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Sample records for functional diffusion maps

  1. Mapping distributed brain function and networks with diffuse optical tomography

    NASA Astrophysics Data System (ADS)

    Eggebrecht, Adam T.; Ferradal, Silvina L.; Robichaux-Viehoever, Amy; Hassanpour, Mahlega S.; Dehghani, Hamid; Snyder, Abraham Z.; Hershey, Tamara; Culver, Joseph P.

    2014-06-01

    Mapping of human brain function has revolutionized systems neuroscience. However, traditional functional neuroimaging by positron emission tomography or functional magnetic resonance imaging cannot be used when applications require portability, or are contraindicated because of ionizing radiation (positron emission tomography) or implanted metal (functional magnetic resonance imaging). Optical neuroimaging offers a non-invasive alternative that is radiation free and compatible with implanted metal and electronic devices (for example, pacemakers). However, optical imaging technology has heretofore lacked the combination of spatial resolution and wide field of view sufficient to map distributed brain functions. Here, we present a high-density diffuse optical tomography imaging array that can map higher-order, distributed brain function. The system was tested by imaging four hierarchical language tasks and multiple resting-state networks including the dorsal attention and default mode networks. Finally, we imaged brain function in patients with Parkinson's disease and implanted deep brain stimulators that preclude functional magnetic resonance imaging.

  2. Functional diffusion map: a noninvasive MRI biomarker for early stratification of clinical brain tumor response.

    PubMed

    Moffat, Bradford A; Chenevert, Thomas L; Lawrence, Theodore S; Meyer, Charles R; Johnson, Timothy D; Dong, Qian; Tsien, Christina; Mukherji, Suresh; Quint, Douglas J; Gebarski, Stephen S; Robertson, Patricia L; Junck, Larry R; Rehemtulla, Alnawaz; Ross, Brian D

    2005-04-12

    Assessment of radiation and chemotherapy efficacy for brain cancer patients is traditionally accomplished by measuring changes in tumor size several months after therapy has been administered. The ability to use noninvasive imaging during the early stages of fractionated therapy to determine whether a particular treatment will be effective would provide an opportunity to optimize individual patient management and avoid unnecessary systemic toxicity, expense, and treatment delays. We investigated whether changes in the Brownian motion of water within tumor tissue as quantified by using diffusion MRI could be used as a biomarker for early prediction of treatment response in brain cancer patients. Twenty brain tumor patients were examined by standard and diffusion MRI before initiation of treatment. Additional images were acquired 3 weeks after initiation of chemo- and/or radiotherapy. Images were coregistered to pretreatment scans, and changes in tumor water diffusion values were calculated and displayed as a functional diffusion map (fDM) for correlation with clinical response. Of the 20 patients imaged during the course of therapy, 6 were classified as having a partial response, 6 as stable disease, and 8 as progressive disease. The fDMs were found to predict patient response at 3 weeks from the start of treatment, revealing that early changes in tumor diffusion values could be used as a prognostic indicator of subsequent volumetric tumor response. Overall, fDM analysis provided an early biomarker for predicting treatment response in brain tumor patients. PMID:15805192

  3. Orientability and Diffusion Maps

    PubMed Central

    Singer, Amit; Wu, Hau-tieng

    2010-01-01

    One of the main objectives in the analysis of a high dimensional large data set is to learn its geometric and topological structure. Even though the data itself is parameterized as a point cloud in a high dimensional ambient space ℝp, the correlation between parameters often suggests the “manifold assumption” that the data points are distributed on (or near) a low dimensional Riemannian manifold ℳd embedded in ℝp, with d ≪ p. We introduce an algorithm that determines the orientability of the intrinsic manifold given a sufficiently large number of sampled data points. If the manifold is orientable, then our algorithm also provides an alternative procedure for computing the eigenfunctions of the Laplacian that are important in the diffusion map framework for reducing the dimensionality of the data. If the manifold is non-orientable, then we provide a modified diffusion mapping of its orientable double covering. PMID:21765628

  4. sfDM: Open-Source Software for Temporal Analysis and Visualization of Brain Tumor Diffusion MR Using Serial Functional Diffusion Mapping

    PubMed Central

    Ceschin, Rafael; Panigrahy, Ashok; Gopalakrishnan, Vanathi

    2015-01-01

    A major challenge in the diagnosis and treatment of brain tumors is tissue heterogeneity leading to mixed treatment response. Additionally, they are often difficult or at very high risk for biopsy, further hindering the clinical management process. To overcome this, novel advanced imaging methods are increasingly being adapted clinically to identify useful noninvasive biomarkers capable of disease stage characterization and treatment response prediction. One promising technique is called functional diffusion mapping (fDM), which uses diffusion-weighted imaging (DWI) to generate parametric maps between two imaging time points in order to identify significant voxel-wise changes in water diffusion within the tumor tissue. Here we introduce serial functional diffusion mapping (sfDM), an extension of existing fDM methods, to analyze the entire tumor diffusion profile along the temporal course of the disease. sfDM provides the tools necessary to analyze a tumor data set in the context of spatiotemporal parametric mapping: the image registration pipeline, biomarker extraction, and visualization tools. We present the general workflow of the pipeline, along with a typical use case for the software. sfDM is written in Python and is freely available as an open-source package under the Berkley Software Distribution (BSD) license to promote transparency and reproducibility. PMID:25673970

  5. sfDM: Open-Source Software for Temporal Analysis and Visualization of Brain Tumor Diffusion MR Using Serial Functional Diffusion Mapping.

    PubMed

    Ceschin, Rafael; Panigrahy, Ashok; Gopalakrishnan, Vanathi

    2015-01-01

    A major challenge in the diagnosis and treatment of brain tumors is tissue heterogeneity leading to mixed treatment response. Additionally, they are often difficult or at very high risk for biopsy, further hindering the clinical management process. To overcome this, novel advanced imaging methods are increasingly being adapted clinically to identify useful noninvasive biomarkers capable of disease stage characterization and treatment response prediction. One promising technique is called functional diffusion mapping (fDM), which uses diffusion-weighted imaging (DWI) to generate parametric maps between two imaging time points in order to identify significant voxel-wise changes in water diffusion within the tumor tissue. Here we introduce serial functional diffusion mapping (sfDM), an extension of existing fDM methods, to analyze the entire tumor diffusion profile along the temporal course of the disease. sfDM provides the tools necessary to analyze a tumor data set in the context of spatiotemporal parametric mapping: the image registration pipeline, biomarker extraction, and visualization tools. We present the general workflow of the pipeline, along with a typical use case for the software. sfDM is written in Python and is freely available as an open-source package under the Berkley Software Distribution (BSD) license to promote transparency and reproducibility.

  6. Vector Diffusion Maps and the Connection Laplacian

    PubMed Central

    Singer, A.; Wu, H.-T.

    2013-01-01

    We introduce vector diffusion maps (VDM), a new mathematical framework for organizing and analyzing massive high-dimensional data sets, images, and shapes. VDM is a mathematical and algorithmic generalization of diffusion maps and other nonlinear dimensionality reduction methods, such as LLE, ISOMAP, and Laplacian eigenmaps. While existing methods are either directly or indirectly related to the heat kernel for functions over the data, VDM is based on the heat kernel for vector fields. VDM provides tools for organizing complex data sets, embedding them in a low-dimensional space, and interpolating and regressing vector fields over the data. In particular, it equips the data with a metric, which we refer to as the vector diffusion distance. In the manifold learning setup, where the data set is distributed on a low-dimensional manifold ℳd embedded in ℝp, we prove the relation between VDM and the connection Laplacian operator for vector fields over the manifold. PMID:24415793

  7. On genetic map functions

    SciTech Connect

    Zhao, Hongyu; Speed, T.P.

    1996-04-01

    Various genetic map functions have been proposed to infer the unobservable genetic distance between two loci from the observable recombination fraction between them. Some map functions were found to fit data better than others. When there are more than three markers, multilocus recombination probabilities cannot be uniquely determined by the defining property of map functions, and different methods have been proposed to permit the use of map functions to analyze multilocus data. If for a given map function, there is a probability model for recombination that can give rise to it, then joint recombination probabilities can be deduced from this model. This provides another way to use map functions in multilocus analysis. In this paper we show that stationary renewal processes give rise to most of the map functions in the literature. Furthermore, we show that the interevent distributions of these renewal processes can all be approximated quite well by gamma distributions. 43 refs., 4 figs.

  8. Earthquake-explosion discrimination using diffusion maps

    NASA Astrophysics Data System (ADS)

    Rabin, N.; Bregman, Y.; Lindenbaum, O.; Ben-Horin, Y.; Averbuch, A.

    2016-09-01

    Discrimination between earthquakes and explosions is an essential component of nuclear test monitoring and it is also important for maintaining the quality of earthquake catalogs. Currently used discrimination methods provide a partial solution to the problem. In this work, we apply advanced machine learning methods and in particular diffusion maps for modeling and discriminating between seismic signals. Diffusion maps enable us to construct a geometric representation that capture the intrinsic structure of the seismograms. The diffusion maps are applied after a pre-processing step, in which seismograms are converted to normalized sonograms. The constructed low-dimensional model is used for automatic earthquake-explosion discrimination of data that is collected in single seismic stations. We demonstrate our approach on a data set comprising seismic events from the Dead Sea area. The diffusion-based algorithm provides correct discrimination rate that is higher than 90%.

  9. Diffusion in membranes: Toward a two-dimensional diffusion map

    NASA Astrophysics Data System (ADS)

    Toppozini, Laura; Garcia-Sakai, Victoria; Bewley, Robert; Dalgliesh, Robert; Perring, Toby; Rheinstädter, Maikel C.

    2015-01-01

    For decades, quasi-elastic neutron scattering has been the prime tool for studying molecular diffusion in membranes over relevant nanometer distances. These experiments are essential to our current understanding of molecular dynamics of lipids, proteins and membrane-active molecules. Recently, we presented experimental evidence from X-ray diffraction and quasi-elastic neutron scattering demonstrating that ethanol enhances the permeability of membranes. At the QENS 2014/WINS 2014 conference we presented a novel technique to measure diffusion across membranes employing 2-dimensional quasi-elastic neutron scattering. We present results from our preliminary analysis of an experiment on the cold neutron multi-chopper spectrometer LET at ISIS, where we studied the self-diffusion of water molecules along lipid membranes and have the possibility of studying the diffusion in membranes. By preparing highly oriented membrane stacks and aligning them horizontally in the spectrometer, our aim is to distinguish between lateral and transmembrane diffusion. Diffusion may also be measured at different locations in the membranes, such as the water layer and the hydrocarbon membrane core. With a complete analysis of the data, 2-dimensional mapping will enable us to determine diffusion channels of water and ethanol molecules to quantitatively determine nanoscale membrane permeability.

  10. Mean Apparent Propagator (MAP) MRI: a novel diffusion imaging method for mapping tissue microstructure

    PubMed Central

    Özarslan, Evren; Koay, Cheng Guan; Shepherd, Timothy M.; Komlosh, Michal E.; İrfanoğlu, M. Okan; Pierpaoli, Carlo; Basser, Peter J.

    2014-01-01

    Diffusion-weighted magnetic resonance (MR) signals reflect information about underlying tissue microstructure and cytoarchitecture. We propose a quantitative, efficient, and robust mathematical and physical framework for representing diffusion-weighted MR imaging (MRI) data obtained in “q-space,” and the corresponding “mean apparent propagator (MAP)” describing molecular displacements in “r-space.” We also define and map novel quantitative descriptors of diffusion that can be computed robustly using this MAP-MRI framework. We describe efficient analytical representation of the three-dimensional q-space MR signal in a series expansion of basis functions that accurately describes diffusion in many complex geometries. The lowest order term in this expansion contains a diffusion tensor that characterizes the Gaussian displacement distribution, equivalent to diffusion tensor MRI (DTI). Inclusion of higher order terms enables the reconstruction of the true average propagator whose projection onto the unit “displacement” sphere provides an orientational distribution function (ODF) that contains only the orientational dependence of the diffusion process. The representation characterizes novel features of diffusion anisotropy and the non-Gaussian character of the three-dimensional diffusion process. Other important measures this representation provides include the return-to-the-origin probability (RTOP), and its variants for diffusion in one- and two-dimensions—the return-to-the-plane probability (RTPP), and the return-to-the-axis probability (RTAP), respectively. These zero net displacement probabilities measure the mean compartment (pore) volume and cross-sectional area in distributions of isolated pores irrespective of the pore shape. MAP-MRI represents a new comprehensive framework to model the three-dimensional q-space signal and transform it into diffusion propagators. Experiments on an excised marmoset brain specimen demonstrate that MAP

  11. A Mapping method for mixing with diffusion

    NASA Astrophysics Data System (ADS)

    Schlick, Conor P.; Christov, Ivan C.; Umbanhowar, Paul B.; Ottino, Julio M.; Lueptow, Richard M.

    2012-11-01

    We present an accurate and efficient computational method for solving the advection-diffusion equation in time-periodic chaotic flows. The method uses operator splitting which allows advection and diffusion steps to be treated independently. Taking advantage of flow periodicity, the advection step is solved with a mapping method, and diffusion is added discretely after each iteration of the advection map. This approach allows for a ``composite'' mapping matrix to be constructed for an entire period of a chaotic advection-diffusion process, which provides a natural approach to the spectral analysis of mixing. To test the approach, we consider the two-dimensional time-periodic sine flow. When compared to the exact solution for this simple velocity field, the operator splitting method exhibits qualitative agreement (overall concentration structure) for large time steps and is quantitatively accurate (average and maximum error) for small time steps. We extend the operator splitting approach to three-dimensional chaotic flows. Funded by NSF Grant CMMI-1000469. Present affiliation: Princeton University. Supported by NSF Grant DMS-1104047.

  12. A framework to analyze cerebral mean diffusivity using surface guided diffusion mapping in diffusion tensor imaging

    PubMed Central

    Kwon, Oh-Hun; Park, Hyunjin; Seo, Sang-Won; Na, Duk L.; Lee, Jong-Min

    2015-01-01

    The mean diffusivity (MD) value has been used to describe microstructural properties in Diffusion Tensor Imaging (DTI) in cortical gray matter (GM). Recently, researchers have applied a cortical surface generated from the T1-weighted volume. When the DTI data are analyzed using the cortical surface, it is important to assign an accurate MD value from the volume space to the vertex of the cortical surface, considering the anatomical correspondence between the DTI and the T1-weighted image. Previous studies usually sampled the MD value using the nearest-neighbor (NN) method or Linear method, even though there are geometric distortions in diffusion-weighted volumes. Here we introduce a Surface Guided Diffusion Mapping (SGDM) method to compensate for such geometric distortions. We compared our SGDM method with results using NN and Linear methods by investigating differences in the sampled MD value. We also projected the tissue classification results of non-diffusion-weighted volumes to the cortical midsurface. The CSF probability values provided by the SGDM method were lower than those produced by the NN and Linear methods. The MD values provided by the NN and Linear methods were significantly greater than those of the SGDM method in regions suffering from geometric distortion. These results indicate that the NN and Linear methods assigned the MD value in the CSF region to the cortical midsurface (GM region). Our results suggest that the SGDM method is an effective way to correct such mapping errors. PMID:26236180

  13. Spatiotemporal mapping of diffusion dynamics and organization in plasma membranes

    NASA Astrophysics Data System (ADS)

    Bag, Nirmalya; Ng, Xue Wen; Sankaran, Jagadish; Wohland, Thorsten

    2016-09-01

    Imaging fluorescence correlation spectroscopy (FCS) and the related FCS diffusion law have been applied in recent years to investigate the diffusion modes of lipids and proteins in membranes. These efforts have provided new insights into the membrane structure below the optical diffraction limit, new information on the existence of lipid domains, and on the influence of the cytoskeleton on membrane dynamics. However, there has been no systematic study to evaluate how domain size, domain density, and the probe partition coefficient affect the resulting imaging FCS diffusion law parameters. Here, we characterize the effects of these factors on the FCS diffusion law through simulations and experiments on lipid bilayers and live cells. By segmenting images into smaller 7  ×  7 pixel areas, we can evaluate the FCS diffusion law on areas smaller than 2 µm and thus provide detailed maps of information on the membrane structure and heterogeneity at this length scale. We support and extend this analysis by deriving a mathematical expression to calculate the mean squared displacement (MSDACF) from the autocorrelation function of imaging FCS, and demonstrate that the MSDACF plots depend on the existence of nanoscopic domains. Based on the results, we derive limits for the detection of domains depending on their size, density, and relative viscosity in comparison to the surroundings. Finally, we apply these measurements to bilayers and live cells using imaging total internal reflection FCS and single plane illumination microscopy FCS.

  14. Mapping the exciton diffusion in semiconductor nanocrystal solids.

    PubMed

    Kholmicheva, Natalia; Moroz, Pavel; Bastola, Ebin; Razgoniaeva, Natalia; Bocanegra, Jesus; Shaughnessy, Martin; Porach, Zack; Khon, Dmitriy; Zamkov, Mikhail

    2015-03-24

    Colloidal nanocrystal solids represent an emerging class of functional materials that hold strong promise for device applications. The macroscopic properties of these disordered assemblies are determined by complex trajectories of exciton diffusion processes, which are still poorly understood. Owing to the lack of theoretical insight, experimental strategies for probing the exciton dynamics in quantum dot solids are in great demand. Here, we develop an experimental technique for mapping the motion of excitons in semiconductor nanocrystal films with a subdiffraction spatial sensitivity and a picosecond temporal resolution. This was accomplished by doping PbS nanocrystal solids with metal nanoparticles that force the exciton dissociation at known distances from their birth. The optical signature of the exciton motion was then inferred from the changes in the emission lifetime, which was mapped to the location of exciton quenching sites. By correlating the metal-metal interparticle distance in the film with corresponding changes in the emission lifetime, we could obtain important transport characteristics, including the exciton diffusion length, the number of predissociation hops, the rate of interparticle energy transfer, and the exciton diffusivity. The benefits of this approach to device applications were demonstrated through the use of two representative film morphologies featuring weak and strong interparticle coupling.

  15. Myocardial fiber orientation mapping using reduced encoding diffusion tensor imaging.

    PubMed

    Hsu, E W; Henriquez, C S

    2001-01-01

    A precise knowledge of the myocardial fiber architecture is essential to accurately understand and interpret cardiac electrical and mechanical functions. Diffusion tensor imaging has been used to noninvasively and quantitatively characterize myocardial fiber orientations. However, because the approach necessitates diffusion to be measured in multiple encoding directions and frequently at multiple weighting levels, the required data set size may present a limitation on its acquisition time efficiency. Applying the principles of reduced encoding imaging (REI), four basic reconstruction schemes, keyhole using direct substitution, keyhole with baseline correction, symmetrically encoded REI with generalized-series reconstruction (RIGR), and asymmetrically encoded RIGR, are evaluated in terms of their accuracy in diffusion tensorfiber orientation mapping of excised myocardial samples. Results show that the performances of all REI schemes, at approximately 50% reduced encoding, are at least comparable with that of a control experiment consisting of proportionally reduced number of full k-space images. Moreover, although performances of the symmetrically and asymmetrically encoded RIGR schemes are similar, both methods provide significant improvements over the control experiment and the direct-substitution keyhole technique. These findings demonstrate the potential of the general REI methodology for diffusion tensor imaging and pave the way for modified schemes involving rapid imaging sequences or alternative k-space sampling strategies to achieve even better data acquisition time efficiency and performance.

  16. Mapping Cognitive Function

    PubMed Central

    Stufflebeam, Steven M.; Rosen, Bruce

    2009-01-01

    Synopsis Cognitive functions are fundamental to being human. Although tremendous progress has been made in the science of cognition using neuroimaging, the clinical applications of neuroimaging are just beginning to be realized. A unifying theme of this chapter is the concept that a more complete understanding of cognition only comes through integration of multimodal structural and functional imaging technologies. PMID:17983964

  17. Spatial Mapping of Translational Diffusion Coefficients Using Diffusion Tensor Imaging: A Mathematical Description

    PubMed Central

    SHETTY, ANIL N.; CHIANG, SHARON; MALETIC-SAVATIC, MIRJANA; KASPRIAN, GREGOR; VANNUCCI, MARINA; LEE, WESLEY

    2016-01-01

    In this article, we discuss the theoretical background for diffusion weighted imaging and diffusion tensor imaging. Molecular diffusion is a random process involving thermal Brownian motion. In biological tissues, the underlying microstructures restrict the diffusion of water molecules, making diffusion directionally dependent. Water diffusion in tissue is mathematically characterized by the diffusion tensor, the elements of which contain information about the magnitude and direction of diffusion and is a function of the coordinate system. Thus, it is possible to generate contrast in tissue based primarily on diffusion effects. Expressing diffusion in terms of the measured diffusion coefficient (eigenvalue) in any one direction can lead to errors. Nowhere is this more evident than in white matter, due to the preferential orientation of myelin fibers. The directional dependency is removed by diagonalization of the diffusion tensor, which then yields a set of three eigenvalues and eigenvectors, representing the magnitude and direction of the three orthogonal axes of the diffusion ellipsoid, respectively. For example, the eigenvalue corresponding to the eigenvector along the long axis of the fiber corresponds qualitatively to diffusion with least restriction. Determination of the principal values of the diffusion tensor and various anisotropic indices provides structural information. We review the use of diffusion measurements using the modified Stejskal–Tanner diffusion equation. The anisotropy is analyzed by decomposing the diffusion tensor based on symmetrical properties describing the geometry of diffusion tensor. We further describe diffusion tensor properties in visualizing fiber tract organization of the human brain. PMID:27441031

  18. Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps.

    PubMed

    Boninsegna, Lorenzo; Gobbo, Gianpaolo; Noé, Frank; Clementi, Cecilia

    2015-12-01

    Identification of the collective coordinates that describe rare events in complex molecular transitions such as protein folding has been a key challenge in the theoretical molecular sciences. In the Diffusion Map approach, one assumes that the molecular configurations sampled have been generated by a diffusion process, and one uses the eigenfunctions of the corresponding diffusion operator as reaction coordinates. While diffusion coordinates (DCs) appear to provide a good approximation to the true dynamical reaction coordinates, they are not parametrized using dynamical information. Thus, their approximation quality could not, as yet, be validated, nor could the diffusion map eigenvalues be used to compute relaxation rate constants of the system. Here we combine the Diffusion Map approach with the recently proposed Variational Approach for Conformation Dynamics (VAC). Diffusion Map coordinates are used as a basis set, and their optimal linear combination is sought using the VAC, which employs time-correlation information on the molecular dynamics (MD) trajectories. We have applied this approach to ultra-long MD simulations of the Fip35 WW domain and found that the first DCs are indeed a good approximation to the true reaction coordinates of the system, but they could be further improved using the VAC. Using the Diffusion Map basis, excellent approximations to the relaxation rates of the system are obtained. Finally, we evaluate the quality of different metric spaces and find that pairwise minimal root-mean-square deviation performs poorly, while operating in the recently introduced kinetic maps based on the time-lagged independent component analysis gives the best performance.

  19. EGRET Diffuse Gamma Ray Maps Between 30 MeV and 10 GeV

    NASA Technical Reports Server (NTRS)

    Cillis, A, N.; Hartman, R. C.

    2004-01-01

    This paper presents all-sky maps of diffuse gamma radiation in various energy ranges between 30 MeV and 10 GeV, based on data collected by the EGRET instrument on the Compton Gamma Ray Observatory. Although the maps can be used for a variety of applications. the immediate goal is the generation of diffuse gamma-ray maps which can be used as a diffuse background/foreground for point source analysis of the data to be obtained from new high-energy gamma-ray missions like GLAST and AGILE. To generate the diffuse gamma maps from the raw EGRET maps, the point sources in the Third EGRET Catalog were subtracted out using the appropriate point spread function for each energy range. After that, smoothing was performed to minimize the effects of photon statistical noise. A smoothing length of 1 deg vas used for the Galactic plane maps. For the all-sky maps, a procedure was used which resulted in a smoothing length roughly equivalent to 4 deg. The result of this work is 16 maps of different energy intervals for absolute value of b < or equal to 20 deg, and 32 all-sky maps, 16 in equatorial coordinates (J2000) and 16 in Galactic coordinates.

  20. EGRET Diffuse Gamma Ray Maps Between 30 MeV and 10 GeV

    NASA Technical Reports Server (NTRS)

    Cillis, A. N.; Hartman, R. C.

    2004-01-01

    This paper presents all-sky maps of diffuse gamma radiation in various energy ranges between 30 MeV and 10 GeV, based on data collected by the EGRET instrument on the Compton Gamma Ray Observatory. Although the maps can be used for a variety of applications, the immediate goal is the generation of diffuse gamma-ray maps which can be used as a diffuse background/foreground for point source analysis of the data to be obtained from new high-energy gamma-ray missions like GLAST and AGILE. To generate the diffuse gamma maps from the raw EGRET maps, the point sources in the Third EGRET Catalog were subtracted out using the appropriate point spread function for each energy range. After that, smoothing was performed to minimize the effects of photon statistical noise. A smoothing length of 1deg was used for the Galactic plane maps. For the all-sky maps, a procedure was used which resulted in a smoothing length roughly equivalent to 4deg. The result of this work is 16 maps of different energy intervals for [b]less than or equal to 20deg, and 32 all-sky maps, 16 in equatorial coordinates (J2000) and 16 in Galactic coordinates.

  1. Diffusion maps clustering for magnetic resonance q-ball imaging segmentation.

    PubMed

    Wassermann, Demian; Descoteaux, Maxime; Deriche, Rachid

    2008-01-01

    White matter fiber clustering aims to get insight about anatomical structures in order to generate atlases, perform clear visualizations, and compute statistics across subjects, all important and current neuroimaging problems. In this work, we present a diffusion maps clustering method applied to diffusion MRI in order to segment complex white matter fiber bundles. It is well known that diffusion tensor imaging (DTI) is restricted in complex fiber regions with crossings and this is why recent high-angular resolution diffusion imaging (HARDI) such as Q-Ball imaging (QBI) has been introduced to overcome these limitations. QBI reconstructs the diffusion orientation distribution function (ODF), a spherical function that has its maxima agreeing with the underlying fiber populations. In this paper, we use a spherical harmonic ODF representation as input to the diffusion maps clustering method. We first show the advantage of using diffusion maps clustering over classical methods such as N-Cuts and Laplacian eigenmaps. In particular, our ODF diffusion maps requires a smaller number of hypothesis from the input data, reduces the number of artifacts in the segmentation, and automatically exhibits the number of clusters segmenting the Q-Ball image by using an adaptive scale-space parameter. We also show that our ODF diffusion maps clustering can reproduce published results using the diffusion tensor (DT) clustering with N-Cuts on simple synthetic images without crossings. On more complex data with crossings, we show that our ODF-based method succeeds to separate fiber bundles and crossing regions whereas the DT-based methods generate artifacts and exhibit wrong number of clusters. Finally, we show results on a real-brain dataset where we segment well-known fiber bundles. PMID:18317506

  2. Mapping intracellular diffusion distribution using single quantum dot tracking: compartmentalized diffusion defined by endoplasmic reticulum.

    PubMed

    Li, Hui; Dou, Shuo-Xing; Liu, Yu-Ru; Li, Wei; Xie, Ping; Wang, Wei-Chi; Wang, Peng-Ye

    2015-01-14

    The crowded intracellular environment influences the diffusion-mediated cellular processes, such as metabolism, signaling, and transport. The hindered diffusion of macromolecules in heterogeneous cytoplasm has been studied over years, but the detailed diffusion distribution and its origin still remain unclear. Here, we introduce a novel method to map rapidly the diffusion distribution in single cells based on single-particle tracking (SPT) of quantum dots (QDs). The diffusion map reveals the heterogeneous intracellular environment and, more importantly, an unreported compartmentalization of QD diffusions in cytoplasm. Simultaneous observations of QD motion and green fluorescent protein-tagged endoplasmic reticulum (ER) dynamics provide direct evidence that the compartmentalization results from micron-scale domains defined by ER tubules, and ER cisternae form perinuclear areas that restrict QDs to enter. The same phenomenon was observed using fluorescein isothiocyanate-dextrans, further confirming the compartmentalized diffusion. These results shed new light on the diffusive movements of macromolecules in the cell, and the mapping of intracellular diffusion distribution may be used to develop strategies for nanoparticle-based drug deliveries and therapeutics.

  3. Normal and anomalous diffusion in a deterministic area-preserving map

    NASA Astrophysics Data System (ADS)

    Lebœuf, P.

    1998-05-01

    Chaotic deterministic dynamics of a particle can give rise to diffusive Brownian motion. In this paper, we compute analytically the diffusion coefficient for a particular two-dimensional stochastic layer induced by the kicked Harper map. The variations of the transport coefficient as a control parameter is varied are analyzed in terms of the underlying classical trajectories with particular emphasis on the appearance and bifurcations of periodic orbits. When accelerator modes are present, anomalous diffusion of the Lévy type is observed. The exponent characterizing the anomalous diffusion is computed numerically and analyzed as a function of the parameter.

  4. Granger-causality maps of diffusion processes.

    PubMed

    Wahl, Benjamin; Feudel, Ulrike; Hlinka, Jaroslav; Wächter, Matthias; Peinke, Joachim; Freund, Jan A

    2016-02-01

    Granger causality is a statistical concept devised to reconstruct and quantify predictive information flow between stochastic processes. Although the general concept can be formulated model-free it is often considered in the framework of linear stochastic processes. Here we show how local linear model descriptions can be employed to extend Granger causality into the realm of nonlinear systems. This novel treatment results in maps that resolve Granger causality in regions of state space. Through examples we provide a proof of concept and illustrate the utility of these maps. Moreover, by integration we convert the local Granger causality into a global measure that yields a consistent picture for a global Ornstein-Uhlenbeck process. Finally, we recover invariance transformations known from the theory of autoregressive processes. PMID:26986337

  5. Granger-causality maps of diffusion processes.

    PubMed

    Wahl, Benjamin; Feudel, Ulrike; Hlinka, Jaroslav; Wächter, Matthias; Peinke, Joachim; Freund, Jan A

    2016-02-01

    Granger causality is a statistical concept devised to reconstruct and quantify predictive information flow between stochastic processes. Although the general concept can be formulated model-free it is often considered in the framework of linear stochastic processes. Here we show how local linear model descriptions can be employed to extend Granger causality into the realm of nonlinear systems. This novel treatment results in maps that resolve Granger causality in regions of state space. Through examples we provide a proof of concept and illustrate the utility of these maps. Moreover, by integration we convert the local Granger causality into a global measure that yields a consistent picture for a global Ornstein-Uhlenbeck process. Finally, we recover invariance transformations known from the theory of autoregressive processes.

  6. Putting the Diffuse Interstellar Bands on the Map - Literally!

    NASA Astrophysics Data System (ADS)

    van Loon, J. Th.

    2014-02-01

    In a quest to further our understanding of the diffuse interstellar medium (ISM) as well as the unidentified carriers of the diffuse interstellar bands (DIBs), we are mapping DIBs across the sky using hundreds of hot stars as background torches - globular clusters (in particular ω Centauri), nearby stars in and around the Local Bubble, and stars within the Magellanic Clouds. I describe the results so far obtained and our current experiments.

  7. Influence Function Learning in Information Diffusion Networks

    PubMed Central

    Du, Nan; Liang, Yingyu; Balcan, Maria-Florina; Song, Le

    2015-01-01

    Can we learn the influence of a set of people in a social network from cascades of information diffusion? This question is often addressed by a two-stage approach: first learn a diffusion model, and then calculate the influence based on the learned model. Thus, the success of this approach relies heavily on the correctness of the diffusion model which is hard to verify for real world data. In this paper, we exploit the insight that the influence functions in many diffusion models are coverage functions, and propose a novel parameterization of such functions using a convex combination of random basis functions. Moreover, we propose an efficient maximum likelihood based algorithm to learn such functions directly from cascade data, and hence bypass the need to specify a particular diffusion model in advance. We provide both theoretical and empirical analysis for our approach, showing that the proposed approach can provably learn the influence function with low sample complexity, be robust to the unknown diffusion models, and significantly outperform existing approaches in both synthetic and real world data. PMID:25973445

  8. Polymer reversal rate calculated via locally scaled diffusion map.

    PubMed

    Zheng, Wenwei; Rohrdanz, Mary A; Maggioni, Mauro; Clementi, Cecilia

    2011-04-14

    A recent study on the dynamics of polymer reversal inside a nanopore by Huang and Makarov [J. Chem. Phys. 128, 114903 (2008)] demonstrated that the reaction rate cannot be reproduced by projecting the dynamics onto a single empirical reaction coordinate, a result suggesting the dynamics of this system cannot be correctly described by using a single collective coordinate. To further investigate this possibility we have applied our recently developed multiscale framework, locally scaled diffusion map (LSDMap), to obtain collective reaction coordinates for this system. Using a single diffusion coordinate, we obtain a reversal rate via Kramers expression that is in good agreement with the exact rate obtained from the simulations. Our mathematically rigorous approach accounts for the local heterogeneity of molecular configuration space in constructing a diffusion map, from which collective coordinates emerge. We believe this approach can be applied in general to characterize complex macromolecular dynamics by providing an accurate definition of the collective coordinates associated with processes at different time scales.

  9. Retinotopic mapping of adult human visual cortex with high-density diffuse optical tomography

    PubMed Central

    Zeff, Benjamin W.; White, Brian R.; Dehghani, Hamid; Schlaggar, Bradley L.; Culver, Joseph P.

    2007-01-01

    Functional neuroimaging is a vital element of neuroscience and cognitive research and, increasingly, is an important clinical tool. Diffuse optical imaging is an emerging, noninvasive technique with unique portability and hemodynamic contrast capabilities for mapping brain function in young subjects and subjects in enriched or clinical environments. We have developed a high-performance, high-density diffuse optical tomography (DOT) system that overcomes previous limitations and enables superior image quality. We show herein the utility of the DOT system by presenting functional hemodynamic maps of the adult human visual cortex. The functional brain images have a high contrast-to-noise ratio, allowing visualization of individual activations and highly repeatable mapping within and across subjects. With the improved spatial resolution and localization, we were able to image functional responses of 1.7 cm in extent and shifts of <1 cm. Cortical maps of angle and eccentricity in the visual field are consistent with retinotopic studies using functional MRI and positron-emission tomography. These results demonstrate that high-density DOT is a practical and powerful tool for mapping function in the human cortex. PMID:17616584

  10. Diffusion-convection function of cosmic rays

    NASA Technical Reports Server (NTRS)

    Zhang, G.; Yang, G.

    1985-01-01

    The fundamental properties and some numerical results of the solution of the diffusion equation of an impulsive cosmic-ray point source in an uniform, unbounded and spherically symmetrical moving medium is presented. The diffusion-convection(D-C) function is an elementary composite function of the solution of the D-C equation for the particles injected impulsively from a diffusive point source into the medium. It is the analytic solution derived by the dimensional method for the propagation equation of solar cosmic rays in the heliosphere, i.e. the interplanetary space. Because of the introduction of convection effect of solar wind, a nonhomogeneous term appears in the propagation equation, it is difficult to express its solution in terms of the ordinary special functions. The research made so far has led to a solution containing only the first order approximation of the convection effect.

  11. Enhancing scattering images for orientation recovery with diffusion map

    DOE PAGESBeta

    Winter, Martin; Saalmann, Ulf; Rost, Jan M.

    2016-02-12

    We explore the possibility for orientation recovery in single-molecule coherent diffractive imaging with diffusion map. This algorithm approximates the Laplace-Beltrami operator, which we diagonalize with a metric that corresponds to the mapping of Euler angles onto scattering images. While suitable for images of objects with specific properties we show why this approach fails for realistic molecules. Here, we introduce a modification of the form factor in the scattering images which facilitates the orientation recovery and should be suitable for all recovery algorithms based on the distance of individual images. (C) 2016 Optical Society of America

  12. Chaotic map models of soot fluctuations in turbulent diffusion flames

    SciTech Connect

    Mukerji, S.; McDonough, J.M.; Menguec, M.P.; Manickavasagam, S.; Chung, S.

    1998-10-01

    In this paper, the authors introduce a methodology to characterize time-dependent soot volume fraction fluctuations in turbulent diffusion flames via chaotic maps. The approach is based on the hypothesis that fluctuations of properties in turbulent flames are deterministic in nature, rather than statistical. The objective is to develop models of these fluctuations to be used in comprehensive algorithms to study the nature of turbulent flames and the interaction of turbulence with radiation. To this end the authors measured the time series of soot scattering coefficient in an ethylene diffusion flame from light scattering experiments and fit these data to linear combinations of chaotic maps of the unit interval. Both time series and power spectra can be modeled with reasonable accuracy in this way.

  13. A multiple mapping conditioning model for differential diffusion

    NASA Astrophysics Data System (ADS)

    Dialameh, L.; Cleary, M. J.; Klimenko, A. Y.

    2014-02-01

    This work introduces modeling of differential diffusion within the multiple mapping conditioning (MMC) turbulent mixing and combustion framework. The effect of differential diffusion on scalar variance decay is analyzed and, following a number of publications, is found to scale as Re-1/2. The ability to model the differential decay rates is the most important aim of practical differential diffusion models, and here this is achieved in MMC by introducing what is called the side-stepping method. The approach is practical and, as it does not involve an increase in the number of MMC reference variables, economical. In addition we also investigate the modeling of a more refined and difficult to reproduce differential diffusion effect - the loss of correlation between the different scalars. For this we develop an alternative MMC model with two reference variables but which also makes use of the side-stepping method. The new models are successfully validated against DNS results available in literature for homogenous, isotropic two scalar mixing.

  14. Blogviz: mapping the dynamics of information diffusion in blogspace

    NASA Astrophysics Data System (ADS)

    Lima, Manuel S.

    2006-01-01

    Blogviz is a visualization model for mapping the transmission and internal structure of top links across the blogosphere. It explores the idea of meme propagation by assuming a parallel with the spreading of most cited URLs in daily weblog entries. The main goal of Blogviz is to unravel hidden patterns in the topics diffusion process. What's the life cycle of a topic? How does it start and how does it evolve through time? Are topics constrained to a specific community of users? Who are the most influential and innovative blogs in any topic? Are there any relationships amongst topic proliferators?

  15. Reflectance Diffuse Optical Tomography: Its Application to Human Brain Mapping

    NASA Astrophysics Data System (ADS)

    Ueda, Yukio; Yamanaka, Takeshi; Yamashita, Daisuke; Suzuki, Toshihiko; Ohmae, Etsuko; Oda, Motoki; Yamashita, Yutaka

    2005-09-01

    We report the successful application of reflectance diffuse optical tomography (DOT) using near-infrared light with the new reconstruction algorithm that we developed to the observation of regional hemodynamic changes in the brain under specific mental tasks. Our results reveal the heterogeneous distribution of oxyhemoglobin and deoxyhemoglobin in the brain, showing complementary images of oxyhemoglobin and deoxyhemoglobin changes in certain regions. We conclude that our reflectance DOT has practical potential for human brain mapping, as well as in the diagnostic imaging of brain diseases.

  16. FAST Mapping of Diffuse HI Gas in the Local Universe

    NASA Astrophysics Data System (ADS)

    Zhu, M.; Pisano, D. J.; Ai, M.; Jiao, Q.

    2016-02-01

    We propose to use the Five hundred meter Aperture Spherical radio Telescope (FAST) to map the diffuse intergalactic HI gas in the local universe at column densities of NHI=1018 cm-2 and below. The major science goal is to study gas accretion during galaxy evolution, and trace cosmic web features in the local universe. We disuss the technical feasibilty of such a deep survey, and have conducted test observations with the Arecibo 305 m telescope. Our preliminary results shows that, with about a few thousand hours of observing time, FAST will be able to map several hundred square degree regions at 1 σ of NHI=2×1017 cm-2 level out to a distance of 5-10 Mpc, and with a volume 1000 larger than that of the Local Group.

  17. MAPPING THE DIFFUSE ULTRAVIOLET SKY WITH THE GALAXY EVOLUTION EXPLORER

    SciTech Connect

    Murthy, Jayant; Sujatha, N. V.; Henry, R. C.

    2010-12-01

    We present a map of the diffuse ultraviolet cosmic background in two wavelength bands (FUV: 1530 A and NUV: 2310 A) over almost 75% of the sky using archival data from the Galaxy Evolution Explorer (GALEX) mission. Most of the diffuse flux is due to dust-scattered starlight and follows a cosecant law with slopes of 545 photons cm{sup -2} s{sup -1} sr{sup -1} A{sup -1} and 433 photons cm{sup -2} s{sup -1} sr{sup -1} A{sup -1} in the FUV and NUV bands, respectively. There is a strong correlation with the 100 {mu}m Infrared Astronomy Satellite (IRAS) flux with an average UV/IR ratio of 300 photons cm{sup -2} s{sup -1} sr{sup -1} A{sup -1} (MJy sr{sup -1}){sup -1} in the FUV band and that of 220 photons cm{sup -2} s{sup -1} sr{sup -1} A{sup -1} (MJy sr{sup -1}){sup -1} in the NUV band but with significant variations over the sky. In addition to the large-scale distribution of the diffuse light, we note a number of individual features including bright spots around the hot stars Spica and Achernar.

  18. Planck 2015 results. X. Diffuse component separation: Foreground maps

    NASA Astrophysics Data System (ADS)

    Planck Collaboration; Adam, R.; Ade, P. A. R.; Aghanim, N.; Alves, M. I. R.; Arnaud, M.; Ashdown, M.; Aumont, J.; Baccigalupi, C.; Banday, A. J.; Barreiro, R. B.; Bartlett, J. G.; Bartolo, N.; Battaner, E.; Benabed, K.; Benoît, A.; Benoit-Lévy, A.; Bernard, J.-P.; Bersanelli, M.; Bielewicz, P.; Bock, J. J.; Bonaldi, A.; Bonavera, L.; Bond, J. R.; Borrill, J.; Bouchet, F. R.; Boulanger, F.; Bucher, M.; Burigana, C.; Butler, R. C.; Calabrese, E.; Cardoso, J.-F.; Catalano, A.; Challinor, A.; Chamballu, A.; Chary, R.-R.; Chiang, H. C.; Christensen, P. R.; Clements, D. L.; Colombi, S.; Colombo, L. P. L.; Combet, C.; Couchot, F.; Coulais, A.; Crill, B. P.; Curto, A.; Cuttaia, F.; Danese, L.; Davies, R. D.; Davis, R. J.; de Bernardis, P.; de Rosa, A.; de Zotti, G.; Delabrouille, J.; Désert, F.-X.; Dickinson, C.; Diego, J. M.; Dole, H.; Donzelli, S.; Doré, O.; Douspis, M.; Ducout, A.; Dupac, X.; Efstathiou, G.; Elsner, F.; Enßlin, T. A.; Eriksen, H. K.; Falgarone, E.; Fergusson, J.; Finelli, F.; Forni, O.; Frailis, M.; Fraisse, A. A.; Franceschi, E.; Frejsel, A.; Galeotta, S.; Galli, S.; Ganga, K.; Ghosh, T.; Giard, M.; Giraud-Héraud, Y.; Gjerløw, E.; González-Nuevo, J.; Górski, K. M.; Gratton, S.; Gregorio, A.; Gruppuso, A.; Gudmundsson, J. E.; Hansen, F. K.; Hanson, D.; Harrison, D. L.; Helou, G.; Henrot-Versillé, S.; Hernández-Monteagudo, C.; Herranz, D.; Hildebrandt, S. R.; Hivon, E.; Hobson, M.; Holmes, W. A.; Hornstrup, A.; Hovest, W.; Huffenberger, K. M.; Hurier, G.; Jaffe, A. H.; Jaffe, T. R.; Jones, W. C.; Juvela, M.; Keihänen, E.; Keskitalo, R.; Kisner, T. S.; Kneissl, R.; Knoche, J.; Kunz, M.; Kurki-Suonio, H.; Lagache, G.; Lähteenmäki, A.; Lamarre, J.-M.; Lasenby, A.; Lattanzi, M.; Lawrence, C. R.; Le Jeune, M.; Leahy, J. P.; Leonardi, R.; Lesgourgues, J.; Levrier, F.; Liguori, M.; Lilje, P. B.; Linden-Vørnle, M.; López-Caniego, M.; Lubin, P. M.; Macías-Pérez, J. F.; Maggio, G.; Maino, D.; Mandolesi, N.; Mangilli, A.; Maris, M.; Marshall, D. J.; Martin, P. G.; Martínez-González, E.; Masi, S.; Matarrese, S.; McGehee, P.; Meinhold, P. R.; Melchiorri, A.; Mendes, L.; Mennella, A.; Migliaccio, M.; Mitra, S.; Miville-Deschênes, M.-A.; Moneti, A.; Montier, L.; Morgante, G.; Mortlock, D.; Moss, A.; Munshi, D.; Murphy, J. A.; Naselsky, P.; Nati, F.; Natoli, P.; Netterfield, C. B.; Nørgaard-Nielsen, H. U.; Noviello, F.; Novikov, D.; Novikov, I.; Orlando, E.; Oxborrow, C. A.; Paci, F.; Pagano, L.; Pajot, F.; Paladini, R.; Paoletti, D.; Partridge, B.; Pasian, F.; Patanchon, G.; Pearson, T. J.; Perdereau, O.; Perotto, L.; Perrotta, F.; Pettorino, V.; Piacentini, F.; Piat, M.; Pierpaoli, E.; Pietrobon, D.; Plaszczynski, S.; Pointecouteau, E.; Polenta, G.; Pratt, G. W.; Prézeau, G.; Prunet, S.; Puget, J.-L.; Rachen, J. P.; Reach, W. T.; Rebolo, R.; Reinecke, M.; Remazeilles, M.; Renault, C.; Renzi, A.; Ristorcelli, I.; Rocha, G.; Rosset, C.; Rossetti, M.; Roudier, G.; Rubiño-Martín, J. A.; Rusholme, B.; Sandri, M.; Santos, D.; Savelainen, M.; Savini, G.; Scott, D.; Seiffert, M. D.; Shellard, E. P. S.; Spencer, L. D.; Stolyarov, V.; Stompor, R.; Strong, A. W.; Sudiwala, R.; Sunyaev, R.; Sutton, D.; Suur-Uski, A.-S.; Sygnet, J.-F.; Tauber, J. A.; Terenzi, L.; Toffolatti, L.; Tomasi, M.; Tristram, M.; Tucci, M.; Tuovinen, J.; Umana, G.; Valenziano, L.; Valiviita, J.; Van Tent, F.; Vielva, P.; Villa, F.; Wade, L. A.; Wandelt, B. D.; Wehus, I. K.; Wilkinson, A.; Yvon, D.; Zacchei, A.; Zonca, A.

    2016-09-01

    Planck has mapped the microwave sky in temperature over nine frequency bands between 30 and 857 GHz and in polarization over seven frequency bands between 30 and 353 GHz in polarization. In this paper we consider the problem of diffuse astrophysical component separation, and process these maps within a Bayesian framework to derive an internally consistent set of full-sky astrophysical component maps. Component separation dedicated to cosmic microwave background (CMB) reconstruction is described in a companion paper. For the temperature analysis, we combine the Planck observations with the 9-yr Wilkinson Microwave Anisotropy Probe (WMAP) sky maps and the Haslam et al. 408 MHz map, to derive a joint model of CMB, synchrotron, free-free, spinning dust, CO, line emission in the 94 and 100 GHz channels, and thermal dust emission. Full-sky maps are provided for each component, with an angular resolution varying between 7.´5 and 1deg. Global parameters (monopoles, dipoles, relative calibration, and bandpass errors) are fitted jointly with the sky model, and best-fit values are tabulated. For polarization, the model includes CMB, synchrotron, and thermal dust emission. These models provide excellent fits to the observed data, with rms temperature residuals smaller than 4μK over 93% of the sky for all Planck frequencies up to 353 GHz, and fractional errors smaller than 1% in the remaining 7% of the sky. The main limitations of the temperature model at the lower frequencies are internal degeneracies among the spinning dust, free-free, and synchrotron components; additional observations from external low-frequency experiments will be essential to break these degeneracies. The main limitations of the temperature model at the higher frequencies are uncertainties in the 545 and 857 GHz calibration and zero-points. For polarization, the main outstanding issues are instrumental systematics in the 100-353 GHz bands on large angular scales in the form of temperature

  19. Spatial mapping of fluorophore quantum yield in diffusive media.

    PubMed

    Zhao, Yanyu; Roblyer, Darren

    2015-08-01

    Fluorescence quantum yield (QY) indicates the efficiency of the fluorescence process. The QY of many fluorophores is sensitive to local tissue environments, highlighting the possibility of using QY as an indicator of important parameters such as pH or temperature. QY is commonly measured by comparison to a well-known standard in nonscattering media. We propose a new imaging method, called quantum yield imaging (QYI), to spatially map the QY of a fluorophore within an optically diffusive media. QYI utilizes the wide-field diffuse optical technique spatial frequency domain imaging (SFDI) as well as planar fluorescence imaging. SFDI is used to measure the optical properties of the background media and the absorption contributed by the fluorophore. The unknown QY is then calculated by combining information from both modalities. A fluorescent sample with known QY is used to account for instrument response. To demonstrate QYI, rhodamine B and SNARF-5 were imaged in liquid phantoms with different background optical properties. The methanol:water ratio and pH were changed for rhodamine B and SNARF-5 solvents, respectively, altering the QY of each through a wide range. QY was determined with an agreement of 0.021 and 0.012 for rhodamine B and SNARF-5, respectively. PMID:26308165

  20. Critical properties of lattices of diffusively coupled quadratic maps.

    PubMed

    Van De Water, Willem; Bohr, Tomas

    1993-10-01

    We study the critical properties of lattices of coupled logistic maps in the regime where the individual maps are closely above the onset of chaos. We discuss both spatial and temporal characteristics and especially the link between them. We show that the mutual information function between two points on the lattice decays exponentially with distance. In this way we find support for the relation xi approximately lambda(-1/2) between the coherence length xi and the largest Lyapunov exponent lambda which is further corroborated by a detailed study of the spreading of small perturbations. Finally we study the structure function of the lattice field variable. It shows that at the onset of chaos the lattice remains smooth.

  1. Native Magnetic Resonance T1-Mapping Identifies Diffuse Myocardial Injury in Hypothyroidism

    PubMed Central

    Qu, Aijuan; Chen, Zhe; Jia, Yumei; Yang, Ning; Feng, Xiaomeng; Liu, Jia; Xu, Yuan; Yang, Xinchun; Wang, Guang

    2016-01-01

    Background and Aim Hypothyroidism (HT) is characterized by thyroid hormone deficiencies, which can lead to diffuse myocardial interstitium lesions in patients with HT. Myocardial longitudinal relaxation time (T1) mapping is a potential diagnostic tool for quantifying diffuse myocardial injury. This study aimed to assess the usefulness of T1 mapping in identifying myocardial involvement in HT, and determine the relationship between T1 values and myocardial function. Methods A cross-sectional study was conducted with 30 untreated HT patients alongside 23 age- and sex-matched healthy controls. All subjects underwent cardiac magnetic resonance (CMR) with non-contrast (native) T1 mapping using a modified Look-Locker inversion-recovery (MOLLI) sequence to assess the native T1 values of myocardium and cardiac function. Results Native myocardial T1 values were significantly increased in HT patients, especially those with pericardial effusion (p < 0.05), compared with healthy controls. In addition, significantly reduced peak filling rate (PFR) and prolonged peak filling time (PFT) were obtained (p < 0.05) in HT patients compared with controls. Furthermore, stroke volume (SV) and cardiac index (CI) were significantly lower in HT patients than controls (all p < 0.05). Interestingly, native T1 values were negatively correlated with free triiodothyronine (FT3), PFR, SV and CI (all p < 0.05). Conclusion Diffuse myocardial injuries are common in HT patients, and increased T1 values are correlated with FT3 and cardiac function impairment. These findings indicate that T1 mapping might be useful in evaluating myocardial injuries in HT patients. PMID:26964099

  2. Mapping Prefrontal Cortex Functions in Human Infancy

    ERIC Educational Resources Information Center

    Grossmann, Tobias

    2013-01-01

    It has long been thought that the prefrontal cortex, as the seat of most higher brain functions, is functionally silent during most of infancy. This review highlights recent work concerned with the precise mapping (localization) of brain activation in human infants, providing evidence that prefrontal cortex exhibits functional activation much…

  3. Functional brain mapping of psychopathology

    PubMed Central

    Honey, G; Fletcher, P; Bullmore, E

    2002-01-01

    In this paper, we consider the impact that the novel functional neuroimaging techniques may have upon psychiatric illness. Functional neuroimaging has rapidly developed as a powerful tool in cognitive neuroscience and, in recent years, has seen widespread application in psychiatry. Although such studies have produced evidence for abnormal patterns of brain response in association with some pathological conditions, the core pathophysiologies remain unresolved. Although imaging techniques provide an unprecedented opportunity for investigation of physiological function of the living human brain, there are fundamental questions and assumptions which remain to be addressed. In this review we examine these conceptual issues under three broad sections: (1) characterising the clinical population of interest, (2) defining appropriate levels of description of normal brain function, and (3) relating these models to pathophysiological conditions. Parallel advances in each of these questions will be required before imaging techniques can impact on clinical decisions in psychiatry. PMID:11909899

  4. Intraoperative MRI and functional mapping.

    PubMed

    Gasser, Thomas; Szelenyi, Andrea; Senft, Christian; Muragaki, Yoshihiro; Sandalcioglu, I Erol; Sure, Ulrich; Nimsky, Christopher; Seifert, Volker

    2011-01-01

    The integration of functional and anatomical data into neuronavigation is an established standard of care in many neurosurgical departments. Yet, this method has limitations as in most cases the data are acquired prior to surgery. Due to brain-shift the accurate presentation of functional as well as anatomical structures declines in the course of surgery. In consequence, the acquisition of information during surgery about the brain's current functional state is of specific interest. The advancement of imaging technologies (e.g. fMRI, MEG, Intraoperative Optical Intrinsic Signal Imaging--IOIS) and neurophysiological techniques and the advent of intraoperative MRI all had a major impact on neurosurgery. The combination of modalities such as neurophysiology and intraoperative MRI (ioMRI), as well as the acquisition of functional MRI during surgery (ifMRI) are in the focus of this work. Especially the technical aspects and safety issues are elucidated.

  5. What is a genetic map function?

    SciTech Connect

    Speed, T.P.

    1996-12-31

    We review the reasons that genetic map functions are studied and the way they are used. The connections between chiasma point processes on four-stranded bivalents, crossover point processes on the single strand products of meiosis, multilocus recombination probabilities and map functions are discussed in detail, mainly, but not exclusively under the assumption of no chromatid interference. As a result of this discussion we obtain a number of inequalities constraining map functions which lead to both bound and smoothness constraints. We show that most of the functions proposed as map functions in the literature do in fact arise in association with a stationary renewal chiasma process, and we clarify the relation between their doing so, while failing to be multilocus feasible in the sense of Liberman & Karlin. We emphasize the fact that map functions can in general neither define chiasma nor crossover processes nor multilocus recombination probabilities, nor can they fully reflect the nature of the interference present in a chiasma or crossover process. Our attempt to answer the question in the title of this paper is not wholly successful, but we present some simple necessary conditions which become sufficient when supplemented by two further simple conditions. The paper closes with the statement of several open problems. 64 refs.

  6. Mapping specific soil functions based on digital soil property maps

    NASA Astrophysics Data System (ADS)

    Pásztor, László; Fodor, Nándor; Farkas-Iványi, Kinga; Szabó, József; Bakacsi, Zsófia; Koós, Sándor

    2016-04-01

    Quantification of soil functions and services is a great challenge in itself even if the spatial relevance is supposed to be identified and regionalized. Proxies and indicators are widely used in ecosystem service mapping. Soil services could also be approximated by elementary soil features. One solution is the association of soil types with services as basic principle. Soil property maps however provide quantified spatial information, which could be utilized more versatilely for the spatial inference of soil functions and services. In the frame of the activities referred as "Digital, Optimized, Soil Related Maps and Information in Hungary" (DOSoReMI.hu) numerous soil property maps have been compiled so far with proper DSM techniques partly according to GSM.net specifications, partly by slightly or more strictly changing some of its predefined parameters (depth intervals, pixel size, property etc.). The elaborated maps have been further utilized, since even DOSoReMI.hu was intended to take steps toward the regionalization of higher level soil information (secondary properties, functions, services). In the meantime the recently started AGRAGIS project requested spatial soil related information in order to estimate agri-environmental related impacts of climate change and support the associated vulnerability assessment. One of the most vulnerable services of soils in the context of climate change is their provisioning service. In our work it was approximated by productivity, which was estimated by a sequential scenario based crop modelling. It took into consideration long term (50 years) time series of both measured and predicted climatic parameters as well as accounted for the potential differences in agricultural practice and crop production. The flexible parametrization and multiple results of modelling was then applied for the spatial assessment of sensitivity, vulnerability, exposure and adaptive capacity of soils in the context of the forecasted changes in

  7. A mapping method for distributive mixing with diffusion: Interplay between chaos and diffusion in time-periodic sine flow

    NASA Astrophysics Data System (ADS)

    Schlick, Conor P.; Christov, Ivan C.; Umbanhowar, Paul B.; Ottino, Julio M.; Lueptow, Richard M.

    2013-05-01

    We present an accurate and efficient computational method for solving the advection-diffusion equation in time-periodic chaotic flows. The method uses operator splitting, which allows the advection and diffusion steps to be treated independently. Taking advantage of flow periodicity, the advection step is solved using a mapping method, and diffusion is "added" discretely after each iteration of the advection map. This approach results in the construction of a composite mapping matrix over an entire period of the chaotic advection-diffusion process and provides a natural framework for the analysis of mixing. To test the approach, we consider two-dimensional time-periodic sine flow. By comparing the numerical solutions obtained by our method to reference solutions, we find qualitative agreement for large time steps (structure of concentration profile) and quantitative agreement for small time steps (low error). Further, we study the interplay between mixing through chaotic advection and mixing through diffusion leading to an analytical model for the evolution of the intensity of segregation with time. Additionally, we demonstrate that our operator splitting mapping approach can be readily extended to three dimensions.

  8. Pyramidal tract mapping by diffusion tensor magnetic resonance imaging in multiple sclerosis: improving correlations with disability

    PubMed Central

    Wilson, M; Tench, C; Morgan, P; Blumhardt, L

    2003-01-01

    Background: Current magnetic resonance imaging (MRI) outcome measures such as T2 lesion load correlate poorly with disability in multiple sclerosis. Diffusion tensor imaging (DTI) of the brain can provide unique information regarding the orientation and integrity of white matter tracts in vivo. Objective: To use this information to map the pyramidal tracts of patients with multiple sclerosis, investigate the relation between burden of disease in the tracts and disability, and compare this with more global magnetic resonance estimates of disease burden. Methods: 25 patients with relapsing-remitting multiple sclerosis and 17 healthy volunteers were studied with DTI. An algorithm was used that automatically produced anatomically plausible maps of white matter tracts. The integrity of the pyramidal tracts was assessed using relative anisotropy and a novel measure (Lt) derived from the compounded relative anisotropy along the tracts. The methods were compared with both traditional and more recent techniques for measuring disease burden in multiple sclerosis (T2 lesion load and "whole brain" diffusion histograms). Results: Relative anisotropy and Lt were significantly lower in patients than controls (p < 0.05). Pyramidal tract Lt in the patients correlated significantly with both expanded disability status scale (r = -0.48, p < 0.05), and to a greater degree, the pyramidal Kurtzke functional system score (KFS-p) (r = -0.75, p < 0.0001). T2 lesion load and diffusion histogram parameters did not correlate with disability. Conclusions: Tract mapping using DTI is feasible and may increase the specificity of MRI in multiple sclerosis by matching appropriate tracts with specific clinical scoring systems. These techniques may be applicable to a wide range of neurological conditions. PMID:12531950

  9. A direct approach to generalised multiple mapping conditioning for selected turbulent diffusion flame cases

    NASA Astrophysics Data System (ADS)

    Sundaram, Brruntha; Klimenko, Alexander Yuri; Cleary, Matthew John; Ge, Yipeng

    2016-07-01

    This work presents a direct and transparent interpretation of two concepts for modelling turbulent combustion: generalised Multiple Mapping Conditioning (MMC) and sparse-Lagrangian Large Eddy Simulation (LES). The MMC approach is presented as a hybrid between the Probability Density Function (PDF) method and approaches based on conditioning (e.g. Conditional Moment Closure, flamelet, etc.). The sparse-Lagrangian approach, which allows for a dramatic reduction of computational cost, is viewed as an alternative interpretation of the Filtered Density Function (FDF) methods. This work presents simulations of several turbulent diffusion flame cases and discusses the universality of the localness parameter between these cases and the universality of sparse-Lagrangian FDF methods with MMC.

  10. Temperature dependence of thermal conductivities of coupled rotator lattice and the momentum diffusion in standard map

    NASA Astrophysics Data System (ADS)

    Li, Yunyun; Li, Nianbei; Li, Baowen

    2015-07-01

    In contrary to other 1D momentum-conserving lattices such as the Fermi-Pasta-Ulam β (FPU- β) lattice, the 1D coupled rotator lattice is a notable exception which conserves total momentum while exhibits normal heat conduction behavior. The temperature behavior of the thermal conductivities of 1D coupled rotator lattice had been studied in previous works trying to reveal the underlying physical mechanism for normal heat conduction. However, two different temperature behaviors of thermal conductivities have been claimed for the same coupled rotator lattice. These different temperature behaviors also intrigue the debate whether there is a phase transition of thermal conductivities as the function of temperature. In this work, we will revisit the temperature dependent thermal conductivities for the 1D coupled rotator lattice. We find that the temperature dependence follows a power law behavior which is different with the previously found temperature behaviors. Our results also support the claim that there is no phase transition for 1D coupled rotator lattice. We also give some discussion about the similarity of diffusion behaviors between the 1D coupled rotator lattice and the single kicked rotator also called the Chirikov standard map. It is found that the momentum diffusion constant for 1D coupled rotator lattice follows a power-law temperature dependence of T -3.2 which is close to that of Chirikov standard map which follows a behavior of T -3.

  11. Sub-diffuse structured light imaging provides macroscopic maps of microscopic tissue structure (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Kanick, Stephen C.

    2016-03-01

    The onset and progression of cancer introduces changes to the intra-cellular ultrastructural components and to the morphology of the extracellular matrix. While previous work has shown that localized scatter imaging is sensitive to pathology-induced differences in these aspects of tissue microstructure, wide adaptation this knowledge for surgical guidance is limited by two factors. First, the time required to image with confocal-level localization of the remission signal can be substantial. Second, localized (i.e. sub-diffuse) scatter remission intensity is influenced interchangeably by parameters that define scattering frequency and anisotropy. This similarity relationship must be carefully considered in order to obtain unique estimates of biomarkers that define either the scatter density or features that describe the distribution (e.g. shape, size, and orientation) of scatterers. This study presents a novel approach that uses structured light imaging to address both of these limitations. Monte Carlo data were used to model the reflectance intensity over a wide range of spatial frequencies, reduced scattering coefficients, absorption coefficients, and a metric of the scattering phase function that directly maps to the fractal dimension of scatter sizes. The approach is validated in tissue-simulating phantoms constructed with user-tuned scattering phase functions. The validation analysis shows that the phase function can be described in the presence of different scatter densities or background absorptions. Preliminary data from clinical tissue specimens show quantitative images of both the scatter density and the tissue fractal dimension for various tissue types and pathologies. These data represent a novel wide-field quantitative approach to mapping microscopic structural biomarkers that cannot be obtained with standard diffuse imaging. Implications for the use of this approach to assess surgical margins will be discussed.

  12. Acoustic mapping of diffuse flow at a seafloor hydrothermal site: Monolith Vent, Juan de Fuca Ridge

    NASA Astrophysics Data System (ADS)

    Rona, P. A.; Jackson, D. R.; Wen, T.; Jones, C.; Mitsuzawa, K.; Bemis, K. G.; Dworski, J. G.

    Diffuse flow of hydrothermal solutions commonly occurs in patchy areas up to tens of meters in diameter in seafloor hydrothermal fields. It is recognized as a quantitatively significant component of thermal and chemical fluxes, yet is elusive to map. We report a new acoustic method to detect and map areas of diffuse flow using phase-coherent correlation techniques. The sonar system was modified to record phase information and mounted on DSV SEA CLIFF. The submersible occupied a stationary position on the seafloor and the transducer scanned the seafloor surrounding Monolith Vent, a sulfide edifice venting black smokers, at a nominal range of 17 m at a depth of 2249 m on the Juan de Fuca Ridge. Patchy areas of uncorrelated returns clearly stood out from a background of returns that exhibited ping-to-ping correlation. The areas of uncorrelated returns coincided with areas of diffuse flow as mapped by a video survey with the Navy's Advanced Tethered Vehicle (ATV). Correlated returns were backscattered from invariant seafloor. Uncorrelated returns were distorted by index of refraction inhomogeneities as they passed through diffuse flow between the seafloor and the transducer. The acoustic method presented can synoptically map areas of diffuse flow. When combined with standard in situ measurement and sampling methods the acoustic mapping will facilitate accurate determination of diffuse thermal and chemical fluxes in seafloor hydrothermal fields.

  13. Measuring and mapping cardiac fiber and laminar architecture using diffusion tensor MR imaging.

    PubMed

    Helm, Patrick; Beg, Mirza Faisal; Miller, Michael I; Winslow, Raimond L

    2005-06-01

    The ventricular myocardium is known to exhibit a complex spatial organization, with fiber orientation varying as a function of transmural location. It is now well established that diffusion tensor magnetic resonance imaging (DTMRI) may be used to measure this fiber orientation at high spatial resolution. Cardiac fibers are also known to be organized in sheets with surface orientation varying throughout the ventricles. This article reviews results on use of DTMRI for measuring ventricular fiber orientation, as well as presents new results providing strong evidence that the tertiary eigenvector of the diffusion tensor is aligned locally with the cardiac sheet surface normal. Considered together, these data indicate that DTMRI may be used to reconstruct both ventricular fiber and sheet organization. This article also presents the large deformation diffeomorphic metric mapping (LDDMM) algorithm and shows that this algorithm may be used to bring ensembles of imaged and reconstructed hearts into correspondence (e.g., registration) so that variability of ventricular geometry, fiber, and sheet orientation may be quantified. Ventricular geometry and fiber structure is known to be remodeled in a range of disease processes; however, descriptions of this remodeling have remained subjective and qualitative. We anticipate that use of DTMRI for reconstruction of ventricular anatomy coupled with application of the LDDMM method for image volume registration will enable the detection and quantification of changes in cardiac anatomy that are characteristic of specific disease processes in the heart. Finally, we show that epicardial electrical mapping and DTMRI imaging may be performed in the same hearts. The anatomic data may then be used to simulate electrical conduction in a computational model of the very same heart that was mapped electrically. This facilitates direct comparison and testing of model versus experimental results and opens the door to quantitative measurement

  14. Quantitative analysis of diffusion tensor imaging (DTI) using statistical parametric mapping (SPM) for brain disorders

    NASA Astrophysics Data System (ADS)

    Lee, Jae-Seung; Im, In-Chul; Kang, Su-Man; Goo, Eun-Hoe; Kwak, Byung-Joon

    2013-07-01

    This study aimed to quantitatively analyze data from diffusion tensor imaging (DTI) using statistical parametric mapping (SPM) in patients with brain disorders and to assess its potential utility for analyzing brain function. DTI was obtained by performing 3.0-T magnetic resonance imaging for patients with Alzheimer's disease (AD) and vascular dementia (VD), and the data were analyzed using Matlab-based SPM software. The two-sample t-test was used for error analysis of the location of the activated pixels. We compared regions of white matter where the fractional anisotropy (FA) values were low and the apparent diffusion coefficients (ADCs) were increased. In the AD group, the FA values were low in the right superior temporal gyrus, right inferior temporal gyrus, right sub-lobar insula, and right occipital lingual gyrus whereas the ADCs were significantly increased in the right inferior frontal gyrus and right middle frontal gyrus. In the VD group, the FA values were low in the right superior temporal gyrus, right inferior temporal gyrus, right limbic cingulate gyrus, and right sub-lobar caudate tail whereas the ADCs were significantly increased in the left lateral globus pallidus and left medial globus pallidus. In conclusion by using DTI and SPM analysis, we were able to not only determine the structural state of the regions affected by brain disorders but also quantitatively analyze and assess brain function.

  15. Clinton Woolsey: Functional Brain Mapping Pioneer

    PubMed Central

    Lyon, Will; Mehta, Tej I.; Pointer, Kelli B.; Walden, Daniel; Elmayan, Ardem; Swanson, Kyle I.; Kuo, John S.

    2014-01-01

    Dr. Clinton Woolsey was a leading twentieth century neuroscientist for almost four decades. His most significant achievements were the novel use and refinement of evoked potential techniques to functionally map mammalian brains, the discovery of secondary cortical areas, and a wide repertoire of comparative neurofunctional studies across many species. We discuss his life and work through a historical context with contemporaries, highlight the primitive state of brain mapping before Woolsey, and his involvement in advancing its rapid development through work at both Johns Hopkins University and University of Wisconsin in Madison. Dr. Woolsey’s lasting impact on basic and clinical neuroscience, neurosurgery, and neurology and his important roles as a scientific mentor and leader are also described. PMID:25105696

  16. Planck 2015 results. IX. Diffuse component separation: CMB maps

    NASA Astrophysics Data System (ADS)

    Planck Collaboration; Adam, R.; Ade, P. A. R.; Aghanim, N.; Arnaud, M.; Ashdown, M.; Aumont, J.; Baccigalupi, C.; Banday, A. J.; Barreiro, R. B.; Bartlett, J. G.; Bartolo, N.; Basak, S.; Battaner, E.; Benabed, K.; Benoît, A.; Benoit-Lévy, A.; Bernard, J.-P.; Bersanelli, M.; Bielewicz, P.; Bock, J. J.; Bonaldi, A.; Bonavera, L.; Bond, J. R.; Borrill, J.; Bouchet, F. R.; Boulanger, F.; Bucher, M.; Burigana, C.; Butler, R. C.; Calabrese, E.; Cardoso, J.-F.; Casaponsa, B.; Castex, G.; Catalano, A.; Challinor, A.; Chamballu, A.; Chary, R.-R.; Chiang, H. C.; Christensen, P. R.; Clements, D. L.; Colombi, S.; Colombo, L. P. L.; Combet, C.; Couchot, F.; Coulais, A.; Crill, B. P.; Curto, A.; Cuttaia, F.; Danese, L.; Davies, R. D.; Davis, R. J.; de Bernardis, P.; de Rosa, A.; de Zotti, G.; Delabrouille, J.; Désert, F.-X.; Dickinson, C.; Diego, J. M.; Dole, H.; Donzelli, S.; Doré, O.; Douspis, M.; Ducout, A.; Dupac, X.; Efstathiou, G.; Elsner, F.; Enßlin, T. A.; Eriksen, H. K.; Falgarone, E.; Fantaye, Y.; Fergusson, J.; Finelli, F.; Forni, O.; Frailis, M.; Fraisse, A. A.; Franceschi, E.; Frejsel, A.; Galeotta, S.; Galli, S.; Ganga, K.; Ghosh, T.; Giard, M.; Giraud-Héraud, Y.; Gjerløw, E.; González-Nuevo, J.; Górski, K. M.; Gratton, S.; Gregorio, A.; Gruppuso, A.; Gudmundsson, J. E.; Hansen, F. K.; Hanson, D.; Harrison, D. L.; Helou, G.; Henrot-Versillé, S.; Hernández-Monteagudo, C.; Herranz, D.; Hildebrandt, S. R.; Hivon, E.; Hobson, M.; Holmes, W. A.; Hornstrup, A.; Hovest, W.; Huffenberger, K. M.; Hurier, G.; Jaffe, A. H.; Jaffe, T. R.; Jones, W. C.; Juvela, M.; Keihänen, E.; Keskitalo, R.; Kisner, T. S.; Kneissl, R.; Knoche, J.; Krachmalnicoff, N.; Kunz, M.; Kurki-Suonio, H.; Lagache, G.; Lamarre, J.-M.; Lasenby, A.; Lattanzi, M.; Lawrence, C. R.; Le Jeune, M.; Leonardi, R.; Lesgourgues, J.; Levrier, F.; Liguori, M.; Lilje, P. B.; Linden-Vørnle, M.; López-Caniego, M.; Lubin, P. M.; Macías-Pérez, J. F.; Maggio, G.; Maino, D.; Mandolesi, N.; Mangilli, A.; Maris, M.; Marshall, D. J.; Martin, P. G.; Martínez-González, E.; Masi, S.; Matarrese, S.; McGehee, P.; Meinhold, P. R.; Melchiorri, A.; Mendes, L.; Mennella, A.; Migliaccio, M.; Mitra, S.; Miville-Deschênes, M.-A.; Molinari, D.; Moneti, A.; Montier, L.; Morgante, G.; Mortlock, D.; Moss, A.; Munshi, D.; Murphy, J. A.; Naselsky, P.; Nati, F.; Natoli, P.; Netterfield, C. B.; Nørgaard-Nielsen, H. U.; Noviello, F.; Novikov, D.; Novikov, I.; Oxborrow, C. A.; Paci, F.; Pagano, L.; Pajot, F.; Paladini, R.; Paoletti, D.; Pasian, F.; Patanchon, G.; Pearson, T. J.; Perdereau, O.; Perotto, L.; Perrotta, F.; Pettorino, V.; Piacentini, F.; Piat, M.; Pierpaoli, E.; Pietrobon, D.; Plaszczynski, S.; Pointecouteau, E.; Polenta, G.; Pratt, G. W.; Prézeau, G.; Prunet, S.; Puget, J.-L.; Rachen, J. P.; Racine, B.; Reach, W. T.; Rebolo, R.; Reinecke, M.; Remazeilles, M.; Renault, C.; Renzi, A.; Ristorcelli, I.; Rocha, G.; Rosset, C.; Rossetti, M.; Roudier, G.; Rubiño-Martín, J. A.; Rusholme, B.; Sandri, M.; Santos, D.; Savelainen, M.; Savini, G.; Scott, D.; Seiffert, M. D.; Shellard, E. P. S.; Spencer, L. D.; Stolyarov, V.; Stompor, R.; Sudiwala, R.; Sunyaev, R.; Sutton, D.; Suur-Uski, A.-S.; Sygnet, J.-F.; Tauber, J. A.; Terenzi, L.; Toffolatti, L.; Tomasi, M.; Tristram, M.; Trombetti, T.; Tucci, M.; Tuovinen, J.; Valenziano, L.; Valiviita, J.; Van Tent, F.; Vielva, P.; Villa, F.; Wade, L. A.; Wandelt, B. D.; Wehus, I. K.; Yvon, D.; Zacchei, A.; Zonca, A.

    2016-08-01

    We present foreground-reduced cosmic microwave background (CMB) maps derived from the full Planck data set in both temperature and polarization. Compared to the corresponding Planck 2013 temperature sky maps, the total data volume is larger by a factor of 3.2 for frequencies between 30 and 70 GHz, and by 1.9 for frequencies between 100 and 857 GHz. In addition, systematic errors in the forms of temperature-to-polarization leakage, analogue-to-digital conversion uncertainties, and very long time constant errors have been dramatically reduced, to the extent that the cosmological polarization signal may now be robustly recovered on angular scales ℓ ≳ 40. On the very largest scales, instrumental systematic residuals are still non-negligible compared to the expected cosmological signal, and modes with ℓ< 20 are accordingly suppressed in the current polarization maps by high-pass filtering. As in 2013, four different CMB component separation algorithms are applied to these observations, providing a measure of stability with respect to algorithmic and modelling choices. The resulting polarization maps have rms instrumental noise ranging between 0.21 and 0.27μK averaged over 55' pixels, and between 4.5 and 6.1μK averaged over 3.4 parcm pixels. The cosmological parameters derived from the analysis of temperature power spectra are in agreement at the 1σ level with the Planck 2015 likelihood. Unresolved mismatches between the noise properties of the data and simulations prevent a satisfactory description of the higher-order statistical properties of the polarization maps. Thus, the primary applications of these polarization maps are those that do not require massive simulations for accurate estimation of uncertainties, for instance estimation of cross-spectra and cross-correlations, or stacking analyses. However, the amplitude of primordial non-Gaussianity is consistent with zero within 2σ for all local, equilateral, and orthogonal configurations of the bispectrum

  17. Quantification of diffusion-weighted images (DWI) and apparent diffusion coefficient maps (ADC) in the detection of acute stroke

    NASA Astrophysics Data System (ADS)

    Tulipano, P. Karina; Millar, William S.; Imielinska, Celina; Liu, Xin; Rosiene, Joel; D'Ambrosio, Anthony L.

    2006-03-01

    Magnetic resonance (MR) imaging is an imaging modality that is used in the management and diagnosis of acute stroke. Common MR imaging techniques such as diffusion weighted imaging (DWI) and apparent diffusion coefficient maps (ADC) are used routinely in the diagnosis of acute infarcts. However, advances in radiology information systems and imaging protocols have led to an overload of image information that can be difficult to manage and time consuming. Automated techniques to assist in the identification of acute ischemic stroke can prove beneficial to 1) the physician by providing a mechanism for early detection and 2) the patient by providing effective stroke therapy at an early stage. We have processed DW images and ADC maps using a novel automated Relative Difference Map (RDM) method that was tailored to the identification and delineation of the stroke region. Results indicate that the technique can delineate regions of acute infarctions on DW images and ADC maps. A formal evaluation of the RDM algorithm was performed by comparing accuracy measurements between 1) expert generated ground truths with the RDM delineated DWI infarcts and 2) RDM delineated DWI infarcts with RDM delineated ADC infarcts. The accuracy measurements indicate that the RDM delineated DWI infarcts are comparable to the expert generated ground truths. The true positive volume fraction value (TPVF), between RDM delineated DWI and ADC infarcts, is nonzero for all cases with an acute infarct while the value for non-acute cases remains zero.

  18. Efficient numerical solution of the time fractional diffusion equation by mapping from its Brownian counterpart

    NASA Astrophysics Data System (ADS)

    Stokes, Peter W.; Philippa, Bronson; Read, Wayne; White, Ronald D.

    2015-02-01

    The solution of a Caputo time fractional diffusion equation of order 0 < α < 1 is expressed in terms of the solution of a corresponding integer order diffusion equation. We demonstrate a linear time mapping between these solutions that allows for accelerated computation of the solution of the fractional order problem. In the context of an N-point finite difference time discretisation, the mapping allows for an improvement in time computational complexity from O (N2) to O (Nα), given a precomputation of O (N 1 + α ln ⁡ N). The mapping is applied successfully to the least squares fitting of a fractional advection-diffusion model for the current in a time-of-flight experiment, resulting in a computational speed up in the range of one to three orders of magnitude for realistic problem sizes.

  19. Efficient global fiber tracking on multi-dimensional diffusion direction maps

    NASA Astrophysics Data System (ADS)

    Klein, Jan; Köhler, Benjamin; Hahn, Horst K.

    2012-02-01

    Global fiber tracking algorithms have recently been proposed which were able to compute results of unprecedented quality. They account for avoiding accumulation errors by a global optimization process at the cost of a high computation time of several hours or even days. In this paper, we introduce a novel global fiber tracking algorithm which, for the first time, globally optimizes the underlying diffusion direction map obtained from DTI or HARDI data, instead of single fiber segments. As a consequence, the number of iterations in the optimization process can drastically be reduced by about three orders of magnitude. Furthermore, in contrast to all previous algorithms, the density of the tracked fibers can be adjusted after the optimization within a few seconds. We evaluated our method for diffusion-weighted images obtained from software phantoms, healthy volunteers, and tumor patients. We show that difficult fiber bundles, e.g., the visual pathways or tracts for different motor functions can be determined and separated in an excellent quality. Furthermore, crossing and kissing bundles are correctly resolved. On current standard hardware, a dense fiber tracking result of a whole brain can be determined in less than half an hour which is a strong improvement compared to previous work.

  20. Analytical correlation functions for motion through diffusivity landscapes.

    PubMed

    Roosen-Runge, Felix; Bicout, Dominique J; Barrat, Jean-Louis

    2016-05-28

    Diffusion of a particle through an energy and diffusivity landscape is a very general phenomenon in numerous systems of soft and condensed matter. On the one hand, theoretical frameworks such as Langevin and Fokker-Planck equations present valuable accounts to understand these motions in great detail, and numerous studies have exploited these approaches. On the other hand, analytical solutions for correlation functions, as, e.g., desired by experimentalists for data fitting, are only available for special cases. We explore the possibility to use different theoretical methods in the specific picture of time-dependent switching between diffusive states to derive analytical functions that allow to link experimental and simulation results to theoretical calculations. In particular, we present a closed formula for diffusion switching between two states, as well as a general recipe of how to generalize the formula to multiple states. PMID:27250281

  1. Analytical correlation functions for motion through diffusivity landscapes

    NASA Astrophysics Data System (ADS)

    Roosen-Runge, Felix; Bicout, Dominique J.; Barrat, Jean-Louis

    2016-05-01

    Diffusion of a particle through an energy and diffusivity landscape is a very general phenomenon in numerous systems of soft and condensed matter. On the one hand, theoretical frameworks such as Langevin and Fokker-Planck equations present valuable accounts to understand these motions in great detail, and numerous studies have exploited these approaches. On the other hand, analytical solutions for correlation functions, as, e.g., desired by experimentalists for data fitting, are only available for special cases. We explore the possibility to use different theoretical methods in the specific picture of time-dependent switching between diffusive states to derive analytical functions that allow to link experimental and simulation results to theoretical calculations. In particular, we present a closed formula for diffusion switching between two states, as well as a general recipe of how to generalize the formula to multiple states.

  2. Isotropic diffusion weighting for measurement of a high-resolution apparent diffusion coefficient map using a single radial scan in MRI

    NASA Astrophysics Data System (ADS)

    Seo, Hyunseok; Choi, Joonsung; Oh, Changheun; Han, Yeji; Park, HyunWook

    2014-10-01

    This work proposes an isotropic diffusion weighting method for a high-resolution diffusion-weighted image and for a high-resolution apparent diffusion coefficient (ADC) map using a single radial scan in MRI. By using a conventional radial imaging technique, a high-resolution diffusion-weighted (DW) image can be obtained at the cost of a long imaging time. To reduce the imaging time, the proposed method acquires a DW image by altering the diffusion gradient directions for each radial spoke. The acquisition order and directions of the diffusion gradients for an accurate DW image and an ADC map are also proposed by modifying the golden angle ratio in 3D space. In addition, an individual-direction diffusion-weighted (id-DW) image can also be obtained by a diffusion gradient direction, which is one of the multiple directions used in isotropic diffusion weighting. Computer simulations and experiment results show that the proposed method is more accurate and faster than the conventional radial diffusion-weighted imaging. This study suggests that the proposed isotropic diffusion-weighted imaging can be used to obtain a DW image and a high-resolution ADC map accurately in a single radial scan, while reducing the artifacts caused by the diffusion anisotropy, compared to the diffusion-weighted echo-planar-imaging.

  3. A photometric function for diffuse reflection by particulate materials

    NASA Technical Reports Server (NTRS)

    Meador, W. E.; Weaver, W. R.

    1975-01-01

    A photometric function is proposed to describe the diffuse reflection of radiation by particulate materials. Both multiple scattering and the dominant effects of particle shadowing are included and the function is verified by comparisons with the photometries of laboratory surfaces. Brightness measurements of planetary and other diffusely scattering surfaces can be used to calculate the brightness for geometries other than those used in the measurements and for which the Minnaert function does not apply. The measurements also can be directly related to such surface characteristics as particle size, single-particle albedo, and compactness.

  4. Eloquent Brain, Ethical Challenges: Functional Brain Mapping in Neurosurgery.

    PubMed

    Klein, Eran

    2015-06-01

    Functional brain mapping is an increasingly relied upon tool in presurgical planning and intraoperative decision making. Mapping allows personalization of structure-function relationships when surgical or other treatment of pathology puts eloquent functioning like language or vision at risk. As an innovative technology, functional brain mapping holds great promise but also raises important ethical questions. In this article, recent work in neuroethics on functional imaging and functional neurosurgery is explored and applied to functional brain mapping. Specific topics discussed in this article are incidental findings, responsible innovation, and informed consent.

  5. Integrating Concept Mapping and the Learning Cycle To Teach Diffusion and Osmosis Concepts to High School Biology Students.

    ERIC Educational Resources Information Center

    Odom, Arthur L.; Kelly, Paul V.

    2001-01-01

    Explores the effectiveness of concept mapping, the learning cycle, expository instruction, and a combination of concept mapping/learning cycle in promoting conceptual understanding of diffusion and osmosis. Concludes that the concept mapping/learning cycle and concept mapping treatment groups significantly outperformed the expository treatment…

  6. Mapping the functional yeast ABC transporter interactome

    PubMed Central

    Snider, Jamie; Hanif, Asad; Lee, Mid Eum; Jin, Ke; Yu, Analyn R.; Graham, Chris; Chuk, Matthew; Damjanovic, Dunja; Wierzbicka, Marta; Tang, Priscilla; Balderes, Dina; Wong, Victoria; Jessulat, Matthew; Darowski, Katelyn D.; Luis, Bryan-Joseph San; Shevelev, Igor; Sturley, Stephen L; Boone, Charles; Greenblatt, Jack F.; Zhang, Zhaolei; Paumi, Christian M.; Babu, Mohan; Park, Hay-Oak; Michaelis, Susan; Stagljar, Igor

    2013-01-01

    ABC transporters are a ubiquitous class of integral membrane proteins of immense clinical interest because of their strong association with human disease and pharmacology. To improve our understanding of these proteins, we used Membrane Yeast Two-Hybrid (MYTH) technology to map the protein interactome of all non-mitochondrial ABC transporters in the model organism Saccharomy cescerevisiae, and combined this data with previously reported yeast ABC transporter interactions in the BioGRID database to generate a comprehensive, integrated interactome. We show that ABC transporters physically associate with proteins involved in a surprisingly diverse range of functions. We specifically examine the importance of the physical interactions of ABC transporters in both the regulation of one another and in the modulation of proteins involved in zinc homeostasis. The interaction network presented here will be a powerful resource for increasing our fundamental understanding of the cellular role and regulation of ABC transporters. PMID:23831759

  7. Remediating High School Students' Misconceptions Concerning Diffusion and Osmosis through Concept Mapping and Conceptual Change Text.

    ERIC Educational Resources Information Center

    Tekkaya, Ceren

    2003-01-01

    Investigates the effectiveness of combining conceptual change text and concept mapping strategies on students' understanding of diffusion and osmosis. Results indicate that while the average percentage of students in the experimental group holding a scientifically correct view rose, the percentage of correct responses in the control group…

  8. Mapping turbulent diffusivity associated with oceanic internal lee waves offshore Costa Rica

    NASA Astrophysics Data System (ADS)

    Fortin, Will F. J.; Holbrook, W. Steven; Schmitt, Raymond W.

    2016-04-01

    Breaking internal waves play a primary role in maintaining the meridional overturning circulation. Oceanic lee waves are known to be a significant contributor to diapycnal mixing associated with internal wave dissipation, but direct measurement is difficult with standard oceanographic sampling methods due to the limited spatial extent of standing lee waves. Here, we present an analysis of oceanic internal lee waves observed offshore eastern Costa Rica using seismic imaging and estimate the turbulent diffusivity via a new seismic slope spectrum method that extracts diffusivities directly from seismic images, using tracked reflections only to scale diffusivity values. The result provides estimates of turbulent diffusivities throughout the water column at scales of a few hundred meters laterally and 10 m vertically. Synthetic tests demonstrate the method's ability to resolve turbulent structures and reproduce accurate diffusivities. A turbulence map of our seismic section in the western Caribbean shows elevated turbulent diffusivities near rough seafloor topography as well as in the mid-water column where observed lee wave propagation terminates. Mid-water column hotspots of turbulent diffusivity show levels 5 times higher than surrounding waters and 50 times greater than typical open-ocean diffusivities. This site has steady currents that make it an exceptionally accessible laboratory for the study of lee-wave generation, propagation, and decay.

  9. Quantitative mapping of the per‐axon diffusion coefficients in brain white matter

    PubMed Central

    Kruggel, Frithjof; Alexander, Daniel C.

    2015-01-01

    Purpose This article presents a simple method for estimating the effective diffusion coefficients parallel and perpendicular to the axons unconfounded by the intravoxel fiber orientation distribution. We also call these parameters the per‐axon or microscopic diffusion coefficients. Theory and Methods Diffusion MR imaging is used to probe the underlying tissue material. The key observation is that for a fixed b‐value the spherical mean of the diffusion signal over the gradient directions does not depend on the axon orientation distribution. By exploiting this invariance property, we propose a simple, fast, and robust estimator of the per‐axon diffusion coefficients, which we refer to as the spherical mean technique. Results We demonstrate quantitative maps of the axon‐scale diffusion process, which has factored out the effects due to fiber dispersion and crossing, in human brain white matter. These microscopic diffusion coefficients are estimated in vivo using a widely available off‐the‐shelf pulse sequence featuring multiple b‐shells and high‐angular gradient resolution. Conclusion The estimation of the per‐axon diffusion coefficients is essential for the accurate recovery of the fiber orientation distribution. In addition, the spherical mean technique enables us to discriminate microscopic tissue features from fiber dispersion, which potentially improves the sensitivity and/or specificity to various neurological conditions. Magn Reson Med, 2015. Magn Reson Med 75:1752–1763, 2016. © 2015 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. PMID:25974332

  10. Eulerian Mapping Closure Approach for Probability Density Function of Concentration in Shear Flows

    NASA Technical Reports Server (NTRS)

    He, Guowei; Bushnell, Dennis M. (Technical Monitor)

    2002-01-01

    The Eulerian mapping closure approach is developed for uncertainty propagation in computational fluid mechanics. The approach is used to study the Probability Density Function (PDF) for the concentration of species advected by a random shear flow. An analytical argument shows that fluctuation of the concentration field at one point in space is non-Gaussian and exhibits stretched exponential form. An Eulerian mapping approach provides an appropriate approximation to both convection and diffusion terms and leads to a closed mapping equation. The results obtained describe the evolution of the initial Gaussian field, which is in agreement with direct numerical simulations.

  11. Raman and CT scan mapping of chalcogenide glass diffusion generated gradient index profiles

    NASA Astrophysics Data System (ADS)

    Lindberg, G. P.; Berg, R. H.; Deegan, J.; Benson, R.; Salvaggio, P. S.; Gross, N.; Weinstein, B. A.; Gibson, D.; Bayya, S.; Sanghera, J.; Nguyen, V.; Kotov, M.

    2016-05-01

    Metrology of a gradient index (GRIN) material is non-trivial, especially in the realm of infrared and large refractive index. Traditional methods rely on index matching fluids which are not available for indexes as high as those found in the chalcogenide glasses (2.4-3.2). By diffusing chalcogenide glasses of similar composition one can blend the properties in a continuous way. In an effort to measure this we will present data from both x-ray computed tomography scans (CT scans) and Raman mapping scans of the diffusion profiles. Proof of concept measurements on undiffused bonded sheets of chalcogenide glasses were presented previously. The profiles measured will be of axially stacked sheets of chalcogenide glasses diffused to create a linear GRIN profile and nested tubes of chalcogenide glasses diffused to create a radial parabolic GRIN profile. We will show that the x-ray absorption in the CT scan and the intensity of select Raman peaks spatially measured through the material are indicators of the concentration of the diffusion ions and correlate to the spatial change in refractive index. We will also present finite element modeling (FEM) results and compare them to post precision glass molded (PGM) elements that have undergone CT and Raman mapping.

  12. Fast and simplified mapping of mean axon diameter using temporal diffusion spectroscopy.

    PubMed

    Xu, Junzhong; Li, Hua; Li, Ke; Harkins, Kevin D; Jiang, Xiaoyu; Xie, Jingping; Kang, Hakmook; Dortch, Richard D; Anderson, Adam W; Does, Mark D; Gore, John C

    2016-04-01

    Mapping axon diameter is of interest for the potential diagnosis and monitoring of various neuronal pathologies. Advanced diffusion-weighted MRI methods have been developed to measure mean axon diameters non-invasively, but suffer major drawbacks that prevent their direct translation into clinical practice, such as complex non-linear data fitting and, more importantly, long scanning times that are usually not tolerable for most human subjects. In the current study, temporal diffusion spectroscopy using oscillating diffusion gradients was used to measure mean axon diameters with high sensitivity to small axons in the central nervous system. Axon diameters have been found to be correlated with a novel metric, DDR⊥ (the rate of dispersion of the perpendicular diffusion coefficient with gradient frequency), which is a model-free quantity that does not require complex data analyses and can be obtained from two diffusion coefficient measurements in clinically relevant times with conventional MRI machines. A comprehensive investigation including computer simulations and animal experiments ex vivo showed that measurements of DDR⊥ agree closely with histological data. In humans in vivo, DDR⊥ was also found to correlate well with reported mean axon diameters in human corpus callosum, and the total scan time was only about 8 min. In conclusion, DDR⊥ may have potential to serve as a fast, simple and model-free approach to map the mean axon diameter of white matter in clinics for assessing axon diameter changes. PMID:27077155

  13. Fast and simplified mapping of mean axon diameter using temporal diffusion spectroscopy.

    PubMed

    Xu, Junzhong; Li, Hua; Li, Ke; Harkins, Kevin D; Jiang, Xiaoyu; Xie, Jingping; Kang, Hakmook; Dortch, Richard D; Anderson, Adam W; Does, Mark D; Gore, John C

    2016-04-01

    Mapping axon diameter is of interest for the potential diagnosis and monitoring of various neuronal pathologies. Advanced diffusion-weighted MRI methods have been developed to measure mean axon diameters non-invasively, but suffer major drawbacks that prevent their direct translation into clinical practice, such as complex non-linear data fitting and, more importantly, long scanning times that are usually not tolerable for most human subjects. In the current study, temporal diffusion spectroscopy using oscillating diffusion gradients was used to measure mean axon diameters with high sensitivity to small axons in the central nervous system. Axon diameters have been found to be correlated with a novel metric, DDR⊥ (the rate of dispersion of the perpendicular diffusion coefficient with gradient frequency), which is a model-free quantity that does not require complex data analyses and can be obtained from two diffusion coefficient measurements in clinically relevant times with conventional MRI machines. A comprehensive investigation including computer simulations and animal experiments ex vivo showed that measurements of DDR⊥ agree closely with histological data. In humans in vivo, DDR⊥ was also found to correlate well with reported mean axon diameters in human corpus callosum, and the total scan time was only about 8 min. In conclusion, DDR⊥ may have potential to serve as a fast, simple and model-free approach to map the mean axon diameter of white matter in clinics for assessing axon diameter changes.

  14. Functional Mapping with Simultaneous MEG and EEG

    PubMed Central

    Liu, Hesheng; Tanaka, Naoaki; Stufflebeam, Steven; Ahlfors, Seppo; Hämäläinen, Matti

    2010-01-01

    We use magnetoencephalography (MEG) and electroencephalography (EEG) to locate and determine the temporal evolution in brain areas involved in the processing of simple sensory stimuli. We will use somatosensory stimuli to locate the hand somatosensory areas, auditory stimuli to locate the auditory cortices, visual stimuli in four quadrants of the visual field to locate the early visual areas. These type of experiments are used for functional mapping in epileptic and brain tumor patients to locate eloquent cortices. In basic neuroscience similar experimental protocols are used to study the orchestration of cortical activity. The acquisition protocol includes quality assurance procedures, subject preparation for the combined MEG/EEG study, and acquisition of evoked-response data with somatosensory, auditory, and visual stimuli. We also demonstrate analysis of the data using the equivalent current dipole model and cortically-constrained minimum-norm estimates. Anatomical MRI data are employed in the analysis for visualization and for deriving boundaries of tissue boundaries for forward modeling and cortical location and orientation constraints for the minimum-norm estimates. PMID:20567210

  15. A radial basis function Galerkin method for inhomogeneous nonlocal diffusion

    DOE PAGESBeta

    Lehoucq, Richard B.; Rowe, Stephen T.

    2016-02-01

    We introduce a discretization for a nonlocal diffusion problem using a localized basis of radial basis functions. The stiffness matrix entries are assembled by a special quadrature routine unique to the localized basis. Combining the quadrature method with the localized basis produces a well-conditioned, sparse, symmetric positive definite stiffness matrix. We demonstrate that both the continuum and discrete problems are well-posed and present numerical results for the convergence behavior of the radial basis function method. As a result, we explore approximating the solution to anisotropic differential equations by solving anisotropic nonlocal integral equations using the radial basis function method.

  16. Numerical solution of convection-diffusion problems in irregular domains mapped onto a circle

    NASA Astrophysics Data System (ADS)

    Asako, Yutaka; Nakamura, Hiroshi; Faghri, Mohammad; Asaba, Makoto

    1991-01-01

    A coordinate transformation methodology has been developed for convection-diffusion problems with an arbitrary solution domain. An algebraic coordinate transformation is used that maps the solution domain onto a circle. The transformed conservation equations are discretized by a control-volume finite difference technique. Sample computations are performed for fully developed flow and heat transfer in a polygonal duct, and for natural convection in a square cavity, to validate the present methodology. The numerical results obtained compared reasonably well, even in the extreme case of a rectangular domain mapped onto a circle.

  17. Damage detection on mesosurfaces using distributed sensor network and spectral diffusion maps

    NASA Astrophysics Data System (ADS)

    Chinde, V.; Cao, L.; Vaidya, U.; Laflamme, S.

    2016-04-01

    In this work, we develop a data-driven method for the diagnosis of damage in mesoscale mechanical structures using an array of distributed sensor networks. The proposed approach relies on comparing intrinsic geometries of data sets corresponding to the undamaged and damaged states of the system. We use a spectral diffusion map approach to identify the intrinsic geometry of the data set. In particular, time series data from distributed sensors is used for the construction of diffusion maps. The low dimensional embedding of the data set corresponding to different damage levels is obtained using a singular value decomposition of the diffusion map. We construct appropriate metrics in the diffusion space to compare the different data sets corresponding to different damage cases. The developed algorithm is applied for damage diagnosis of wind turbine blades. To achieve this goal, we developed a detailed finite element-based model of CX-100 blade in ANSYS using shell elements. Typical damage, such as crack or delamination, will lead to a loss of stiffness, is modeled by altering the stiffness of the laminate layer. One of the main challenges in the development of health monitoring algorithms is the ability to use sensor data with a relatively small signal-to-noise ratio. Our developed diffusion map-based algorithm is shown to be robust to the presence of sensor noise. The proposed diffusion map-based algorithm is advantageous by enabling the comparison of data from numerous sensors of similar or different types of data through data fusion, hereby making it attractive to exploit the distributed nature of sensor arrays. This distributed nature is further exploited for the purpose of damage localization. We perform extensive numerical simulations to demonstrate that the proposed method can successfully determine the extent of damage on the wind turbine blade and also localize the damage. We also present preliminary results for the application of the developed algorithm on

  18. Structural and functional correlates of visual field asymmetry in the human brain by diffusion kurtosis MRI and functional MRI.

    PubMed

    O'Connell, Caitlin; Ho, Leon C; Murphy, Matthew C; Conner, Ian P; Wollstein, Gadi; Cham, Rakie; Chan, Kevin C

    2016-11-01

    Human visual performance has been observed to show superiority in localized regions of the visual field across many classes of stimuli. However, the underlying neural mechanisms remain unclear. This study aims to determine whether the visual information processing in the human brain is dependent on the location of stimuli in the visual field and the corresponding neuroarchitecture using blood-oxygenation-level-dependent functional MRI (fMRI) and diffusion kurtosis MRI, respectively, in 15 healthy individuals at 3 T. In fMRI, visual stimulation to the lower hemifield showed stronger brain responses and larger brain activation volumes than the upper hemifield, indicative of the differential sensitivity of the human brain across the visual field. In diffusion kurtosis MRI, the brain regions mapping to the lower visual field showed higher mean kurtosis, but not fractional anisotropy or mean diffusivity compared with the upper visual field. These results suggested the different distributions of microstructural organization across visual field brain representations. There was also a strong positive relationship between diffusion kurtosis and fMRI responses in the lower field brain representations. In summary, this study suggested the structural and functional brain involvements in the asymmetry of visual field responses in humans, and is important to the neurophysiological and psychological understanding of human visual information processing.

  19. Intra-retinal layer segmentation of 3D optical coherence tomography using coarse grained diffusion map

    PubMed Central

    Kafieh, Raheleh; Rabbani, Hossein; Abramoff, Michael D.; Sonka, Milan

    2013-01-01

    Optical coherence tomography (OCT) is a powerful and noninvasive method for retinal imaging. In this paper, we introduce a fast segmentation method based on a new variant of spectral graph theory named diffusion maps. The research is performed on spectral domain (SD) OCT images depicting macular and optic nerve head appearance. The presented approach does not require edge-based image information in localizing most of boundaries and relies on regional image texture. Consequently, the proposed method demonstrates robustness in situations of low image contrast or poor layer-to-layer image gradients. Diffusion mapping applied to 2D and 3D OCT datasets is composed of two steps, one for partitioning the data into important and less important sections, and another one for localization of internal layers. In the first step, the pixels/voxels are grouped in rectangular/cubic sets to form a graph node. The weights of the graph are calculated based on geometric distances between pixels/voxels and differences of their mean intensity. The first diffusion map clusters the data into three parts, the second of which is the area of interest. The other two sections are eliminated from the remaining calculations. In the second step, the remaining area is subjected to another diffusion map assessment and the internal layers are localized based on their textural similarities. The proposed method was tested on 23 datasets from two patient groups (glaucoma and normals). The mean unsigned border positioning errors (mean ± SD) was 8.52 ± 3.13 and 7.56 ± 2.95 μm for the 2D and 3D methods, respectively. PMID:23837966

  20. Shape-Based Image Matching Using Heat Kernels and Diffusion Maps

    NASA Astrophysics Data System (ADS)

    Vizilter, Yu. V.; Gorbatsevich, V. S.; Rubis, A. Yu.; Zheltov, S. Yu.

    2014-08-01

    2D image matching problem is often stated as an image-to-shape or shape-to-shape matching problem. Such shape-based matching techniques should provide the matching of scene image fragments registered in various lighting, weather and season conditions or in different spectral bands. Most popular shape-to-shape matching technique is based on mutual information approach. Another wellknown approach is a morphological image-to-shape matching proposed by Pytiev. In this paper we propose the new image-to-shape matching technique based on heat kernels and diffusion maps. The corresponding Diffusion Morphology is proposed as a new generalization of Pytiev morphological scheme. The fast implementation of morphological diffusion filtering is described. Experimental comparison of new and aforementioned shape-based matching techniques is reported applying to the TV and IR image matching problem.

  1. Typical diffusion behaviour in packaging polymers - application to functional barriers.

    PubMed

    Dole, Patrice; Feigenbaum, Alexandre E; De La Cruz, Carlos; Pastorelli, Sara; Paseiro, Perfecto; Hankemeier, Thomas; Voulzatis, Yiannis; Aucejo, Susana; Saillard, Philippe; Papaspyrides, Costas

    2006-02-01

    When plastics are collected for recycling, possibly contaminated articles might be recycled into food packaging, and thus the contaminants might subsequently migrate into the food. Multilayer functional barriers may be used to delay and to reduce such migration. The contribution of the work reported here is to establish reference values (at 40 degrees C) of diffusion coefficients and of activation energies to predict the functional barrier efficiency of a broad range of polymers (polyolefins, polystyrene, polyamide, PVC, PET, PVDC, [ethylene vinyl alcohol copolymer], polyacrylonitrile and [ethylene vinyl acetate copolymer]). Diffusion coefficients (D) and activation energies (Ea) were measured and were compiled together with literature data. This allowed identification of new trends for the log D=f(molecular weight) relationships. The slopes were a function of the barrier efficiency of the polymer and temperature. The apparent activation energy of diffusion displayed two domains of variation with molecular weight (M). For low M (gases), there was little variation of Ea. Focusing on larger molecules, high barrier polymers displayed a larger dependence of Ea with M. The apparent activation energy decreased with T. These results suggest a discontinuity between rubbery and glassy polymers.

  2. Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

    NASA Astrophysics Data System (ADS)

    Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G.; Hummer, Gerhard

    2014-09-01

    Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.

  3. Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

    SciTech Connect

    Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G. E-mail: gerhard.hummer@biophys.mpg.de; Hummer, Gerhard E-mail: gerhard.hummer@biophys.mpg.de

    2014-09-21

    Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.

  4. Systematic characterization of protein folding pathways using diffusion maps: Application to Trp-cage miniprotein

    SciTech Connect

    Kim, Sang Beom; Dsilva, Carmeline J.; Debenedetti, Pablo G.; Kevrekidis, Ioannis G.

    2015-02-28

    Understanding the mechanisms by which proteins fold from disordered amino-acid chains to spatially ordered structures remains an area of active inquiry. Molecular simulations can provide atomistic details of the folding dynamics which complement experimental findings. Conventional order parameters, such as root-mean-square deviation and radius of gyration, provide structural information but fail to capture the underlying dynamics of the protein folding process. It is therefore advantageous to adopt a method that can systematically analyze simulation data to extract relevant structural as well as dynamical information. The nonlinear dimensionality reduction technique known as diffusion maps automatically embeds the high-dimensional folding trajectories in a lower-dimensional space from which one can more easily visualize folding pathways, assuming the data lie approximately on a lower-dimensional manifold. The eigenvectors that parametrize the low-dimensional space, furthermore, are determined systematically, rather than chosen heuristically, as is done with phenomenological order parameters. We demonstrate that diffusion maps can effectively characterize the folding process of a Trp-cage miniprotein. By embedding molecular dynamics simulation trajectories of Trp-cage folding in diffusion maps space, we identify two folding pathways and intermediate structures that are consistent with the previous studies, demonstrating that this technique can be employed as an effective way of analyzing and constructing protein folding pathways from molecular simulations.

  5. Mapping mean axon diameter and axonal volume fraction by MRI using temporal diffusion spectroscopy

    PubMed Central

    Xu, Junzhong; Li, Hua; Harkins, Kevin D.; Jiang, Xiaoyu; Xie, Jingping; Kang, Hakmook; Does, Mark D.; Gore, John C.

    2014-01-01

    Mapping mean axon diameter and intra-axonal volume fraction may have significant clinical potential because nerve conduction velocity is directly dependent on axon diameter, and several neurodegenerative diseases affect axons of specific sizes and alter axon counts. Diffusion-weighted MRI methods based on the pulsed gradient spin echo (PGSE) sequence have been reported to be able to assess axon diameter and volume fraction non-invasively. However, due to the relatively long diffusion times used, e.g. > 20 ms, the sensitivity to small axons (diameter < 2 µm) is low, and the derived mean axon diameter has been reported to be overestimated. In the current study, oscillating gradient spin echo (OGSE) diffusion sequences with variable frequency gradients were used to assess rat spinal white matter tracts with relatively short effective diffusion times (1 – 5 ms). In contrast to previous PGSE-based methods, the extra-axonal diffusion cannot be modeled as hindered (Gaussian) diffusion when short diffusion times are used. Appropriate frequency-dependent rates are therefore incorporated into our analysis and validated by histology-based computer simulation of water diffusion. OGSE data were analyzed to derive mean axon diameters and intra-axonal volume fractions of rat spinal white matter tracts (mean axon diameter ~ 1.27 – 5.54 µm). The estimated values were in good agreement with histology, including the small axon diameters (< 2.5 µm). This study establishes a framework for quantification of nerve morphology using the OGSE method with high sensitivity to small axons. PMID:25225002

  6. Atlas-based diffusion tensor imaging correlates of executive function

    PubMed Central

    Nowrangi, Milap A.; Okonkwo, Ozioma; Lyketsos, Constantine; Oishi, Kenichi; Mori, Susumu; Albert, Marilyn; Mielke, Michelle M.

    2015-01-01

    Impairment in executive function (EF) is commonly found in Alzheimer’s Dementia (AD) and Mild Cognitive Impairment (MCI). Atlas-based Diffusion Tensor Imaging (DTI) methods may be useful in relating regional integrity to EF measures in MCI and AD. 66 participants (25 NC, 22 MCI, and 19 AD) received DTI scans and clinical evaluation. DTI scans were applied to a pre-segmented atlas and fractional anisotropy (FA) and mean diffusivity (MD) were calculated. ANOVA was used to assess group differences in frontal, parietal, and cerebellar regions. For regions differing between groups (p<0.01), linear regression examined the relationship between EF scores and regional FA and MD. Anisotropy and diffusivity in frontal and parietal lobe white matter (WM) structures were associated with EF scores in MCI and only frontal lobe structures in AD. EF was more strongly associated with FA than MD. The relationship between EF and anisotropy and diffusivity was strongest in MCI. These results suggest that regional WM integrity is compromised in MCI and AD and that FA may be a better correlate of EF than MD. PMID:25318544

  7. Response variance in functional maps: neural darwinism revisited.

    PubMed

    Takahashi, Hirokazu; Yokota, Ryo; Kanzaki, Ryohei

    2013-01-01

    The mechanisms by which functional maps and map plasticity contribute to cortical computation remain controversial. Recent studies have revisited the theory of neural Darwinism to interpret the learning-induced map plasticity and neuronal heterogeneity observed in the cortex. Here, we hypothesize that the Darwinian principle provides a substrate to explain the relationship between neuron heterogeneity and cortical functional maps. We demonstrate in the rat auditory cortex that the degree of response variance is closely correlated with the size of its representational area. Further, we show that the response variance within a given population is altered through training. These results suggest that larger representational areas may help to accommodate heterogeneous populations of neurons. Thus, functional maps and map plasticity are likely to play essential roles in Darwinian computation, serving as effective, but not absolutely necessary, structures to generate diverse response properties within a neural population.

  8. Effect of disease and recovery on functional anatomy in brain tumor patients: insights from functional MRI and diffusion tensor imaging

    PubMed Central

    Abd-El-Barr, Muhammad M; Saleh, Emam; Huang, Raymond Y; Golby, Alexandra J

    2014-01-01

    Patients with brain tumors provide a unique opportunity to understand functional brain plasticity. Using advanced imaging techniques, such as functional MRI and diffusion tensor imaging, we have gained tremendous knowledge of brain tumor behavior, transformation, infiltration and destruction of nearby structures. Using these advanced techniques as an adjunct with more proven techniques, such as direct cortical stimulation, intraoperative navigation and advanced microsurgical techniques, we now are able to better formulate safer resection trajectories, perform larger resections at reduced risk and better counsel patients and their families about possible complications. Brain mapping in patients with brain tumors and other lesions has shown us that the old idea of fixed function of the adult cerebral cortex is not entirely true. Improving care for patients with brain lesions in the future will depend on better understanding of the functional organization and plasticity of the adult brain. Advanced noninvasive brain imaging will undoubtedly play a role in advancing this understanding. PMID:24660024

  9. Real space mapping of oxygen vacancy diffusion and electrochemical transformations by hysteretic current reversal curve measurements

    DOEpatents

    Kalinin, Sergei V.; Balke, Nina; Borisevich, Albina Y.; Jesse, Stephen; Maksymovych, Petro; Kim, Yunseok; Strelcov, Evgheni

    2014-06-10

    An excitation voltage biases an ionic conducting material sample over a nanoscale grid. The bias sweeps a modulated voltage with increasing maximal amplitudes. A current response is measured at grid locations. Current response reversal curves are mapped over maximal amplitudes of the bias cycles. Reversal curves are averaged over the grid for each bias cycle and mapped over maximal bias amplitudes for each bias cycle. Average reversal curve areas are mapped over maximal amplitudes of the bias cycles. Thresholds are determined for onset and ending of electrochemical activity. A predetermined number of bias sweeps may vary in frequency where each sweep has a constant number of cycles and reversal response curves may indicate ionic diffusion kinetics.

  10. Benchmark calculations of excess electrons in water cluster cavities: balancing the addition of atom-centered diffuse functions versus floating diffuse functions.

    PubMed

    Zhang, Changzhe; Bu, Yuxiang

    2016-09-14

    Diffuse functions have been proved to be especially crucial for the accurate characterization of excess electrons which are usually bound weakly in intermolecular zones far away from the nuclei. To examine the effects of diffuse functions on the nature of the cavity-shaped excess electrons in water cluster surroundings, both the HOMO and LUMO distributions, vertical detachment energies (VDEs) and visible absorption spectra of two selected (H2O)24(-) isomers are investigated in the present work. Two main types of diffuse functions are considered in calculations including the Pople-style atom-centered diffuse functions and the ghost-atom-based floating diffuse functions. It is found that augmentation of atom-centered diffuse functions contributes to a better description of the HOMO (corresponding to the VDE convergence), in agreement with previous studies, but also leads to unreasonable diffuse characters of the LUMO with significant red-shifts in the visible spectra, which is against the conventional point of view that the more the diffuse functions, the better the results. The issue of designing extra floating functions for excess electrons has also been systematically discussed, which indicates that the floating diffuse functions are necessary not only for reducing the computational cost but also for improving both the HOMO and LUMO accuracy. Thus, the basis sets with a combination of partial atom-centered diffuse functions and floating diffuse functions are recommended for a reliable description of the weakly bound electrons. This work presents an efficient way for characterizing the electronic properties of weakly bound electrons accurately by balancing the addition of atom-centered diffuse functions and floating diffuse functions and also by balancing the computational cost and accuracy of the calculated results, and thus is very useful in the relevant calculations of various solvated electron systems and weakly bound anionic systems.

  11. Benchmark calculations of excess electrons in water cluster cavities: balancing the addition of atom-centered diffuse functions versus floating diffuse functions.

    PubMed

    Zhang, Changzhe; Bu, Yuxiang

    2016-09-14

    Diffuse functions have been proved to be especially crucial for the accurate characterization of excess electrons which are usually bound weakly in intermolecular zones far away from the nuclei. To examine the effects of diffuse functions on the nature of the cavity-shaped excess electrons in water cluster surroundings, both the HOMO and LUMO distributions, vertical detachment energies (VDEs) and visible absorption spectra of two selected (H2O)24(-) isomers are investigated in the present work. Two main types of diffuse functions are considered in calculations including the Pople-style atom-centered diffuse functions and the ghost-atom-based floating diffuse functions. It is found that augmentation of atom-centered diffuse functions contributes to a better description of the HOMO (corresponding to the VDE convergence), in agreement with previous studies, but also leads to unreasonable diffuse characters of the LUMO with significant red-shifts in the visible spectra, which is against the conventional point of view that the more the diffuse functions, the better the results. The issue of designing extra floating functions for excess electrons has also been systematically discussed, which indicates that the floating diffuse functions are necessary not only for reducing the computational cost but also for improving both the HOMO and LUMO accuracy. Thus, the basis sets with a combination of partial atom-centered diffuse functions and floating diffuse functions are recommended for a reliable description of the weakly bound electrons. This work presents an efficient way for characterizing the electronic properties of weakly bound electrons accurately by balancing the addition of atom-centered diffuse functions and floating diffuse functions and also by balancing the computational cost and accuracy of the calculated results, and thus is very useful in the relevant calculations of various solvated electron systems and weakly bound anionic systems. PMID:27522987

  12. Functional imaging of small tissue volumes with diffuse optical tomography

    NASA Astrophysics Data System (ADS)

    Klose, Alexander D.; Hielscher, Andreas H.

    2006-03-01

    Imaging of dynamic changes in blood parameters, functional brain imaging, and tumor imaging are the most advanced application areas of diffuse optical tomography (DOT). When dealing with the image reconstruction problem one is faced with the fact that near-infrared photons, unlike X-rays, are highly scattered when they traverse biological tissue. Image reconstruction schemes are required that model the light propagation inside biological tissue and predict measurements on the tissue surface. By iteratively changing the tissue-parameters until the predictions agree with the real measurements, a spatial distribution of optical properties inside the tissue is found. The optical properties can be related to the tissue oxygenation, inflammation, or to the fluorophore concentration of a biochemical marker. If the model of light propagation is inaccurate, the reconstruction process will lead to an inaccurate result as well. Here, we focus on difficulties that are encountered when DOT is employed for functional imaging of small tissue volumes, for example, in cancer studies involving small animals, or human finger joints for early diagnosis of rheumatoid arthritis. Most of the currently employed image reconstruction methods rely on the diffusion theory that is an approximation to the equation of radiative transfer. But, in the cases of small tissue volumes and tissues that contain low scattering regions diffusion theory has been shown to be of limited applicability Therefore, we employ a light propagation model that is based on the equation of radiative transfer, which promises to overcome the limitations.

  13. Characterizing the structure of diffuse emission in Hi-GAL maps

    SciTech Connect

    Elia, D.; Molinari, S.; Rygl, K. L. J.; Di Giorgio, A. M.; Pestalozzi, M.; Liu, S. J.; Strafella, F.; Maruccia, Y.; Schneider, N.; Paladini, R.; Vavrek, R.; Noriega-Crespo, A.; Pezzuto, S.; Schisano, E.; Traficante, A.; Calzoletti, L.; Natoli, P.; Martin, P.; Fukui, Y.; and others

    2014-06-10

    We present a study of the structure of the Galactic interstellar medium (ISM) through the Δ-variance technique, related to the power spectrum and the fractal properties of infrared/submillimeter maps. Through this method, it is possible to provide quantitative parameters, which are useful for characterizing different morphological and physical conditions, and better constraining the theoretical models. In this respect, the Herschel Infrared Galactic Plane Survey, carried out at five photometric bands from 70 to 500 μm, constitutes a unique database for applying statistical tools to a variety of regions across the Milky Way. In this paper, we derive a robust estimate of the power-law portion of the power spectrum of four contiguous 2° × 2° Hi-GAL tiles located in the third Galactic quadrant (217° ≲ ℓ ≲ 225°, –2° ≲ b ≲ 0°). The low level of confusion along the line of sight, testified by CO observations, makes this region an ideal case. We find very different values for the power spectrum slope from tile to tile but also from wavelength to wavelength (2 ≲ β ≲ 3), with similarities between fields attributable to components located at the same distance. Thanks to comparisons with models of turbulence, an explanation of the determined slopes in terms of the fractal geometry is also provided, and possible relations with the underlying physics are investigated. In particular, an anti-correlation between ISM fractal dimension and star formation efficiency is found for the two main distance components observed in these fields. A possible link between the fractal properties of the diffuse emission and the resulting clump mass function is discussed.

  14. Diffusion-Weighted Magnetic Resonance Imaging to Evaluate Major Salivary Gland Function Before and After Radiotherapy

    SciTech Connect

    Dirix, Piet Keyzer, Frederik de; Vandecaveye, Vincent; Stroobants, Sigrid; Hermans, Robert; Nuyts, Sandra

    2008-08-01

    Purpose: To evaluate diffusion-weighted (DW)-MRI as a noninvasive tool to investigate major salivary gland function before and after radiotherapy (RT) for head and neck cancer (HNC). Methods and Materials: DW-MRI was performed in 8 HNC patients before and after parotid-sparing RT (mean dose to the contralateral parotid gland <26 Gy). A DW sequence was performed once at rest and then repeated continuously during salivary stimulation. Apparent diffusion coefficient (ADC) maps for both parotid and submandibular glands were calculated. Findings were compared with salivary gland scintigraphy. Results: Before RT, the mean ADC value at rest was significantly lower in the parotid than in the submandibular glands. During the first 5 min of stimulation, the ADC value of the salivary glands showed a decrease, followed by a steady increase until a peak ADC, significantly higher than the baseline value, was reached after a median of 17 min. The baseline ADC value at rest was significantly higher after RT than before RT in the nonspared salivary glands but not in the spared parotid glands. In the contralateral parotid glands, the same response was seen as before RT. This pattern was completely lost in the nonspared glands. These results corresponded with remaining or loss of salivary function, respectively, as confirmed by salivary gland scintigraphy. Conclusions: Diffusion-weighted-MRI allows noninvasive evaluation of functional changes in the major salivary glands after RT and is a promising tool for investigating radiation-induced xerostomia.

  15. Remediating High School Students' Misconceptions Concerning Diffusion and Osmosis through Concept Mapping and Conceptual Change Text

    NASA Astrophysics Data System (ADS)

    Tekkaya, Ceren

    2003-01-01

    This study investigated the effectiveness of combining conceptual change text and concept mapping strategy on students' understanding of diffusion and osmosis. Students' conceptual understanding of diffusion and osmosis was measured using the Diffusion and Osmosis Diagnostic Test developed by Odom and Barrow (1995). The test was administered as pretest and post-test to a total of 44 ninth-grade students in two intact classes of the same high school located in an urban area. The experimental group was a class of 24 students who received concept mapping and conceptual change text instruction. A class of 20 students comprised the control group who received a traditional instruction. Group Assessment of Logical Thinking Test (GALT) and pretest scores were used as covariates in this study. A pretest-post-test control group design utilising the analysis of covariance (ANCOVA) showed a statistically significant difference between the experimental and control groups in the favour of the experimental group after treatment. The results indicated that while the average percentage of students in the experimental group holding a scientifically correct view had risen from 22.5% to 54.1%, a gain of 31.6%, the percentage of correct responses of the students in the control group had increased from 19.1% to 38.7%, a gain of 19.6% after treatment.

  16. Fine genetic mapping of diffuse non-epidermolytic palmoplantar keratoderma to chromosome 12q11-q13: exclusion of the mapped type II keratins.

    PubMed

    Kelsell, D P; Stevens, H P; Purkis, P E; Talas, U; Rustin, M H; Leigh, I M

    1999-10-01

    Diffuse non-epidermolytic palmoplantar keratoderma (NEPPK) belongs to the heterogeneous group of skin diseases characterized by thickening of the stratum corneum of the palms and soles (1). This autosomal dominant PPK is characterized by a diffuse pattern of palmar and plantar hyperkeratosis giving the affected areas a thickened yellowish appearance with a marked erythematous edge. Linkage of diffuse NEPPK to chromosome 12q11-q13 has been demonstrated in two independent reports (2, 3). In this study, we describe detailed haplotyping with microsatellite markers mapping to this chromosomal region in three diffuse NEPPK pedigrees from the south of England. Fine mapping of a previously identified recombination event and the identification of a common disease haplotype segregating in the three pedigrees places the diffuse NEPPK locus proximal to the type II keratin gene cluster.

  17. Sub-diffusive scattering parameter maps recovered using wide-field high-frequency structured light imaging

    PubMed Central

    Kanick, Stephen Chad; McClatchy, David M.; Krishnaswamy, Venkataramanan; Elliott, Jonathan T.; Paulsen, Keith D.; Pogue, Brian W.

    2014-01-01

    This study investigates the hypothesis that structured light reflectance imaging with high spatial frequency patterns (fx) can be used to quantitatively map the anisotropic scattering phase function distribution (P(θs)) in turbid media. Monte Carlo simulations were used in part to establish a semi-empirical model of demodulated reflectance (Rd) in terms of dimensionless scattering (μs′fx−1) and γ, a metric of the first two moments of the P(θs) distribution. Experiments completed in tissue-simulating phantoms showed that simultaneous analysis of Rd spectra sampled at multiple fx in the frequency range [0.05-0.5] mm−1 allowed accurate estimation of both μs′(λ) in the relevant tissue range [0.4-1.8] mm−1, and γ(λ) in the range [1.4-1.75]. Pilot measurements of a healthy volunteer exhibited γ-based contrast between scar tissue and surrounding normal skin, which was not as apparent in wide field diffuse imaging. These results represent the first wide-field maps to quantify sub-diffuse scattering parameters, which are sensitive to sub-microscopic tissue structures and composition, and therefore, offer potential for fast diagnostic imaging of ultrastructure on a size scale that is relevant to surgical applications. PMID:25360357

  18. Fiber-bundle microendoscopy with sub-diffuse reflectance spectroscopy and intensity mapping for multimodal optical biopsy of stratified epithelium

    PubMed Central

    Greening, Gage J.; James, Haley M.; Powless, Amy J.; Hutcheson, Joshua A.; Dierks, Mary K.; Rajaram, Narasimhan; Muldoon, Timothy J.

    2015-01-01

    Early detection of structural or functional changes in dysplastic epithelia may be crucial for improving long-term patient care. Recent work has explored myriad non-invasive or minimally invasive “optical biopsy” techniques for diagnosing early dysplasia, such as high-resolution microendoscopy, a method to resolve sub-cellular features of apical epithelia, as well as broadband sub-diffuse reflectance spectroscopy, a method that evaluates bulk health of a small volume of tissue. We present a multimodal fiber-based microendoscopy technique that combines high-resolution microendoscopy, broadband (450-750 nm) sub-diffuse reflectance spectroscopy (sDRS) at two discrete source-detector separations (374 and 730 μm), and sub-diffuse reflectance intensity mapping (sDRIM) using a 635 nm laser. Spatial resolution, magnification, field-of-view, and sampling frequency were determined. Additionally, the ability of the sDRS modality to extract optical properties over a range of depths is reported. Following this, proof-of-concept experiments were performed on tissue-simulating phantoms made with poly(dimethysiloxane) as a substrate material with cultured MDA-MB-468 cells. Then, all modalities were demonstrated on a human melanocytic nevus from a healthy volunteer and on resected colonic tissue from a murine model. Qualitative in vivo image data is correlated with reduced scattering and absorption coefficients. PMID:26713207

  19. Fiber-bundle microendoscopy with sub-diffuse reflectance spectroscopy and intensity mapping for multimodal optical biopsy of stratified epithelium.

    PubMed

    Greening, Gage J; James, Haley M; Powless, Amy J; Hutcheson, Joshua A; Dierks, Mary K; Rajaram, Narasimhan; Muldoon, Timothy J

    2015-12-01

    Early detection of structural or functional changes in dysplastic epithelia may be crucial for improving long-term patient care. Recent work has explored myriad non-invasive or minimally invasive "optical biopsy" techniques for diagnosing early dysplasia, such as high-resolution microendoscopy, a method to resolve sub-cellular features of apical epithelia, as well as broadband sub-diffuse reflectance spectroscopy, a method that evaluates bulk health of a small volume of tissue. We present a multimodal fiber-based microendoscopy technique that combines high-resolution microendoscopy, broadband (450-750 nm) sub-diffuse reflectance spectroscopy (sDRS) at two discrete source-detector separations (374 and 730 μm), and sub-diffuse reflectance intensity mapping (sDRIM) using a 635 nm laser. Spatial resolution, magnification, field-of-view, and sampling frequency were determined. Additionally, the ability of the sDRS modality to extract optical properties over a range of depths is reported. Following this, proof-of-concept experiments were performed on tissue-simulating phantoms made with poly(dimethysiloxane) as a substrate material with cultured MDA-MB-468 cells. Then, all modalities were demonstrated on a human melanocytic nevus from a healthy volunteer and on resected colonic tissue from a murine model. Qualitative in vivo image data is correlated with reduced scattering and absorption coefficients.

  20. Random walks, diffusion limited aggregation in a wedge, and average conformal maps.

    PubMed

    Sander, Leonard M; Somfai, Ellák

    2005-06-01

    We investigate diffusion-limited aggregation (DLA) in a wedge geometry. Arneodo and collaborators have suggested that the ensemble average of DLA cluster density should be close to the noise-free selected Saffman-Taylor finger. We show that a different, but related, ensemble average, that of the conformal maps associated with random clusters, yields a nontrivial shape which is also not far from the Saffman-Taylor finger. However, we have previously demonstrated that the same average of DLA in a channel geometry is not the Saffman-Taylor finger. This casts doubt on the idea that the average of noisy diffusion-limited growth is governed by a simple transcription of noise-free results. PMID:16035911

  1. Photoelectric scanner makes detailed work function maps of metal surface

    NASA Technical Reports Server (NTRS)

    Rasor, N. S.

    1966-01-01

    Photoelectric scanning device maps the work function of a metal surface by scanning it with a light spot and measuring the resulting photocurrent. The device is capable of use over a range of surface temperatures.

  2. Coarse-grained particle model for pedestrian flow using diffusion maps

    NASA Astrophysics Data System (ADS)

    Marschler, Christian; Starke, Jens; Liu, Ping; Kevrekidis, Ioannis G.

    2014-01-01

    Interacting particle systems constitute the dynamic model of choice in a variety of application areas. A prominent example is pedestrian dynamics, where good design of escape routes for large buildings and public areas can improve evacuation in emergency situations, avoiding exit blocking and the ensuing panic. Here we employ diffusion maps to study the coarse-grained dynamics of two pedestrian crowds trying to pass through a door from opposite sides. These macroscopic variables and the associated smooth embeddings lead to a better description and a clearer understanding of the nature of the transition to oscillatory dynamics. We also compare the results to those obtained through intuitively chosen macroscopic variables.

  3. Joint brain connectivity estimation from diffusion and functional MRI data

    NASA Astrophysics Data System (ADS)

    Chu, Shu-Hsien; Lenglet, Christophe; Parhi, Keshab K.

    2015-03-01

    Estimating brain wiring patterns is critical to better understand the brain organization and function. Anatomical brain connectivity models axonal pathways, while the functional brain connectivity characterizes the statistical dependencies and correlation between the activities of various brain regions. The synchronization of brain activity can be inferred through the variation of blood-oxygen-level dependent (BOLD) signal from functional MRI (fMRI) and the neural connections can be estimated using tractography from diffusion MRI (dMRI). Functional connections between brain regions are supported by anatomical connections, and the synchronization of brain activities arises through sharing of information in the form of electro-chemical signals on axon pathways. Jointly modeling fMRI and dMRI data may improve the accuracy in constructing anatomical connectivity as well as functional connectivity. Such an approach may lead to novel multimodal biomarkers potentially able to better capture functional and anatomical connectivity variations. We present a novel brain network model which jointly models the dMRI and fMRI data to improve the anatomical connectivity estimation and extract the anatomical subnetworks associated with specific functional modes by constraining the anatomical connections as structural supports to the functional connections. The key idea is similar to a multi-commodity flow optimization problem that minimizes the cost or maximizes the efficiency for flow configuration and simultaneously fulfills the supply-demand constraint for each commodity. In the proposed network, the nodes represent the grey matter (GM) regions providing brain functionality, and the links represent white matter (WM) fiber bundles connecting those regions and delivering information. The commodities can be thought of as the information corresponding to brain activity patterns as obtained for instance by independent component analysis (ICA) of fMRI data. The concept of information

  4. Joint brain connectivity estimation from diffusion and functional MRI data

    NASA Astrophysics Data System (ADS)

    Chu, Shu-Hsien; Lenglet, Christophe; Parhi, Keshab K.

    2015-03-01

    Estimating brain wiring patterns is critical to better understand the brain organization and function. Anatomical brain connectivity models axonal pathways, while the functional brain connectivity characterizes the statistical dependencies and correlation between the activities of various brain regions. The synchronization of brain activity can be inferred through the variation of blood-oxygen-level dependent (BOLD) signal from functional MRI (fMRI) and the neural connections can be estimated using tractography from diffusion MRI (dMRI). Functional connections between brain regions are supported by anatomical connections, and the synchronization of brain activities arises through sharing of information in the form of electro-chemical signals on axon pathways. Jointly modeling fMRI and dMRI data may improve the accuracy in constructing anatomical connectivity as well as functional connectivity. Such an approach may lead to novel multimodal biomarkers potentially able to better capture functional and anatomical connectivity variations. We present a novel brain network model which jointly models the dMRI and fMRI data to improve the anatomical connectivity estimation and extract the anatomical subnetworks associated with specific functional modes by constraining the anatomical connections as structural supports to the functional connections. The key idea is similar to a multi-commodity flow optimization problem that minimizes the cost or maximizes the efficiency for flow configuration and simultaneously fulfills the supply-demand constraint for each commodity. In the proposed network, the nodes represent the grey matter (GM) regions providing brain functionality, and the links represent white matter (WM) fiber bundles connecting those regions and delivering information. The commodities can be thought of as the information corresponding to brain activity patterns as obtained for instance by independent component analysis (ICA) of fMRI data. The concept of information

  5. Diffusion of innovations dynamics, biological growth and catenary function

    NASA Astrophysics Data System (ADS)

    Guseo, Renato

    2016-12-01

    The catenary function has a well-known role in determining the shape of chains and cables supported at their ends under the force of gravity. This enables design using a specific static equilibrium over space. Its reflected version, the catenary arch, allows the construction of bridges and arches exploiting the dual equilibrium property under uniform compression. In this paper, we emphasize a further connection with well-known aggregate biological growth models over time and the related diffusion of innovation key paradigms (e.g., logistic and Bass distributions over time) that determine self-sustaining evolutionary growth dynamics in naturalistic and socio-economic contexts. Moreover, we prove that the 'local entropy function', related to a logistic distribution, is a catenary and vice versa. This special invariance may be explained, at a deeper level, through the Verlinde's conjecture on the origin of gravity as an effect of the entropic force.

  6. Cubic map algebra functions for spatio-temporal analysis

    USGS Publications Warehouse

    Mennis, J.; Viger, R.; Tomlin, C.D.

    2005-01-01

    We propose an extension of map algebra to three dimensions for spatio-temporal data handling. This approach yields a new class of map algebra functions that we call "cube functions." Whereas conventional map algebra functions operate on data layers representing two-dimensional space, cube functions operate on data cubes representing two-dimensional space over a third-dimensional period of time. We describe the prototype implementation of a spatio-temporal data structure and selected cube function versions of conventional local, focal, and zonal map algebra functions. The utility of cube functions is demonstrated through a case study analyzing the spatio-temporal variability of remotely sensed, southeastern U.S. vegetation character over various land covers and during different El Nin??o/Southern Oscillation (ENSO) phases. Like conventional map algebra, the application of cube functions may demand significant data preprocessing when integrating diverse data sets, and are subject to limitations related to data storage and algorithm performance. Solutions to these issues include extending data compression and computing strategies for calculations on very large data volumes to spatio-temporal data handling.

  7. Mapping Spatio-Temporal Diffusion inside the Human Brain Using a Numerical Solution of the Diffusion Equation

    PubMed Central

    Zhan, Wang; Jiang, Li; Loew, Murray; Yang, Yihong

    2008-01-01

    Diffusion is an important mechanism for molecular transport in living biological tissues. Diffusion magnetic resonance imaging (dMRI) provides a unique probe to examine microscopic structures of the tissues in vivo, but current dMRI techniques usually ignore the spatio-temporal evolution process of the diffusive medium. In the present study, we demonstrate the feasibility to reveal the spatio-temporal diffusion process inside the human brain based on a numerical solution of the diffusion equation. Normal human subjects were scanned with a diffusion tensor imaging (DTI) technique on a 3-Tesla MRI scanner, and the diffusion tensor in each voxel was calculated from the DTI data. The diffusion equation, a partial-derivative description of Fick’s Law for the diffusion process, was discretized into equivalent algebraic equations. A finite-difference method was employed to obtain the numerical solution of the diffusion equation with a Crank-Nicholson iteration scheme to enhance the numerical stability. By specifying boundary and initial conditions, the spatio-temporal evolution of the diffusion process inside the brain can be virtually reconstructed. Our results exhibit similar medium profiles and diffusion coefficients as those of light fluorescence dextrans measured in integrative optical imaging experiments. The proposed method highlights the feasibility to non-invasively estimate the macroscopic diffusive transport time for a molecule in a given region of the brain. PMID:18440744

  8. Rapid exploration of configuration space with diffusion-map-directed molecular dynamics.

    PubMed

    Zheng, Wenwei; Rohrdanz, Mary A; Clementi, Cecilia

    2013-10-24

    The gap between the time scale of interesting behavior in macromolecular systems and that which our computational resources can afford often limits molecular dynamics (MD) from understanding experimental results and predicting what is inaccessible in experiments. In this paper, we introduce a new sampling scheme, named diffusion-map-directed MD (DM-d-MD), to rapidly explore molecular configuration space. The method uses a diffusion map to guide MD on the fly. DM-d-MD can be combined with other methods to reconstruct the equilibrium free energy, and here, we used umbrella sampling as an example. We present results from two systems: alanine dipeptide and alanine-12. In both systems, we gain tremendous speedup with respect to standard MD both in exploring the configuration space and reconstructing the equilibrium distribution. In particular, we obtain 3 orders of magnitude of speedup over standard MD in the exploration of the configurational space of alanine-12 at 300 K with DM-d-MD. The method is reaction coordinate free and minimally dependent on a priori knowledge of the system. We expect wide applications of DM-d-MD to other macromolecular systems in which equilibrium sampling is not affordable by standard MD.

  9. Application of diffusion maps to identify human factors of self-reported anomalies in aviation.

    PubMed

    Andrzejczak, Chris; Karwowski, Waldemar; Mikusinski, Piotr

    2012-01-01

    A study investigating what factors are present leading to pilots submitting voluntary anomaly reports regarding their flight performance was conducted. Diffusion Maps (DM) were selected as the method of choice for performing dimensionality reduction on text records for this study. Diffusion Maps have seen successful use in other domains such as image classification and pattern recognition. High-dimensionality data in the form of narrative text reports from the NASA Aviation Safety Reporting System (ASRS) were clustered and categorized by way of dimensionality reduction. Supervised analyses were performed to create a baseline document clustering system. Dimensionality reduction techniques identified concepts or keywords within records, and allowed the creation of a framework for an unsupervised document classification system. Results from the unsupervised clustering algorithm performed similarly to the supervised methods outlined in the study. The dimensionality reduction was performed on 100 of the most commonly occurring words within 126,000 text records describing commercial aviation incidents. This study demonstrates that unsupervised machine clustering and organization of incident reports is possible based on unbiased inputs. Findings from this study reinforced traditional views on what factors contribute to civil aviation anomalies, however, new associations between previously unrelated factors and conditions were also found.

  10. Regional myocardial contractile function: multiparametric strain mapping.

    PubMed

    Cupps, Brian P; Taggar, Ajay K; Reynolds, Lina M; Lawton, Jennifer S; Pasque, Michael K

    2010-06-01

    Magnetic resonance imaging (MRI) with tissue tagging enables the quantification of multiple strain indices that can be combined through normalization into a single multiparametric index of regional myocardial contractile function. The aim of this study was to test the ability of multiparametric strain analysis to quantify regional differences in contractile function in an ovine model of myocardial injury. Regional variance in myocardial contractile function was induced in eight sheep by the ligation of the blood supply to the anterior and apical left ventricular (LV) myocardial walls. LV systolic strain was obtained from tissue tagged MRI images. A normal strain database (n=50) defines all parameters of systolic strain and allows normalization of regional function at 15,300 LV points by calculation of a z-score. Multiparametric systolic strain z-scores were therefore determined for 15,300 points in each injured sheep left ventricle. Multiparametric z-scores were found to vary significantly by region (P<0.001). z-Scores in regions remote to the infarct were found to be significantly smaller than those in the regions most likely to include infarcted myocardium. In this pre-clinical evaluation of MRI-based multiparametric strain analysis, it accurately quantified and visually defined regional differences in myocardial contractile function.

  11. Mapping of health system functions to strengthen priority programs. The case of maternal health in Mexico

    PubMed Central

    2011-01-01

    Background Health system strengthening is critical to ensure the integration and scaling-up of priority health promotion, disease prevention and control programs. Normative guidelines are available to address health system function imbalances while strategic and analytical frameworks address critical functions in complex systems. Tacit knowledge-based health system constructs can help identify actors' perspectives, contributing to improve strengthening strategies. Using maternal health as an example, this paper maps and analyses the health system functions that critical actors charged with formulating and delivering priority health programs consider important for their success. Methods Using concept mapping qualitative and statistical methods, health system functions were mapped for different categories of actors in high maternal mortality states of Mexico and at the federal level. Functions within and across maps were analyzed for degree of classification, importance, feasibility and coding. Results Hospital infrastructure and human resource training are the most prominent functions in the maternal health system, associated to federal efforts to support emergency obstetric care. Health policy is a highly diffuse function while program development, intercultural and community participation and social networks are clearly stated although less focused and with lower perceived importance. The importance of functions is less correlated between federal and state decision makers, between federal decision makers and reproductive health/local health area program officers and between state decision makers and system-wide support officers. Two sets of oppositions can be observed in coding across functions: health sector vs. social context; and given structures vs. manageable processes. Conclusions Concept mapping enabled the identification of critical functions constituting adaptive maternal health systems, including aspects of actor perspectives that are seldom included in

  12. Diffusion of responsibility attenuates altruistic punishment: A functional magnetic resonance imaging effective connectivity study.

    PubMed

    Feng, Chunliang; Deshpande, Gopikrishna; Liu, Chao; Gu, Ruolei; Luo, Yue-Jia; Krueger, Frank

    2016-02-01

    Humans altruistically punish violators of social norms to enforce cooperation and pro-social behaviors. However, such altruistic behaviors diminish when others are present, due to a diffusion of responsibility. We investigated the neural signatures underlying the modulations of diffusion of responsibility on altruistic punishment, conjoining a third-party punishment task with event-related functional magnetic resonance imaging and multivariate Granger causality mapping. In our study, participants acted as impartial third-party decision-makers and decided how to punish norm violations under two different social contexts: alone (i.e., full responsibility) or in the presence of putative other third-party decision makers (i.e., diffused responsibility). Our behavioral results demonstrated that the diffusion of responsibility served as a mediator of context-dependent punishment. In the presence of putative others, participants who felt less responsible also punished less severely in response to norm violations. Our neural results revealed that underlying this behavioral effect was a network of interconnected brain regions. For unfair relative to fair splits, the presence of others led to attenuated responses in brain regions implicated in signaling norm violations (e.g., AI) and to increased responses in brain regions implicated in calculating values of norm violations (e.g., vmPFC, precuneus) and mentalizing about others (dmPFC). The dmPFC acted as the driver of the punishment network, modulating target regions, such as AI, vmPFC, and precuneus, to adjust altruistic punishment behavior. Our results uncovered the neural basis of the influence of diffusion of responsibility on altruistic punishment and highlighted the role of the mentalizing network in this important phenomenon. Hum Brain Mapp 37:663-677, 2016. © 2015 Wiley Periodicals, Inc.

  13. A large deformation diffeomorphic metric mapping solution for diffusion spectrum imaging datasets.

    PubMed

    Hsu, Yung-Chin; Hsu, Ching-Han; Tseng, Wen-Yih Isaac

    2012-11-01

    Spatial transformation for diffusion spectrum imaging (DSI) is an important step for group analyses of DSI datasets. In this study, we developed a transformation method for DSI datasets under the framework of large deformation diffeomorphic metric mapping (LDDMM), which is termed LDDMM-DSI. The proposed method made use of the fact that a DSI dataset is 6D, and generalized the original 2D/3D LDDMM algorithm to the 6D case with some modifications made for the DSI datasets. In this manner, the conventional reorientation problem that arises from transforming diffusion-weighted datasets was avoided by making the DSI datasets capable of being freely deformed in the q-space. The algorithm treated the data-matching task as a variational problem under the LDDMM framework and sought optimal velocity fields from which the generated transformations were diffeomorphic and the transformation curve was a geodesic. The mathematical materials and numerical implementation are detailed in the paper, and experiments were performed to analyze the proposed method on real brain DSI datasets. The results showed that the method was capable of registering different DSI datasets in both global structural shapes and local diffusion profiles. In conclusion, the proposed method can facilitate group analyses of DSI datasets and the generation of a DSI template.

  14. Detecting Buried Archaeological Remains by the Use of Geophysical Data Processing with 'Diffusion Maps' Methodology

    NASA Astrophysics Data System (ADS)

    Eppelbaum, Lev

    2015-04-01

    Geophysical methods are prompt, non-invasive and low-cost tool for quantitative delineation of buried archaeological targets. However, taking into account the complexity of geological-archaeological media, some unfavourable environments and known ambiguity of geophysical data analysis, a single geophysical method examination might be insufficient (Khesin and Eppelbaum, 1997). Besides this, it is well-known that the majority of inverse-problem solutions in geophysics are ill-posed (e.g., Zhdanov, 2002), which means, according to Hadamard (1902), that the solution does not exist, or is not unique, or is not a continuous function of observed geophysical data (when small perturbations in the observations will cause arbitrary mistakes in the solution). This fact has a wide application for informational, probabilistic and wavelet methodologies in archaeological geophysics (Eppelbaum, 2014a). The goal of the modern geophysical data examination is to detect the geophysical signatures of buried targets at noisy areas via the analysis of some physical parameters with a minimal number of false alarms and miss-detections (Eppelbaum et al., 2011; Eppelbaum, 2014b). The proposed wavelet approach to recognition of archaeological targets (AT) by the examination of geophysical method integration consists of advanced processing of each geophysical method and nonconventional integration of different geophysical methods between themselves. The recently developed technique of diffusion clustering combined with the abovementioned wavelet methods was utilized to integrate the geophysical data and detect existing irregularities. The approach is based on the wavelet packet techniques applied as to the geophysical images (or graphs) versus coordinates. For such an analysis may be utilized practically all geophysical methods (magnetic, gravity, seismic, GPR, ERT, self-potential, etc.). On the first stage of the proposed investigation a few tens of typical physical-archaeological models (PAM

  15. Two-dimensional finite element neutron diffusion analysis using hierarchic shape functions

    SciTech Connect

    Carpenter, D.C.

    1997-04-01

    Recent advances have been made in the use of p-type finite element method (FEM) for structural and fluid dynamics problems that hold promise for reactor physics problems. These advances include using hierarchic shape functions, element-by-element iterative solvers and more powerful mapping techniques. Use of the hierarchic shape functions allows greater flexibility and efficiency in implementing energy-dependent flux expansions and incorporating localized refinement of the solution space. The irregular matrices generated by the p-type FEM can be solved efficiently using element-by-element conjugate gradient iterative solvers. These solvers do not require storage of either the global or local stiffness matrices and can be highly vectorized. Mapping techniques based on blending function interpolation allow exact representation of curved boundaries using coarse element grids. These features were implemented in a developmental two-dimensional neutron diffusion program based on the use of hierarchic shape functions (FEM2DH). Several aspects in the effective use of p-type analysis were explored. Two choices of elemental preconditioning were examined--the proper selection of the polynomial shape functions and the proper number of functions to use. Of the five shape function polynomials tested, the integral Legendre functions were the most effective. The serendipity set of functions is preferable over the full tensor product set. Two global preconditioners were also examined--simple diagonal and incomplete Cholesky. The full effectiveness of the finite element methodology was demonstrated on a two-region, two-group cylindrical problem but solved in the x-y coordinate space, using a non-structured element grid. The exact, analytic eigenvalue solution was achieved with FEM2DH using various combinations of element grids and flux expansions.

  16. Spectral analysis of mixing in chaotic flows via the mapping matrix formalism: Inclusion of molecular diffusion and quantitative eigenvalue estimate in the purely convective limit

    NASA Astrophysics Data System (ADS)

    Gorodetskyi, O.; Giona, M.; Anderson, P. D.

    2012-07-01

    This paper extends the mapping matrix formalism to include the effects of molecular diffusion in the analysis of mixing processes in chaotic flows. The approach followed is Lagrangian, by considering the stochastic formulation of advection-diffusion processes via the Langevin equation for passive fluid particle motion. In addition, the inclusion of diffusional effects in the mapping matrix formalism permits to frame the spectral properties of mapping matrices in the purely convective limit in a quantitative way. Specifically, the effects of coarse graining can be quantified by means of an effective Péclet number that scales as the second power of the linear lattice size. This simple result is sufficient to predict the scaling exponents characterizing the behavior of the eigenvalue spectrum of the advection-diffusion operator in chaotic flows as a function of the Péclet number, exclusively from purely kinematic data, by varying the grid resolution. Simple but representative model systems and realistic physically realizable flows are considered under a wealth of different kinematic conditions-from the presence of large quasi-periodic islands intertwined by chaotic regions, to almost globally chaotic conditions, to flows possessing "sticky islands"-providing a fairly comprehensive characterization of the different numerical phenomenologies that may occur in the quantitative analysis of mapping matrices, and ultimately of chaotic mixing processes.

  17. Intraoperative Functional Mapping and Monitoring during Glioma Surgery

    PubMed Central

    SAITO, Taiichi; MURAGAKI, Yoshihiro; MARUYAMA, Takashi; TAMURA, Manabu; NITTA, Masayuki; OKADA, Yoshikazu

    2015-01-01

    Glioma surgery represents a significant advance with respect to improving resection rates using new surgical techniques, including intraoperative functional mapping, monitoring, and imaging. Functional mapping under awake craniotomy can be used to detect individual eloquent tissues of speech and/or motor functions in order to prevent unexpected deficits and promote extensive resection. In addition, monitoring the patient’s neurological findings during resection is also very useful for maximizing the removal rate and minimizing deficits by alarming that the touched area is close to eloquent regions and fibers. Assessing several types of evoked potentials, including motor evoked potentials (MEPs), sensory evoked potentials (SEPs) and visual evoked potentials (VEPs), is also helpful for performing surgical monitoring in patients under general anesthesia (GA). We herein review the utility of intraoperative mapping and monitoring the assessment of neurological findings, with a particular focus on speech and the motor function, in patients undergoing glioma surgery. PMID:25744346

  18. Intraoperative Functional Mapping and Monitoring during Glioma Surgery.

    PubMed

    Saito, Taiichi; Muragaki, Yoshihiro; Maruyama, Takashi; Tamura, Manabu; Nitta, Masayuki; Okada, Yoshikazu

    2015-01-01

    Glioma surgery represents a significant advance with respect to improving resection rates using new surgical techniques, including intraoperative functional mapping, monitoring, and imaging. Functional mapping under awake craniotomy can be used to detect individual eloquent tissues of speech and/or motor functions in order to prevent unexpected deficits and promote extensive resection. In addition, monitoring the patient’s neurological findings during resection is also very useful for maximizing the removal rate and minimizing deficits by alarming that the touched area is close to eloquent regions and fibers. Assessing several types of evoked potentials, including motor evoked potentials (MEPs), sensory evoked potentials (SEPs) and visual evoked potentials (VEPs), is also helpful for performing surgical monitoring in patients under general anesthesia (GA). We herein review the utility of intraoperative mapping and monitoring the assessment of neurological findings, with a particular focus on speech and the motor function, in patients undergoing glioma surgery. PMID:26236798

  19. Using Immediate-Early Genes to Map Hippocampal Subregional Functions

    ERIC Educational Resources Information Center

    Kubik, Stepan; Miyashita, Teiko; Guzowski, John F.

    2007-01-01

    Different functions have been suggested for the hippocampus and its subdivisions along both transversal and longitudinal axes. Expression of immediate-early genes (IEGs) has been used to map specific functions onto neuronal activity in different areas of the brain including the hippocampus (IEG imaging). Here we review IEG studies on hippocampal…

  20. Diffeomorphic metric mapping and probabilistic atlas generation of hybrid diffusion imaging based on BFOR signal basis.

    PubMed

    Du, Jia; Hosseinbor, A Pasha; Chung, Moo K; Bendlin, Barbara B; Suryawanshi, Gaurav; Alexander, Andrew L; Qiu, Anqi

    2014-10-01

    We first propose a large deformation diffeomorphic metric mapping algorithm to align multiple b-value diffusion weighted imaging (mDWI) data, specifically acquired via hybrid diffusion imaging (HYDI). We denote this algorithm as LDDMM-HYDI. We then propose a Bayesian probabilistic model for estimating the white matter atlas from HYDIs. We adopt the work given in Hosseinbor et al. (2013) and represent the q-space diffusion signal with the Bessel Fourier orientation reconstruction (BFOR) signal basis. The BFOR framework provides the representation of mDWI in the q-space and the analytic form of the emsemble average propagator (EAP) reconstruction, as well as reduces memory requirement. In addition, since the BFOR signal basis is orthonormal, the L(2) norm that quantifies the differences in the q-space signals of any two mDWI datasets can be easily computed as the sum of the squared differences in the BFOR expansion coefficients. In this work, we show that the reorientation of the q-space signal due to spatial transformation can be easily defined on the BFOR signal basis. We incorporate the BFOR signal basis into the LDDMM framework and derive the gradient descent algorithm for LDDMM-HYDI with explicit orientation optimization. Additionally, we extend the previous Bayesian atlas estimation framework for scalar-valued images to HYDIs and derive the expectation-maximization algorithm for solving the HYDI atlas estimation problem. Using real HYDI datasets, we show that the Bayesian model generates the white matter atlas with anatomical details. Moreover, we show that it is important to consider the variation of mDWI reorientation due to a small change in diffeomorphic transformation in the LDDMM-HYDI optimization and to incorporate the full information of HYDI for aligning mDWI. Finally, we show that the LDDMM-HYDI outperforms the LDDMM algorithm with diffusion tensors generated from each shell of HYDI.

  1. Improved fidelity of brain microstructure mapping from single-shell diffusion MRI.

    PubMed

    Taquet, Maxime; Scherrer, Benoit; Boumal, Nicolas; Peters, Jurriaan M; Macq, Benoit; Warfield, Simon K

    2015-12-01

    Diffusion weighted imaging (DWI) is sensitive to alterations in the diffusion of water molecules caused by microstructural barriers. Different microstructural compartments are characterized by differences in DWI signal. Diffusion tensor imaging conflates the signal from these compartments into a single tensor, which poorly represents multiple white matter fascicles and extra-axonal space. Diffusion compartment imaging (DCI) models overcome this limitation by providing parametric representations for the signal contribution of each compartment, thereby improving the fidelity of brain microstructure mapping. However, current approaches fail to identify DCI model parameters from conventional single-shell DWI with the desired accuracy. It has been demonstrated that part of this inaccuracy is due to the ill-posedness of the estimation of DCI model parameters from conventional single-shell acquisitions. In this paper, we propose to regularize the estimation problem for single-shell DWI by learning a prior distribution of DCI model parameters from DWI acquired at multiple b-values in an external population of subjects. We demonstrate that this population-informed prior enables, for the first time, accurate estimation of DCI models from single-shell DWI typically acquired in clinical practice. We validated our approach on synthetic and in vivo data of healthy subjects and patients with autism spectrum disorder. We applied the approach to population studies of brain microstructure in autism and found that introducing a population-informed prior leads to reliable detection of group differences. Our algorithm enables novel investigation from large existing DWI datasets in normal development and in disease and injury. PMID:26529580

  2. Mapping brain function in freely moving subjects

    PubMed Central

    Holschneider, Daniel P.; Maarek, Jean-Michel I.

    2014-01-01

    Expression of many fundamental mammalian behaviors such as, for example, aggression, mating, foraging or social behaviors, depend on locomotor activity. A central dilemma in the functional neuroimaging of these behaviors has been the fact that conventional neuroimaging techniques generally rely on immobilization of the subject, which extinguishes all but the simplest activity. Ideally, imaging could occur in freely moving subjects, while presenting minimal interference with the subject’s natural behavior. Here we provide an overview of several approaches that have been undertaken in the past to achieve this aim in both tethered and freely moving animals, as well as in nonrestrained human subjects. Applications of specific radiotracers to single photon emission computed tomography and positron emission tomography are discussed in which brain activation is imaged after completion of the behavioral task and capture of the tracer. Potential applications to clinical neuropsychiatry are discussed, as well as challenges inherent to constraint-free functional neuroimaging. Future applications of these methods promise to increase our understanding of the neural circuits underlying mammalian behavior in health and disease. PMID:15465134

  3. Antibody mapping of functional domains in vinculin.

    PubMed Central

    Westmeyer, A; Ruhnau, K; Wegner, A; Jockusch, B M

    1990-01-01

    We have analyzed the functional domain structure of vinculin, a protein involved in linking microfilaments to the cytoplasmic face of cell membranes in animal cells. For this purpose, we used several monoclonal antibodies raised against chicken gizzard vinculin whose epitopes could be assigned to discrete regions in the vinculin sequence by immunoblotting of proteolytic fragments combined with N-terminal amino acid sequencing. Two of these antibodies induced the disruption of stress fibers and changed the number of morphology of focal contacts after microinjection in chicken embryo fibroblasts. Based on the location of its epitope in comparison with vinculin domains previously identified by other groups, we propose that one of these antibodies (15B7) interferes with the binding of vinculin to talin, the most peripheral of the microfilament proteins. The second antibody (14C10) binds within a region comprising three internal repeats and might therefore distort the inner architecture of vinculin. A third antibody (As3) inhibited the binding of F-actin to vinculin in an in vitro assay but had no effect on the microfilament system in cells. These data emphasize the role of vinculin as a key protein in microfilament-membrane linkage and support previous work on a direct interaction between vinculin and actin. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 6. Fig. 7. Fig. 8. PMID:1694125

  4. Mapping functional regions of transcription factor TFIIIA.

    PubMed Central

    Vrana, K E; Churchill, M E; Tullius, T D; Brown, D D

    1988-01-01

    Functional deletion mutants of the trans-acting factor TFIIIA, truncated at both ends of the molecule, have been expressed by in vitro transcription of a cDNA clone and subsequent cell-free translation of the synthetic mRNAs. A region of TFIIIA 19 amino acids or less, near the carboxyl terminus, is critical for maximal transcription and lies outside the DNA-binding domain. The elongated protein can be aligned over the internal control region (ICR) of the Xenopus 5S RNA gene with its carboxyl terminus oriented toward the 5' end of the gene and its amino terminus oriented toward the 3' end of the gene. The nine "zinc fingers" and the linkers that separate them comprise 80% of the protein mass and correspond to the DNA-binding domain of TFIIIA. The zinc fingers near the amino terminus of the protein contribute more to the overall binding energy of the protein to the ICR than do the zinc fingers near the carboxyl end. The most striking feature of TFIIIA is its modular structure. This is demonstrated by the fact that each zinc finger binds to just one of three short nucleotide sequences within the ICR. Images PMID:2837652

  5. Mapping functional regions of transcription factor TFIIIA.

    PubMed

    Vrana, K E; Churchill, M E; Tullius, T D; Brown, D D

    1988-04-01

    Functional deletion mutants of the trans-acting factor TFIIIA, truncated at both ends of the molecule, have been expressed by in vitro transcription of a cDNA clone and subsequent cell-free translation of the synthetic mRNAs. A region of TFIIIA 19 amino acids or less, near the carboxyl terminus, is critical for maximal transcription and lies outside the DNA-binding domain. The elongated protein can be aligned over the internal control region (ICR) of the Xenopus 5S RNA gene with its carboxyl terminus oriented toward the 5' end of the gene and its amino terminus oriented toward the 3' end of the gene. The nine "zinc fingers" and the linkers that separate them comprise 80% of the protein mass and correspond to the DNA-binding domain of TFIIIA. The zinc fingers near the amino terminus of the protein contribute more to the overall binding energy of the protein to the ICR than do the zinc fingers near the carboxyl end. The most striking feature of TFIIIA is its modular structure. This is demonstrated by the fact that each zinc finger binds to just one of three short nucleotide sequences within the ICR.

  6. Mapping a Discharge Zone of Arsenic-Contaminated Ground Water Using Diffusion Samplers

    NASA Astrophysics Data System (ADS)

    Vroblesky, D. A.

    2001-05-01

    Arsenic, iron, and manganese are present at elevated concentrations in ground water at the Naval Air Station Fort Worth Joint Reserve Base in Texas. The source of the metals is thought to be mobilization from naturally occurring minerals as a result of reducing conditions produced by petroleum hydrocarbon degradation. Previous work showed that the metals are in a plume oriented along the ground-water flowpath toward an unnamed tributary of the Trinity River. Concentrations of arsenic in ground water at wells within the plume range from about 75 micrograms per liter (mg/L) in upgradient areas to about 4 mg/L near the tributary. Eight diffusion samplers, each consisting of anaerobic deionized water in a 25 milliliter plastic jar with 250-micron nylon mesh covering the mouth were buried in bottom sediment of the unnamed tributary along a 200-foot (ft) reach. Arsenic was not detected in the samplers at 0 and 200 ft and was at concentrations less than 15 mg/L in the samplers at 93 and 153 ft along the traverse. However, arsenic concentrations in excess of 50 mg/L were found in the 60-ft reach between 93 and 153 ft, coinciding with the projected discharge point of the ground-water arsenic plume. Iron also was elevated in this zone as well as in the contaminated ground water. The data show that this type of diffusion sampler is an effective tool for mapping zones where metals-containing ground-water discharge to surface water

  7. [Functional magnetic resonance imaging for cortical mapping in epilepsy].

    PubMed

    Lajos, Rudolf Kozák; Tóth, Vivien; Barsi, Péter; Rudas, Gábor

    2011-09-30

    It is not only the total curative resection of pathological tissue or the minimization of symptoms to be considered in epilepsy surgery or other neurosurgical procedures, it is equally desirable to maintain the best possible quality of life. Cortical mapping methods can help achieve this goal by delineating eloquent areas, i.e. brain regions that are vital for providing an acceptable quality of life, albeit not prone to compensatory reorganization. These areas include among others the Broca and Wernicke regions for speech, the primary motor, sensory and visual cortices. Functional MRI gained importance in the last decade as a non-invasive clinical cortical mapping technique. This method is capable of localizing cortical areas selectively activated by a given task condition. Thus, selecting appropriate tasks can help mapping eloquent brain regions. Using functional MRI provides information that is complementary to other mapping methods. Moreover, it can replace invasive methods such as the Wada test. Here, we explain the background of functional MRI, compare it to other clinical mapping methods, explain the intricacies of paradigm selection, and show the limitations of the technique while also pointing out alternative uses.

  8. Segmentation and grading of brain tumors on apparent diffusion coefficient images using self-organizing maps.

    PubMed

    Vijayakumar, C; Damayanti, Gharpure; Pant, R; Sreedhar, C M

    2007-10-01

    An accurate computer-assisted method to perform segmentation of brain tumor on apparent diffusion coefficient (ADC) images and evaluate its grade (malignancy state) has been designed using a mixture of unsupervised artificial neural networks (ANN) and hierarchical multiresolution wavelet. Firstly, the ADC images are decomposed by multiresolution wavelets, which are subsequently selectively reconstructed to form wavelet filtered images. These wavelet filtered images along with FLAIR and T2 weighted images have been utilized as the features to unsupervised neural network - self organizing maps (SOM) - to segment the tumor, edema, necrosis, CSF and normal tissue and grade the malignant state of the tumor. A novel segmentation algorithm based on the number of hits experienced by Best Matching Units (BMU) on SOM maps is proposed. The results shows that the SOM performs well in differentiating the tumor, edema, necrosis, CSF and normal tissue pattern vectors on ADC images. Using the trained SOM and proposed segmentation algorithm, we are able to identify high or low grade tumor, edema, necrosis, CSF and normal tissue. The results are validated against manually segmented images and sensitivity and the specificity are observed to be 0.86 and 0.93, respectively. PMID:17572068

  9. Glioma grading using apparent diffusion coefficient map: application of histogram analysis based on automatic segmentation.

    PubMed

    Lee, Jeongwon; Choi, Seung Hong; Kim, Ji-Hoon; Sohn, Chul-Ho; Lee, Sooyeul; Jeong, Jaeseung

    2014-09-01

    The accurate diagnosis of glioma subtypes is critical for appropriate treatment, but conventional histopathologic diagnosis often exhibits significant intra-observer variability and sampling error. The aim of this study was to investigate whether histogram analysis using an automatically segmented region of interest (ROI), excluding cystic or necrotic portions, could improve the differentiation between low-grade and high-grade gliomas. Thirty-two patients (nine low-grade and 23 high-grade gliomas) were included in this retrospective investigation. The outer boundaries of the entire tumors were manually drawn in each section of the contrast-enhanced T1 -weighted MR images. We excluded cystic or necrotic portions from the entire tumor volume. The histogram analyses were performed within the ROI on normalized apparent diffusion coefficient (ADC) maps. To evaluate the contribution of the proposed method to glioma grading, we compared the area under the receiver operating characteristic (ROC) curves. We found that an ROI excluding cystic or necrotic portions was more useful for glioma grading than was an entire tumor ROI. In the case of the fifth percentile values of the normalized ADC histogram, the area under the ROC curve for the tumor ROIs excluding cystic or necrotic portions was significantly higher than that for the entire tumor ROIs (p < 0.005). The automatic segmentation of a cystic or necrotic area probably improves the ability to differentiate between high- and low-grade gliomas on an ADC map. PMID:25042540

  10. In vivo inflammation mapping of periodontal disease based on diffuse reflectance spectral imaging: a clinical study

    NASA Astrophysics Data System (ADS)

    Prasanth, Chandra Sekhar; Betsy, Joseph; Jayanthi, Jayaraj L.; Nisha, Unni G.; Prasantila, Janam; Subhash, Narayanan

    2013-02-01

    Since conventional techniques using periodontal probes have inherent drawbacks in the diagnosis of different grades of gingival inflammation, development of noninvasive screening devices becomes significant. Diffuse reflectance (DR) spectra recorded with white light illumination is utilized to detect periodontal inflammation from the oxygenated hemoglobin absorption ratio R620/R575. A multispectral imaging system is utilized to record narrow-band DR images at 575 and 620 nm from the anterior sextant of the gingivia of 15 healthy volunteers and 25 patients (N=40). An experienced periodontist assesses the level of gingival inflammation at each site through periodontal probing and assigns diagnosis as healthy, mild, moderate, or severe inflammation. The DR image ratio R620/R575 computed for each pixel (8-μm resolution) from the monochrome images is pseudo-color-mapped to identify gingival inflammation sites. The DR image ratio values at each site are compared with clinical diagnosis to estimate the specificity and sensitivity of the DR imaging technique in inflammation mapping. The high diagnostic accuracy is utilized to detect underlying inflammation in six patients with a previous history of periodontitis.

  11. In vivo isotropic 3D diffusion tensor mapping of the rat brain using diffusion-weighted 3D MP-RAGE MRI.

    PubMed

    Numano, Tomokazu; Homma, Kazuhiro; Iwasaki, Nobuaki; Hyodo, Koji; Nitta, Naotaka; Hirose, Takeshi

    2006-04-01

    The purpose of this study was to examine the potential of diffusion-weighted (DW) three-dimensional (3D) MP-RAGE MRI for diffusion-tensor mapping of the rat brain in vivo. A DW-3D-MP-RAGE (3D-DWI) sequence was implemented at 2.0 T using six gradient orientations and a b value of 1000 s/mm2. In this sequence, the preparation sequence with a "90 degrees RF-motion proving gradient (MPG): MPG-180 degrees RF-MPG-90 degrees RF" pulse train (DW driven equilibrium Fourier transform) was used to sensitize the magnetization to diffusion. A centric k-space acquisition order was necessary to minimize saturation effects (T1 contamination) from tissues with short relaxation time. The image matrix was 128x128x128 (interpolated from 64x64x64 acquisitions), which resulted in small isotropic DW image data (voxel size: 0.273x0.273x0.273 mm3). Moreover, 3D-DWI-derived maps of the fractional anisotropy (FA), relative anisotropy (RA) and main-diffusion direction were completely free of susceptibility-induced signal losses and geometric distortions. Two well-known commissural fibers, the corpus callosum and anterior commissure, were indicated and shown to be in agreement with the locations of these known stereotaxic atlases. The experiment took 45 min, and shorter times should be possible in clinical application. The 3D-DWI sequence allows for in vivo 3D diffusion-tensor mapping of the rat brain without motion artifacts and susceptibility to distortion. PMID:16563958

  12. Degradation nonuniformity in the solar diffuser bidirectional reflectance distribution function.

    PubMed

    Sun, Junqiang; Chu, Mike; Wang, Menghua

    2016-08-01

    The assumption of angular dependence stability of the solar diffuser (SD) throughout degradation is critical to the on-orbit calibration of the reflective solar bands (RSBs) in many satellite sensors. Recent evidence has pointed to the contrary, and in this work, we present a thorough investigative effort into the angular dependence of the SD degradation for the Visible Infrared Imaging Radiometer Suite (VIIRS) onboard the Suomi National Polar-orbiting Partnership (SNPP) satellite and for the twin Moderate-resolution Imaging Spectroradiometer (MODIS) onboard Terra and Aqua spacecrafts. One common key step in the RSB calibration is the use of the SD degradation performance measured by an accompanying solar diffuser stability monitor (SDSM) as a valid substitute for the SD degradation factor in the direction of the RSB view. If SD degradations between these two respective directions do not maintain the same relative relationship over time, then the unmitigated use of the SDSM-measured SD degradation factor in the RSB calibration calculation will generate bias, and consequently, long-term drift in derived science products. We exploit the available history of the on-orbit calibration events to examine the response of the SDSM and the RSB detectors to the incident illumination reflecting off SD versus solar declination angle and show that the angular dependency, particularly at short wavelengths, evolves with respect to time. The generalized and the decisive conclusion is that the bidirectional reflectance distribution function (BRDF) of the SD degrades nonuniformly with respect to both incident and outgoing directions. Thus, the SDSM-based measurements provide SD degradation factors that are biased relative to the RSB view direction with respect to the SD. The analysis also reveals additional interesting phenomena, for example, the sharp behavioral change in the evolving angular dependence observed in Terra MODIS and SNPP VIIRS. For SNPP VIIRS the mitigation for this

  13. Degradation nonuniformity in the solar diffuser bidirectional reflectance distribution function.

    PubMed

    Sun, Junqiang; Chu, Mike; Wang, Menghua

    2016-08-01

    The assumption of angular dependence stability of the solar diffuser (SD) throughout degradation is critical to the on-orbit calibration of the reflective solar bands (RSBs) in many satellite sensors. Recent evidence has pointed to the contrary, and in this work, we present a thorough investigative effort into the angular dependence of the SD degradation for the Visible Infrared Imaging Radiometer Suite (VIIRS) onboard the Suomi National Polar-orbiting Partnership (SNPP) satellite and for the twin Moderate-resolution Imaging Spectroradiometer (MODIS) onboard Terra and Aqua spacecrafts. One common key step in the RSB calibration is the use of the SD degradation performance measured by an accompanying solar diffuser stability monitor (SDSM) as a valid substitute for the SD degradation factor in the direction of the RSB view. If SD degradations between these two respective directions do not maintain the same relative relationship over time, then the unmitigated use of the SDSM-measured SD degradation factor in the RSB calibration calculation will generate bias, and consequently, long-term drift in derived science products. We exploit the available history of the on-orbit calibration events to examine the response of the SDSM and the RSB detectors to the incident illumination reflecting off SD versus solar declination angle and show that the angular dependency, particularly at short wavelengths, evolves with respect to time. The generalized and the decisive conclusion is that the bidirectional reflectance distribution function (BRDF) of the SD degrades nonuniformly with respect to both incident and outgoing directions. Thus, the SDSM-based measurements provide SD degradation factors that are biased relative to the RSB view direction with respect to the SD. The analysis also reveals additional interesting phenomena, for example, the sharp behavioral change in the evolving angular dependence observed in Terra MODIS and SNPP VIIRS. For SNPP VIIRS the mitigation for this

  14. Self-Organizing Maps and Parton Distribution Functions

    SciTech Connect

    K. Holcomb, Simonetta Liuti, D. Z. Perry

    2011-05-01

    We present a new method to extract parton distribution functions from high energy experimental data based on a specific type of neural networks, the Self-Organizing Maps. We illustrate the features of our new procedure that are particularly useful for an anaysis directed at extracting generalized parton distributions from data. We show quantitative results of our initial analysis of the parton distribution functions from inclusive deep inelastic scattering.

  15. Human brain somatic representation: a functional magnetic resonance mapping

    NASA Astrophysics Data System (ADS)

    Romero-Romo, Juan; Rojas, Rafael; Salgado, Perla; Sánchez-Cortázar, Julián; Vazquez-Vela, Arturo; Barrios, Fernando A.

    2001-10-01

    Central nervous system studies of injury and plasticity for the reorganization in the phantom limb sensation area presented. In particular functional magnetic resonance imaging (fMRI) mapping of the somatic and motor cortex of amputee patients, in the case of referred sensations. Using fMRI we can show the correlation between structure and functional field and study the reorganization due to plasticity in the brain.

  16. Insight from uncertainty: bootstrap-derived diffusion metrics differentially predict memory function among older adults.

    PubMed

    Vorburger, Robert S; Habeck, Christian G; Narkhede, Atul; Guzman, Vanessa A; Manly, Jennifer J; Brickman, Adam M

    2016-01-01

    Diffusion tensor imaging suffers from an intrinsic low signal-to-noise ratio. Bootstrap algorithms have been introduced to provide a non-parametric method to estimate the uncertainty of the measured diffusion parameters. To quantify the variability of the principal diffusion direction, bootstrap-derived metrics such as the cone of uncertainty have been proposed. However, bootstrap-derived metrics are not independent of the underlying diffusion profile. A higher mean diffusivity causes a smaller signal-to-noise ratio and, thus, increases the measurement uncertainty. Moreover, the goodness of the tensor model, which relies strongly on the complexity of the underlying diffusion profile, influences bootstrap-derived metrics as well. The presented simulations clearly depict the cone of uncertainty as a function of the underlying diffusion profile. Since the relationship of the cone of uncertainty and common diffusion parameters, such as the mean diffusivity and the fractional anisotropy, is not linear, the cone of uncertainty has a different sensitivity. In vivo analysis of the fornix reveals the cone of uncertainty to be a predictor of memory function among older adults. No significant correlation occurs with the common diffusion parameters. The present work not only demonstrates the cone of uncertainty as a function of the actual diffusion profile, but also discloses the cone of uncertainty as a sensitive predictor of memory function. Future studies should incorporate bootstrap-derived metrics to provide more comprehensive analysis.

  17. Exact maps in density functional theory for lattice models

    NASA Astrophysics Data System (ADS)

    Dimitrov, Tanja; Appel, Heiko; Fuks, Johanna I.; Rubio, Angel

    2016-08-01

    In the present work, we employ exact diagonalization for model systems on a real-space lattice to explicitly construct the exact density-to-potential and graphically illustrate the complete exact density-to-wavefunction map that underly the Hohenberg-Kohn theorem in density functional theory. Having the explicit wavefunction-to-density map at hand, we are able to construct arbitrary observables as functionals of the ground-state density. We analyze the density-to-potential map as the distance between the fragments of a system increases and the correlation in the system grows. We observe a feature that gradually develops in the density-to-potential map as well as in the density-to-wavefunction map. This feature is inherited by arbitrary expectation values as functional of the ground-state density. We explicitly show the excited-state energies, the excited-state densities, and the correlation entropy as functionals of the ground-state density. All of them show this exact feature that sharpens as the coupling of the fragments decreases and the correlation grows. We denominate this feature as intra-system steepening and discuss how it relates to the well-known inter-system derivative discontinuity. The inter-system derivative discontinuity is an exact concept for coupled subsystems with degenerate ground state. However, the coupling between subsystems as in charge transfer processes can lift the degeneracy. An important conclusion is that for such systems with a near-degenerate ground state, the corresponding cut along the particle number N of the exact density functionals is differentiable with a well-defined gradient near integer particle number.

  18. Exact maps in density functional theory for lattice models

    NASA Astrophysics Data System (ADS)

    Dimitrov, Tanja; Appel, Heiko; Fuks, Johanna I.; Rubio, Angel

    2016-08-01

    In the present work, we employ exact diagonalization for model systems on a real-space lattice to explicitly construct the exact density-to-potential and graphically illustrate the complete exact density-to-wavefunction map that underly the Hohenberg–Kohn theorem in density functional theory. Having the explicit wavefunction-to-density map at hand, we are able to construct arbitrary observables as functionals of the ground-state density. We analyze the density-to-potential map as the distance between the fragments of a system increases and the correlation in the system grows. We observe a feature that gradually develops in the density-to-potential map as well as in the density-to-wavefunction map. This feature is inherited by arbitrary expectation values as functional of the ground-state density. We explicitly show the excited-state energies, the excited-state densities, and the correlation entropy as functionals of the ground-state density. All of them show this exact feature that sharpens as the coupling of the fragments decreases and the correlation grows. We denominate this feature as intra-system steepening and discuss how it relates to the well-known inter-system derivative discontinuity. The inter-system derivative discontinuity is an exact concept for coupled subsystems with degenerate ground state. However, the coupling between subsystems as in charge transfer processes can lift the degeneracy. An important conclusion is that for such systems with a near-degenerate ground state, the corresponding cut along the particle number N of the exact density functionals is differentiable with a well-defined gradient near integer particle number.

  19. A Method for Automated Classification of Parkinson's Disease Diagnosis Using an Ensemble Average Propagator Template Brain Map Estimated from Diffusion MRI.

    PubMed

    Banerjee, Monami; Okun, Michael S; Vaillancourt, David E; Vemuri, Baba C

    2016-01-01

    Parkinson's disease (PD) is a common and debilitating neurodegenerative disorder that affects patients in all countries and of all nationalities. Magnetic resonance imaging (MRI) is currently one of the most widely used diagnostic imaging techniques utilized for detection of neurologic diseases. Changes in structural biomarkers will likely play an important future role in assessing progression of many neurological diseases inclusive of PD. In this paper, we derived structural biomarkers from diffusion MRI (dMRI), a structural modality that allows for non-invasive inference of neuronal fiber connectivity patterns. The structural biomarker we use is the ensemble average propagator (EAP), a probability density function fully characterizing the diffusion locally at a voxel level. To assess changes with respect to a normal anatomy, we construct an unbiased template brain map from the EAP fields of a control population. Use of an EAP captures both orientation and shape information of the diffusion process at each voxel in the dMRI data, and this feature can be a powerful representation to achieve enhanced PD brain mapping. This template brain map construction method is applicable to small animal models as well as to human brains. The differences between the control template brain map and novel patient data can then be assessed via a nonrigid warping algorithm that transforms the novel data into correspondence with the template brain map, thereby capturing the amount of elastic deformation needed to achieve this correspondence. We present the use of a manifold-valued feature called the Cauchy deformation tensor (CDT), which facilitates morphometric analysis and automated classification of a PD versus a control population. Finally, we present preliminary results of automated discrimination between a group of 22 controls and 46 PD patients using CDT. This method may be possibly applied to larger population sizes and other parkinsonian syndromes in the near future.

  20. A Method for Automated Classification of Parkinson’s Disease Diagnosis Using an Ensemble Average Propagator Template Brain Map Estimated from Diffusion MRI

    PubMed Central

    Banerjee, Monami; Okun, Michael S.; Vaillancourt, David E.; Vemuri, Baba C.

    2016-01-01

    Parkinson’s disease (PD) is a common and debilitating neurodegenerative disorder that affects patients in all countries and of all nationalities. Magnetic resonance imaging (MRI) is currently one of the most widely used diagnostic imaging techniques utilized for detection of neurologic diseases. Changes in structural biomarkers will likely play an important future role in assessing progression of many neurological diseases inclusive of PD. In this paper, we derived structural biomarkers from diffusion MRI (dMRI), a structural modality that allows for non-invasive inference of neuronal fiber connectivity patterns. The structural biomarker we use is the ensemble average propagator (EAP), a probability density function fully characterizing the diffusion locally at a voxel level. To assess changes with respect to a normal anatomy, we construct an unbiased template brain map from the EAP fields of a control population. Use of an EAP captures both orientation and shape information of the diffusion process at each voxel in the dMRI data, and this feature can be a powerful representation to achieve enhanced PD brain mapping. This template brain map construction method is applicable to small animal models as well as to human brains. The differences between the control template brain map and novel patient data can then be assessed via a nonrigid warping algorithm that transforms the novel data into correspondence with the template brain map, thereby capturing the amount of elastic deformation needed to achieve this correspondence. We present the use of a manifold-valued feature called the Cauchy deformation tensor (CDT), which facilitates morphometric analysis and automated classification of a PD versus a control population. Finally, we present preliminary results of automated discrimination between a group of 22 controls and 46 PD patients using CDT. This method may be possibly applied to larger population sizes and other parkinsonian syndromes in the near future. PMID

  1. An optimal strategy for functional mapping of dynamic trait loci.

    PubMed

    Jin, Tianbo; Li, Jiahan; Guo, Ying; Zhou, Xiaojing; Yang, Runqing; Wu, Rongling

    2010-02-01

    As an emerging powerful approach for mapping quantitative trait loci (QTLs) responsible for dynamic traits, functional mapping models the time-dependent mean vector with biologically meaningful equations and are likely to generate biologically relevant and interpretable results. Given the autocorrelation nature of a dynamic trait, functional mapping needs the implementation of the models for the structure of the covariance matrix. In this article, we have provided a comprehensive set of approaches for modelling the covariance structure and incorporated each of these approaches into the framework of functional mapping. The Bayesian information criterion (BIC) values are used as a model selection criterion to choose the optimal combination of the submodels for the mean vector and covariance structure. In an example for leaf age growth from a rice molecular genetic project, the best submodel combination was found between the Gaussian model for the correlation structure, power equation of order 1 for the variance and the power curve for the mean vector. Under this combination, several significant QTLs for leaf age growth trajectories were detected on different chromosomes. Our model can be well used to study the genetic architecture of dynamic traits of agricultural values. PMID:20196894

  2. Prognostic value of combined visualization of MR diffusion and perfusion maps in glioblastoma.

    PubMed

    Deike, Katerina; Wiestler, Benedikt; Graf, Markus; Reimer, Caroline; Floca, Ralf O; Bäumer, Philipp; Kickingereder, Philipp; Heiland, Sabine; Schlemmer, Heinz-Peter; Wick, Wolfgang; Bendszus, Martin; Radbruch, Alexander

    2016-02-01

    We analyzed whether the combined visualization of decreased apparent diffusion coefficient (ADC) values and increased cerebral blood volume (CBV) in perfusion imaging can identify prognosis-related growth patterns in patients with newly diagnosed glioblastoma. Sixty-five consecutive patients were examined with diffusion and dynamic susceptibility-weighted contrast-enhanced perfusion weighted MRI. ADC and CBV maps were co-registered on the T1-w image and a region of interest (ROI) was manually delineated encompassing the enhancing lesion. Within this ROI pixels with ADC values the 70th percentile (CBVmax) and the intersection of pixels with ADCmin and CBVmax were automatically calculated and visualized. Initially, all tumors with a mean intersection greater than the upper quartile of the normally distributed mean intersection of all patients were subsumed to the first growth pattern termed big intersection (BI). Subsequently, the remaining tumors' growth patterns were categorized depending on the qualitative representation of ADCmin, CBVmax and their intersection. Log-rank test exposed a significantly longer overall survival of BI (n = 16) compared to non-BI group (n = 49) (p = 0.0057). Thirty-one, four and 14 patients of the non-BI group were classified as predominant ADC-, CBV- and mixed growth group, respectively. In a multivariate Cox regression model, the BI-, CBV- and mixed groups had significantly lower adjusted hazard ratios (p-value, α(Bonferroni) < 0.006) when compared to the reference group ADC: 0.29 (0.0027), 0.11 (0.038) and 0.33 (0.0059). Our study provides evidence that the combination of diffusion and perfusion imaging allows visualization of different glioblastoma growth patterns that are associated with prognosis. A possible biological hypothesis for this finding could be the interpretation of the ADCmin fraction as the invasion-front of tumor cells while the CBVmax fraction might represent

  3. A comprehensive neuropsychological mapping battery for functional magnetic resonance imaging.

    PubMed

    Karakas, Sirel; Baran, Zeynel; Ceylan, Arzu Ozkan; Tileylioglu, Emre; Tali, Turgut; Karakas, Hakki Muammer

    2013-11-01

    Existing batteries for FMRI do not precisely meet the criteria for comprehensive mapping of cognitive functions within minimum data acquisition times using standard scanners and head coils. The goal was to develop a battery of neuropsychological paradigms for FMRI that can also be used in other brain imaging techniques and behavioural research. Participants were 61 healthy, young adult volunteers (48 females and 13 males, mean age: 22.25 ± 3.39 years) from the university community. The battery included 8 paradigms for basic (visual, auditory, sensory-motor, emotional arousal) and complex (language, working memory, inhibition/interference control, learning) cognitive functions. Imaging was performed using standard functional imaging capabilities (1.5-T MR scanner, standard head coil). Structural and functional data series were analysed using Brain Voyager QX2.9 and Statistical Parametric Mapping-8. For basic processes, activation centres for individuals were within a distance of 3-11 mm of the group centres of the target regions and for complex cognitive processes, between 7 mm and 15 mm. Based on fixed-effect and random-effects analyses, the distance between the activation centres was 0-4 mm. There was spatial variability between individual cases; however, as shown by the distances between the centres found with fixed-effect and random-effects analyses, the coordinates for individual cases can be used to represent those of the group. The findings show that the neuropsychological brain mapping battery described here can be used in basic science studies that investigate the relationship of the brain to the mind and also as functional localiser in clinical studies for diagnosis, follow-up and pre-surgical mapping.

  4. A functional map of the nopaline synthase promoter.

    PubMed Central

    Shaw, C H; Carter, G H; Watson, M D; Shaw, C H

    1984-01-01

    This paper describes the first functional map of a promoter expressed from the plant chromosome. We have constructed a series of overlapping deletion mutants within the region upstream of the Ti-plasmid encoded nopaline synthase (nos) gene. By monitoring nos expression in tumour tissue we have inferred a functional map of the nos promoter. The maximum length of sequence upstream of the transcription initiation point required to express wild type levels of nopaline synthase is 88 bp. Within this region, the "CAAT" box is essential for maximal activity; deletion of this sequence reduced apparent nos expression by over 80%. Presence of an intact or partial "TATA" box in the absence of the "CAAT" box supports a barely detectable level of nopaline synthase. Removal of all sequences upstream of the nos coding sequence results in no detectable activity. PMID:6493982

  5. Coarse-grained variables for particle-based models: diffusion maps and animal swarming simulations

    NASA Astrophysics Data System (ADS)

    Liu, Ping; Safford, Hannah R.; Couzin, Iain D.; Kevrekidis, Ioannis G.

    2014-12-01

    As microscopic (e.g. atomistic, stochastic, agent-based, particle-based) simulations become increasingly prevalent in the modeling of complex systems, so does the need to systematically coarse-grain the information they provide. Before even starting to formulate relevant coarse-grained equations, we need to determine the right macroscopic observables—the right variables in terms of which emergent behavior will be described. This paper illustrates the use of data mining (and, in particular, diffusion maps, a nonlinear manifold learning technique) in coarse-graining the dynamics of a particle-based model of animal swarming. Our computational data-driven coarse-graining approach extracts two coarse (collective) variables from the detailed particle-based simulations, and helps formulate a low-dimensional stochastic differential equation in terms of these two collective variables; this allows the efficient quantification of the interplay of "informed" and "naive" individuals in the collective swarm dynamics. We also present a brief exploration of swarm breakup and use data-mining in an attempt to identify useful predictors for it. In our discussion of the scope and limitations of the approach we focus on the key step of selecting an informative metric, allowing us to usefully compare different particle swarm configurations.

  6. A high throughput and efficient visualization method for diffusion tensor imaging of human brain white matter employing diffusion-map space.

    PubMed

    Aarabi, Mohammad Hadi; Kazerooni, Anahita Fathi; Salehi, Narges; Rad, Hamidreza Saligheh

    2014-01-01

    Diffusion tensor imaging (DTI) possesses high dimension and complex structure, so that detecting available pattern information and its analysis based on conventional linear statistics and classification methods become inefficient. In order to facilitate classification, segmentation, compression or visualization of the data, dimension reduction is far-reaching. There have been many approaches proposed for this purpose, which mostly rely on complex low dimensional manifold embedding of the high-dimensional space. Dimension reduction is commonly applicable through linear algorithms, such as principal component analysis and multi-dimensional scaling; however, they are not able to deal with complex and high dimensional data. In this light, nonlinear algorithms with the capability to preserve the distance of high dimensional data have been developed. The purpose of this paper is to propose a new method for meaningful visualization of brain white matter using diffusion tensor data to map the 6-dimensional tensor to a three dimensional space employing Markov random walk and diffusion distance algorithms, leading to a new distance-preserving map for the DTI data with lower dimension and higher throughput information. PMID:25570465

  7. MarsAtlas: A cortical parcellation atlas for functional mapping.

    PubMed

    Auzias, Guillaume; Coulon, Olivier; Brovelli, Andrea

    2016-04-01

    An open question in neuroimaging is how to develop anatomical brain atlases for the analysis of functional data. Here, we present a cortical parcellation model based on macroanatomical information and test its validity on visuomotor-related cortical functional networks. The parcellation model is based on a recently developed cortical parameterization method (Auzias et al., [2013]: IEEE Trans Med Imaging 32:873-887), called HIP-HOP. This method exploits a set of primary and secondary sulci to create an orthogonal coordinate system on the cortical surface. A natural parcellation scheme arises from the axes of the HIP-HOP model running along the fundus of selected sulci. The resulting parcellation scheme, called MarsAtlas, complies with dorsoventral/rostrocaudal direction fields and allows inter-subject matching. To test it for functional mapping, we analyzed a MEG dataset collected from human participants performing an arbitrary visuomotor mapping task. Single-trial high-gamma activity, HGA (60-120 Hz), was estimated using spectral analysis and beamforming techniques at cortical areas arising from a Talairach atlas (i.e., Brodmann areas) and MarsAtlas. Using both atlases, we confirmed that visuomotor associations involve an increase in HGA over the sensorimotor and fronto-parietal network, in addition to medial prefrontal areas. However, MarsAtlas provided: (1) crucial functional information along both the dorsolateral and rostrocaudal direction; (2) an increase in statistical significance. To conclude, our results suggest that the MarsAtlas is a valid anatomical atlas for functional mapping, and represents a potential anatomical framework for integration of functional data arising from multiple techniques such as MEG, intracranial EEG and fMRI. PMID:26813563

  8. The Transition from Diffuse to Dense Gas in Herschel Dust Emission Maps

    NASA Astrophysics Data System (ADS)

    Goldsmith, Paul

    Dense cores in dark clouds are the sites where young stars form. These regions manifest as relatively small (<0.1pc) pockets of cold and dense gas. If we wish to understand the star formation process, we have to understand the physical conditions in dense cores. This has been a main aim of star formation research in the past decade. Today, we do indeed possess a good knowledge of the density and velocity structure of cores, as well as their chemical evolution and physical lifetime. However, we do not understand well how dense cores form out of the diffuse gas clouds surrounding them. It is crucial that we constrain the relationship between dense cores and their environment: if we only understand dense cores, we may be able to understand how individual stars form --- but we would not know how the star forming dense cores themselves come into existence. We therefore propose to obtain data sets that reveal both dense cores and the clouds containing them in the same map. Based on these maps, we will study how dense cores form out of their natal clouds. Since cores form stars, this knowledge is crucial for the development of a complete theoretical and observational understanding of the formation of stars and their planets, as envisioned in NASA's Strategic Science Plan. Fortunately, existing archival data allow to derive exactly the sort of maps we need for our analysis. Here, we describe a program that exclusively builds on PACS and SPIRE dust emission imaging data from the NASA-supported Herschel mission. The degree-sized wide-field Herschel maps of the nearby (<260pc) Polaris Flare and Aquila Rift clouds are ideal for our work. They permit to resolve dense cores (<0.1pc), while the maps also reveal large-scale cloud structure (5pc and larger). We will generate column density maps from these dust emission maps and then run a tree-based hierarchical multi-scale structure analysis on them. Only this procedure permits to exploit the full potential of the maps: we will

  9. Green's Function Nodal Algorithm for the Diffusion Equation.

    1989-12-04

    Version 00 GRENADE is a coarse-mesh program designed for neutronic flux and power calculations in nuclear reactors. It solves the static diffusion equation for neutrons in multidimensional problems, assuming Cartesian Geometry. The program yields flux and power distributions and the effective neutron multiplication factor .

  10. Multiconfiguration Pair-Density Functional Theory Spectral Calculations Are Stable to Adding Diffuse Basis Functions.

    PubMed

    Hoyer, Chad E; Gagliardi, Laura; Truhlar, Donald G

    2015-11-01

    Time-dependent Kohn-Sham density functional theory (TD-KS-DFT) is useful for calculating electronic excitation spectra of large systems, but the low-energy spectra are often complicated by artificially lowered higher-energy states. This affects even the lowest energy excited states. Here, by calculating the lowest energy spin-conserving excited state for atoms from H to K and for formaldehyde, we show that this problem does not occur in multiconfiguration pair-density functional theory (MC-PDFT). We use the tPBE on-top density functional, which is a translation of the PBE exchange-correlation functional. We compare to a robust multireference method, namely, complete active space second-order perturbation theory (CASPT2), and to TD-KS-DFT with two popular exchange-correlation functionals, PBE and PBE0. We find for atoms that the mean unsigned error (MUE) of MC-PDFT with the tPBE functional improves from 0.42 to 0.40 eV with a double set of diffuse functions, whereas the MUEs for PBE and PBE0 drastically increase from 0.74 to 2.49 eV and from 0.45 to 1.47 eV, respectively.

  11. Multiconfiguration Pair-Density Functional Theory Spectral Calculations Are Stable to Adding Diffuse Basis Functions.

    PubMed

    Hoyer, Chad E; Gagliardi, Laura; Truhlar, Donald G

    2015-11-01

    Time-dependent Kohn-Sham density functional theory (TD-KS-DFT) is useful for calculating electronic excitation spectra of large systems, but the low-energy spectra are often complicated by artificially lowered higher-energy states. This affects even the lowest energy excited states. Here, by calculating the lowest energy spin-conserving excited state for atoms from H to K and for formaldehyde, we show that this problem does not occur in multiconfiguration pair-density functional theory (MC-PDFT). We use the tPBE on-top density functional, which is a translation of the PBE exchange-correlation functional. We compare to a robust multireference method, namely, complete active space second-order perturbation theory (CASPT2), and to TD-KS-DFT with two popular exchange-correlation functionals, PBE and PBE0. We find for atoms that the mean unsigned error (MUE) of MC-PDFT with the tPBE functional improves from 0.42 to 0.40 eV with a double set of diffuse functions, whereas the MUEs for PBE and PBE0 drastically increase from 0.74 to 2.49 eV and from 0.45 to 1.47 eV, respectively. PMID:26722961

  12. The value of preoperative functional cortical mapping using navigated TMS.

    PubMed

    Lefaucheur, Jean-Pascal; Picht, Thomas

    2016-04-01

    The surgical removal of brain tumours in so-called eloquent regions is frequently associated with a high risk of causing disabling postoperative deficits. Among the preoperative techniques proposed to help neurosurgical planning and procedure, navigated transcranial magnetic stimulation (nTMS) is increasingly performed. A high level of evidence is now available in the literature regarding the anatomical and functional accuracy of this mapping technique. This article presents the principles and facts demonstrating the value of using nTMS in clinical practice to preserve motor or language functions from deleterious lesions secondary to brain tumour resection or epilepsy surgery. PMID:27229765

  13. The value of preoperative functional cortical mapping using navigated TMS.

    PubMed

    Lefaucheur, Jean-Pascal; Picht, Thomas

    2016-04-01

    The surgical removal of brain tumours in so-called eloquent regions is frequently associated with a high risk of causing disabling postoperative deficits. Among the preoperative techniques proposed to help neurosurgical planning and procedure, navigated transcranial magnetic stimulation (nTMS) is increasingly performed. A high level of evidence is now available in the literature regarding the anatomical and functional accuracy of this mapping technique. This article presents the principles and facts demonstrating the value of using nTMS in clinical practice to preserve motor or language functions from deleterious lesions secondary to brain tumour resection or epilepsy surgery.

  14. Spatial mapping of structural and connectional imaging data for the developing human brain with diffusion tensor imaging.

    PubMed

    Ouyang, Austin; Jeon, Tina; Sunkin, Susan M; Pletikos, Mihovil; Sedmak, Goran; Sestan, Nenad; Lein, Ed S; Huang, Hao

    2015-02-01

    During human brain development from fetal stage to adulthood, the white matter (WM) tracts undergo dramatic changes. Diffusion tensor imaging (DTI), a widely used magnetic resonance imaging (MRI) modality, offers insight into the dynamic changes of WM fibers as these fibers can be noninvasively traced and three-dimensionally (3D) reconstructed with DTI tractography. The DTI and conventional T1 weighted MRI images also provide sufficient cortical anatomical details for mapping the cortical regions of interests (ROIs). In this paper, we described basic concepts and methods of DTI techniques that can be used to trace major WM tracts noninvasively from fetal brain of 14 postconceptional weeks (pcw) to adult brain. We applied these techniques to acquire DTI data and trace, reconstruct and visualize major WM tracts during development. After categorizing major WM fiber bundles into five unique functional tract groups, namely limbic, brain stem, projection, commissural and association tracts, we revealed formation and maturation of these 3D reconstructed WM tracts of the developing human brain. The structural and connectional imaging data offered by DTI provides the anatomical backbone of transcriptional atlas of the developing human brain.

  15. Spatial Mapping of Structural and Connectional Imaging Data for the Developing Human Brain with Diffusion Tensor Imaging

    PubMed Central

    Ouyang, Austin; Jeon, Tina; Sunkin, Susan M.; Pletikos, Mihovil; Sedmak, Goran; Sestan, Nenad; Lein, Ed S.; Huang, Hao

    2014-01-01

    During human brain development from fetal stage to adulthood, the white matter (WM) tracts undergo dramatic changes. Diffusion tensor imaging (DTI), a widely used magnetic resonance imaging (MRI) modality, offers insight into the dynamic changes of WM fibers as these fibers can be noninvasively traced and three-dimensionally (3D) reconstructed with DTI tractography. The DTI and conventional T1 weighted MRI images also provide sufficient cortical anatomical details for mapping the cortical regions of interests (ROIs). In this paper, we described basic concepts and methods of DTI techniques that can be used to trace major WM tracts noninvasively from fetal brain of 14 postconceptional weeks (pcw) to adult brain. We applied these techniques to acquire DTI data and trace, reconstruct and visualize major WM tracts during development. After categorizing major WM fiber bundles into five unique functional tract groups, namely limbic, brain stem, projection, commissural and association tracts, we revealed formation and maturation of these 3D reconstructed WM tracts of the developing human brain. The structural and connectional imaging data offered by DTI provides the anatomical backbone of transcriptional atlas of the developing human brain. PMID:25448302

  16. From chemotaxis to the cognitive map: The function of olfaction

    PubMed Central

    Jacobs, Lucia F.

    2012-01-01

    A paradox of vertebrate brain evolution is the unexplained variability in the size of the olfactory bulb (OB), in contrast to other brain regions, which scale predictably with brain size. Such variability appears to be the result of selection for olfactory function, yet there is no obvious concordance that would predict the causal relationship between OB size and behavior. This discordance may derive from assuming the primary function of olfaction is odorant discrimination and acuity. If instead the primary function of olfaction is navigation, i.e., predicting odorant distributions in time and space, variability in absolute OB size could be ascribed and explained by variability in navigational demand. This olfactory spatial hypothesis offers a single functional explanation to account for patterns of olfactory system scaling in vertebrates, the primacy of olfaction in spatial navigation, even in visual specialists, and proposes an evolutionary scenario to account for the convergence in olfactory structure and function across protostomes and deuterostomes. In addition, the unique percepts of olfaction may organize odorant information in a parallel map structure. This could have served as a scaffold for the evolution of the parallel map structure of the mammalian hippocampus, and possibly the arthropod mushroom body, and offers an explanation for similar flexible spatial navigation strategies in arthropods and vertebrates. PMID:22723365

  17. Automatic Detection and Quantification of Acute Cerebral Infarct by Fuzzy Clustering and Histographic Characterization on Diffusion Weighted MR Imaging and Apparent Diffusion Coefficient Map

    PubMed Central

    Tsai, Jang-Zern; Chen, Yu-Wei; Wang, Kuo-Wei; Wu, Hsiao-Kuang; Lin, Yun-Yu; Lee, Ying-Ying; Chen, Chi-Jen; Lin, Huey-Juan; Smith, Eric Edward; Hsin, Yue-Loong

    2014-01-01

    Determination of the volumes of acute cerebral infarct in the magnetic resonance imaging harbors prognostic values. However, semiautomatic method of segmentation is time-consuming and with high interrater variability. Using diffusion weighted imaging and apparent diffusion coefficient map from patients with acute infarction in 10 days, we aimed to develop a fully automatic algorithm to measure infarct volume. It includes an unsupervised classification with fuzzy C-means clustering determination of the histographic distribution, defining self-adjusted intensity thresholds. The proposed method attained high agreement with the semiautomatic method, with similarity index 89.9 ± 6.5%, in detecting cerebral infarct lesions from 22 acute stroke patients. We demonstrated the accuracy of the proposed computer-assisted prompt segmentation method, which appeared promising to replace the laborious, time-consuming, and operator-dependent semiautomatic segmentation. PMID:24738080

  18. THE HALO MASS FUNCTION FROM EXCURSION SET THEORY. II. THE DIFFUSING BARRIER

    SciTech Connect

    Maggiore, Michele; Riotto, Antonio

    2010-07-01

    In excursion set theory, the computation of the halo mass function is mapped into a first-passage time process in the presence of a barrier, which in the spherical collapse model is a constant and in the ellipsoidal collapse model is a fixed function of the variance of the smoothed density field. However, N-body simulations show that dark matter halos grow through a mixture of smooth accretion, violent encounters, and fragmentations, and modeling halo collapse as spherical, or even as ellipsoidal, is a significant oversimplification. In addition, the very definition of what is a dark matter halo, both in N-body simulations and observationally, is a difficult problem. We propose that some of the physical complications inherent to a realistic description of halo formation can be included in the excursion set theory framework, at least at an effective level, by taking into account that the critical value for collapse is not a fixed constant {delta}{sub c}, as in the spherical collapse model, nor a fixed function of the variance {sigma} of the smoothed density field, as in the ellipsoidal collapse model, but rather is itself a stochastic variable, whose scatter reflects a number of complicated aspects of the underlying dynamics. Solving the first-passage time problem in the presence of a diffusing barrier we find that the exponential factor in the Press-Schechter mass function changes from exp{l_brace}-{delta}{sup 2}{sub c}/2{sigma}{sup 2{r_brace}} to exp{l_brace}-a{delta}{sup 2}{sub c}/2{sigma}{sup 2{r_brace}}, where a = 1/(1 + D{sub B}) and D{sub B} is the diffusion coefficient of the barrier. The numerical value of D{sub B} , and therefore the corresponding value of a, depends among other things on the algorithm used for identifying halos. We discuss the physical origin of the stochasticity of the barrier and, from recent N-body simulations that studied the properties of the collapse barrier, we deduce a value D{sub B} {approx_equal} 0.25. Our model then predicts a

  19. Functional mapping of seasonal transition in perennial plants.

    PubMed

    Ye, Meixia; Jiang, Libo; Mao, Ke; Wang, Yaqun; Wang, Zhong; Wu, Rongling

    2015-05-01

    Unlike annuals, all perennial plants undergo seasonal transitions during ontogeny. As an adaptive response to seasonal changes in climate, the seasonal pattern of growth is likely to be under genetic control, although its underlying genetic basis remains unknown. Here, we develop a computational model that can map specific quantitative trait loci (QTLs) responsible for seasonal transitions of growth in perennials. The model is founded on functional mapping, a statistical framework to map developmental dynamics, which is reformed to integrate a seasonally adjusted growth function. The new model is equipped with a capacity to characterize the genetic effects of QTLs on seasonal alternation at different ages and then to better elucidate the genetic architecture of development. The model is implemented with a series of testing procedures, including (i) how a QTL controls an overall ontogenetic growth curve, (ii) how the QTL determines seasonal trajectories of growth within years and (iii) how it determines the dynamic nature of age-specific season response. The model was validated through computer simulation. The extension of season adjustment to other types of biological curves is statistically straightforward, facilitating a wider variety of genetic studies into ontogenetic growth and development in perennial plants.

  20. Computational study of influence of diffuse basis functions on geometry optimization and spectroscopic properties of losartan potassium

    NASA Astrophysics Data System (ADS)

    Mizera, Mikołaj; Lewadowska, Kornelia; Talaczyńska, Alicja; Cielecka-Piontek, Judyta

    2015-02-01

    The work was aimed at investigating the influence of diffusion of basis functions on the geometry optimization of molecule of losartan in acidic and salt form. Spectroscopic properties of losartan potassium were also calculated and compared with experiment. Density functional theory method with various basis sets: 6-31G(d,p) and its diffused variations 6-31G(d,p)+ and 6-31G(d,p)++ was used. Application of diffuse basis functions in geometry optimization resulted in significant change of total molecule energy. Total molecule energy of losartan potassium decreased by 112.91 kJ/mol and 114.32 kJ/mol for 6-31G(d,p)+ and 6-31G(d,p)++ basis sets, respectively. Almost the same decrease was observed for losartan: 114.99 kJ/mol and 117.08 kJ/mol respectively for 6-31G(d,p)+ and 6-31G(d,p)++ basis sets. Further investigation showed significant difference within geometries of losartan potassium optimized with investigated basis sets. Application of diffused basis functions resulted in average 1.29 Å difference in relative position between corresponding atoms of three obtained geometries. Similar study taken on losartan resulted in only average 0.22 Å of dislocation. Extensive analysis of geometry changes in molecules obtained with diffused and non-diffuse basis functions was carried out in order to elucidate observed changes. The analysis was supported by electrostatic potential maps and calculation of natural atomic charges. UV, FT-IR and Raman spectra of losartan potassium were calculated and compared with experimental results. No crucial differences between Raman spectra obtained with different basis sets were observed. However, FT-IR spectra of geometry of losartan potassium optimized with 6-31G(d,p)++ basis set resulted in 40% better correlation with experimental FT-IR spectra than FT-IR calculated with geometry optimized with 6-31G(d,p) basis set. Therefore, it is highly advisable to optimize geometry of molecules with ionic interactions using diffuse basis functions

  1. Computational study of influence of diffuse basis functions on geometry optimization and spectroscopic properties of losartan potassium.

    PubMed

    Mizera, Mikołaj; Lewadowska, Kornelia; Talaczyńska, Alicja; Cielecka-Piontek, Judyta

    2015-02-25

    The work was aimed at investigating the influence of diffusion of basis functions on the geometry optimization of molecule of losartan in acidic and salt form. Spectroscopic properties of losartan potassium were also calculated and compared with experiment. Density functional theory method with various basis sets: 6-31G(d,p) and its diffused variations 6-31G(d,p)+ and 6-31G(d,p)++ was used. Application of diffuse basis functions in geometry optimization resulted in significant change of total molecule energy. Total molecule energy of losartan potassium decreased by 112.91kJ/mol and 114.32kJ/mol for 6-31G(d,p)+ and 6-31G(d,p)++ basis sets, respectively. Almost the same decrease was observed for losartan: 114.99kJ/mol and 117.08kJ/mol respectively for 6-31G(d,p)+ and 6-31G(d,p)++ basis sets. Further investigation showed significant difference within geometries of losartan potassium optimized with investigated basis sets. Application of diffused basis functions resulted in average 1.29Å difference in relative position between corresponding atoms of three obtained geometries. Similar study taken on losartan resulted in only average 0.22Å of dislocation. Extensive analysis of geometry changes in molecules obtained with diffused and non-diffuse basis functions was carried out in order to elucidate observed changes. The analysis was supported by electrostatic potential maps and calculation of natural atomic charges. UV, FT-IR and Raman spectra of losartan potassium were calculated and compared with experimental results. No crucial differences between Raman spectra obtained with different basis sets were observed. However, FT-IR spectra of geometry of losartan potassium optimized with 6-31G(d,p)++ basis set resulted in 40% better correlation with experimental FT-IR spectra than FT-IR calculated with geometry optimized with 6-31G(d,p) basis set. Therefore, it is highly advisable to optimize geometry of molecules with ionic interactions using diffuse basis functions when

  2. Functionally-defined Therapeutic Targets in Diffuse Intrinsic Pontine Glioma

    PubMed Central

    Grasso, Catherine S.; Tang, Yujie; Truffaux, Nathalene; Berlow, Noah E.; Liu, Lining; Debily, Marie-Anne; Quist, Michael J.; Davis, Lara E.; Huang, Elaine C.; Woo, Pamelyn J; Ponnuswami, Anitha; Chen, Spenser; Johung, Tessa B.; Sun, Wenchao; Kogiso, Mari; Du, Yuchen; Lin, Qi; Huang, Yulun; Hütt-Cabezas, Marianne; Warren, Katherine E.; Dret, Ludivine Le; Meltzer, Paul S.; Mao, Hua; Quezado, Martha; van Vuurden, Dannis G.; Abraham, Jinu; Fouladi, Maryam; Svalina, Matthew N.; Wang, Nicholas; Hawkins, Cynthia; Nazarian, Javad; Alonso, Marta M.; Raabe, Eric; Hulleman, Esther; Spellman, Paul T.; Li, Xiao-Nan; Keller, Charles; Pal, Ranadip; Grill, Jacques; Monje, Michelle

    2015-01-01

    Diffuse Intrinsic Pontine Glioma (DIPG) is a fatal childhood cancer. We performed a chemical screen in patient-derived DIPG cultures along with RNAseq analyses and integrated computational modeling to identify potentially effective therapeutic strategies. The multi-histone deacetylase inhibitor panobinostat demonstrated efficacy in vitro and in DIPG orthotopic xenograft models. Combination testing of panobinostat with histone demethylase inhibitor GSKJ4 revealed synergy. Together, these data suggest a promising therapeutic strategy for DIPG. PMID:25939062

  3. MAPPING THE INTERSTELLAR MEDIUM WITH NEAR-INFRARED DIFFUSE INTERSTELLAR BANDS

    SciTech Connect

    Zasowski, G.; Ménard, B.; Bizyaev, D.; García-Hernández, D. A.; Pérez, A. E. García; Majewski, S. R.; Hayden, M. R.; Holtzman, J.; Kinemuchi, K.; Johnson, J. A.; Wilson, J. C.; Nidever, D. L.; Shetrone, M.

    2015-01-01

    We map the distribution and properties of the Milky Way's interstellar medium as traced by diffuse interstellar bands (DIBs) detected in near-infrared stellar spectra from the SDSS-III/APOGEE survey. Focusing exclusively on the strongest DIB in the H band, at λ ∼ 1.527 μm, we present a projected map of the DIB absorption field in the Galactic plane, using a set of about 60,000 sightlines that reach up to 15 kpc from the Sun and probe up to 30 mag of visual extinction. The strength of this DIB is linearly correlated with dust reddening over three orders of magnitude in both DIB equivalent width (W {sub DIB}) and extinction, with a power law index of 1.01 ± 0.01, a mean relationship of W {sub DIB}/A{sub V} = 0.1 Å mag{sup –1} and a dispersion of ∼0.05 Å mag{sup –1} at extinctions characteristic of the Galactic midplane. These properties establish this DIB as a powerful, independent probe of dust extinction over a wide range of A{sub V} values. The subset of about 14,000 robustly detected DIB features have a W {sub DIB} distribution that follows an exponential trend. We empirically determine the intrinsic rest wavelength of this transition to be λ{sub 0} = 15 272.42 Å  and use it to calculate absolute radial velocities of the carrier, which display the kinematical signature of the rotating Galactic disk. We probe the DIB carrier distribution in three dimensions and show that it can be characterized by an exponential disk model with a scale height of about 100 pc and a scale length of about 5 kpc. Finally, we show that the DIB distribution also traces large-scale Galactic structures, including the Galactic long bar and the warp of the outer disk.

  4. Diffusion Tensor Imaging as a Predictor of Locomotor Function after Experimental Spinal Cord Injury and Recovery

    PubMed Central

    Kelley, Brian J.; Harel, Noam Y.; Kim, Chang-Yeon; Papademetris, Xenophon; Coman, Daniel; Wang, Xingxing; Hasan, Omar; Kaufman, Adam; Globinsky, Ronen; Staib, Lawrence H.; Cafferty, William B.J.; Hyder, Fahmeed

    2014-01-01

    Abstract Traumatic spinal cord injury (SCI) causes long-term disability with limited functional recovery linked to the extent of axonal connectivity. Quantitative diffusion tensor imaging (DTI) of axonal integrity has been suggested as a potential biomarker for prognostic and therapeutic evaluation after trauma, but its correlation with functional outcomes has not been clearly defined. To examine this application, female Sprague-Dawley rats underwent midthoracic laminectomy followed by traumatic spinal cord contusion of differing severities or laminectomy without contusion. Locomotor scores and hindlimb kinematic data were collected for 4 weeks post-injury. Ex vivo DTI was then performed to assess axonal integrity using tractography and fractional anisotropy (FA), a numerical measure of relative white matter integrity, at the injury epicenter and at specific intervals rostral and caudal to the injury site. Immunohistochemistry for tissue sparing was also performed. Statistical correlation between imaging data and functional performance was assessed as the primary outcome. All injured animals showed some recovery of locomotor function, while hindlimb kinematics revealed graded deficits consistent with injury severity. Standard T2 magnetic resonance sequences illustrated conventional spinal cord morphology adjacent to contusions while corresponding FA maps indicated graded white matter pathology within these adjacent regions. Positive correlations between locomotor (Basso, Beattie, and Bresnahan score and gait kinematics) and imaging (FA values) parameters were also observed within these adjacent regions, most strongly within caudal segments beyond the lesion. Evaluation of axonal injury by DTI provides a mechanism for functional recovery assessment in a rodent SCI model. These findings suggest that focused DTI analysis of caudal spinal cord should be studied in human cases in relationship to motor outcome to augment outcome biomarkers for clinical cases. PMID

  5. Traveling wave solutions of density-dependent nonlinear reaction-diffusion equation via the extended generalized Riccati equation mapping method

    NASA Astrophysics Data System (ADS)

    Kengne, Emmanuel; Saydé, Michel; Ben Hamouda, Fathi; Lakhssassi, Ahmed

    2013-11-01

    Analytical entire traveling wave solutions to the 1+1 density-dependent nonlinear reaction-diffusion equation via the extended generalized Riccati equation mapping method are presented in this paper. This equation can be regarded as an extension case of the Fisher-Kolmogoroff equation, which is used for studying insect and animal dispersal with growth dynamics. The analytical solutions are then used to investigate the effect of equation parameters on the population distribution.

  6. Synthetic protein interactions reveal a functional map of the cell

    PubMed Central

    Berry, Lisa K; Ólafsson, Guðjón; Ledesma-Fernández, Elena; Thorpe, Peter H

    2016-01-01

    To understand the function of eukaryotic cells, it is critical to understand the role of protein-protein interactions and protein localization. Currently, we do not know the importance of global protein localization nor do we understand to what extent the cell is permissive for new protein associations – a key requirement for the evolution of new protein functions. To answer this question, we fused every protein in the yeast Saccharomyces cerevisiae with a partner from each of the major cellular compartments and quantitatively assessed the effects upon growth. This analysis reveals that cells have a remarkable and unanticipated tolerance for forced protein associations, even if these associations lead to a proportion of the protein moving compartments within the cell. Furthermore, the interactions that do perturb growth provide a functional map of spatial protein regulation, identifying key regulatory complexes for the normal homeostasis of eukaryotic cells. DOI: http://dx.doi.org/10.7554/eLife.13053.001 PMID:27098839

  7. How MAP kinase modules function as robust, yet adaptable, circuits

    PubMed Central

    Tian, Tianhai; Harding, Angus

    2014-01-01

    Genetic and biochemical studies have revealed that the diversity of cell types and developmental patterns evident within the animal kingdom is generated by a handful of conserved, core modules. Core biological modules must be robust, able to maintain functionality despite perturbations, and yet sufficiently adaptable for random mutations to generate phenotypic variation during evolution. Understanding how robust, adaptable modules have influenced the evolution of eukaryotes will inform both evolutionary and synthetic biology. One such system is the MAP kinase module, which consists of a 3-tiered kinase circuit configuration that has been evolutionarily conserved from yeast to man. MAP kinase signal transduction pathways are used across eukaryotic phyla to drive biological functions that are crucial for life. Here we ask the fundamental question, why do MAPK modules follow a conserved 3-tiered topology rather than some other number? Using computational simulations, we identify a fundamental 2-tiered circuit topology that can be readily reconfigured by feedback loops and scaffolds to generate diverse signal outputs. When this 2-kinase circuit is connected to proximal input kinases, a 3-tiered modular configuration is created that is both robust and adaptable, providing a biological circuit that can regulate multiple phenotypes and maintain functionality in an uncertain world. We propose that the 3-tiered signal transduction module has been conserved through positive selection, because it facilitated the generation of phenotypic variation during eukaryotic evolution. PMID:25483189

  8. Functionally defined therapeutic targets in diffuse intrinsic pontine glioma.

    PubMed

    Grasso, Catherine S; Tang, Yujie; Truffaux, Nathalene; Berlow, Noah E; Liu, Lining; Debily, Marie-Anne; Quist, Michael J; Davis, Lara E; Huang, Elaine C; Woo, Pamelyn J; Ponnuswami, Anitha; Chen, Spenser; Johung, Tessa B; Sun, Wenchao; Kogiso, Mari; Du, Yuchen; Qi, Lin; Huang, Yulun; Hütt-Cabezas, Marianne; Warren, Katherine E; Le Dret, Ludivine; Meltzer, Paul S; Mao, Hua; Quezado, Martha; van Vuurden, Dannis G; Abraham, Jinu; Fouladi, Maryam; Svalina, Matthew N; Wang, Nicholas; Hawkins, Cynthia; Nazarian, Javad; Alonso, Marta M; Raabe, Eric H; Hulleman, Esther; Spellman, Paul T; Li, Xiao-Nan; Keller, Charles; Pal, Ranadip; Grill, Jacques; Monje, Michelle

    2015-06-01

    Diffuse intrinsic pontine glioma (DIPG) is a fatal childhood cancer. We performed a chemical screen in patient-derived DIPG cultures along with RNA-seq analyses and integrated computational modeling to identify potentially effective therapeutic strategies. The multi-histone deacetylase inhibitor panobinostat demonstrated therapeutic efficacy both in vitro and in DIPG orthotopic xenograft models. Combination testing of panobinostat and the histone demethylase inhibitor GSK-J4 revealed that the two had synergistic effects. Together, these data suggest a promising therapeutic strategy for DIPG.

  9. Diffusion-relaxation distribution functions of sedimentary rocks in different saturation states.

    PubMed

    Hürlimann, M D; Flaum, M; Venkataramanan, L; Flaum, C; Freedman, R; Hirasaki, G J

    2003-01-01

    We present diffusion-relaxation distribution functions measured on four rock cores that were prepared in a succession of different saturation states of brine and crude oil. The measurements were performed in a static gradient field at a Larmor frequency of 1.76 MHz. The diffusion-relaxation distribution functions clearly separate the contributions from the two fluid phases. The results can be used to identify the wetting and non-wetting phase, to infer fluid properties of the phases, and to obtain additional information on the geometrical arrangement of the phases. We also observe effects due to restricted diffusion and susceptibility induced internal gradients.

  10. High-resolution mapping of protein sequence-function relationships.

    PubMed

    Fowler, Douglas M; Araya, Carlos L; Fleishman, Sarel J; Kellogg, Elizabeth H; Stephany, Jason J; Baker, David; Fields, Stanley

    2010-09-01

    We present a large-scale approach to investigate the functional consequences of sequence variation in a protein. The approach entails the display of hundreds of thousands of protein variants, moderate selection for activity and high-throughput DNA sequencing to quantify the performance of each variant. Using this strategy, we tracked the performance of >600,000 variants of a human WW domain after three and six rounds of selection by phage display for binding to its peptide ligand. Binding properties of these variants defined a high-resolution map of mutational preference across the WW domain; each position had unique features that could not be captured by a few representative mutations. Our approach could be applied to many in vitro or in vivo protein assays, providing a general means for understanding how protein function relates to sequence.

  11. The effect of meditation on brain structure: cortical thickness mapping and diffusion tensor imaging

    PubMed Central

    Kang, Do-Hyung; Jo, Hang Joon; Jung, Wi Hoon; Kim, Sun Hyung; Jung, Ye-Ha; Choi, Chi-Hoon; Lee, Ul Soon; An, Seung Chan; Jang, Joon Hwan

    2013-01-01

    A convergent line of neuroscientific evidence suggests that meditation alters the functional and structural plasticity of distributed neural processes underlying attention and emotion. The purpose of this study was to examine the brain structural differences between a well-matched sample of long-term meditators and controls. We employed whole-brain cortical thickness analysis based on magnetic resonance imaging, and diffusion tensor imaging to quantify white matter integrity in the brains of 46 experienced meditators compared with 46 matched meditation-naïve volunteers. Meditators, compared with controls, showed significantly greater cortical thickness in the anterior regions of the brain, located in frontal and temporal areas, including the medial prefrontal cortex, superior frontal cortex, temporal pole and the middle and interior temporal cortices. Significantly thinner cortical thickness was found in the posterior regions of the brain, located in the parietal and occipital areas, including the postcentral cortex, inferior parietal cortex, middle occipital cortex and posterior cingulate cortex. Moreover, in the region adjacent to the medial prefrontal cortex, both higher fractional anisotropy values and greater cortical thickness were observed. Our findings suggest that long-term meditators have structural differences in both gray and white matter. PMID:22569185

  12. Functional imaging and assessment of the glucose diffusion rate in epithelial tissues in optical coherence tomography

    SciTech Connect

    Larin, K V; Tuchin, V V

    2008-06-30

    Functional imaging, monitoring and quantitative description of glucose diffusion in epithelial and underlying stromal tissues in vivo and controlling of the optical properties of tissues are extremely important for many biomedical applications including the development of noninvasive or minimally invasive glucose sensors as well as for therapy and diagnostics of various diseases, such as cancer, diabetic retinopathy, and glaucoma. Recent progress in the development of a noninvasive molecular diffusion biosensor based on optical coherence tomography (OCT) is described. The diffusion of glucose was studied in several epithelial tissues both in vitro and in vivo. Because OCT provides depth-resolved imaging of tissues with high in-depth resolution, the glucose diffusion is described not only as a function of time but also as a function of depth. (special issue devoted to application of laser technologies in biophotonics and biomedical studies)

  13. A minimally diffusive interface function steepening approach for compressible multiphase flows

    NASA Astrophysics Data System (ADS)

    Regele, Jonathan

    2015-11-01

    Interface capturing methods for contacts and shocks are commonly used in compressible multiphase flows. Artificial diffusion is inherently necessary to stabilize jump discontinuities across shocks and contacts. Contacts suffer from diffusion more severely than shock waves because their characteristics are not convergent like shocks. Interface steepening procedures are commonly used to counteract numerical diffusion necessary to maintain a sharp interface function. In this work, a modification to the sharpening approach used in Shukla, Pantano, and Freund [J. Comp. Phys, 229, 2010] is developed that minimizes the artificial diffusion across the interface while maintaining a monotonic interface function. The method requires fewer iterations for convergence and provides a steeper interface function. Examples in one and two dimensions demonstrate the method's performance.

  14. Functional imaging and assessment of the glucose diffusion rate in epithelial tissues in optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Larin, K. V.; Tuchin, V. V.

    2008-06-01

    Functional imaging, monitoring and quantitative description of glucose diffusion in epithelial and underlying stromal tissues in vivo and controlling of the optical properties of tissues are extremely important for many biomedical applications including the development of noninvasive or minimally invasive glucose sensors as well as for therapy and diagnostics of various diseases, such as cancer, diabetic retinopathy, and glaucoma. Recent progress in the development of a noninvasive molecular diffusion biosensor based on optical coherence tomography (OCT) is described. The diffusion of glucose was studied in several epithelial tissues both in vitro and in vivo. Because OCT provides depth-resolved imaging of tissues with high in-depth resolution, the glucose diffusion is described not only as a function of time but also as a function of depth.

  15. 2D Potential theory using complex functions and conformal mapping

    NASA Astrophysics Data System (ADS)

    Le Maire, Pauline; Munschy, Marc

    2016-04-01

    For infinitely horizontally extended bodies, functions that describe potential and field equations (gravity and magnetics) outside bodies are 2D and harmonic. The consequence of this property is that potential and field equations can be written as complex analytic functions. We define these complex functions whose real part is the commonly used real function and imaginary part is its Hilbert transform. Using data or synthetic cases the transformation is easily performed in the Fourier domain by setting to zero all values for negative frequencies. Written as complex functions of the complex variable, equations of potential and field in gravity and magnetics for different kinds of geometries are simple and correspond to powers of the inverse of the distance. For example, it is easily shown that for a tilted dyke, the dip and the apparent inclination have the same effect on the function and consequently that it is not possible, with data, to compute one of both values without knowing the other. Conformal mapping is an original way to display potential field functions. Considering that the complex variable corresponds to the real axis, complex potential field functions resume to a limaçon, a curve formed by the path of the point fixed to a circle when that circle rolls around the outside of another circle. For example, the point corresponding to the maximum distance to the origin of the complex magnetic field due to a cylinder, corresponds to the maximum of the analytic signal as defined by Nabighan in 1972 and its phase corresponds to the apparent inclination. Several applications are shown in different geological contexts using aeromagnetic data.

  16. Functional Topography of Human Corpus Callosum: An fMRI Mapping Study

    PubMed Central

    Fabri, Mara; Polonara, Gabriele

    2013-01-01

    The concept of a topographical map of the corpus callosum (CC) has emerged from human lesion studies and from electrophysiological and anatomical tracing investigations in other mammals. Over the last few years a rising number of researchers have been reporting functional magnetic resonance imaging (fMRI) activation in white matter, particularly the CC. In this study the scope for describing CC topography with fMRI was explored by evoking activation through simple sensory stimulation and motor tasks. We reviewed our published and unpublished fMRI and diffusion tensor imaging data on the cortical representation of tactile, gustatory, auditory, and visual sensitivity and of motor activation, obtained in 36 normal volunteers and in 6 patients with partial callosotomy. Activation foci were consistently detected in discrete CC regions: anterior (taste stimuli), central (motor tasks), central and posterior (tactile stimuli), and splenium (auditory and visual stimuli). Reconstruction of callosal fibers connecting activated primary gustatory, motor, somatosensory, auditory, and visual cortices by diffusion tensor tracking showed bundles crossing, respectively, through the genu, anterior and posterior body, and splenium, at sites harboring fMRI foci. These data confirm that the CC commissure has a topographical organization and demonstrate that its functional topography can be explored with fMRI. PMID:23476810

  17. Complementary aspects of diffusion imaging and fMRI; I: structure and function.

    PubMed

    Mulkern, Robert V; Davis, Peter E; Haker, Steven J; Estepar, Raul San Jose; Panych, Lawrence P; Maier, Stephan E; Rivkin, Michael J

    2006-05-01

    Studying the intersection of brain structure and function is an important aspect of modern neuroscience. The development of magnetic resonance imaging (MRI) over the last 25 years has provided new and powerful tools for the study of brain structure and function. Two tools in particular, diffusion imaging and functional MRI (fMRI), are playing increasingly important roles in elucidating the complementary aspects of brain structure and function. In this work, we review basic technical features of diffusion imaging and fMRI for studying the integrity of white matter structural components and for determining the location and extent of cortical activation in gray matter, respectively. We then review a growing body of literature in which the complementary aspects of diffusion imaging and fMRI, applied as separate examinations but analyzed in tandem, have been exploited to enhance our knowledge of brain structure and function. PMID:16677953

  18. Mapping the Transmission Functions of Single-Molecule Junctions.

    PubMed

    Capozzi, Brian; Low, Jonathan Z; Xia, Jianlong; Liu, Zhen-Fei; Neaton, Jeffrey B; Campos, Luis M; Venkataraman, Latha

    2016-06-01

    Charge transport phenomena in single-molecule junctions are often dominated by tunneling, with a transmission function dictating the probability that electrons or holes tunnel through the junction. Here, we present a new and simple technique for measuring the transmission functions of molecular junctions in the coherent tunneling limit, over an energy range of 1.5 eV around the Fermi energy. We create molecular junctions in an ionic environment with electrodes having different exposed areas, which results in the formation of electric double layers of dissimilar density on the two electrodes. This allows us to electrostatically shift the molecular resonance relative to the junction Fermi levels in a manner that depends on the sign of the applied bias, enabling us to map out the junction's transmission function and determine the dominant orbital for charge transport in the molecular junction. We demonstrate this technique using two groups of molecules: one group having molecular resonance energies relatively far from EF and one group having molecular resonance energies within the accessible bias window. Our results compare well with previous electrochemical gating data and with transmission functions computed from first principles. Furthermore, with the second group of molecules, we are able to examine the behavior of a molecular junction as a resonance shifts into the bias window. This work provides a new, experimentally simple route for exploring the fundamentals of charge transport at the nanoscale. PMID:27186894

  19. Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function.

    PubMed

    Floyd, Brendan J; Wilkerson, Emily M; Veling, Mike T; Minogue, Catie E; Xia, Chuanwu; Beebe, Emily T; Wrobel, Russell L; Cho, Holly; Kremer, Laura S; Alston, Charlotte L; Gromek, Katarzyna A; Dolan, Brendan K; Ulbrich, Arne; Stefely, Jonathan A; Bohl, Sarah L; Werner, Kelly M; Jochem, Adam; Westphall, Michael S; Rensvold, Jarred W; Taylor, Robert W; Prokisch, Holger; Kim, Jung-Ja P; Coon, Joshua J; Pagliarini, David J

    2016-08-18

    Mitochondria are essential for numerous cellular processes, yet hundreds of their proteins lack robust functional annotation. To reveal functions for these proteins (termed MXPs), we assessed condition-specific protein-protein interactions for 50 select MXPs using affinity enrichment mass spectrometry. Our data connect MXPs to diverse mitochondrial processes, including multiple aspects of respiratory chain function. Building upon these observations, we validated C17orf89 as a complex I (CI) assembly factor. Disruption of C17orf89 markedly reduced CI activity, and its depletion is found in an unresolved case of CI deficiency. We likewise discovered that LYRM5 interacts with and deflavinates the electron-transferring flavoprotein that shuttles electrons to coenzyme Q (CoQ). Finally, we identified a dynamic human CoQ biosynthetic complex involving multiple MXPs whose topology we map using purified components. Collectively, our data lend mechanistic insight into respiratory chain-related activities and prioritize hundreds of additional interactions for further exploration of mitochondrial protein function. PMID:27499296

  20. Director orientations in lyotropic liquid crystals: diffusion MRI mapping of the Saupe order tensor.

    PubMed

    Topgaard, Daniel

    2016-03-28

    The macroscopic physical properties of a liquid crystalline material depend on both the properties of the individual crystallites and the details of their spatial arrangement. We propose a diffusion MRI method to estimate the director orientations of a lyotropic liquid crystal as a spatially resolved field of Saupe order tensors. The method relies on varying the shape of the diffusion-encoding tensor to disentangle the effects of voxel-scale director orientational order and the local diffusion anisotropy of the solvent. Proof-of-concept experiments are performed on water in lamellar and reverse hexagonal liquid crystalline systems with intricate patterns of director orientations.

  1. Calculation of the second term of the exact Green's function of the diffusion equation for diffusion-controlled chemical reactions

    NASA Astrophysics Data System (ADS)

    Plante, Ianik

    2016-01-01

    The exact Green's function of the diffusion equation (GFDE) is often considered to be the gold standard for the simulation of partially diffusion-controlled reactions. As the GFDE with angular dependency is quite complex, the radial GFDE is more often used. Indeed, the exact GFDE is expressed as a Legendre expansion, the coefficients of which are given in terms of an integral comprising Bessel functions. This integral does not seem to have been evaluated analytically in existing literature. While the integral can be evaluated numerically, the Bessel functions make the integral oscillate and convergence is difficult to obtain. Therefore it would be of great interest to evaluate the integral analytically. The first term was evaluated previously, and was found to be equal to the radial GFDE. In this work, the second term of this expansion was evaluated. As this work has shown that the first two terms of the Legendre polynomial expansion can be calculated analytically, it raises the question of the possibility that an analytical solution exists for the other terms.

  2. Local analyses of Planck maps with Minkowski functionals

    NASA Astrophysics Data System (ADS)

    Novaes, C. P.; Bernui, A.; Marques, G. A.; Ferreira, I. S.

    2016-09-01

    Minkowski functionals (MF) are excellent tools to investigate the statistical properties of the cosmic background radiation (CMB) maps. Between their notorious advantages is the possibility to use them efficiently in patches of the CMB sphere, which allow studies in masked skies, inclusive analyses of small sky regions. Then, possible deviations from Gaussianity are investigated by comparison with MF obtained from a set of Gaussian isotropic simulated CMB maps to which are applied the same cut-sky masks. These analyses are sensitive enough to detect contaminations of small intensity like primary and secondary CMB anisotropies. Our methodology uses the MF, widely employed to study non-Gaussianities in CMB data, and asserts Gaussian deviations only when all of them points out an exceptional χ2 value, at more than 2.2σ confidence level, in a given sky patch. Following this rigorous procedure, we find 13 regions in the foreground-cleaned Planck maps that evince such high levels of non-Gaussian deviations. According to our results, these non-Gaussian contributions show signatures that can be associated to the presence of hot or cold spots in such regions. Moreover, some of these non-Gaussian deviations signals suggest the presence of foreground residuals in those regions located near the Galactic plane. Additionally, we confirm that most of the regions revealed in our analyses, but not all, have been recently reported in studies done by the Planck collaboration. Furthermore, we also investigate whether these non-Gaussian deviations can be possibly sourced by systematics, like inhomogeneous noise and beam effect in the released Planck data, or perhaps due to residual Galactic foregrounds.

  3. Resecting diffuse low-grade gliomas to the boundaries of brain functions: a new concept in surgical neuro-oncology.

    PubMed

    Duffau, H

    2015-12-01

    The traditional dilemma making surgery for diffuse low-grade gliomas (DLGGs) challenging is underlain by the need to optimize tumor resection in order to significantly increase survival versus the risk of permanent neurological morbidity. Development of neuroimaging led neurosurgeons to achieve tumorectomy according to the oncological limits provided by preoperative or intraoperative structural and metabolic imaging. However, this principle is not coherent, neither with the infiltrative nature of DLGGs nor with the limited resolution of current neuroimaging. Indeed, despite technical advances, MRI still underestimates the actual spatial extent of gliomas, since tumoral cells are present several millimeters to centimeters beyond the area of signal abnormalities. Furthermore, cortical and subcortical structures may be still crucial for brain functions despite their invasion by this diffuse tumoral disease. Finally, the lack of reliability of functional MRI has also been demonstrated. Therefore, to talk about "maximal safe resection" based upon neuroimaging is a non-sense, because oncological MRI does not show the tumor and functional MRI does not show critical neural pathways. This review proposes an original concept in neuro-oncological surgery, i.e. to resect DLGG to the boundaries of brain functions, thanks to intraoperative electrical mapping performed in awake patients. This paradigmatic shift from image-guided resection to functional mapping-guided resection, based upon an accurate study of brain connectomics and neuroplasticity in each patient throughout tumor removal has permitted to solve the classical dilemma, by increasing both survival and quality of life in DLGG patients. With this in mind, brain surgeons should also be neuroscientists.

  4. Functional mapping of reaction norms to multiple environmental signals.

    PubMed

    Wu, Jiasheng; Zeng, Yanru; Huang, Jianqing; Hou, Wei; Zhu, Jun; Wu, Rongling

    2007-02-01

    Whether there are different genes involved in response to different environmental signals and how these genes interact to determine the final expression of the trait are of fundamental importance in agricultural and biological research. We present a statistical framework for mapping environment-induced genes (or quantitative trait loci, QTLs) of major effects on the expression of a trait that respond to changing environments. This framework is constructed with a maximum-likelihood-based mixture model, in which the mean and covariance structure of environment-induced responses is modelled. The means for responses to continuous environmental states, referred to as reaction norms, are approximated for different QTL genotypes by mathematical equations that were derived from fundamental biological principles or based on statistical goodness-of-fit to observational data. The residual covariance between different environmental states was modelled by autoregressive processes. Such an approach to studying the genetic control of reaction norms can be expected to be advantageous over traditional mapping approaches in which no biological principles and statistical structures are considered. We demonstrate the analytical procedure and power of this approach by modelling the photosynthetic rate process as a function of temperature and light irradiance. Our approach allows for testing how a QTL affects the reaction norm of photosynthetic rate to a specific environment and whether there exist different QTLs to mediate photosynthetic responses to temperature and light irradiance, respectively. PMID:17517157

  5. The time dependent propensity function for acceleration of spatial stochastic simulation of reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Fu, Jin; Wu, Sheng; Li, Hong; Petzold, Linda R.

    2014-10-01

    The inhomogeneous stochastic simulation algorithm (ISSA) is a fundamental method for spatial stochastic simulation. However, when diffusion events occur more frequently than reaction events, simulating the diffusion events by ISSA is quite costly. To reduce this cost, we propose to use the time dependent propensity function in each step. In this way we can avoid simulating individual diffusion events, and use the time interval between two adjacent reaction events as the simulation stepsize. We demonstrate that the new algorithm can achieve orders of magnitude efficiency gains over widely-used exact algorithms, scales well with increasing grid resolution, and maintains a high level of accuracy.

  6. The Time Dependent Propensity Function for Acceleration of Spatial Stochastic Simulation of Reaction-Diffusion Systems

    PubMed Central

    Wu, Sheng; Li, Hong; Petzold, Linda R.

    2015-01-01

    The inhomogeneous stochastic simulation algorithm (ISSA) is a fundamental method for spatial stochastic simulation. However, when diffusion events occur more frequently than reaction events, simulating the diffusion events by ISSA is quite costly. To reduce this cost, we propose to use the time dependent propensity function in each step. In this way we can avoid simulating individual diffusion events, and use the time interval between two adjacent reaction events as the simulation stepsize. We demonstrate that the new algorithm can achieve orders of magnitude efficiency gains over widely-used exact algorithms, scales well with increasing grid resolution, and maintains a high level of accuracy. PMID:26609185

  7. The time dependent propensity function for acceleration of spatial stochastic simulation of reaction–diffusion systems

    SciTech Connect

    Fu, Jin; Wu, Sheng; Li, Hong; Petzold, Linda R.

    2014-10-01

    The inhomogeneous stochastic simulation algorithm (ISSA) is a fundamental method for spatial stochastic simulation. However, when diffusion events occur more frequently than reaction events, simulating the diffusion events by ISSA is quite costly. To reduce this cost, we propose to use the time dependent propensity function in each step. In this way we can avoid simulating individual diffusion events, and use the time interval between two adjacent reaction events as the simulation stepsize. We demonstrate that the new algorithm can achieve orders of magnitude efficiency gains over widely-used exact algorithms, scales well with increasing grid resolution, and maintains a high level of accuracy.

  8. Probing dissociative molecular dications by mapping vibrational wave functions

    SciTech Connect

    Puettner, R.; Sekushin, V.; Kaindl, G.; Arion, T.; Lischke, T.; Mucke, M.; Hergenhahn, U.; Foerstel, M.; Bradshaw, A. M.

    2011-04-15

    We present high-resolution photoelectron-Auger-electron coincidence spectra of methane (CH{sub 4}). Since the vibrational structure in the photoelectron spectrum is resolved, the Auger spectra corresponding to different vibrational levels can be separated. The seven final states of CH{sub 4}{sup 2+} are either dissociative or metastable, but in any case are populated in a repulsive part of their potential-energy curve via the Auger decay. The Auger line shapes can therefore be obtained by mapping the vibrational wave functions of the core-hole state into energy space. We have implemented this connection in the data analysis. By simultaneously fitting the different Auger spectra, detailed information on the energies of the dicationic states and their repulsive potential-energy curves is derived.

  9. Velocity Autocorrelation Functions and Diffusion of Dusty Plasma

    SciTech Connect

    Ramazanov, T. S.; Dzhumagulova, K. N.; Daniyarov, T. T.; Dosbolayev, M. K.; Jumabekov, A. N.

    2008-09-07

    The velocity autocorrelation functions and square displacements were calculated on the basis of experimental data obtained on experimental setup with dc discharge. Computer simulation of the system of dust particles by the method of the Langevin dynamics was performed. The comparisons of experimental and theoretical results are given.

  10. Solitary fibrous tumor of the pleura: apparent diffusion coefficient (ADC) value and ADC map to predict malignant transformation.

    PubMed

    Inaoka, Tsutomu; Takahashi, Koji; Miyokawa, Naoyuki; Ohsaki, Yoshinobu; Aburano, Tamio

    2007-07-01

    Solitary fibrous tumors (SFTs) of the pleura are rare soft-tissue tumors that are presumed to be of mesenchymal origin. Most SFTs are histologically benign, but up to 20% of SFTs may be malignant. In addition, malignant transformation may occur within histologically benign SFTs, though it is rare. However, it is difficult to diagnose malignant SFTs of the pleura by means of conventional computed tomography and magnetic resonance imaging (MRI). In this article we present the first case of malignant SFT of the pleura in an 81-year-old man in which the apparent diffusion coefficient (ADC) value and ADC map based on diffusion-weighted MRI were very useful for identifying malignant transformation.

  11. Site and Orbit Repeatabilities using Adaptive Mapping Functions

    NASA Astrophysics Data System (ADS)

    Desjardins, Camille; Gegout, Pascal; Soudarin, Laurent; Biancale, Richard; Perosanz, Felix

    2015-04-01

    The electromagnetic signals emitted by the satellite positioning systems travel at the speed of light in a straight line in a vacuum but are modified in their propagation through the neutral atmosphere by temporal and spatial changes of density, and composition and refractivity. These waves are slowed down and their trajectories are bent. This presentation summarizes the performances of the modeling of the tropospheric propagation by the ray tracing technique through the assimilations of the European Meteorological Centre (ECMWF) in the framework of realizing the geodetic reference frame. This goal is achieved by modeling the spatial variability of the propagation using the time variable three-dimensional physical parameters of the atmosphere. The tropospheric delays obtained by ray tracing in all directions throughout the meteorological model surrounding the geodetic site, are fitted by Adaptive Mapping Functions (AMF) parameterized by several tens of coefficients. The delays produced by the Horizon software are then experimented, kept unchanged or adjusted, when recovering a reference frame based on hundred sites using the GINS software. Without any adjustments of the tropospheric modeling, the subcentimetric performances of the AMF are demonstrated by the repeatability of sites positions and GPS satellites orbits. When some AMF coefficients are adjusted, the accuracy of orbits recovery in term of quadratic mean is 7 to 8 millimeters. This limit is imposed by the lack or deficiency of other models, such as non-tidal and tidal loading respectively. Hence the repeatability of the vertical position is not enhanced by changing the propagation model. At the contrary, the repeatability of the horizontal position of geodetic sites is greatly enhanced by accounting for the azimuthal variability provided by the realistic 3D shapes of the Atmosphere and the Earth and the rigorous interpolations of atmospheric parameters included in Adaptive Mapping Functions with respect

  12. Maps of current density using density-functional methods

    NASA Astrophysics Data System (ADS)

    Soncini, A.; Teale, A. M.; Helgaker, T.; de Proft, F.; Tozer, D. J.

    2008-08-01

    The performance of several density-functional theory (DFT) methods for the calculation of current densities induced by a uniform magnetic field is examined. Calculations are performed using the BLYP and KT3 generalized-gradient approximations, together with the B3LYP hybrid functional. For the latter, both conventional and optimized effective potential (OEP) approaches are used. Results are also determined from coupled-cluster singles-and-doubles (CCSD) electron densities by a DFT constrained search procedure using the approach of Wu and Yang (WY). The current densities are calculated within the CTOCD-DZ2 distributed origin approach. Comparisons are made with results from Hartree-Fock (HF) theory. Several small molecules for which correlation is known to be especially important in the calculation of magnetic response properties are considered-namely, O3, CO, PN, and H2CO. As examples of aromatic and antiaromatic systems, benzene and planarized cyclooctatetraene molecules are considered, with specific attention paid to the ring current phenomenon and its Kohn-Sham orbital origin. Finally, the o-benzyne molecule is considered as a computationally challenging case. The HF and DFT induced current maps show qualitative differences, while among the DFT methods the maps show a similar qualitative structure. To assess quantitative differences in the calculated current densities with different methods, the maximal moduli of the induced current densities are compared and integration of the current densities to yield shielding constants is performed. In general, the maximal modulus is reduced in moving from HF to B3LYP and BLYP, and further reduced in moving to KT3, OEP(B3LYP), and WY(CCSD). The latter three methods offer the most accurate shielding constants in comparison with both experimental and ab initio data and hence the more reliable route to DFT calculation of induced current density in molecules.

  13. Correlation function induced by a generalized diffusion equation with the presence of a harmonic potential

    SciTech Connect

    Fa, Kwok Sau

    2015-02-15

    An integro-differential diffusion equation with linear force, based on the continuous time random walk model, is considered. The equation generalizes the ordinary and fractional diffusion equations, which includes short, intermediate and long-time memory effects described by the waiting time probability density function. Analytical expression for the correlation function is obtained and analyzed, which can be used to describe, for instance, internal motions of proteins. The result shows that the generalized diffusion equation has a broad application and it may be used to describe different kinds of systems. - Highlights: • Calculation of the correlation function. • The correlation function is connected to the survival probability. • The model can be applied to the internal dynamics of proteins.

  14. Mapping Multiplex Hubs in Human Functional Brain Networks.

    PubMed

    De Domenico, Manlio; Sasai, Shuntaro; Arenas, Alex

    2016-01-01

    Typical brain networks consist of many peripheral regions and a few highly central ones, i.e., hubs, playing key functional roles in cerebral inter-regional interactions. Studies have shown that networks, obtained from the analysis of specific frequency components of brain activity, present peculiar architectures with unique profiles of region centrality. However, the identification of hubs in networks built from different frequency bands simultaneously is still a challenging problem, remaining largely unexplored. Here we identify each frequency component with one layer of a multiplex network and face this challenge by exploiting the recent advances in the analysis of multiplex topologies. First, we show that each frequency band carries unique topological information, fundamental to accurately model brain functional networks. We then demonstrate that hubs in the multiplex network, in general different from those ones obtained after discarding or aggregating the measured signals as usual, provide a more accurate map of brain's most important functional regions, allowing to distinguish between healthy and schizophrenic populations better than conventional network approaches. PMID:27471443

  15. Mapping Multiplex Hubs in Human Functional Brain Networks

    PubMed Central

    De Domenico, Manlio; Sasai, Shuntaro; Arenas, Alex

    2016-01-01

    Typical brain networks consist of many peripheral regions and a few highly central ones, i.e., hubs, playing key functional roles in cerebral inter-regional interactions. Studies have shown that networks, obtained from the analysis of specific frequency components of brain activity, present peculiar architectures with unique profiles of region centrality. However, the identification of hubs in networks built from different frequency bands simultaneously is still a challenging problem, remaining largely unexplored. Here we identify each frequency component with one layer of a multiplex network and face this challenge by exploiting the recent advances in the analysis of multiplex topologies. First, we show that each frequency band carries unique topological information, fundamental to accurately model brain functional networks. We then demonstrate that hubs in the multiplex network, in general different from those ones obtained after discarding or aggregating the measured signals as usual, provide a more accurate map of brain's most important functional regions, allowing to distinguish between healthy and schizophrenic populations better than conventional network approaches. PMID:27471443

  16. Mapping

    ERIC Educational Resources Information Center

    Kinney, Douglas M.; McIntosh, Willard L.

    1978-01-01

    Geologic mapping in the United States increased by about one-quarter in the past year. Examinations of mapping trends were in the following categories: (1) Mapping at scales of 1:100, 000; (2) Metric-scale base maps; (3) International mapping, and (4) Planetary mapping. (MA)

  17. Classification and Approximate Functional Separable Solutions to the Generalized Diffusion Equations with Perturbation

    NASA Astrophysics Data System (ADS)

    Ji, Fei-Yu; Zhang, Shun-Li

    2013-11-01

    In this paper, the generalized diffusion equation with perturbation ut = A(u;ux)uII+eB(u;ux) is studied in terms of the approximate functional variable separation approach. A complete classification of these perturbed equations which admit approximate functional separable solutions is presented. Some approximate solutions to the resulting perturbed equations are obtained by examples.

  18. Can Native T1 Mapping Differentiate between Healthy and Diffuse Diseased Myocardium in Clinical Routine Cardiac MR Imaging?

    PubMed Central

    Goebel, Juliane; Seifert, Ingmar; Nensa, Felix; Schemuth, Haemi P.; Maderwald, Stefan; Quick, Harald H.; Schlosser, Thomas; Jensen, Christoph; Bruder, Oliver; Nassenstein, Kai

    2016-01-01

    Objectives T1 mapping allows quantitative myocardial assessment, but its value in clinical routine remains unclear. We investigated, whether the average native myocardial T1 value can be used as a diagnostic classifier between healthy and diffuse diseased myocardium. Methods Native T1 mapping was performed in 54 persons with healthy hearts and in 150 patients with diffuse myocardial pathologies (coronary artery disease (CAD): n = 76, acute myocarditis: n = 19, convalescent myocarditis: n = 26, hypertrophic cardiomyopathy (HCM): n = 12, dilated cardiomyopathy (DCM): n = 17) at 1.5 Tesla in a mid-ventricular short axis slice using a modified Look-Locker inversion recovery (MOLLI) sequence. The average native myocardial T1 value was measured using dedicated software for each patient. The mean as well as the range of the observed average T1 values were calculated for each group, and compared using t-test. The ability of T1 mapping to differentiate between healthy and diffuse diseased myocardium was assessed using receiver operating characteristic analysis (ROC). Results The mean T1 value of the group “healthy hearts” (955±34ms) differed significantly from that of the groups DCM (992±37ms, p<0.001), HCM (980±44ms, p = 0.035), and acute myocarditis (974±36ms, p = 0.044). No significant difference was observed between the groups “healthy hearts” and CAD (951±37ms, p = 0.453) or convalescent myocarditis (965±40ms, p = 0.240). The average native T1 value varied considerably within all groups (range: healthy hearts, 838-1018ms; DCM, 882-1034ms; HCM, 897-1043ms; acute myocarditis, 925-1025ms; CAD, 867-1082ms; convalescent myocarditis, 890-1071ms) and overlapped broadly between all groups. ROC analysis showed, that the average native T1 value does not allow for differentiating between healthy and diffuse diseased myocardium, except for the subgroup of DCM. Conclusions The average native T1 value in cardiac MR imaging does not allow differentiating between healthy

  19. Reconstruction of optical absorption coefficient maps of heterogeneous media by photoacoustic tomography coupled with diffusion equation based regularized Newton method.

    PubMed

    Yuan, Zhen; Wang, Qiang; Jiang, Huabei

    2007-12-24

    We describe a novel reconstruction method that allows for quantitative recovery of optical absorption coefficient maps of heterogeneous media using tomographic photoacoustic measurements. Images of optical absorption coefficient are obtained from a diffusion equation based regularized Newton method where the absorbed energy density distribution from conventional photoacoustic tomography serves as the measured field data. We experimentally demonstrate this new method using tissue-mimicking phantom measurements and simulations. The reconstruction results show that the optical absorption coefficient images obtained are quantitative in terms of the shape, size, location and optical property values of the heterogeneities examined.

  20. Nanoscale mapping of ion diffusion in a lithium-ion battery cathode

    SciTech Connect

    Balke, N.; Jesse, S.; Morozovska, A.; Eliseev, E.; Chung, D.; Kim, Y.; Adamczyk, L.; Garcia, R.

    2010-08-29

    The movement of lithium ions into and out of electrodes is central to the operation of lithium-ion batteries. Although this process has been extensively studied at the device level, it remains insufficiently characterized at the nanoscale level of grain clusters, single grains and defects. Here, we probe the spatial variation of lithium-ion diffusion times in the battery-cathode material LiCoO{sub 2} at a resolution of ~100 nm by using an atomic force microscope to both redistribute lithium ions and measure the resulting cathode deformation. The relationship between diffusion and single grains and grain boundaries is observed, revealing that the diffusion coefficient increases for certain grain orientations and single-grain boundaries. This knowledge provides feedback to improve understanding of the nanoscale mechanisms underpinning lithium-ion battery operation.

  1. Nondestructive Method for Mapping Metal Contact Diffusion in In2O3 Thin-Film Transistors.

    PubMed

    Kryvchenkova, Olga; Abdullah, Isam; Macdonald, John Emyr; Elliott, Martin; Anthopoulos, Thomas D; Lin, Yen-Hung; Igić, Petar; Kalna, Karol; Cobley, Richard J

    2016-09-28

    The channel width-to-length ratio is an important transistor parameter for integrated circuit design. Contact diffusion into the channel during fabrication or operation alters the channel width and this important parameter. A novel methodology combining atomic force microscopy and scanning Kelvin probe microscopy (SKPM) with self-consistent modeling is developed for the nondestructive detection of contact diffusion on active devices. Scans of the surface potential are modeled using physically based Technology Computer Aided Design (TCAD) simulations when the transistor terminals are grounded and under biased conditions. The simulations also incorporate the tip geometry to investigate its effect on the measurements due to electrostatic tip-sample interactions. The method is particularly useful for semiconductor- and metal-semiconductor interfaces where the potential contrast resulting from dopant diffusion is below that usually detectable with scanning probe microscopy. PMID:27581104

  2. Non Gaussian Minkowski functionals and extrema counts for CMB maps

    NASA Astrophysics Data System (ADS)

    Pogosyan, Dmitri; Codis, Sandrine; Pichon, Christophe

    2016-10-01

    In the conference presentation we have reviewed the theory of non-Gaussian geometrical measures for 3D Cosmic Web of the matter distribution in the Universe and 2D sky data, such as Cosmic Microwave Background (CMB) maps that was developed in a series of our papers. The theory leverages symmetry of isotropic statistics such as Minkowski functionals and extrema counts to develop post Gaussian expansion of the statistics in orthogonal polynomials of invariant descriptors of the field, its first and second derivatives. The application of the approach to 2D fields defined on a spherical sky was suggested, but never rigorously developed. In this paper we present such development treating the effects of the curvature and finiteness of the spherical space $S_2$ exactly, without relying on flat-sky approximation. We present Minkowski functionals, including Euler characteristic and extrema counts to the first non-Gaussian correction, suitable for weakly non-Gaussian fields on a sphere, of which CMB is the prime example.

  3. Mapping the trajectory of the stria terminalis of the human limbic system using high spatial resolution diffusion tensor tractography.

    PubMed

    Kamali, Arash; Yousem, David M; Lin, Doris D; Sair, Haris I; Jasti, Siva P; Keser, Zafer; Riascos, Roy F; Hasan, Khader M

    2015-11-01

    The human limbic system is composed of gray and white matter structures which have been known to have a role in core processes such as motivation, memory, emotion, social behavior, self-awareness as well as certain primitive instincts. Multiple functional studies investigated some of these brain tasks in human brain limbic system. However, the underlying fine fiber pathways of the limbic system including the trajectory of the stria terminalis have not been delineated separately by prior diffusion weighted imaging. The ability to trace the underlying fiber anatomy noninvasively using diffusion tensor tractography (DTT) would be helpful to study the neurophysiology of these tracts in different functions in future functional studies. Few studies have focused on the stria terminalis using diffusion tensor tractography. Yet, the trajectory of the stria terminalis and some fine subtrajectories of the fornix have not been elucidated by prior DTT studies. We decided to further investigate these fine neuronal trajectory using tractography and high spatial resolution diffusion tensor imaging on 3T. Fifteen healthy right-handed men (age range 24-37 years) were studied. We delineated the detailed trajectories of the stria terminalis and fornix bilaterally in fifteen normal adult human brains. Using a high resolution DTT technique, we demonstrate for the first time, the trajectory of stria terminalis as well as detailed precommissural and postcommissural connectivity of the forniceal columns.

  4. Density functional theory calculations of stability and diffusion mechanisms of impurity atoms in Ge crystals

    NASA Astrophysics Data System (ADS)

    Maeta, Takahiro; Sueoka, Koji

    2014-08-01

    Ge-based substrates are being developed for applications in advanced nano-electronic devices because of their higher intrinsic carrier mobility than Si. The stability and diffusion mechanism of impurity atoms in Ge are not well known in contrast to those of Si. Systematic studies of the stable sites of 2nd to 6th row element impurity atoms in Ge crystal were undertaken with density functional theory (DFT) and compared with those in Si crystal. It was found that most of the impurity atoms in Ge were stable at substitutional sites, while transition metals in Si were stable at interstitial sites and the other impurity atoms in Si were stable at substitutional sites. Furthermore, DFT calculations were carried out to clarify the mechanism responsible for the diffusion of impurity atoms in Ge crystals. The diffusion mechanism for 3d transition metals in Ge was found to be an interstitial-substitutional diffusion mechanism, while in Si this was an interstitial diffusion mechanism. The diffusion barriers in the proposed diffusion mechanisms in Ge and Si were quantitatively verified by comparing them to the experimental values in the literature.

  5. Density functional theory calculations of stability and diffusion mechanisms of impurity atoms in Ge crystals

    SciTech Connect

    Maeta, Takahiro; Sueoka, Koji

    2014-08-21

    Ge-based substrates are being developed for applications in advanced nano-electronic devices because of their higher intrinsic carrier mobility than Si. The stability and diffusion mechanism of impurity atoms in Ge are not well known in contrast to those of Si. Systematic studies of the stable sites of 2nd to 6th row element impurity atoms in Ge crystal were undertaken with density functional theory (DFT) and compared with those in Si crystal. It was found that most of the impurity atoms in Ge were stable at substitutional sites, while transition metals in Si were stable at interstitial sites and the other impurity atoms in Si were stable at substitutional sites. Furthermore, DFT calculations were carried out to clarify the mechanism responsible for the diffusion of impurity atoms in Ge crystals. The diffusion mechanism for 3d transition metals in Ge was found to be an interstitial-substitutional diffusion mechanism, while in Si this was an interstitial diffusion mechanism. The diffusion barriers in the proposed diffusion mechanisms in Ge and Si were quantitatively verified by comparing them to the experimental values in the literature.

  6. Cognitive activity, cognitive function, and brain diffusion characteristics in old age.

    PubMed

    Arfanakis, Konstantinos; Wilson, Robert S; Barth, Christopher M; Capuano, Ana W; Vasireddi, Anil; Zhang, Shengwei; Fleischman, Debra A; Bennett, David A

    2016-06-01

    The objective of this work was to test the hypotheses that a) more frequent cognitive activity in late life is associated with higher brain diffusion anisotropy and lower trace of the diffusion tensor, and b) brain diffusion characteristics partially mediate the association of late life cognitive activity with cognition. As part of a longitudinal cohort study, 379 older people without dementia rated their frequency of participation in cognitive activities, completed a battery of cognitive function tests, and underwent diffusion tensor imaging. We used tract-based spatial statistics to test the association between late life cognitive activity and brain diffusion characteristics. Clusters with statistically significant findings defined regions of interest in which we tested the hypothesis that diffusion characteristics partially mediate the association of late life cognitive activity with cognition. More frequent cognitive activity in late life was associated with higher level of global cognition after adjustment for age, sex, education, and indicators of early life cognitive enrichment (p = 0.001). More frequent cognitive activity was also related to higher fractional anisotropy in the left superior and inferior longitudinal fasciculi, left fornix, and corpus callosum, and lower trace in the thalamus (p < 0.05, FWE-corrected). After controlling for fractional anisotropy or trace from these regions, the regression coefficient for the association of late life cognitive activity with cognition was reduced by as much as 26 %. These findings suggest that the association of late life cognitive activity with cognition may be partially mediated by brain diffusion characteristics.

  7. Remote sensing of prefrontal cortex function with diffusive light

    NASA Astrophysics Data System (ADS)

    Zhao, Zhongyao; Wang, Xin C.; Chance, Britton

    2004-12-01

    A data bank on prefrontal imaging under stressful conditions including deceit, has been gathered over several years on National and International populations using a contact imager pad consisting of 16 detectors and 4 sources, validating the concept of imaging prefrontal responses to stress, not only following the response of the PFC to imaging stress but especially of precognitive activations. We designed a new portable and non-invasive optical detecting system for remote sensing of deceit at 1~2m distance. The signals of pre- and post-cognitive function in deceit can be detected with very high sensitivity for blood volume and blood oxygenation detection at depths sufficient for PFC imaging and sensitivities of sub-micromolar oxy-hemoglobin and blood concentration detection. Thus, remote imaging of the process of decision making seems possible and examples will be presented using both contact and flying spot remote sensing.

  8. A Mapping of the Electron Localization Function for Earth Materials

    SciTech Connect

    Gibbs, Gerald V.; Cox, David F.; Ross, Nancy; Crawford, T Daniel; Burt, Jason; Rosso, Kevin M.

    2005-06-01

    The electron localization function, ELF, generated for a number of geometry-optimized earth materials, provides a graphical representation of the spatial localization of the probability electron density distribution as embodied in domains ascribed to localized bond and lone pair electrons. The lone pair domains, displayed by the silica polymorphs quartz, coesite and cristobalite, are typically banana-shaped and oriented perpendicular to the plane of the SiOSi angle at ~0.60 Å from the O atom on the reflex side of the angle. With decreasing angle, the domains increase in magnitude, indicating an increase in the nucleophilic character of the O atom, rendering it more susceptible to potential electrophilic attack. The Laplacian isosurface maps of the experimental and theoretical electron density distribution for coesite substantiates the increase in the size of the domain with decreasing angle. Bond pair domains are displayed along each of the SiO bond vectors as discrete concave hemispherically-shaped domains at ~0.70 Å from the O atom. For more closed-shell ionic bonded interactions, the bond and lone pair domains are often coalesced, resulting in concave hemispherical toroidal-shaped domains with local maxima centered along the bond vectors. As the shared covalent character of the bonded interactions increases, the bond and lone pair domains are better developed as discrete domains. ELF isosurface maps generated for the earth materials tremolite, diopside, talc and dickite display banana-shaped lone pair domains associated with the bridging O atoms of SiOSi angles and concave hemispherical toroidal bond pair domains associated with the nonbridging ones. The lone pair domains in dickite and talc provide a basis for understanding the bonded interactions between the adjacent neutral layers. Maps were also generated for beryl, cordierite, quartz, low albite, forsterite, wadeite, åkermanite, pectolite, periclase, hurlbutite, thortveitite and vanthoffite. Strategies

  9. Spatial resolution versus data acquisition efficiency in mapping an inhomogeneous system with species diffusion

    PubMed Central

    Chen, Fengxiang; Zhang, Yong; Gfroerer, T. H.; Finger, A. N.; Wanlass, M. W.

    2015-01-01

    Traditionally, spatially-resolved photoluminescence (PL) has been performed using a point-by-point scan mode with both excitation and detection occurring at the same spatial location. But with the availability of high quality detector arrays like CCDs, an imaging mode has become popular for performing spatially-resolved PL. By illuminating the entire area of interest and collecting the data simultaneously from all spatial locations, the measurement efficiency can be greatly improved. However, this new approach has proceeded under the implicit assumption of comparable spatial resolution. We show here that when carrier diffusion is present, the spatial resolution can actually differ substantially between the two modes, with the less efficient scan mode being far superior. We apply both techniques in investigation of defects in a GaAs epilayer – where isolated singlet and doublet dislocations can be identified. A superposition principle is developed for solving the diffusion equation to extract the intrinsic carrier diffusion length, which can be applied to a system with arbitrarily distributed defects. The understanding derived from this work is significant for a broad range of problems in physics and beyond (for instance biology) – whenever the dynamics of generation, diffusion, and annihilation of species can be probed with either measurement mode. PMID:26035409

  10. Spatial Resolution Versus Data Acquisition Efficiency in Mapping an Inhomogeneous System with Species Diffusion

    SciTech Connect

    Chen, Fengxiang; Zhang, Yong; Gfroerer, T. H.; Finger, A. N.; Mark W. Wanlass

    2015-06-02

    Traditionally, spatially-resolved photoluminescence (PL) has been performed using a point-by-point scan mode with both excitation and detection occurring at the same spatial location. But with the availability of high quality detector arrays like CCDs, an imaging mode has become popular for performing spatially-resolved PL. By illuminating the entire area of interest and collecting the data simultaneously from all spatial locations, the measurement efficiency can be greatly improved. However, this new approach has proceeded under the implicit assumption of comparable spatial resolution. We show here that when carrier diffusion is present, the spatial resolution can actually differ substantially between the two modes, with the less efficient scan mode being far superior. We apply both techniques in investigation of defects in a GaAs epilayer – where isolated singlet and doublet dislocations can be identified. A superposition principle is developed for solving the diffusion equation to extract the intrinsic carrier diffusion length, which can be applied to a system with arbitrarily distributed defects. The understanding derived from this work is significant for a broad range of problems in physics and beyond (for instance biology) – whenever the dynamics of generation, diffusion, and annihilation of species can be probed with either measurement mode.

  11. Spatial Resolution Versus Data Acquisition Efficiency in Mapping an Inhomogeneous System with Species Diffusion

    DOE PAGESBeta

    Chen, Fengxiang; Zhang, Yong; Gfroerer, T. H.; Finger, A. N.; Mark W. Wanlass

    2015-06-02

    Traditionally, spatially-resolved photoluminescence (PL) has been performed using a point-by-point scan mode with both excitation and detection occurring at the same spatial location. But with the availability of high quality detector arrays like CCDs, an imaging mode has become popular for performing spatially-resolved PL. By illuminating the entire area of interest and collecting the data simultaneously from all spatial locations, the measurement efficiency can be greatly improved. However, this new approach has proceeded under the implicit assumption of comparable spatial resolution. We show here that when carrier diffusion is present, the spatial resolution can actually differ substantially between the twomore » modes, with the less efficient scan mode being far superior. We apply both techniques in investigation of defects in a GaAs epilayer – where isolated singlet and doublet dislocations can be identified. A superposition principle is developed for solving the diffusion equation to extract the intrinsic carrier diffusion length, which can be applied to a system with arbitrarily distributed defects. The understanding derived from this work is significant for a broad range of problems in physics and beyond (for instance biology) – whenever the dynamics of generation, diffusion, and annihilation of species can be probed with either measurement mode.« less

  12. A functional technique based on the Euclidean algorithm with applications to 2-D acoustic diffractal diffusers

    NASA Astrophysics Data System (ADS)

    Cortés-Vega, Luis

    2015-09-01

    We built, based on the Euclidean algorithm, a functional technique, which allows to discover a direct proof of Chinese Remainder Theorem. Afterwards, by using this functional approach, we present some applications to 2-D acoustic diffractal diffusers. The novelty of the method is their functional algorithmic character, which improves ideas, as well as, other results of the author and his collaborators in a previous work.

  13. Estimating diffusion propagator and its moments using directional radial basis functions

    PubMed Central

    Ning, Lipeng; Westin, Carl-Fredrik; Rathi, Yogesh

    2015-01-01

    The ensemble average diffusion propagator (EAP) obtained from diffusion MRI (dMRI) data captures important structural properties of the underlying tissue. As such, it is imperative to derive an accurate estimate of the EAP from the acquired diffusion data. In this work, we propose a novel method for estimating the EAP by representing the diffusion signal as a linear combination of directional radial basis functions scattered in q-space. In particular, we focus on a special case of anisotropic Gaussian basis functions and derive analytical expressions for the diffusion orientation distribution function (ODF), the return-to-origin probability (RTOP), and mean-squared-displacement (MSD). A significant advantage of the proposed method is that the second and the fourth order moment tensors of the EAP can be computed explicitly. This allows for computing several novel scalar indices (from the moment tensors) such as mean-fourth-order-displacement (MFD) and generalized kurtosis (GK) – which is a generalization of the mean kurtosis measure used in diffusion kurtosis imaging. Additionally, we also propose novel scalar indices computed from the signal in q-space, called the q-space mean-squared-displacement (QMSD) and the q-space mean-fourth-order-displacement (QMFD), which are sensitive to short diffusion time scales. We validate our method extensively on data obtained from a physical phantom with known crossing angle as well as on in-vivo human brain data. Our experiments demonstrate the robustness of our method for different combinations of b-values and number of gradient directions. PMID:25838518

  14. Signal detection using the radial basis function coupled map lattice.

    PubMed

    Leung, H; Hennessey, G; Drosopoulos, A

    2000-01-01

    Conventional detection methods used in current marine radar systems do not perform efficiently in detecting small targets embedded in a clutter environment. Based on a recent observation that sea clutter, radar echoes from a sea surface, is chaotic rather than random, we propose using a spatial temporal predictor to reconstruct the chaotic dynamic of sea clutter because electromagnetic wave scattering is a spatial temporal phenomenon which is physically modeled by partial differential equations. The spatial temporal predictor used here is called radial basis function coupled map lattice (RBF-CML) which uses a linear combiner to fuse either measurements in different spatial domains for an RBF prediction or predictions from several RBF nets operated on different spatial regions. Using real-life radar data, it is shown that the RBF-CML is an effective method to reconstruct the sea clutter dynamic. The RBF-CML predictor is then applied to detect small targets in sea clutter using the constant false alarm rate (CFAR) principle. The spatial temporal approach is shown, both theoretically and experimentally, to be superior to a conventional CFAR detector.

  15. Topographic Brain Mapping: A Window on Brain Function?

    ERIC Educational Resources Information Center

    Karniski, Walt M.

    1989-01-01

    The article reviews the method of topographic mapping of the brain's electrical activity. Multiple electroencephalogram (EEG) electrodes and computerized analysis of the EEG signal are used to generate maps of frequency and voltage (evoked potential). This relatively new technique holds promise in the evaluation of children with behavioral and…

  16. Identity Diffusion as a Function of Sex-Roles in Adult Women.

    ERIC Educational Resources Information Center

    Jabury, Donald Eugene

    This study sought to demonstrate that the relative degree of adult female identity diffusion, as well as certain personality correlates, would be a function of specific sex roles and their combinations. Three groups of 32 women each were selected as married and noncareer, married and career, or unmarried and career women. They were administered a…

  17. Nonlinear stability in reaction-diffusion systems via optimal Lyapunov functions

    NASA Astrophysics Data System (ADS)

    Lombardo, S.; Mulone, G.; Trovato, M.

    2008-06-01

    We define optimal Lyapunov functions to study nonlinear stability of constant solutions to reaction-diffusion systems. A computable and finite radius of attraction for the initial data is obtained. Applications are given to the well-known Brusselator model and a three-species model for the spatial spread of rabies among foxes.

  18. Relation of the diffuse reflectance remission function to the fundamental optical parameters.

    NASA Technical Reports Server (NTRS)

    Simmons, E. L.

    1972-01-01

    The Kubelka-Munk equations describing the diffuse reflectance of a powdered sample were compared to equations obtained using a uniformly-sized rough-surfaced spherical particle model. The comparison resulted in equations relating the remission function and the Kubelka-Munk constants to the index of refraction, the absorption coefficient, and the average particle diameter of a powdered sample. Published experimental results were used to test the equation relating to the remission function to the fundamental optical parameters.

  19. Bidirectional scattering distribution function measurements from volume diffusers: correction factors and associated uncertainties.

    PubMed

    Germer, Thomas A

    2016-09-01

    We consider the effect of volume diffusion on measurements of the bidirectional scattering distribution function when a finite distance is used for the solid angle defining aperture. We derive expressions for correction factors that can be used when the reduced scattering coefficients and the index of refraction are known. When these quantities are not known, the expressions can be used to guide the assessment of measurement uncertainty. We find that some measurement geometries reduce the effect of volume diffusion compared to their reciprocal geometries. PMID:27607273

  20. Mapping a kingdom-specific functional domain of squalene synthase.

    PubMed

    Linscott, Kristin B; Niehaus, Thomas D; Zhuang, Xun; Bell, Stephen A; Chappell, Joe

    2016-09-01

    Squalene synthase catalyzes the first committed step in sterol biosynthesis and consists of both an amino-terminal catalytic domain and a carboxy-terminal domain tethering the enzyme to the ER membrane. While the overall architecture of this enzyme is identical in eukaryotes, it was previously shown that plant and animal genes cannot complement a squalene synthase knockout mutation in yeast unless the carboxy-terminal domain is swapped for one of fungal origin. This implied a unique component of the fungal carboxy-terminal domain was responsible for the complementation phenotype. To identify this motif, we used Saccharomyces cerevisiae with a squalene synthase knockout mutation, and expressed intact and chimeric squalene synthases originating from fungi, plants, and animals. In contrast to previous observations, all enzymes tested could partially complement the knockout mutation when the genes were weakly expressed. However, when highly expressed, non-fungal squalene synthases could not complement the yeast mutation and instead led to the accumulation of a toxic intermediate(s) as defined by mutations of genes downstream in the ergosterol pathway. Restoration of the complete complementation phenotype was mapped to a 26-amino acid hinge region linking the catalytic and membrane-spanning domains specific to fungal squalene synthases. Over-expression of the C-terminal domain containing a hinge domain from fungi, not from animals or plants, led to growth inhibition of wild-type yeast. Because this hinge region is unique to and highly conserved within each kingdom of life, the data suggests that the hinge domain plays an essential functional role, such as assembly of ergosterol multi-enzyme complexes in fungi.

  1. Diffusivity of Er3+ into LiNbO3 as a function of stoichiometry

    NASA Astrophysics Data System (ADS)

    Zhang, De-Long; Hua, Ping-Rang; Yang, Qing-Zhong; Liu, Hong-Li; Cui, Yu-Ming; Pun, E. Y. B.

    2009-01-01

    Diffusivity of Er3+ into LiNbO3 crystal has been studied as a function of Li2O content and crystal orientation. The Li2O content in single-crystal LiNbO3 plates was adjusted by Li-rich vapor transport equilibration (VTE) technique. Five X-cut and five Z-cut congruent substrates were VTE treated at first at 1100 °C for different durations ranging from 6 to 74 h, and then were subjected to a special post-VTE anneal procedure at the same temperature for 60 h to obtain homogeneous Li2O content. The Li2O content was determined from the measured fundamental optical absorption edge. Its homogeneity is verified by measuring the optical absorption edge as a function of the crystal thickness. After the composition characterization, the substrates were coated with 45 nm thick Er film and annealed at 1130 °C for 40 h in argon atmosphere. The Er3+ profile was analyzed by secondary ion mass spectrometry. The results show that the Er3+ diffusivity decreases monoexponentially with the increase in the Li2O content in both cases of X- and Z-cut. As the Li2O content is increased from the congruent point (48.4 mol %) to the near-stoichiometric composition (˜49.9 mol %), the diffusivity decreases from 0.107 (0.072) to 0.017 (0.018) μm2/h for the Z (X)-cut substrate. The diffusion shows considerable anisotropy for the lower Li2O content and the diffusivity in a Z-cut substrate is larger. The anisotropy weakens gradually with the increase in the Li2O content, and the diffusivities in the X- and Z-cut substrates ultimately tend to a same value (˜0.02 μm2/h) at the Li-rich phase boundary. After the Er diffusion procedure, endface coupling experiment was carried out to check if a planar waveguide layer was formed near the Er-diffused surface due to the Li outdiffusion. The results show that the Li outdiffusion did not accompany the Er diffusion procedure.

  2. Particle tracking single protein-functionalized quantum dot diffusion and binding at silica surfaces.

    PubMed

    Rife, Jack C; Long, James P; Wilkinson, John; Whitman, Lloyd J

    2009-04-01

    We evaluate commercial QD585 and QD605 streptavidin-functionalized quantum dots (QDs) for single-particle tracking microscopy at surfaces using total internal reflectance fluorescence and measure single QD diffusion and nonspecific binding at silica surfaces in static and flow conditions. The QD diffusion coefficient on smooth, near-ideal, highly hydroxylated silica surfaces is near bulk-solution diffusivity, as expected for repulsive surfaces, but many QD trajectories on rougher, less-than-ideal surfaces or regions display transient adsorptions. We attribute the binding to defect sites or adsorbates, possibly in conjunction with protein conformation changes, and estimate binding energies from the transient adsorption lifetimes. We also assess QD parameters relevant to tracking, including hydrodynamic radius, charge state, signal levels, blinking reduction with reducing solutions, and photoinduced blueing and bleaching.

  3. H2O2: a Ca(2+) or Mg(2+)-sensing function in statin passive diffusion.

    PubMed

    Guillaume, Yves Claude; Lethier, Lydie; André, Claire

    2015-09-01

    In a previous paper Guillaume's group demonstrated that magnesium (Mg(2+) concentration range 0.00-2.60 mm) increased the passive diffusion of statins and thus played a role in their potential toxicity. In order to confirm an increase in this passive diffusion by divalent salt cations, the role of calcium chloride (CaCl2) on the statin-immobilized artificial membrane (IAM) association was studied. It was demonstrated that calcium supplementation (Ca(2+) concentration range 0.00-3.25 mm) increases the statin passive diffusion. In addition, it was shown that the Ca(2+) effect on the statin-IAM association is higher than that of Mg(2+). These results show that Ca(2+) enhances the passive diffusion of drugs into biological membranes and thus their potential toxicity. Also, addition of H2O2 to the medium showed a hyperbolic response for the statin passive diffusion and this effect was enhanced for the highest Ca(2+) or Mg(2+) concentrations in the medium. H2O2 is likely to interact with the polar head groups of the IAM through dipole-dipole interactions. The conformational changes in H2O2-IAM result in a higher degree of exposure of hydrophobic areas, thus explaining why the binding of pravastatin, which showed the lowest logP value, was less affected by H2O2. This result shows the significant contribution of H2O2 and thus the oxidative stress on the statin passive diffusion. Much of the sensitivity derives from the action of Ca(2+) or Mg(2+), in turn supported the idea that H2O2 may serve a Ca(2+) or Mg(2+) sensing function in statin passive diffusion.

  4. Required distribution of noise sources for Green's function recovery in diffusive fields

    NASA Astrophysics Data System (ADS)

    Shamsalsadati, S.; Weiss, C. J.

    2011-12-01

    In the most general sense, noise is the part of the signal of little or no interest, due to a multitude of reasons such as operator error, imperfect instrumentation, experiment design, or inescapable background interference. Considering the latter, it has been shown that Green's function can be extracted from cross-correlation of the ambient, diffusive wavefields arising from background random noise sources. Pore pressure and low-frequency electromagnetic induction are two such examples of diffusive fields. In theory, applying Green's function method in geophysical exploration requires infinity of volumetrically distributed sources; however, in the real world the number of noise sources in an area is limited, and furthermore, unevenly distributed in time, space and spectral content. Hence, quantification of the requisite noise sources that enable us to calculate Green's function acceptably well remains an open research question. The purpose of this study is to find the area of noise sources that contribute most to the Green's function estimation in diffusive systems. We call such a region the Volume of Relevance (VoR). Our analysis builds upon recent work in 1D homogeneous system where it was shown that sources located between two receivers positions are the most important ones for the purpose of Green's function recovery. Our results confirm the previous finding but we also examine the effect of heterogeneity, dimensionality and receiver location in both 1D and 2D at a fixed frequency. We demonstrate that for receivers located symmetrically across an interface between regions of contrasting diffusivity, the VoR rapidly shifts from one side of the interface to the other, and back again, as receiver separation increases. We also demonstrate that where the receiver pair is located on the interface itself, the shifting is less rapid, and for moderate to high diffusivity contrasts, the VoR remains entirely on the more diffusive side. In addition, because classical

  5. Real space mapping of ionic diffusion and electrochemical activity in energy storage and conversion materials

    SciTech Connect

    Kalinin, Sergei V; Balke, Nina; Kumar, Amit; Dudney, Nancy J; Jesse, Stephen

    2014-05-06

    A method and system for probing mobile ion diffusivity and electrochemical reactivity on a nanometer length scale of a free electrochemically active surface includes a control module that biases the surface of the material. An electrical excitation signal is applied to the material and induces the movement of mobile ions. An SPM probe in contact with the surface of the material detects the displacement of mobile ions at the surface of the material. A detector measures an electromechanical strain response at the surface of the material based on the movement and reactions of the mobile ions. The use of an SPM tip to detect local deformations allows highly reproducible measurements in an ambient environment without visible changes in surface structure. The measurements illustrate effective spatial resolution comparable with defect spacing and well below characteristic grain sizes of the material.

  6. Nanometer-scale electrochemical intercalation and diffusion mapping of Li-ion battery materials

    SciTech Connect

    Balke, Nina; Jesse, Stephen; Morozovska, A. N.; Eliseev, E. A.; Chung, Ding-wen; Garcia, R. Edwin; Dudney, Nancy J; Kalinin, Sergei V

    2010-01-01

    The electrochemical energy storage systems based on Li-based insertion and reconstitution chemistries are a vital component of future energy technologies. Development of high energy and power density materials demands detailed understanding of the nanoscale mechanisms involved in Li-battery operation, including the interplay between the interfacial electrochemical reactions, electron and Li-ion diffusion, and structural defects. We demonstrate that strong coupling between Li-ion concentration and lattice parameters can be used as an efficient basis for real-space imaging of Li-ion currents and electrochemical reactivity on the nanometer length scales, providing what until now has been an elusive view of the electrochemical reactivity on a level of single structural element.

  7. Mapping of soot particles in a weakly sooting diffusion flame by aerosol techniques

    SciTech Connect

    Hepp, H.; Siegmann, K.

    1998-10-01

    The evolution of detailed particle size distributions has been measured along the centerline of an axisymmetric diffusion flame of CH{sub 4} + Ar burning in air at 1 atm. Soot particles with mean diameters of 3--18 nm were observed. Changes in the size distribution exhibited zones where either nucleation, coagulation, or destruction of soot particles dominated. These highly sensitive measurements were made by microprobe sampling with an immediate dilution of 1:400, to quench the aerosol, and by subsequent application of aerosol measurement techniques. In parallel, the yield of photoemitted electrons from size-selected particles was determined. The yield shows a characteristic dependence on location in the flame, indicating changes of the particle`s surface. Multiphoton, time-of-flight mass spectrometry was used to investigate the correlation between polycyclic aromatic hydrocarbons in the flame and enhanced photoemission yield from the soot particles.

  8. Mapping.

    ERIC Educational Resources Information Center

    Kinney, Douglas M.; McIntosh, Willard L.

    1979-01-01

    The area of geological mapping in the United States in 1978 increased greatly over that reported in 1977; state geological maps were added for California, Idaho, Nevada, and Alaska last year. (Author/BB)

  9. Carbon diffusion in solid iron as function of pressure and temperature

    NASA Astrophysics Data System (ADS)

    Stagno, V.; Crispin, K. L.; Fei, Y.

    2012-12-01

    pressure is required to affect the mobility of carbon through metallic iron by almost the same order of magnitude as cooling. The variation of the diffusion coefficient as function of temperature and pressure will be used to determine the activation energy and volume. It is known that the stability of carbide phases in the Earth's interior is mainly governed by the local Fe/C ratios. In the case of enriched mantle model, for instance, carbon in form of diamond will coexist with Fe7C3 for small amounts of metallic iron. In contrast, this would imply that at low carbon contents (<50 ppm) typical of a depleted mantle source, and at oxygen fugacity conditions lower than EMOD buffer, the transport of carbon will likely occur by diffusion through the coexisting metal phase. Results from this study will improve our understanding on the transport of carbon by diffusion at conditions of the Earth's interior and will provide new thermodynamic data to explain the fractionation of carbon by diffusion in other planetary bodies.

  10. Mapping of ApoE4 related white matter damage using diffusion MRI

    NASA Astrophysics Data System (ADS)

    Tsao, Sinchai; Gajawelli, Niharika; Hwang, Darryl H.; Kriger, Stephen; Law, Meng; Chui, Helena; Weiner, Michael; Lepore, Natasha

    2014-04-01

    ApoliopoproteinE Ɛ4 (ApoE-Ɛ4) polymorphism is the most well known genetic risk factor for developing Alzheimers Disease. The exact mechanism through which ApoE 4 increases AD risk is not fully known, but may be related to decreased clearance and increased oligomerization of Aβ. By making measurements of white matter integrity via diffusion MR and correlating the metrics in a voxel-based statistical analysis with ApoE-Ɛ4 genotype (whilst controlling for vascular risk factor, gender, cognitive status and age) we are able to identify changes in white matter associated with carrying an ApoE Ɛ4 allele. We found potentially significant regions (Puncorrected < 0:05) near the hippocampus and the posterior cingulum that were independent of voxels that correlated with age or clinical dementia rating (CDR) status suggesting that ApoE may affect cognitive decline via a pathway in dependent of normal aging and acute insults that can be measured by CDR and Framingham Coronary Risk Score (FCRS).

  11. Investigating the Diffuse Ionized Gas in the Magellanic Stream with Mapped WHAM Observations

    NASA Astrophysics Data System (ADS)

    Smart, Brianna; Haffner, L. Matthew; Barger, Kathleen; Hernandez, Mike

    2016-01-01

    We present early stages of an Hα survey of the Magellanic Stream using the Wisconsin H-Alpha Mapper (WHAM). While the neutral component of the Stream may extend 200° across the sky (Nidever et al. 2010), its ionized gas has not yet been studied in detail. Fox et al. 2014 find that the tidal debris in the Magellanic System contains twice as much ionized gas as neutral and may extend 30° away from the H I emission. However, such absorption-line studies are not sensitive to the overall morphology of the ionized gas. Using targeted Hα emission observations of the Magellanic Stream, Barger et al. 2015 find that although the warm ionized gas tracks the neutral gas, it often spans a few degrees away from the H I emission at slightly offset velocities. Using WHAM's unprecedented sensitivity to diffuse emission (~ 10s of mR) and its velocity resolution (12 km/s) to isolate Stream emission, we are now conducting the first full Hα survey of its ionized component. Here we present early results, including spatial and kinematic comparisons to the well-established neutral profile of the Stream. WHAM research and operations are supported through NSF Award AST-1108911.

  12. Nodal predictive error model and Bayesian approach for thermal diffusivity and heat source mapping

    NASA Astrophysics Data System (ADS)

    Massard, H.; Fudym, Olivier; Orlande, H. R. B.; Batsale, J. C.

    2010-07-01

    This article aims at solving a two-dimensional inverse heat conduction problem in order to retrieve both the thermal diffusivity and heat source field in a thin plate. A spatial random heat pulse is applied to the plate and the thermal response is analysed. The inverse approach is based on the minimisation of a nodal predictive error model, which yields a linear estimation problem. As a result of this approach, the sensitivity matrix is directly filled with experimental data, and thus is partially noisy. Bayesian estimators, such as the Maximum A Posteriori and a Markov Chain Monte Carlo approach (Metropolis-Hastings), are implemented and compared with the Ordinary Least Squares solution. Simulated temperature measurements are used in the inverse analysis. The nodal strategy relies on the availability of temperature measurements with fine spatial resolution and high frequency, typical of nowadays infrared cameras. The effects of both the measurement errors and of the model errors on the inverse problem solution are also analysed.

  13. Spectral and geometrical variation of the bidirectional reflectance distribution function of diffuse reflectance standards.

    PubMed

    Ferrero, Alejandro; Rabal, Ana María; Campos, Joaquín; Pons, Alicia; Hernanz, María Luisa

    2012-12-20

    A study on the variation of the spectral bidirectional reflectance distribution function (BRDF) of four diffuse reflectance standards (matte ceramic, BaSO(4), Spectralon, and white Russian opal glass) is accomplished through this work. Spectral BRDF measurements were carried out and, using principal components analysis, its spectral and geometrical variation respect to a reference geometry was assessed from the experimental data. Several descriptors were defined in order to compare the spectral BRDF variation of the four materials.

  14. Local thermodynamic mapping for effective liquid density-functional theory

    NASA Technical Reports Server (NTRS)

    Kyrlidis, Agathagelos; Brown, Robert A.

    1992-01-01

    The structural-mapping approximation introduced by Lutsko and Baus (1990) in the generalized effective-liquid approximation is extended to include a local thermodynamic mapping based on a spatially dependent effective density for approximating the solid phase in terms of the uniform liquid. This latter approximation, called the local generalized effective-liquid approximation (LGELA) yields excellent predictions for the free energy of hard-sphere solids and for the conditions of coexistence of a hard-sphere fcc solid with a liquid. Moreover, the predicted free energy remains single valued for calculations with more loosely packed crystalline structures, such as the diamond lattice. The spatial dependence of the weighted density makes the LGELA useful in the study of inhomogeneous solids.

  15. Mapping baroreceptor function to genome: a mathematical modeling approach.

    PubMed Central

    Kendziorski, C M; Cowley, A W; Greene, A S; Salgado, H C; Jacob, H J; Tonellato, P J

    2002-01-01

    To gain information about the genetic basis of a complex disease such as hypertension, blood pressure averages are often obtained and used as phenotypes in genetic mapping studies. In contrast, direct measurements of physiological regulatory mechanisms are not often obtained, due in large part to the time and expense required. As a result, little information about the genetic basis of physiological controlling mechanisms is available. Such information is important for disease diagnosis and treatment. In this article, we use a mathematical model of blood pressure to derive phenotypes related to the baroreceptor reflex, a short-term controller of blood pressure. The phenotypes are then used in a quantitative trait loci (QTL) mapping study to identify a potential genetic basis of this controller. PMID:11973321

  16. Dynamics of a Diffusive Predator-Prey Model with General Nonlinear Functional Response

    PubMed Central

    2014-01-01

    We study a diffusive predator-prey model with nonconstant death rate and general nonlinear functional response. Firstly, stability analysis of the equilibrium for reduced ODE system is discussed. Secondly, sufficient and necessary conditions which guarantee the predator and the prey species to be permanent are obtained. Furthermore, sufficient conditions for the global asymptotical stability of the unique positive equilibrium of the system are derived by using the method of Lyapunov function. Finally, we show that there are no nontrivial steady state solutions for certain parameter configuration. PMID:24688422

  17. Jigsaw puzzle metasurface for multiple functions: polarization conversion, anomalous reflection and diffusion.

    PubMed

    Zhao, Yi; Cao, Xiangyu; Gao, Jun; Liu, Xiao; Li, Sijia

    2016-05-16

    We demonstrate a simple reconfigurable metasurface with multiple functions. Anisotropic tiles are investigated and manufactured as fundamental elements. Then, the tiles are combined in a certain sequence to construct a metasurface. Each of the tiles can be adjusted independently which is like a jigsaw puzzle and the whole metasurface can achieve diverse functions by different layouts. For demonstration purposes, we realize polarization conversion, anomalous reflection and diffusion by a jigsaw puzzle metasurface with 6 × 6 pieces of anisotropic tile. Simulated and measured results prove that our method offers a simple and effective strategy for metasurface design. PMID:27409942

  18. A Dynamic Density Functional Theory Approach to Diffusion in White Dwarfs and Neutron Star Envelopes

    NASA Astrophysics Data System (ADS)

    Diaw, A.; Murillo, M. S.

    2016-09-01

    We develop a multicomponent hydrodynamic model based on moments of the Born-Bogolyubov-Green-Kirkwood-Yvon hierarchy equations for physical conditions relevant to astrophysical plasmas. These equations incorporate strong correlations through a density functional theory closure, while transport enters through a relaxation approximation. This approach enables the introduction of Coulomb coupling correction terms into the standard Burgers equations. The diffusive currents for these strongly coupled plasmas is self-consistently derived. The settling of impurities and its impact on cooling can be greatly affected by strong Coulomb coupling, which we show can be quantified using the direct correlation function.

  19. A Radiation Chemistry Code Based on the Greens Functions of the Diffusion Equation

    NASA Technical Reports Server (NTRS)

    Plante, Ianik; Wu, Honglu

    2014-01-01

    Ionizing radiation produces several radiolytic species such as.OH, e-aq, and H. when interacting with biological matter. Following their creation, radiolytic species diffuse and chemically react with biological molecules such as DNA. Despite years of research, many questions on the DNA damage by ionizing radiation remains, notably on the indirect effect, i.e. the damage resulting from the reactions of the radiolytic species with DNA. To simulate DNA damage by ionizing radiation, we are developing a step-by-step radiation chemistry code that is based on the Green's functions of the diffusion equation (GFDE), which is able to follow the trajectories of all particles and their reactions with time. In the recent years, simulations based on the GFDE have been used extensively in biochemistry, notably to simulate biochemical networks in time and space and are often used as the "gold standard" to validate diffusion-reaction theories. The exact GFDE for partially diffusion-controlled reactions is difficult to use because of its complex form. Therefore, the radial Green's function, which is much simpler, is often used. Hence, much effort has been devoted to the sampling of the radial Green's functions, for which we have developed a sampling algorithm This algorithm only yields the inter-particle distance vector length after a time step; the sampling of the deviation angle of the inter-particle vector is not taken into consideration. In this work, we show that the radial distribution is predicted by the exact radial Green's function. We also use a technique developed by Clifford et al. to generate the inter-particle vector deviation angles, knowing the inter-particle vector length before and after a time step. The results are compared with those predicted by the exact GFDE and by the analytical angular functions for free diffusion. This first step in the creation of the radiation chemistry code should help the understanding of the contribution of the indirect effect in the

  20. THE QUaD GALACTIC PLANE SURVEY. I. MAPS AND ANALYSIS OF DIFFUSE EMISSION

    SciTech Connect

    Culverhouse, T.; Friedman, R.; Ade, P.; Bowden, M.; Gear, W. K.; Gupta, S.; Melhuish, S. J.; Orlando, A.; Bock, J.; Leitch, E.; Brown, M. L.; Cahill, G.; Murphy, J. A.; Castro, P. G.; Memari, Y.; Church, S. E.; Hinderks, J. R.; Ganga, K.; Lange, A. E.

    2010-10-20

    We present a survey of {approx}800 deg{sup 2} of the galactic plane observed with the QUaD telescope. The primary products of the survey are maps of Stokes I, Q, and U parameters at 100 and 150 GHz, with spatial resolution of 5' and 3.'5, respectively. Two regions are covered, spanning approximately 245{sup 0}-295{sup 0} and 315{sup 0}-5{sup 0} in the galactic longitude l and -4{sup 0} < b < +4{sup 0} in the galactic latitude b. At 0.{sup 0}02 square pixel size, the median sensitivity is 74 and 107 kJy sr{sup -1} at 100 GHz and 150 GHz respectively in I, and 98 and 120 kJy sr{sup -1} for Q and U. In total intensity, we find an average spectral index of {alpha} = 2.35 {+-} 0.01(stat) {+-} 0.02(sys) for |b| {<=} 1{sup 0}, indicative of emission components other than thermal dust. A comparison to published dust, synchrotron, and free-free models implies an excess of emission in the 100 GHz QUaD band, while better agreement is found at 150 GHz. A smaller excess is observed when comparing QUaD 100 GHz data to the WMAP five-year W band; in this case, the excess is likely due to the wider bandwidth of QUaD. Combining the QUaD and WMAP data, a two-component spectral fit to the inner galactic plane (|b| {<=} 1{sup 0}) yields mean spectral indices of {alpha}{sub s} = -0.32 {+-} 0.03 and {alpha}{sub d} = 2.84 {+-} 0.03; the former is interpreted as a combination of the spectral indices of synchrotron, free-free, and dust, while the second is largely attributed to the thermal dust continuum. In the same galactic latitude range, the polarization data show a high degree of alignment perpendicular to the expected galactic magnetic field direction, and exhibit mean polarization fraction 1.38 {+-} 0.08(stat) {+-} 0.1(sys)% at 100 GHz and 1.70 {+-} 0.06(stat) {+-} 0.1(sys)% at 150 GHz. We find agreement in polarization fraction between QUaD 100 GHz and the WMAP W band, the latter giving 1.1% {+-} 0.4%.

  1. Parcellation of parietal cortex: convergence between lesion-symptom mapping and mapping of the intact functioning brain.

    PubMed

    Vandenberghe, Rik; Gillebert, Céline R

    2009-05-16

    Spatial-attentional deficits are highly prevalent following stroke. They can be clinically detected by means of conventional bedside tests such as target cancellation, line bisection and the visual extinction test. Until recently, lesion mapping studies and functional imaging of the intact brain did not agree very well on exactly which parietal areas play a key role in selective attention: the inferior parietal lobule or the intraparietal sulcus. Recently, the use of a contrastive approach in patients akin to that commonly used in functional imaging studies in healthy volunteers together with voxel-based lesion-symptom mapping have allowed to bring the patient lesion mapping much closer to the functional imaging results obtained in healthy controls. In this review we focus on converging evidence obtained from patient lesion studies and from fMRI studies in the intact brain in humans. This has yielded novel insights into the functional segregation between the middle third of the intraparietal sulcus, the superior parietal lobule and the temporoparietal junction in the intact brain and also enhanced our understanding of the pathogenetic mechanisms underlying deficits arising in patients. PMID:19118580

  2. Technique for examining biological materials using diffuse reflectance spectroscopy and the kubelka-munk function

    DOEpatents

    Alfano, Robert R.; Yang, Yuanlong

    2003-09-02

    Method and apparatus for examining biological materials using diffuse reflectance spectroscopy and the Kubelka-Munk function. In one aspect, the method is used to determine whether a tissue sample is cancerous or not and comprises the steps of (a) measuring the diffuse reflectance from the tissue sample at a first wavelength and at a second wavelength, wherein the first wavelength is a wavelength selected from the group consisting of 255-265 nm and wherein the second wavelength is a wavelength selected from the group consisting of 275-285 nm; (b) using the Kubelka-Munk function to transform the diffuse reflectance measurement obtained at the first and second wavelengths; and (c) comparing a ratio or a difference of the transformed Kubelka-Munk measurements at the first and second wavelengths to appropriate standards determine whether or not the tissue sample is cancerous. One can use the spectral profile of KMF between 250 nm to 300 nm to determine whether or not the tissue sample is cancerous or precancerous. According to the value at the first and second wavelengths determine whether or not the malignant tissue is invasive or mixed invasive and in situ or carcinoma in situ.

  3. Integrating Functional and Diffusion Magnetic Resonance Imaging for Analysis of Structure-Function Relationship in the Human Language Network

    PubMed Central

    Morgan, Victoria L.; Mishra, Arabinda; Newton, Allen T.; Gore, John C.; Ding, Zhaohua

    2009-01-01

    Background The capabilities of magnetic resonance imaging (MRI) to measure structural and functional connectivity in the human brain have motivated growing interest in characterizing the relationship between these measures in the distributed neural networks of the brain. In this study, we attempted an integration of structural and functional analyses of the human language circuits, including Wernicke's (WA), Broca's (BA) and supplementary motor area (SMA), using a combination of blood oxygen level dependent (BOLD) and diffusion tensor MRI. Methodology/Principal Findings Functional connectivity was measured by low frequency inter-regional correlations of BOLD MRI signals acquired in a resting steady-state, and structural connectivity was measured by using adaptive fiber tracking with diffusion tensor MRI data. The results showed that different language pathways exhibited different structural and functional connectivity, indicating varying levels of inter-dependence in processing across regions. Along the path between BA and SMA, the fibers tracked generally formed a single bundle and the mean radius of the bundle was positively correlated with functional connectivity. However, fractional anisotropy was found not to be correlated with functional connectivity along paths connecting either BA and SMA or BA and WA. Conclusions/Significance These findings suggest that structure-function relations in the human language circuits may involve a number of confounding factors that need to be addressed. Nevertheless, the insights gained from this work offers a useful guidance for continued studies that may provide a non-invasive means to evaluate brain network integrity in vivo for use in diagnosing and determining disease progression and recovery. PMID:19684850

  4. On the possibility of obtaining non-diffused proximity functions from cloud-chamber data: I. Fourier deconvolution.

    PubMed

    Zaider, M; Minerbo, G N

    1988-11-01

    A mathematical procedure, using Fourier deconvolution, is described whereby diffusion-free proximity functions can be obtained from cloud-chamber data. Such non-diffused distributions can be used to obtain further microdosimetric and nanodosimetric quantities hitherto not available from experiments, thus making the cloud chamber an almost ideal nanodosimeter.

  5. Stable learning of functional maps in self-organizing spiking neural networks with continuous synaptic plasticity

    PubMed Central

    Srinivasa, Narayan; Jiang, Qin

    2013-01-01

    This study describes a spiking model that self-organizes for stable formation and maintenance of orientation and ocular dominance maps in the visual cortex (V1). This self-organization process simulates three development phases: an early experience-independent phase, a late experience-independent phase and a subsequent refinement phase during which experience acts to shape the map properties. The ocular dominance maps that emerge accommodate the two sets of monocular inputs that arise from the lateral geniculate nucleus (LGN) to layer 4 of V1. The orientation selectivity maps that emerge feature well-developed iso-orientation domains and fractures. During the last two phases of development the orientation preferences at some locations appear to rotate continuously through ±180° along circular paths and referred to as pinwheel-like patterns but without any corresponding point discontinuities in the orientation gradient maps. The formation of these functional maps is driven by balanced excitatory and inhibitory currents that are established via synaptic plasticity based on spike timing for both excitatory and inhibitory synapses. The stability and maintenance of the formed maps with continuous synaptic plasticity is enabled by homeostasis caused by inhibitory plasticity. However, a prolonged exposure to repeated stimuli does alter the formed maps over time due to plasticity. The results from this study suggest that continuous synaptic plasticity in both excitatory neurons and interneurons could play a critical role in the formation, stability, and maintenance of functional maps in the cortex. PMID:23450808

  6. Step-by-Step Simulation of Radiation Chemistry Using Green Functions for Diffusion-Influenced Reactions

    NASA Technical Reports Server (NTRS)

    Plante, Ianik; Cucinotta, Francis A.

    2011-01-01

    Radiolytic species are formed approximately 1 ps after the passage of ionizing radiation through matter. After their formation, they diffuse and chemically react with other radiolytic species and neighboring biological molecules, leading to various oxidative damage. Therefore, the simulation of radiation chemistry is of considerable importance to understand how radiolytic species damage biological molecules [1]. The step-by-step simulation of chemical reactions is difficult, because the radiolytic species are distributed non-homogeneously in the medium. Consequently, computational approaches based on Green functions for diffusion-influenced reactions should be used [2]. Recently, Green functions for more complex type of reactions have been published [3-4]. We have developed exact random variate generators of these Green functions [5], which will allow us to use them in radiation chemistry codes. Moreover, simulating chemistry using the Green functions is which is computationally very demanding, because the probabilities of reactions between each pair of particles should be evaluated at each timestep [2]. This kind of problem is well adapted for General Purpose Graphic Processing Units (GPGPU), which can handle a large number of similar calculations simultaneously. These new developments will allow us to include more complex reactions in chemistry codes, and to improve the calculation time. This code should be of importance to link radiation track structure simulations and DNA damage models.

  7. A spline approach to trial wave functions for variational and diffusion Monte Carlo

    NASA Astrophysics Data System (ADS)

    Bressanini, Dario; Fabbri, Giordano; Mella, Massimo; Morosi, Gabriele

    1999-10-01

    We describe how to combine the variational Monte Carlo method with a spline description of the wave function to obtain a powerful and flexible method to optimize electronic and nuclear wave functions. A property of this method is that the optimization is performed "locally": During the optimization, the attention is focused on a region of the wave function at a certain time, with little or no perturbation in far away regions. This allows a fine tuning of the wave function even in cases where there is no experience on how to choose a good functional form and a good basis set. After the optimization, the splines were fitted using more familiar analytical global functions. The flexibility of the method is shown by calculating the electronic wave function for some two and three electron systems, and the nuclear wave function for the helium trimer. For 4He3, using a two-body helium-helium potential, we obtained the best variational function to date, which allows us to estimate the exact energy with a very small variance by a diffusion Monte Carlo simulation.

  8. Modeling of the Zodiacal Emission for the AKARI/IRC Mid-infrared All-sky Diffuse Maps

    NASA Astrophysics Data System (ADS)

    Kondo, Toru; Ishihara, Daisuke; Kaneda, Hidehiro; Nakamichi, Keichiro; Takaba, Sachi; Kobayashi, Hiroshi; Ootsubo, Takafumi; Pyo, Jeonghyun; Onaka, Takashi

    2016-03-01

    The zodiacal emission, which is the thermal infrared (IR) emission from the interplanetary dust (IPD) in our solar system, has been studied for a long time. Nevertheless, accurate modeling of the zodiacal emission has not been successful to reproduce the all-sky spatial distribution of the zodiacal emission, especially in the mid-IR where the zodiacal emission peaks. Therefore, we aim to improve the IPD cloud model based on Kelsall et al., using the AKARI 9 and 18 μm all-sky diffuse maps. By adopting a new fitting method based on the total brightness, we have succeeded in reducing the residual levels after subtraction of the zodiacal emission from the AKARI data and thus in improving the modeling of the zodiacal emission. Comparing the AKARI and the COBE data, we confirm that the changes from the previous model to our new model are mostly due to model improvements, but not temporal variations between the AKARI and the COBE epoch, except for the position of the Earth-trailing blob. Our results suggest that the size of the smooth cloud, a dominant component in the model, is about 10% more compact than previously thought, and that the dust sizes are not large enough to emit blackbody radiation in the mid-IR. Furthermore, we detect a significant isotropically distributed IPD component, owing to an accurate baseline measurement with AKARI.

  9. Modeling structure-function relationships for diffusive drug transport in inert porous geopolymer matrices.

    PubMed

    Jämstorp, Erik; Strømme, Maria; Frenning, Göran

    2011-10-01

    A unique structure-function relationship investigation of mechanically strong geopolymer drug delivery vehicles for sustained release of potent substances is presented. The effect of in-synthesis water content on geopolymer pore structure and diffusive drug transport is investigated. Scanning electron microscopy, N2 gas adsorption, mercury intrusion porosimetry, compression strength test, drug permeation, and release experiments are performed. Effective diffusion coefficients are measured and compared with corresponding theoretical values as derived from pore size distribution and connectivity via pore-network modeling. By solely varying the in-synthesis water content, mesoporous and mechanically strong geopolymers with porosities of 8%-45% are obtained. Effective diffusion coefficients of the model drugs Saccharin and Zolpidem are observed to span two orders of magnitude (∼1.6-120 × 10(-8) cm(2) /s), comparing very well to theoretical estimations. The ability to predict drug permeation and release from geopolymers, and materials alike, allows future formulations to be tailored on a structural and chemical level for specific applications such as controlled drug delivery of highly potent substances.

  10. Dynamics of supercooled water in nanotubes: Cage correlation function and diffusion coefficient

    NASA Astrophysics Data System (ADS)

    Khademi, Mahdi; Kalia, Rajiv K.; Sahimi, Muhammad

    2015-09-01

    Dynamics of low-temperature water in nanostructured materials is important to a variety of phenomena, ranging from transport in cement and asphaltene, to conformational dynamics of proteins in "crowded" cellular environments, survival of microorganisms at very low temperatures, and diffusion in nanogeoscience. Using silicon-carbide nanotubes as a prototype of nanostructured materials, extensive molecular dynamics simulations were carried out to study the cage correlation function C (t ) and self-diffusivity D of supercooled water in the nanotubes. C (t ) , which measures changes in the atomic surroundings inside the nanotube, follows the Kohlrausch-Williams-Watts law, C (t ) ˜exp[-(t/τ ) β] , where τ is a relaxation time and β is a topological exponent. For the temperature range 220 Kdiffusivity manifests a transition around 230 K, very close to 228 K, the temperature at which a fragile-to-strong dynamic crossover is supposed to happen. Thus the results indicate that water does not freeze in the nanotube over the studied temperature range, and that the Stokes-Einstein relation breaks down.

  11. Toward reliable retrieval of functional information of papillary dermis using spatially resolved diffuse reflectance spectroscopy

    PubMed Central

    Chen, Yu-Wen; Guo, Jun-Yen; Tzeng, Shih-Yu; Chou, Ting-Chun; Lin, Ming-Jen; Huang, Lynn Ling-Huei; Yang, Chao-Chun; Hsu, Chao-Kai; Tseng, Sheng-Hao

    2016-01-01

    Spatially resolved diffuse reflectance spectroscopy (SRDRS) has been employed to quantify tissue optical properties and its interrogation volume is majorly controlled by the source-to-detector separations (SDSs). To noninvasively quantify properties of dermis, a SRDRS setup that includes SDS shorter than 1 mm is required. It will be demonstrated in this study that Monte Carlo simulations employing the Henyey-Greenstein phase function cannot always precisely predict experimentally measured diffuse reflectance at such short SDSs, and we speculated this could be caused by the non-negligible backward light scattering at short SDSs that cannot be properly modeled by the Henyey-Greenstein phase function. To accurately recover the optical properties and functional information of dermis using SRDRS, we proposed the use of the modified two-layer (MTL) geometry. Monte Carlo simulations and phantom experiment results revealed that the MTL probing geometry was capable of faithfully recovering the optical properties of upper dermis. The capability of the MTL geometry in probing the upper dermis properties was further verified through a swine study, and it was found that the measurement results were reasonably linked to histological findings. Finally, the MTL probe was utilized to study psoriatic lesions. Our results showed that the MTL probe was sensitive to the physiological condition of tissue volumes within the papillary dermis and could be used in studying the physiology of psoriasis. PMID:26977361

  12. cAMP diffusion in Dictyostelium discoideum: A Green's function method

    NASA Astrophysics Data System (ADS)

    Calovi, Daniel S.; Brunnet, Leonardo G.; de Almeida, Rita M. C.

    2010-07-01

    A Green’s function method is developed to approach the spatiotemporal equations describing the cAMP production in Dictyostelium discoideum, markedly reducing numerical calculations times: cAMP concentrations and gradients are calculated just at the amoeba locations. A single set of parameters is capable of reproducing the different observed behaviors, from cAMP synchronization, spiral waves and reaction-diffusion patterns to streaming and mound formation. After aggregation, the emergence of a circular motion of amoebas, breaking the radial cAMP field symmetry, is observed.

  13. Resolution below the point spread function for diffuse optical imaging using fluorescence lifetime multiplexing

    PubMed Central

    Rice, William L.; Hou, Steven; Kumar, Anand T. N.

    2014-01-01

    We show that asymptotic lifetime-based fluorescence tomography can localize multiple-lifetime targets separated well below the diffuse point spread function of a turbid medium. This is made possible due to a complete diagonalization of the time domain forward problem in the asymptotic limit. We also show that continuous wave or direct time gate approaches to fluorescence tomography are unable to achieve this separation, indicating the unique advantage of a decay-amplitude-based approach for tomographic lifetime multiplexing with time domain data. PMID:23938969

  14. Quantum diffusion wave-function approach to two-dimensional vibronic spectroscopy

    SciTech Connect

    Wehner, Johannes; Falge, Mirjam; Engel, Volker; Strunz, Walter T.

    2014-10-07

    We apply the quantum diffusion wavefunction approach to calculate vibronic two-dimensional (2D) spectra. As an example, we use a system consisting of two electronic states with harmonic oscillator potentials which are coupled to a bath and interact with three time-delayed laser pulses. The first- and second-order perturbative wave functions which enter into the expression for the third-order polarization are determined for a sufficient number of stochastic runs. The wave-packet approach, besides being an alternative technique to calculate the spectra, offers an intuitive insight into the dissipation dynamics and its relation to the 2D vibronic spectra.

  15. Concepts of soil mapping as a basis for the assessment of soil functions

    NASA Astrophysics Data System (ADS)

    Baumgarten, Andreas

    2014-05-01

    Soil mapping systems in Europe have been designed mainly as a tool for the description of soil characteristics from a morphogenetic viewpoint. Contrasting to the American or FAO system, the soil development has been in the main focus of European systems. Nevertheless , recent developments in soil science stress the importance of the functions of soils with respect to the ecosystems. As soil mapping systems usually offer a sound and extensive database, the deduction of soil functions from "classic" mapping parameters can be used for local and regional assessments. According to the used pedo-transfer functions and mapping systems, tailored approaches can be chosen for different applications. In Austria, a system mainly for spatial planning purposes has been developed that will be presented and illustrated by means of best practice examples.

  16. Diffuse traumatic brain injury affects chronic corticosterone function in the rat

    PubMed Central

    Rowe, Rachel K; Rumney, Benjamin M; May, Hazel G; Permana, Paska; Adelson, P David; Harman, S Mitchell; Lifshitz, Jonathan

    2016-01-01

    As many as 20–55% of patients with a history of traumatic brain injury (TBI) experience chronic endocrine dysfunction, leading to impaired quality of life, impaired rehabilitation efforts and lowered life expectancy. Endocrine dysfunction after TBI is thought to result from acceleration–deceleration forces to the brain within the skull, creating enduring hypothalamic and pituitary neuropathology, and subsequent hypothalamic–pituitary endocrine (HPE) dysfunction. These experiments were designed to test the hypothesis that a single diffuse TBI results in chronic dysfunction of corticosterone (CORT), a glucocorticoid released in response to stress and testosterone. We used a rodent model of diffuse TBI induced by midline fluid percussion injury (mFPI). At 2months postinjury compared with uninjured control animals, circulating levels of CORT were evaluated at rest, under restraint stress and in response to dexamethasone, a synthetic glucocorticoid commonly used to test HPE axis regulation. Testosterone was evaluated at rest. Further, we assessed changes in injury-induced neuron morphology (Golgi stain), neuropathology (silver stain) and activated astrocytes (GFAP) in the paraventricular nucleus (PVN) of the hypothalamus. Resting plasma CORT levels were decreased at 2months postinjury and there was a blunted CORT increase in response to restraint induced stress. No changes in testosterone were measured. These changes in CORT were observed concomitantly with altered complexity of neuron processes in the PVN over time, devoid of neuropathology or astrocytosis. Results provide evidence that a single moderate diffuse TBI leads to changes in CORT function, which can contribute to the persistence of symptoms related to endocrine dysfunction. Future experiments aim to evaluate additional HP-related hormones and endocrine circuit pathology following diffuse TBI. PMID:27317610

  17. Diffuse traumatic brain injury affects chronic corticosterone function in the rat.

    PubMed

    Rowe, Rachel K; Rumney, Benjamin M; May, Hazel G; Permana, Paska; Adelson, P David; Harman, S Mitchell; Lifshitz, Jonathan; Thomas, Theresa C

    2016-07-01

    As many as 20-55% of patients with a history of traumatic brain injury (TBI) experience chronic endocrine dysfunction, leading to impaired quality of life, impaired rehabilitation efforts and lowered life expectancy. Endocrine dysfunction after TBI is thought to result from acceleration-deceleration forces to the brain within the skull, creating enduring hypothalamic and pituitary neuropathology, and subsequent hypothalamic-pituitary endocrine (HPE) dysfunction. These experiments were designed to test the hypothesis that a single diffuse TBI results in chronic dysfunction of corticosterone (CORT), a glucocorticoid released in response to stress and testosterone. We used a rodent model of diffuse TBI induced by midline fluid percussion injury (mFPI). At 2months postinjury compared with uninjured control animals, circulating levels of CORT were evaluated at rest, under restraint stress and in response to dexamethasone, a synthetic glucocorticoid commonly used to test HPE axis regulation. Testosterone was evaluated at rest. Further, we assessed changes in injury-induced neuron morphology (Golgi stain), neuropathology (silver stain) and activated astrocytes (GFAP) in the paraventricular nucleus (PVN) of the hypothalamus. Resting plasma CORT levels were decreased at 2months postinjury and there was a blunted CORT increase in response to restraint induced stress. No changes in testosterone were measured. These changes in CORT were observed concomitantly with altered complexity of neuron processes in the PVN over time, devoid of neuropathology or astrocytosis. Results provide evidence that a single moderate diffuse TBI leads to changes in CORT function, which can contribute to the persistence of symptoms related to endocrine dysfunction. Future experiments aim to evaluate additional HP-related hormones and endocrine circuit pathology following diffuse TBI. PMID:27317610

  18. Application of an evidential belief function model in landslide susceptibility mapping

    NASA Astrophysics Data System (ADS)

    Althuwaynee, Omar F.; Pradhan, Biswajeet; Lee, Saro

    2012-07-01

    The objective of this paper is to exploit the potential application of an evidential belief function model to landslide susceptibility mapping at Kuala Lumpur city and surrounding areas using geographic information system (GIS). At first, a landslide inventory map was prepared using aerial photographs, high resolution satellite images and field survey. A total 220 landslides were mapped and an inventory map was prepared. Then the landslide inventory was randomly split into a testing dataset 70% (153 landslides) and remaining 30% (67 landslides) data was used for validation purpose. Fourteen landslide conditioning factors such as slope, aspect, curvature, altitude, surface roughness, lithology, distance from faults, ndvi (normalized difference vegetation index), land cover, distance from drainage, distance from road, spi (stream power index), soil type, precipitation, were used as thematic layers in the analysis. The Dempster-Shafer theory of evidence model was applied to prepare the landslide susceptibility maps. The validation of the resultant susceptibility maps were performed using receiver operating characteristics (ROC) and area under the curve (AUC). The validation results show that the area under the curve for the evidential belief function (the belief map) model is 0.82 (82%) with prediction accuracy 0.75 (75%). The results of this study indicated that the EBF model can be effectively used in preparation of landslide susceptibility maps.

  19. Dendritic atrophy constricts functional maps in resonance and impedance properties of hippocampal model neurons

    PubMed Central

    Dhupia, Neha; Rathour, Rahul K.; Narayanan, Rishikesh

    2015-01-01

    A gradient in the density of hyperpolarization-activated cyclic-nucleotide gated (HCN) channels is necessary for the emergence of several functional maps within hippocampal pyramidal neurons. Here, we systematically analyzed the impact of dendritic atrophy on nine such functional maps, related to input resistance and local/transfer impedance properties, using conductance-based models of hippocampal pyramidal neurons. We introduced progressive dendritic atrophy in a CA1 pyramidal neuron reconstruction through a pruning algorithm, measured all functional maps in each pruned reconstruction, and arrived at functional forms for the dependence of underlying measurements on dendritic length. We found that, across frequencies, atrophied neurons responded with higher efficiency to incoming inputs, and the transfer of signals across the dendritic tree was more effective in an atrophied reconstruction. Importantly, despite the presence of identical HCN-channel density gradients, spatial gradients in input resistance, local/transfer resonance frequencies and impedance profiles were significantly constricted in reconstructions with dendritic atrophy, where these physiological measurements across dendritic locations converged to similar values. These results revealed that, in atrophied dendritic structures, the presence of an ion channel density gradient alone was insufficient to sustain homologous functional maps along the same neuronal topograph. We assessed the biophysical basis for these conclusions and found that this atrophy-induced constriction of functional maps was mediated by an enhanced spatial spread of the influence of an HCN-channel cluster in atrophied trees. These results demonstrated that the influence fields of ion channel conductances need to be localized for channel gradients to express themselves as homologous functional maps, suggesting that ion channel gradients are necessary but not sufficient for the emergence of functional maps within single neurons

  20. The use of evidential belief functions for mineral potential mapping in the Nanling belt, South China

    NASA Astrophysics Data System (ADS)

    Liu, Yue; Cheng, Qiuming; Xia, Qinglin; Wang, Xinqing

    2015-06-01

    In this study, the evidential belief functions (EBFs) were applied for mapping tungsten polymetallic potential in the Nanling belt, South China. Seven evidential layers (e.g., geological, geochemical, and geophysical) related to tungsten polymetallic deposits were extracted from a multi-source geospatial database. The relationships between evidential layers and the target deposits were quantified using EBFs model. Four EBF maps (belief map, disbelief map, uncertainty map, and plausibility map) are generated by integrating seven evidential layers which provide meaningful interpretations for tungsten polymetallic potential. On the final predictive map, the study area was divided into three target zones of high potential, moderate potential, and low potential areas, among which high potential and moderate potential areas accounted for 17.8% of the total area, containing 81% of the total deposits. To evaluate the success rate accuracy, the receiver operating characteristic (ROC) curves and the area under the curves (AUC) for the belief map were calculated. The area under the curve is 0.81 which indicates that the capability for correctly classifying the areas with existing mineral deposits is satisfactory. The results of this study indicate that the EBFs were effectively used for mapping mineral potential and for managing uncertainties associated with evidential layers.

  1. Mapping Variation in Vegetation Functioning with Imaging Spectroscopy

    NASA Astrophysics Data System (ADS)

    Townsend, P. A.; Couture, J. J.; Kruger, E. L.; Serbin, S.; Singh, A.

    2015-12-01

    Imaging spectroscopy (otherwise known as hyperspectral remote sensing) offers the potential to characterize the spatial and temporal variation in biophysical and biochemical properties of vegetation that can be costly or logistically difficult to measure comprehensively using traditional methods. A number of recent studies have illustrated the capacity for imaging spectroscopy data, such as from NASA's AVIRIS sensor, to empirically estimate functional traits related to foliar chemistry and physiology (Singh et al. 2015, Serbin et al. 2015). Here, we present analyses that illustrate the implications of those studies to characterize within-field or -stand variability in ecosystem functioning. In agricultural ecosystems, within-field photosynthetic capacity can vary by 30-50%, likely due to within-field variations in water availability and soil fertility. In general, the variability of foliar traits is lower in forests than agriculture, but can still be significant. Finally, we demonstrate that functional trait variability at the stand scale is strongly related to vegetation diversity. These results have two significant implications: 1) reliance on a small number of field samples to broadly estimate functional traits likely underestimates variability in those traits, and 2) if trait estimations from imaging spectroscopy are reliable, such data offer the opportunity to greatly increase the density of measurements we can use to predict ecosystem function.

  2. Structure-function relationships underlying calculation: a combined diffusion tensor imaging and fMRI study.

    PubMed

    van Eimeren, L; Grabner, R H; Koschutnig, K; Reishofer, G; Ebner, F; Ansari, D

    2010-08-01

    Both neuropsychological and functional neuroimaging studies have identified brain regions that are critical for the neurocognitive processes related to the calculation of arithmetic problems. In particular, the left angular gyrus (lAG) has been repeatedly implicated in arithmetic problem solving and found to be most activated during the retrieval of arithmetic facts. While significant progress has been made in determining the functional role of specific grey matter areas underlying calculation, very little is known about the relationship between these activated regions and their underlying white matter structures. In this study, we collected both diffusion tensor imaging (DTI) and functional magnetic resonance imaging (fMRI) data while participants performed a mental arithmetic task. Fractional anisotropy (FA) values were extracted from predefined, hypothesis-driven, white matter regions and correlated with fMRI activation values, which were extracted from anatomically defined grey matter regions. Results indicated structure-function relationships on multiple levels. Specifically, a link between the integrity of the left superior corona radiata (SCR) and neural activity in the lAG during calculation was observed, which was found to be particularly strong for problems that have a high probability of being solved via the retrieval of arithmetic facts (problems with a relatively small problem size). The findings reported provide a link between functional activation and structural integrity of grey and white matter regions in the left temporoparietal cortex, thereby contributing to our understanding of the role of both the function and structure of this brain region in calculation. PMID:20382234

  3. Integrating impairments in reaction time and executive function using a diffusion model framework

    PubMed Central

    Karalunas, Sarah L.; Huang-Pollock, Cynthia L.

    2013-01-01

    Using Ratcliff’s diffusion model and ex-Gaussian decomposition, we directly evaluate the role individual differences in reaction time (RT) distribution components play in the prediction of inhibitory control and working memory (WM) capacity in children with and without ADHD. Children with (n=92, x̄ age= 10.2 years, 67% male) and without ADHD (n=62, x̄ age=10.6 years, 46% male) completed four tasks of WM and a stop signal reaction time (SSRT) task. Children with ADHD had smaller WM capacities and less efficient inhibitory control. Diffusion model analyses revealed that children with ADHD had slower drift rates (v) and faster non-decision times (Ter), but there were no group differences in boundary separations (a). Similarly, using an ex-Gaussian approach, children with ADHD had larger τ values than non-ADHD controls, but did not differ in µ or σ distribution components. Drift rate mediated the association between ADHD status and performance on both inhibitory control and WM capacity. τ also mediated the ADHD-executive function impairment associations; however, models were a poorer fit to the data. Impaired performance on RT and executive functioning tasks has long been associated with childhood ADHD. Both are believed to be important cognitive mechanisms to the disorder. We demonstrate here that drift rate, or the speed at which information accumulates towards a decision, is able to explain both. PMID:23334775

  4. Extraction of thermal Green's function using diffuse fields: a passive approach applied to thermography

    NASA Astrophysics Data System (ADS)

    Capriotti, Margherita; Sternini, Simone; Lanza di Scalea, Francesco; Mariani, Stefano

    2016-04-01

    In the field of non-destructive evaluation, defect detection and visualization can be performed exploiting different techniques relying either on an active or a passive approach. In the following paper the passive technique is investigated due to its numerous advantages and its application to thermography is explored. In previous works, it has been shown that it is possible to reconstruct the Green's function between any pair of points of a sensing grid by using noise originated from diffuse fields in acoustic environments. The extraction of the Green's function can be achieved by cross-correlating these random recorded waves. Averaging, filtering and length of the measured signals play an important role in this process. This concept is here applied in an NDE perspective utilizing thermal fluctuations present on structural materials. Temperature variations interacting with thermal properties of the specimen allow for the characterization of the material and its health condition. The exploitation of the thermographic image resolution as a dense grid of sensors constitutes the basic idea underlying passive thermography. Particular attention will be placed on the creation of a proper diffuse thermal field, studying the number, placement and excitation signal of heat sources. Results from numerical simulations will be presented to assess the capabilities and performances of the passive thermal technique devoted to defect detection and imaging of structural components.

  5. Mapping Dopamine Function in Primates Using Pharmacologic Magnetic Resonance Imaging

    PubMed Central

    Sanchez-Pernaute, Rosario; Brownell, Anna-Liisa; Chen, Yin-Ching Iris; Isacson, Ole

    2008-01-01

    Dopamine (DA) receptors play a central role in such diverse pathologies as Parkinson's disease, schizophrenia, and drug abuse. We used an amphetamine challenge combined with pharmacologic magnetic resonance imaging (phMRI) to map DA-associated circuitry in nonhuman primates with high sensitivity and spatial resolution. Seven control cynomolgous monkeys and 10 MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine)-treated parkinsonian primates were studied longitudinally using both positron emission tomography (PET) and phMRI. Amphetamine challenge (2.5 mg/kg, i.v.) in control monkeys increased relative cerebral blood volume (rCBV) in a number of brain regions not described previously, such as parafascicular thalamus, precentral gyrus, and dentate nucleus of the cerebellum. With the high spatial resolution, we were also able to readily identify changes in rCBV in the anterior cingulate, substantia nigra, ventral tegmental area, caudate (tail and head), putamen, and nucleus accumbens. Amphetamine induced decreases in rCBV in occipital and posterior parietal cortices. Parkinsonian primates had a prominent loss of response to amphetamine, with relative sparing of the nucleus accumbens and parafascicular thalamus. There was a significant correlation between rCBV loss in the substantia nigra and both PET imaging of dopamine transporters and behavioral measures. Monkeys with partial lesions as defined by 2β-carbomethoxy-3β-(4-fluorophenyl) tropane binding to dopamine transporters showed recruitment of premotor and motor cortex after amphetamine stimulus similar to what has been noted in Parkinson's patients during motor tasks. These data indicate that phMRI is a powerful tool for assessment of dynamic changes associated with normal and dysfunctional DA brain circuitry in primates. PMID:15509742

  6. Three-dimensional dynamic functional mapping of cardiac mechanics

    NASA Astrophysics Data System (ADS)

    Taratorin, Alexander M.; Sideman, Samuel; Beyar, R.

    1993-07-01

    The heart is an organ which functions by a periodic change of the three dimensional (3D) spatially distributed parameters; malfunctions of the heart's operating systems are manifested by changes of the spatio-temporal heart shape dynamics. This paper attempts to present a set of image analysis tools aimed at a thorough study of the left ventricular (LV) shape-function relationship based on Cine-CT data. Data processing methodologies aimed at analysis and interpretation of the dynamic 3D LV shape, thickening and motion are described. These include the computerized detection of the LV boundaries, dynamic reconstruction of 3D LV shape, the LV shape parameters and their spatio-temporal evolution. The procedures are demonstrated using Cine-CT images of the human LV is normal and pathological cases.

  7. Invariant tori of the Poincare return map as solutions of functional difference equations

    SciTech Connect

    Warnock, R.L.

    1991-01-01

    Functional difference equations characterize the invariant surfaces of the Poincare return map of a general Hamiltonian system. Two different functional equations are derived. The first is analogous to the Hamilton-Jacobi equation and the second is a generalization of Moser's equation. Some properties of the equations, and schemes for solving them numerically, are discussed. 7 refs., 1 fig.

  8. Mapping Language Function in the Brain: A Review of the Recent Literature.

    ERIC Educational Resources Information Center

    Crafton, Robert E.; Kido, Elissa

    2000-01-01

    Considers the potential importance of brain study for composition instruction, briefly describes functional imaging techniques, and reviews the findings of recent brain-mapping studies investigating the neurocognitive systems involved in language function. Presents a review of the recent literature and considers the possible implications of this…

  9. Bells Galore: Oscillations and circle-map dynamics from space-filling fractal functions

    SciTech Connect

    Puente, C.E.; Cortis, A.; Sivakumar, B.

    2008-10-15

    The construction of a host of interesting patterns over one and two dimensions, as transformations of multifractal measures via fractal interpolating functions related to simple affine mappings, is reviewed. It is illustrated that, while space-filling fractal functions most commonly yield limiting Gaussian distribution measures (bells), there are also situations (depending on the affine mappings parameters) in which there is no limit. Specifically, the one-dimensional case may result in oscillations between two bells, whereas the two-dimensional case may give rise to unexpected circle map dynamics of an arbitrary number of two-dimensional circular bells. It is also shown that, despite the multitude of bells over two dimensions, whose means dance making regular polygons or stars inscribed on a circle, the iteration of affine maps yields exotic kaleidoscopes that decompose such an oscillatory pattern in a way that is similar to the many cases that converge to a single bell.

  10. Diffusion MRI

    NASA Astrophysics Data System (ADS)

    Fukuyama, Hidenao

    Recent advances of magnetic resonance imaging have been described, especially stressed on the diffusion sequences. We have recently applied the diffusion sequence to functional brain imaging, and found the appropriate results. In addition to the neurosciences fields, diffusion weighted images have improved the accuracies of clinical diagnosis depending upon magnetic resonance images in stroke as well as inflammations.

  11. A quantitative spatial comparison of high-density diffuse optical tomography and fMRI cortical mapping

    PubMed Central

    Eggebrecht, Adam T.; White, Brian R.; Ferradal, Silvina L.; Chen, Chunxiao; Zhan, Yuxuan; Snyder, Abraham Z.; Dehghani, Hamid; Culver, Joseph P.

    2012-01-01

    Functional neuroimaging commands a dominant role in current neuroscience research. However its use in bedside clinical and certain neuro-scientific studies has been limited because the current tools lack the combination of being non-invasive, non-ionizing and portable while maintaining moderate resolution and localization accuracy. Optical neuroimaging satisfies many of these requirements, but, until recent advances in high-density diffuse optical tomography (HD-DOT), has been hampered by limited resolution. While early results of HD-DOT have been promising, a quantitative voxel-wise comparison and validation of HD-DOT against the gold standard of functional magnetic resonance imaging (fMRI) has been lacking. Herein, we provide such an analysis within the visual cortex using matched visual stimulation protocols in a single group of subjects (n=5) during separate HD-DOT and fMRI scanning sessions. To attain the needed voxel-to-voxel co-registration between HD-DOT and fMRI image spaces, we implemented subject-specific head modeling that incorporated MRI anatomy, detailed segmentation, and alignment of source and detector positions. Comparisons of the visual responses found an average localization error between HD-DOT and fMRI of 4.4 +/− 1 mm, significantly less than the average distance between cortical gyri. This specificity demonstrates that HD-DOT has sufficient image quality to be useful as a surrogate for fMRI. PMID:22330315

  12. Spatial mapping of functional pelvic bone marrow using FLT PET

    PubMed Central

    McGuire, Sarah M.; Menda, Yusuf; Boles Ponto, Laura L.; Gross, Brandie; TenNapel, Mindi; Smith, Brian; Bayouth, John E.

    2014-01-01

    The purpose of this study was to determine the ability of regions identified with bony landmarks on CT imaging to accurately represent active bone marrow when compared to FLT PET imaging. These surrogate regions could then be used to create a bone marrow sparing radiation therapy plan when FLT PET imaging is not available. WB FLT PET images were obtained of 18 subjects prior to chemoradiation therapy. The FLT image of each subject was registered to a CT image acquired for that subject to obtain anatomic information of the pelvis. Seventeen regions were identified based on features of the pelvic bones, sacrum, and femoral heads. The probability of FLT uptake being located in each of 17 different CT-based regions of the bony pelvis was calculated using Tukey’s multiple comparison test. Statistical analysis of FLT uptake in the pelvis indicated 4 distinct groups within the 17 regions that had similar levels of activity. Regions located in the central part of the pelvis including the superior part of the sacrum, the inner halves of the iliac crests and the L5 vertebral body had greater FLT uptake than those in the peripheral regions (p < 0.05). We have developed a method to use CT defined pelvic bone regions to represent FLT PET identified functional bone marrow. Individual regions that have a statistically significant probability of containing functional bone marrow can be used as avoidance regions to reduce radiation dose to functional bone marrow in radiation therapy planning. However, because likely active bone marrow regions and pelvic targets typically overlap, patient specific spatial detail may be advantageous in IMRT planning scenarios and may best be provided using FLT PET imaging. PMID:25207403

  13. Pushing spatial and temporal resolution for functional and diffusion MRI in the Human Connectome Project

    PubMed Central

    Uğurbil, Kamil; Xu, Junqian; Auerbach, Edward J.; Moeller, Steen; Vu, An; Duarte-Carvajalino, Julio M.; Lenglet, Christophe; Wu, Xiaoping; Schmitter, Sebastian; Van de Moortele, Pierre Francois; Strupp, John; Sapiro, Guillermo; De Martino, Federico; Wang, Dingxin; Harel, Noam; Garwood, Michael; Chen, Liyong; Feinberg, David A.; Smith, Stephen M.; Miller, Karla L.; Sotiropoulos, Stamatios N; Jbabdi, Saad; Andersson, Jesper L; Behrens, Timothy EJ; Glasser, Matthew F.; Van Essen, David; Yacoub, Essa

    2013-01-01

    The human connectome project (HCP) relies primarily on three complementary magnetic resonance (MR) methods. These are: 1) resting state functional MR imaging (rfMRI) which uses correlations in the temporal fluctuations in an fMRI time series to deduce ‘functional connectivity’; 2) diffusion imaging (dMRI), which provides the input for tractography algorithms used for the reconstruction of the complex axonal fiber architecture; and 3) task based fMRI (tfMRI), which is employed to identify functional parcellation in the human brain in order to assist analyses of data obtained with the first two methods. We describe technical improvements and optimization of these methods as well as instrumental choices that impact speed of acquisition of fMRI and dMRI images at 3 Tesla, leading to whole brain coverage with 2 mm isotropic resolution in 0.7 second for fMRI, and 1.25 mm isotropic resolution dMRI data for tractography analysis with three-fold reduction in total data acquisition time. Ongoing technical developments and optimization for acquisition of similar data at 7 Tesla magnetic field are also presented, targeting higher resolution, specificity of functional imaging signals, mitigation of the inhomogeneous radio frequency (RF) fields and power deposition. Results demonstrate that overall, these approaches represent a significant advance in MR imaging of the human brain to investigate brain function and structure. PMID:23702417

  14. Mapping kinematic functional abilities of the hand to three dimensional shapes for inclusive design.

    PubMed

    Leitkam, Samuel T; Bix, Laura; de la Fuente, Javier; Reid Bush, Tamara

    2015-08-20

    Loss of hand function can have adverse effects on an individual's ability to maintain independence. The ability to perform daily activities, such as food preparation and medication delivery, is dependent on the hand's ability to grasp and manipulate objects. Therefore, the goal of this research was to demonstrate that three dimensional (3D) modeling of hand function can be used to improve the accessibility of handheld objects for individuals with reduced functionality through informed design. Individual models of hand functionality were created for 43 participants and group models were developed for groups of individuals without (Healthy) and with reduced functionality due to arthritis (RFA) of the hand. Cylindrical models representative of auto-injectors of varying diameters were analyzed in 3D space relative to hand function. The individual model mappings showed the cylinder diameter with the highest mapped functional values varied depending on the type of functional weighting chosen: kinematic redundancy of fingertip pad positional placement, fingertip pad orientation, or finger force directionality. The group mappings showed that for a cylinder to be grasped in a power grasp by at least 75% of the Healthy or RFA groups, a diameter of 40mm was required. This research utilizes a new hand model to objectively compare design parameters across three different kinematic factors of hand function and across groups with different functional abilities. The ability to conduct these comparisons enables the creation of designs that are universal to all - including accommodation of individuals with limits in their functional abilities.

  15. Characteristics of the probability function for three random-walk models of reaction-diffusion processes

    NASA Astrophysics Data System (ADS)

    Musho, Matthew K.; Kozak, John J.

    1984-10-01

    A method is presented for calculating exactly the relative width (σ2)1/2/, the skewness γ1, and the kurtosis γ2 characterizing the probability distribution function for three random-walk models of diffusion-controlled processes. For processes in which a diffusing coreactant A reacts irreversibly with a target molecule B situated at a reaction center, three models are considered. The first is the traditional one of an unbiased, nearest-neighbor random walk on a d-dimensional periodic/confining lattice with traps; the second involves the consideration of unbiased, non-nearest-neigh bor (i.e., variable-step length) walks on the same d-dimensional lattice; and, the third deals with the case of a biased, nearest-neighbor walk on a d-dimensional lattice (wherein a walker experiences a potential centered at the deep trap site of the lattice). Our method, which has been described in detail elsewhere [P.A. Politowicz and J. J. Kozak, Phys. Rev. B 28, 5549 (1983)] is based on the use of group theoretic arguments within the framework of the theory of finite Markov processes. The approach allows the separate effects of geometry (system size N, dimensionality d, and valency ν), of the governing potential and of the medium temperature to be assessed and their respective influence on (σ2)1/2/, γ1, and γ2 to be studied quantitatively. We determine the classes of potential functions and the regimes of temperature for which allowing variable-length jumps or admitting a bias in the site-to-site trajectory of the walker produces results which are significantly different (both quantitatively and qualitatively) from those calculated assuming only unbiased, nearest-neighbor random walks. Finally, we demonstrate that the approach provides a method for determining a continuous probability (density) distribution function consistent with the numerical data on (σ2)1/2/, γ1, and γ2 for the processes described above. In particular we show that the first of the above reaction-diffusion

  16. Asymmetric neighborhood functions accelerate ordering process of self-organizing maps

    SciTech Connect

    Ota, Kaiichiro; Aoki, Takaaki; Kurata, Koji; Aoyagi, Toshio

    2011-02-15

    A self-organizing map (SOM) algorithm can generate a topographic map from a high-dimensional stimulus space to a low-dimensional array of units. Because a topographic map preserves neighborhood relationships between the stimuli, the SOM can be applied to certain types of information processing such as data visualization. During the learning process, however, topological defects frequently emerge in the map. The presence of defects tends to drastically slow down the formation of a globally ordered topographic map. To remove such topological defects, it has been reported that an asymmetric neighborhood function is effective, but only in the simple case of mapping one-dimensional stimuli to a chain of units. In this paper, we demonstrate that even when high-dimensional stimuli are used, the asymmetric neighborhood function is effective for both artificial and real-world data. Our results suggest that applying the asymmetric neighborhood function to the SOM algorithm improves the reliability of the algorithm. In addition, it enables processing of complicated, high-dimensional data by using this algorithm.

  17. Hydration and diffusion processes shape microbial community organization and function in model soil aggregates

    NASA Astrophysics Data System (ADS)

    Ebrahimi, Ali; Or, Dani

    2015-12-01

    The constantly changing soil hydration status affects gas and nutrient diffusion through soil pores and thus the functioning of soil microbial communities. The conditions within soil aggregates are of particular interest due to limitations to oxygen diffusion into their core, and the presence of organic carbon often acting as binding agent. We developed a model for microbial life in simulated soil aggregates comprising of 3-D angular pore network model (APNM) that mimics soil hydraulic and transport properties. Within these APNM, we introduced individual motile (flagellated) microbial cells with different physiological traits that grow, disperse, and respond to local nutrients and oxygen concentrations. The model quantifies the dynamics and spatial extent of anoxic regions that vary with hydration conditions, and their role in shaping microbial community size and activity and the spatial (self) segregation of anaerobes and aerobes. Internal carbon source and opposing diffusion directions of oxygen and carbon within an aggregate were essential to emergence of stable coexistence of aerobic and anaerobic communities (anaerobes become extinct when carbon sources are external). The model illustrates a range of hydration conditions that promote or suppress denitrification or decomposition of organic matter and thus affect soil GHG emissions. Model predictions of CO2 and N2O production rates were in good agreement with limited experimental data. These limited tests support the dynamic modeling approach whereby microbial community size, composition, and spatial arrangement emerge from internal interactions within soil aggregates. The upscaling of the results to a population of aggregates of different sizes embedded in a soil profile is underway.

  18. Functional Connectivity-Based Parcellation of Amygdala Using Self-Organized Mapping: A Data Driven Approach

    PubMed Central

    Mishra, Arabinda; Rogers, Baxter P.; Chen, Li Min; Gore, John C.

    2013-01-01

    The overall goal of this work is to demonstrate how resting state functional magnetic resonance imaging (fMRI) signals may be used to objectively parcellate functionally heterogeneous subregions of the human amygdala into structures characterized by similar patterns of functional connectivity. We hypothesize that similarity of functional connectivity of subregions with other parts of the brain can be a potential basis to segment and cluster voxels using data driven approaches. In this work, self-organizing map (SOM) was implemented to cluster the connectivity maps associated with each voxel of the human amygdala, thereby defining distinct subregions. The functional separation was optimized by evaluating the overall differences in functional connectivity between the subregions at group level. Analysis of 25 resting state fMRI data sets suggests that SOM can successfully identify functionally independent nuclei based on differences in their inter subregional functional connectivity, evaluated statistically at various confidence levels. Although amygdala contains several nuclei whose distinct roles are implicated in various functions, our objective approach discerns at least two functionally distinct volumes comparable to previous parcellation results obtained using probabilistic tractography and cytoarchitectonic analysis. Association of these nuclei with various known functions and a quantitative evaluation of their differences in overall functional connectivity with lateral orbital frontal cortex and temporal pole confirms the functional diversity of amygdala. The data driven approach adopted here may be used as a powerful indicator of structure–function relationships in the amygdala and other functionally heterogeneous structures as well. PMID:23418140

  19. Functional brain mapping of the relaxation response and meditation.

    PubMed

    Lazar, S W; Bush, G; Gollub, R L; Fricchione, G L; Khalsa, G; Benson, H

    2000-05-15

    Meditation is a conscious mental process that induces a set of integrated physiologic changes termed the relaxation response. Functional magnetic resonance imaging (fMRI) was used to identify and characterize the brain regions that are active during a simple form of meditation. Significant (p<10(-7)) signal increases were observed in the group-averaged data in the dorsolateral prefrontal and parietal cortices, hippocampus/parahippocampus, temporal lobe, pregenual anterior cingulate cortex, striatum, and pre- and post-central gyri during meditation. Global fMRI signal decreases were also noted, although these were probably secondary to cardiorespiratory changes that often accompany meditation. The results indicate that the practice of meditation activates neural structures involved in attention and control of the autonomic nervous system.

  20. Resting state functional connectivity magnetic resonance imaging integrated with intraoperative neuronavigation for functional mapping after aborted awake craniotomy

    PubMed Central

    Batra, Prag; Bandt, S. Kathleen; Leuthardt, Eric C.

    2016-01-01

    Background: Awake craniotomy is currently the gold standard for aggressive tumor resections in eloquent cortex. However, a significant subset of patients is unable to tolerate this procedure, particularly the very young or old or those with psychiatric comorbidities, cardiopulmonary comorbidities, or obesity, among other conditions. In these cases, typical alternative procedures include biopsy alone or subtotal resection, both of which are associated with diminished surgical outcomes. Case Description: Here, we report the successful use of a preoperatively obtained resting state functional connectivity magnetic resonance imaging (MRI) integrated with intraoperative neuronavigation software in order to perform functional cortical mapping in the setting of an aborted awake craniotomy due to loss of airway. Conclusion: Resting state functional connectivity MRI integrated with intraoperative neuronavigation software can provide an alternative option for functional cortical mapping in the setting of an aborted awake craniotomy. PMID:26958419

  1. A bridge-functional-based classical mapping method for predicting the correlation functions of uniform electron gases at finite temperature

    SciTech Connect

    Liu, Yu; Wu, Jianzhong

    2014-02-28

    Efficient and accurate prediction of the correlation functions of uniform electron gases is of great importance for both practical and theoretical applications. This paper presents a bridge-functional-based classical mapping method for calculating the correlation functions of uniform spin-unpolarized electron gases at finite temperature. The bridge functional is formulated by following Rosenfeld's universality ansatz in combination with the modified fundamental measure theory. The theoretical predictions are in good agreement with recent quantum Monte Carlo results but with negligible computational cost, and the accuracy is better than a previous attempt based on the hypernetted-chain approximation. We find that the classical mapping method is most accurate if the effective mass of electrons increases as the density falls.

  2. Discussion on the Reliability of the Mapping Function from Standard Atmosphere

    NASA Astrophysics Data System (ADS)

    Hong, Z. J.; Guo, P.

    2004-02-01

    With the development of the modern space techniques, the errors of atmospheric refractive delay has become one of the main keys in improving computation accuracy. In order to reduce the influence of the selection of atmospheric profile on the mapping function of atmospheric refractive delay, the adopted atmospheric profile has gradually changed from theoretical atmosphere models (Marini 1972, Davis et al. 1985, Yan and Ping 1995) to radiosonde atmospheric profiles (Herring 1992, Niell 1996, Mendes et al. 2002). Incorporated with two representative radiosonde stations data, it has compared the mapping functions from the Standard Atmosphere with that from radiosonde data ray-tracking technique, and assessed the reliability of the mapping function from the Standard Atmosphere. A brief discussion on the choice of meteorological and geophysical parameters has been made by simulation computations.

  3. Structure-function correlation in the human placenta: the morphometric diffusing capacity for oxygen at full term.

    PubMed Central

    Mayhew, T M; Joy, C F; Haas, J D

    1984-01-01

    A combination of stereology and physiology is used to estimate the morphometric diffusing capacity for oxygen of the normal human placenta at term. The morphometric diffusing capacity is found to be higher than published values determined by physiological methods. The most likely explanation for this discrepancy is that physiological values are too low because of the effects of shunts, placental oxygen consumption and uneven diffusion:perfusion ratios. Despite the discrepancy, morphometry of histological sections offers a valuable and practicable alternative for comparing the functional potential of the placenta in different species, during normal gestation, disease, experimental treatment and environmental hypoxic stress. Images Fig. 2 PMID:6526720

  4. Mapping Depression in Schizophrenia: A Functional Magnetic Resonance Imaging Study.

    PubMed

    Kumari, Veena; Peters, Emmanuelle; Guinn, Ashley; Fannon, Dominic; Russell, Tamara; Sumich, Alexander; Kuipers, Elizabeth; Williams, Steven C R; Ffytche, Dominic H

    2016-05-01

    Depressive symptoms are common in schizophrenia, often left untreated, and associated with a high relapse rate, suicidal ideation, increased mortality, reduced social adjustment and poor quality of life. The neural mechanisms underlying depression in psychosis are poorly understood. Given reports of altered brain response to negative facial affect in depressive disorders, we examined brain response to emotive facial expressions in relation to levels of depression in people with psychosis. Seventy outpatients (final N= 63) and 20 healthy participants underwent functional magnetic resonance imaging during an implicit affect processing task involving presentation of facial expressions of fear, anger, happiness as well as neutral expressions and a (no face) control condition. All patients completed Beck Depression Inventory (BDI-II) and had their symptoms assessed on the Positive and Negative Syndrome Scale (PANSS). In patients, depression (BDI-II) scores associated positively with activation of the left thalamus, extending to the putamen-globus pallidus, insula, inferior-middle frontal and para-post-pre-central gyri during fearful expressions. Furthermore, patients with moderate-to-severe depression had significantly higher activity in these brain regions during fearful expressions relative to patients with no, minimal, or mild depression and healthy participants. The study provides first evidence of enhanced brain response to fearful facial expressions, which signal an uncertain source of threat in the environment, in patients with psychosis and a high level of self-reported depression. PMID:26712855

  5. Mapping Depression in Schizophrenia: A Functional Magnetic Resonance Imaging Study

    PubMed Central

    Kumari, Veena; Peters, Emmanuelle; Guinn, Ashley; Fannon, Dominic; Russell, Tamara; Sumich, Alexander; Kuipers, Elizabeth; Williams, Steven C. R.; ffytche, Dominic H.

    2016-01-01

    Depressive symptoms are common in schizophrenia, often left untreated, and associated with a high relapse rate, suicidal ideation, increased mortality, reduced social adjustment and poor quality of life. The neural mechanisms underlying depression in psychosis are poorly understood. Given reports of altered brain response to negative facial affect in depressive disorders, we examined brain response to emotive facial expressions in relation to levels of depression in people with psychosis. Seventy outpatients (final N = 63) and 20 healthy participants underwent functional magnetic resonance imaging during an implicit affect processing task involving presentation of facial expressions of fear, anger, happiness as well as neutral expressions and a (no face) control condition. All patients completed Beck Depression Inventory (BDI-II) and had their symptoms assessed on the Positive and Negative Syndrome Scale (PANSS). In patients, depression (BDI-II) scores associated positively with activation of the left thalamus, extending to the putamen-globus pallidus, insula, inferior-middle frontal and para-post-pre-central gyri during fearful expressions. Furthermore, patients with moderate-to-severe depression had significantly higher activity in these brain regions during fearful expressions relative to patients with no, minimal, or mild depression and healthy participants. The study provides first evidence of enhanced brain response to fearful facial expressions, which signal an uncertain source of threat in the environment, in patients with psychosis and a high level of self-reported depression. PMID:26712855

  6. Evaluation of current tropospheric mapping functions by Deep Space Network very long baseline interferometry

    NASA Astrophysics Data System (ADS)

    Sovers, O. J.; Lanyi, G. E.

    1994-11-01

    To compare the validity of current algorithms that map zenith tropospheric delay to arbitrary elevation angles, 10 different tropospheric mapping functions are used to analyze the current data base of Deep Space Network Mark 3 intercontinental very long baseline interferometric (VLBI) data. This analysis serves as a stringent test because of the high proportion of low-elevation observations necessitated by the extremely long baselines. Postfit delay and delay-rate residuals are examined, as well as the scatter of baseline lengths about the time-linear model that characterizes tectonic motion. Among the functions that utilize surface meteorological data as input parameters, the Lanyi 1984 mapping shows the best performance both for residuals and baselines, through the 1985 Davis function is statistically nearly identical. The next best performance is shown by the recent function of Niell, which is based on an examination of global atmospheric characteristics as a function of season and uses no weather data at the time of the measurements. The Niell function shows a slight improvement in residuals relative to Lanyi, but also an increase in baseline scatter that is significant for the California-Spain baseline. Two variants of the Chao mapping function, as well as the Chao tables used with the interpolation algorithm employed in the Orbit Determination Program software, show substandard behavior for both VLBI residuals and baseline scatter. The length of the California-Australia baseline (10,600 km) in the VLBI solution can vary by as much as 5 to 10 cm for the 10 mapping functions.

  7. Electron Distribution Functions in the Diffusion Region of Asymmetric Magnetic Reconnection

    NASA Technical Reports Server (NTRS)

    Bessho, N.; Chen, L.-J.; Hesse, M.

    2016-01-01

    We study electron distribution functions in a diffusion region of antiparallel asymmetric reconnection by means of particle-in-cell simulations and analytical theory. At the electron stagnation point, the electron distribution comprises a crescent-shaped population and a core component. The crescent-shaped distribution is due to electrons coming from the magnetosheath toward the stagnation point and accelerated mainly by electric field normal to the current sheet. Only a part of magnetosheath electrons can reach the stagnation point and form the crescent-shaped distribution that has a boundary of a parabolic curve. The penetration length of magnetosheath electrons into the magnetosphere is derived. We expect that satellite observations can detect crescent-shaped electron distributions during magnetopause reconnection.

  8. The Use of Legendre and Zernike Moment Functions for the Comparison of 2-D PAGE Maps.

    PubMed

    Marengo, Emilio; Robotti, Elisa; Demartini, Marco

    2016-01-01

    The comparison of 2-D maps is not trivial, the main difficulties being the high complexity of the sample and the large experimental variability characterizing 2-D gel electrophoresis. The comparison of maps from control and treated samples is usually performed by specific software, providing the so-called spot volume dataset where each spot of a specific map is matched to its analogous in other maps, and they are described by their optical density, which is supposed to be related to the underlying protein amount. Here, a different approach is presented, based on the direct comparison of 2-D map images: each map is decomposed in terms of moment functions, successively applying the multivariate tools usually adopted in image analysis problems. The moments calculated are then treated with multivariate classification techniques. Here, two types of moment functions are presented (Legendre and Zernike moments), while linear discriminant analysis and partial least squares discriminant analysis are exploited as classification tools to provide the classification of the samples. The procedure is applied to a sample dataset to prove its effectiveness.

  9. Green functions and Langevin equations for nonlinear diffusion equations: A comment on ‘Markov processes, Hurst exponents, and nonlinear diffusion equations’ by Bassler et al.

    NASA Astrophysics Data System (ADS)

    Frank, T. D.

    2008-02-01

    We discuss two central claims made in the study by Bassler et al. [K.E. Bassler, G.H. Gunaratne, J.L. McCauley, Physica A 369 (2006) 343]. Bassler et al. claimed that Green functions and Langevin equations cannot be defined for nonlinear diffusion equations. In addition, they claimed that nonlinear diffusion equations are linear partial differential equations disguised as nonlinear ones. We review bottom-up and top-down approaches that have been used in the literature to derive Green functions for nonlinear diffusion equations and, in doing so, show that the first claim needs to be revised. We show that the second claim as well needs to be revised. To this end, we point out similarities and differences between non-autonomous linear Fokker-Planck equations and autonomous nonlinear Fokker-Planck equations. In this context, we raise the question whether Bassler et al.’s approach to financial markets is physically plausible because it necessitates the introduction of external traders and causes. Such external entities can easily be eliminated when taking self-organization principles and concepts of nonextensive thermostatistics into account and modeling financial processes by means of nonlinear Fokker-Planck equations.

  10. Combined diffusion and strain MRI reveals structure and function of human myocardial laminar sheets in vivo.

    PubMed

    Dou, Jiangang; Tseng, Wen-Yih I; Reese, Timothy G; Wedeen, Van J

    2003-07-01

    The mechanism of ventricular thickening in normal humans was investigated using in vivo MRI. The hypothesis that myocardial laminar sheets contribute to ventricular thickening predominantly via sheet shear and sheet extension, as previously found invasively in canine studies at particular ventricular sites, was tested. In normal human subjects, registered images of myocardial sheet architecture and strain at the mid-left ventricle (mid-LV) at mid-systole were acquired with diffusion and strain MRI. Sheet function was analyzed by computing myocardial strain in the local fiber-sheet coordinates. In general, myocardial sheets contribute to ventricular thickening through all three cross-fiber strain components: sheet shear, sheet extension, and sheet-normal thickening (previously undocumented). Each of these components demonstrated substantial spatial heterogeneity, with sheet shear and sheet extension usually predominant in the anterior free wall, and sheet-normal thickening predominant near the right ventricular (RV) insertions. However, considerable intersubject variability was also found. In all cases, the contributions to thickening of fiber strains were small. Sheet function in normal humans was found to be heterogeneous and variable, contrasting with the uniform and symmetric ventricular patterns of fiber shortening and wall thickening. The study demonstrates that noninvasive NMR imaging is a promising tool for investigations of myocardial sheet architecture and function, and is particularly suited to the evident complexity of this field of study.

  11. Leveraging Functional-Annotation Data in Trans-ethnic Fine-Mapping Studies.

    PubMed

    Kichaev, Gleb; Pasaniuc, Bogdan

    2015-08-01

    Localization of causal variants underlying known risk loci is one of the main research challenges following genome-wide association studies. Risk loci are typically dissected through fine-mapping experiments in trans-ethnic cohorts for leveraging the variability in the local genetic structure across populations. More recent works have shown that genomic functional annotations (i.e., localization of tissue-specific regulatory marks) can be integrated for increasing fine-mapping performance within single-population studies. Here, we introduce methods that integrate the strength of association between genotype and phenotype, the variability in the genetic backgrounds across populations, and the genomic map of tissue-specific functional elements to increase trans-ethnic fine-mapping accuracy. Through extensive simulations and empirical data, we have demonstrated that our approach increases fine-mapping resolution over existing methods. We analyzed empirical data from a large-scale trans-ethnic rheumatoid arthritis (RA) study and showed that the functional genetic architecture of RA is consistent across European and Asian ancestries. In these data, we used our proposed methods to reduce the average size of the 90% credible set from 29 variants per locus for standard non-integrative approaches to 22 variants.

  12. Mapping functional traits: comparing abundance and presence-absence estimates at large spatial scales.

    PubMed

    Newbold, Tim; Butchart, Stuart H M; Sekercioğlu, Cağan H; Purves, Drew W; Scharlemann, Jörn P W

    2012-01-01

    Efforts to quantify the composition of biological communities increasingly focus on functional traits. The composition of communities in terms of traits can be summarized in several ways. Ecologists are beginning to map the geographic distribution of trait-based metrics from various sources of data, but the maps have not been tested against independent data. Using data for birds of the Western Hemisphere, we test for the first time the most commonly used method for mapping community trait composition - overlaying range maps, which assumes that the local abundance of a given species is unrelated to the traits in question - and three new methods that as well as the range maps include varying degrees of information about interspecific and geographic variation in abundance. For each method, and for four traits (body mass, generation length, migratory behaviour, diet) we calculated community-weighted mean of trait values, functional richness and functional divergence. The maps based on species ranges and limited abundance data were compared with independent data on community species composition from the American Christmas Bird Count (CBC) scheme coupled with data on traits. The correspondence with observed community composition at the CBC sites was mostly positive (62/73 correlations) but varied widely depending on the metric of community composition and method used (R(2): 5.6 × 10(-7) to 0.82, with a median of 0.12). Importantly, the commonly-used range-overlap method resulted in the best fit (21/22 correlations positive; R(2): 0.004 to 0.8, with a median of 0.33). Given the paucity of data on the local abundance of species, overlaying range maps appears to be the best available method for estimating patterns of community composition, but the poor fit for some metrics suggests that local abundance data are urgently needed to allow more accurate estimates of the composition of communities.

  13. Intraoperative Monitoring and Mapping of the Functional Integrity of the Brainstem

    PubMed Central

    Fernández-Conejero, Isabel

    2016-01-01

    The risk of iatrogenic damage is very high in surgical interventions in or around the brainstem. However, surgical techniques and intraoperative neuromonitoring (ION) have evolved sufficiently to increase the likelihood of successful functional outcomes in many patients. We present a critical review of the methodologies available for intraoperative monitoring and mapping of the brainstem. There are three main groups of techniques that can be used to assess the functional integrity of the brainstem: 1) mapping, which provides rapid anatomical identification of neural structures using electrical stimulation with a hand-held probe, 2) monitoring, which provides real-time information about the functional integrity of the nervous tissue, and 3) techniques involving the examination of brainstem reflexes in the operating room, which allows for the evaluation of the reflex responses that are known to be crucial for most brainstem functions. These include the blink reflex, which is already in use, and other brainstem reflexes that are being explored, such as the masseter H-reflex. This is still under development but is likely to have important functional consequences. Today an abundant armory of ION methods is available for the monitoring and mapping of the functional integrity of the brainstem during surgery. ION methods are essential in surgery either in or around the brainstem; they facilitate the removal of lesions and contribute to notable improvements in the functional outcomes of patients. PMID:27449909

  14. DiffNet: automatic differential functional summarization of dE-MAP networks.

    PubMed

    Seah, Boon-Siew; Bhowmick, Sourav S; Dewey, C Forbes

    2014-10-01

    The study of genetic interaction networks that respond to changing conditions is an emerging research problem. Recently, Bandyopadhyay et al. (2010) proposed a technique to construct a differential network (dE-MAPnetwork) from two static gene interaction networks in order to map the interaction differences between them under environment or condition change (e.g., DNA-damaging agent). This differential network is then manually analyzed to conclude that DNA repair is differentially effected by the condition change. Unfortunately, manual construction of differential functional summary from a dE-MAP network that summarizes all pertinent functional responses is time-consuming, laborious and error-prone, impeding large-scale analysis on it. To this end, we propose DiffNet, a novel data-driven algorithm that leverages Gene Ontology (go) annotations to automatically summarize a dE-MAP network to obtain a high-level map of functional responses due to condition change. We tested DiffNet on the dynamic interaction networks following MMS treatment and demonstrated the superiority of our approach in generating differential functional summaries compared to state-of-the-art graph clustering methods. We studied the effects of parameters in DiffNet in controlling the quality of the summary. We also performed a case study that illustrates its utility.

  15. Contingency Mapping: Use of a Novel Visual Support Strategy as an Adjunct to Functional Equivalence Training

    ERIC Educational Resources Information Center

    Brown, Kenneth E.; Mirenda, Pat

    2006-01-01

    This study evaluated the effectiveness of contingency mapping, a new visual support strategy designed to enhance clients' understanding of the contingencies associated with functional equivalence training (FET). The study was conducted in a general education classroom with an adolescent boy with autism who engaged in prompt dependent behavior. A…

  16. High-Resolution Sequence-Function Mapping of Full-Length Proteins

    PubMed Central

    Kowalsky, Caitlin A.; Klesmith, Justin R.; Stapleton, James A.; Kelly, Vince; Reichkitzer, Nolan; Whitehead, Timothy A.

    2015-01-01

    Comprehensive sequence-function mapping involves detailing the fitness contribution of every possible single mutation to a gene by comparing the abundance of each library variant before and after selection for the phenotype of interest. Deep sequencing of library DNA allows frequency reconstruction for tens of thousands of variants in a single experiment, yet short read lengths of current sequencers makes it challenging to probe genes encoding full-length proteins. Here we extend the scope of sequence-function maps to entire protein sequences with a modular, universal sequence tiling method. We demonstrate the approach with both growth-based selections and FACS screening, offer parameters and best practices that simplify design of experiments, and present analytical solutions to normalize data across independent selections. Using this protocol, sequence-function maps covering full sequences can be obtained in four to six weeks. Best practices introduced in this manuscript are fully compatible with, and complementary to, other recently published sequence-function mapping protocols. PMID:25790064

  17. Further investigation on MODIS solar diffuser screen vignetting function and its implementation in RSB calibration

    NASA Astrophysics Data System (ADS)

    Wang, Zhipeng; Xiong, Xiaoxiong; Barnes, Williams L.

    2011-10-01

    The MODIS high-gain ocean color bands (B8-B16) are calibrated with its solar diffuser screen (SDS) closed to avoid saturation so that the vignetting function (VF) of SDS is necessary for the calculation of the gain coefficients of these detectors. Since there was no pre-launch system level characterization of the VF, a series of yaw maneuvers were carried out at the mission beginning for both Terra and Aqua to enable its on-orbit characterization. Current VF was derived from the low-gain bands (B1-B7 & B17-B19) data and applied to high-gain ocean color bands calibration, with the assumption that all bands and detectors should share the same VF since it is wavelength independent. As expected, error exists and it was carried over into the calibrated gain coefficients of those bands that use the SDS for their on-orbit calibration. In this paper, an improved VF calculation approach, still using the yaw data as input, is presented. The new approach takes the frame-level mismatch between different detector's footprints on the solar diffuser (SD) into account so that a proper SD image frame adjustment is made when the VF of the low-gain bands is translated into high-gain bands VF. A new set of band-and-detector dependent VFs can be derived using this approach. The implementation of the new VF into calibration of high-gain bands gain coefficient has effectively reduced the undesired seasonal oscillations in its trending from up to Terra's 0.6% and Aqua's 1.0% to nearly 0.2%.

  18. In vivo functional and myeloarchitectonic mapping of human primary auditory areas

    PubMed Central

    Dick, Frederic; Tierney, Adam Taylor; Lutti, Antoine; Josephs, Oliver; Sereno, Martin I.; Weiskopf, Nikolaus

    2012-01-01

    In contrast to vision, where retinotopic mapping alone can define areal borders, primary auditory areas such as A1 are best delineated by combining in vivo tonotopic mapping with post mortem cyto- or myelo-architectonics from the same individual. We combined high-resolution (800 μm) quantitative T1 mapping with phase-encoded tonotopic methods to map primary auditory areas (A1 and R) within the ‘auditory core’ of human volunteers. We first quantitatively characterize the highly myelinated auditory core in terms of shape, area, cortical depth profile, and position, with our data showing considerable correspondence to post-mortem myeloarchitectonic studies, both in cross-participant averages and in individuals. The core region contains two ‘mirror-image‘ tonotopic maps oriented along the same axis as observed in macaque and owl monkey. We suggest that thee two maps within the core are the human analogues of primate auditory areas A1 and R. The core occupies a much smaller portion of tonotopically organized cortex on the superior temporal plane and gyrus than is generally supposed. The multi-modal approach to defining the auditory core will facilitate investigations of structure-function relationships, comparative neuroanatomical studies, and promises new biomarkers for diagnosis and clinical studies. PMID:23152594

  19. Improved spatial accuracy of functional maps in the rat olfactory bulb using supervised machine learning approach.

    PubMed

    Murphy, Matthew C; Poplawsky, Alexander J; Vazquez, Alberto L; Chan, Kevin C; Kim, Seong-Gi; Fukuda, Mitsuhiro

    2016-08-15

    Functional MRI (fMRI) is a popular and important tool for noninvasive mapping of neural activity. As fMRI measures the hemodynamic response, the resulting activation maps do not perfectly reflect the underlying neural activity. The purpose of this work was to design a data-driven model to improve the spatial accuracy of fMRI maps in the rat olfactory bulb. This system is an ideal choice for this investigation since the bulb circuit is well characterized, allowing for an accurate definition of activity patterns in order to train the model. We generated models for both cerebral blood volume weighted (CBVw) and blood oxygen level dependent (BOLD) fMRI data. The results indicate that the spatial accuracy of the activation maps is either significantly improved or at worst not significantly different when using the learned models compared to a conventional general linear model approach, particularly for BOLD images and activity patterns involving deep layers of the bulb. Furthermore, the activation maps computed by CBVw and BOLD data show increased agreement when using the learned models, lending more confidence to their accuracy. The models presented here could have an immediate impact on studies of the olfactory bulb, but perhaps more importantly, demonstrate the potential for similar flexible, data-driven models to improve the quality of activation maps calculated using fMRI data. PMID:27236085

  20. Eccentricity mapping of the human visual cortex to evaluate temporal dynamics of functional T1ρ mapping

    PubMed Central

    Heo, Hye-Young; Wemmie, John A; Johnson, Casey P; Thedens, Daniel R; Magnotta, Vincent A

    2015-01-01

    Recent experiments suggest that T1 relaxation in the rotating frame (T1ρ) is sensitive to metabolism and can detect localized activity-dependent changes in the human visual cortex. Current functional magnetic resonance imaging (fMRI) methods have poor temporal resolution due to delays in the hemodynamic response resulting from neurovascular coupling. Because T1ρ is sensitive to factors that can be derived from tissue metabolism, such as pH and glucose concentration via proton exchange, we hypothesized that activity-evoked T1ρ changes in visual cortex may occur before the hemodynamic response measured by blood oxygenation level-dependent (BOLD) and arterial spin labeling (ASL) contrast. To test this hypothesis, functional imaging was performed using T1ρ, BOLD, and ASL in human participants viewing an expanding ring stimulus. We calculated eccentricity phase maps across the occipital cortex for each functional signal and compared the temporal dynamics of T1ρ versus BOLD and ASL. The results suggest that T1ρ changes precede changes in the two blood flow-dependent measures. These observations indicate that T1ρ detects a signal distinct from traditional fMRI contrast methods. In addition, these findings support previous evidence that T1ρ is sensitive to factors other than blood flow, volume, or oxygenation. Furthermore, they suggest that tissue metabolism may be driving activity-evoked T1ρ changes. PMID:25966957

  1. Evaluation of improvement of diffuse optical imaging of brain function by high-density probe arrangements and imaging algorithms

    NASA Astrophysics Data System (ADS)

    Sakakibara, Yusuke; Kurihara, Kazuki; Okada, Eiji

    2016-04-01

    Diffuse optical imaging has been applied to measure the localized hemodynamic responses to brain activation. One of the serious problems with diffuse optical imaging is the limitation of the spatial resolution caused by the sparse probe arrangement and broadened spatial sensitivity profile for each probe pair. High-density probe arrangements and an image reconstruction algorithm considering the broadening of the spatial sensitivity can improve the spatial resolution of the image. In this study, the diffuse optical imaging of the absorption change in the brain is simulated to evaluate the effect of the high-density probe arrangements and imaging methods. The localization error, equivalent full-width half maximum and circularity of the absorption change in the image obtained by the mapping and reconstruction methods from the data measured by five probe arrangements are compared to quantitatively evaluate the imaging methods and probe arrangements. The simple mapping method is sufficient for the density of the measurement points up to the double-density probe arrangement. The image reconstruction method considering the broadening of the spatial sensitivity of the probe pairs can effectively improve the spatial resolution of the image obtained from the probe arrangements higher than the quadruple density, in which the distance between the neighboring measurement points is 10.6 mm.

  2. A posteriori model validation for the temporal order of directed functional connectivity maps.

    PubMed

    Beltz, Adriene M; Molenaar, Peter C M

    2015-01-01

    A posteriori model validation for the temporal order of neural directed functional connectivity maps is rare. This is striking because models that require sequential independence among residuals are regularly implemented. The aim of the current study was (a) to apply to directed functional connectivity maps of functional magnetic resonance imaging data an a posteriori model validation procedure (i.e., white noise tests of one-step-ahead prediction errors combined with decision criteria for revising the maps based upon Lagrange Multiplier tests), and (b) to demonstrate how the procedure applies to single-subject simulated, single-subject task-related, and multi-subject resting state data. Directed functional connectivity was determined by the unified structural equation model family of approaches in order to map contemporaneous and first order lagged connections among brain regions at the group- and individual-levels while incorporating external input, then white noise tests were run. Findings revealed that the validation procedure successfully detected unmodeled sequential dependencies among residuals and recovered higher order (greater than one) simulated connections, and that the procedure can accommodate task-related input. Findings also revealed that lags greater than one were present in resting state data: With a group-level network that contained only contemporaneous and first order connections, 44% of subjects required second order, individual-level connections in order to obtain maps with white noise residuals. Results have broad methodological relevance (e.g., temporal validation is necessary after directed functional connectivity analyses because the presence of unmodeled higher order sequential dependencies may bias parameter estimates) and substantive implications (e.g., higher order lags may be common in resting state data).

  3. A posteriori model validation for the temporal order of directed functional connectivity maps

    PubMed Central

    Beltz, Adriene M.; Molenaar, Peter C. M.

    2015-01-01

    A posteriori model validation for the temporal order of neural directed functional connectivity maps is rare. This is striking because models that require sequential independence among residuals are regularly implemented. The aim of the current study was (a) to apply to directed functional connectivity maps of functional magnetic resonance imaging data an a posteriori model validation procedure (i.e., white noise tests of one-step-ahead prediction errors combined with decision criteria for revising the maps based upon Lagrange Multiplier tests), and (b) to demonstrate how the procedure applies to single-subject simulated, single-subject task-related, and multi-subject resting state data. Directed functional connectivity was determined by the unified structural equation model family of approaches in order to map contemporaneous and first order lagged connections among brain regions at the group- and individual-levels while incorporating external input, then white noise tests were run. Findings revealed that the validation procedure successfully detected unmodeled sequential dependencies among residuals and recovered higher order (greater than one) simulated connections, and that the procedure can accommodate task-related input. Findings also revealed that lags greater than one were present in resting state data: With a group-level network that contained only contemporaneous and first order connections, 44% of subjects required second order, individual-level connections in order to obtain maps with white noise residuals. Results have broad methodological relevance (e.g., temporal validation is necessary after directed functional connectivity analyses because the presence of unmodeled higher order sequential dependencies may bias parameter estimates) and substantive implications (e.g., higher order lags may be common in resting state data). PMID:26379489

  4. Effective Moisture Diffusivity of Fresh Japanese Noodle (udon) as a Function of Temperature.

    PubMed

    Inazu, T; Iwasaki, K

    1999-01-01

    The effect of moisture content and temperature on the effective moisture diffusivity was investigated to identify the optimal drying condition for Japanese noodle (udon) by using a diffusion model. The drying of fresh udon with different moisture contents was carried out under constant conditions of relative humidity and airflow at 20°C, 30°C and 40°C. The effective moisture diffusivity calculated from diffusion model was found to be constant at each temperature, and not to be influenced by the initial moisture content of the fresh udon. The moisture content calculated from the effective moisture diffusivity (2.1-3.7×10(-7) cm(2) s(-1)) agrees well with the experimental data. The effect of temperature on the effective moisture diffusivity was adequately modeled by the Arrhenius relationship. The activation energy was 21.3 kJ mol(-1). PMID:27389099

  5. Automated mapping of the ocean floor using the theory of intrinsic random functions of order k

    USGS Publications Warehouse

    David, M.; Crozel, D.; Robb, James M.

    1986-01-01

    High-quality contour maps can be computer drawn from single track echo-sounding data by combining Universal Kriging and the theory of intrinsic random function of order K (IRFK). These methods interpolate values among the closely spaced points that lie along relatively widely spaced lines. The technique provides a variance which can be contoured as a quantitative measure of map precision. The technique can be used to evaluate alternative survey trackline configurations and data collection intervals, and can be applied to other types of oceanographic data. ?? 1986 D. Reidel Publishing Company.

  6. Functional and structural mapping of human cerebral cortex: solutions are in the surfaces

    NASA Technical Reports Server (NTRS)

    Van Essen, D. C.; Drury, H. A.; Joshi, S.; Miller, M. I.

    1998-01-01

    The human cerebral cortex is notorious for the depth and irregularity of its convolutions and for its variability from one individual to the next. These complexities of cortical geography have been a chronic impediment to studies of functional specialization in the cortex. In this report, we discuss ways to compensate for the convolutions by using a combination of strategies whose common denominator involves explicit reconstructions of the cortical surface. Surface-based visualization involves reconstructing cortical surfaces and displaying them, along with associated experimental data, in various complementary formats (including three-dimensional native configurations, two-dimensional slices, extensively smoothed surfaces, ellipsoidal representations, and cortical flat maps). Generating these representations for the cortex of the Visible Man leads to a surface-based atlas that has important advantages over conventional stereotaxic atlases as a substrate for displaying and analyzing large amounts of experimental data. We illustrate this by showing the relationship between functionally specialized regions and topographically organized areas in human visual cortex. Surface-based warping allows data to be mapped from individual hemispheres to a surface-based atlas while respecting surface topology, improving registration of identifiable landmarks, and minimizing unwanted distortions. Surface-based warping also can aid in comparisons between species, which we illustrate by warping a macaque flat map to match the shape of a human flat map. Collectively, these approaches will allow more refined analyses of commonalities as well as individual differences in the functional organization of primate cerebral cortex.

  7. Functional and structural mapping of human cerebral cortex: Solutions are in the surfaces

    PubMed Central

    Van Essen, David C.; Drury, Heather A.; Joshi, Sarang; Miller, Michael I.

    1998-01-01

    The human cerebral cortex is notorious for the depth and irregularity of its convolutions and for its variability from one individual to the next. These complexities of cortical geography have been a chronic impediment to studies of functional specialization in the cortex. In this report, we discuss ways to compensate for the convolutions by using a combination of strategies whose common denominator involves explicit reconstructions of the cortical surface. Surface-based visualization involves reconstructing cortical surfaces and displaying them, along with associated experimental data, in various complementary formats (including three-dimensional native configurations, two-dimensional slices, extensively smoothed surfaces, ellipsoidal representations, and cortical flat maps). Generating these representations for the cortex of the Visible Man leads to a surface-based atlas that has important advantages over conventional stereotaxic atlases as a substrate for displaying and analyzing large amounts of experimental data. We illustrate this by showing the relationship between functionally specialized regions and topographically organized areas in human visual cortex. Surface-based warping allows data to be mapped from individual hemispheres to a surface-based atlas while respecting surface topology, improving registration of identifiable landmarks, and minimizing unwanted distortions. Surface-based warping also can aid in comparisons between species, which we illustrate by warping a macaque flat map to match the shape of a human flat map. Collectively, these approaches will allow more refined analyses of commonalities as well as individual differences in the functional organization of primate cerebral cortex. PMID:9448242

  8. Functional food and nutraceutical registration processes in Japan and China: a diffusion of innovation perspective.

    PubMed

    Patel, Darshika; Dufour, Yvon; Domigan, Neil

    2008-01-01

    Purpose - This paper looks into the functional food and nutraceutical registration processes in Japan and China. The Japanese have developed the Foods for Specified Health Use (FOSHU) registration process whereas the Chinese have put into place the Health Food (HF) registration process. The aim of this paper is to compare the regulation processes between the two countries in search for answers to three core empirical questions: (1) how have the registration processes developed and changed? (2) What are the similarities and differences between the processes of registration in the two countries investigated? (3) Why are the registration processes similar/different? Method - The study was conducted using secondary sources. The literature surveyed covered academic journals, trade journals, magazine and newspaper articles, market reports, proceedings, books and web pages of relevant regulatory authorities and regulatory consultants. Information from the more recently published sources was used preferentially over older sources. As well as using the most recent sources, information was selected on the basis of which source it was from. Official regulations and SFDA and MHLW websites would contain accurate and up to date information and information from here would be taken as true over other sources of information. Results - The two diagrams of the registration processes respectively in Japan and China clearly show that there are similarities and differences. There are six categories under which these can be found: (1) the scientific evidence required; (2) the application process; (3) the evaluation process; (4) the law and the categories of products; (5) the labels and the types of claims; and finally (6) the cost and the time involved. Conclusions -The data analysis suggests that the process of diffusion of innovation played a role in the development of the regulations. Further it was found that while Japan was at the outset a pioneer innovator in nutraceutical

  9. Improved Learning Performance of Hardware Self-Organizing Map Using a Novel Neighborhood Function.

    PubMed

    Hikawa, Hiroomi; Maeda, Yutaka

    2015-11-01

    Many self-organizing maps (SOMs) implemented on hardware restrict their neighborhood function values to negative powers of two. In this paper, we propose a novel hardware friendly neighborhood function that is aimed to improve the vector quantization performance of hardware SOM. The quantization performance of the hardware SOM with the proposed neighborhood function is examined by simulations. Simulation results show that the proposed function can improve the hardware SOM's vector quantization capability even though the function value is restricted to negative powers of two. Then, the hardware SOM is implemented on field-programmable gate array to find out the hardware cost and performance speed of the proposed neighborhood function. Experimental results show that the proposed neighborhood function can improve SOM's quantization performance without additional hardware cost or slowing down the operating speed. Due to fully parallel operation, the proposed SOM with 16×16 neurons achieves a performance of 25 344 million connections updates per second.

  10. Binding and Diffusion of Lithium in Graphite: Quantum Monte Carlo Benchmarks and Validation of van der Waals Density Functional Methods.

    PubMed

    Ganesh, P; Kim, Jeongnim; Park, Changwon; Yoon, Mina; Reboredo, Fernando A; Kent, Paul R C

    2014-12-01

    Highly accurate diffusion quantum Monte Carlo (QMC) studies of the adsorption and diffusion of atomic lithium in AA-stacked graphite are compared with van der Waals-including density functional theory (DFT) calculations. Predicted QMC lattice constants for pure AA graphite agree with experiment. Pure AA-stacked graphite is shown to challenge many van der Waals methods even when they are accurate for conventional AB graphite. Highest overall DFT accuracy, considering pure AA-stacked graphite as well as lithium binding and diffusion, is obtained by the self-consistent van der Waals functional vdW-DF2, although errors in binding energies remain. Empirical approaches based on point charges such as DFT-D are inaccurate unless the local charge transfer is assessed. The results demonstrate that the lithium-carbon system requires a simultaneous highly accurate description of both charge transfer and van der Waals interactions, favoring self-consistent approaches. PMID:26583215

  11. Binding and Diffusion of Lithium in Graphite: Quantum Monte Carlo Benchmarks and Validation of van der Waals Density Functional Methods

    SciTech Connect

    Ganesh, P.; Kim, Jeongnim; Park, Changwon; Yoon, Mina; Reboredo, Fernando A.; Kent, Paul R. C.

    2014-11-03

    In highly accurate diffusion quantum Monte Carlo (QMC) studies of the adsorption and diffusion of atomic lithium in AA-stacked graphite are compared with van der Waals-including density functional theory (DFT) calculations. Predicted QMC lattice constants for pure AA graphite agree with experiment. Pure AA-stacked graphite is shown to challenge many van der Waals methods even when they are accurate for conventional AB graphite. Moreover, the highest overall DFT accuracy, considering pure AA-stacked graphite as well as lithium binding and diffusion, is obtained by the self-consistent van der Waals functional vdW-DF2, although errors in binding energies remain. Empirical approaches based on point charges such as DFT-D are inaccurate unless the local charge transfer is assessed. Our results demonstrate that the lithium carbon system requires a simultaneous highly accurate description of both charge transfer and van der Waals interactions, favoring self-consistent approaches.

  12. Binding and Diffusion of Lithium in Graphite: Quantum Monte Carlo Benchmarks and Validation of van der Waals Density Functional Methods.

    PubMed

    Ganesh, P; Kim, Jeongnim; Park, Changwon; Yoon, Mina; Reboredo, Fernando A; Kent, Paul R C

    2014-12-01

    Highly accurate diffusion quantum Monte Carlo (QMC) studies of the adsorption and diffusion of atomic lithium in AA-stacked graphite are compared with van der Waals-including density functional theory (DFT) calculations. Predicted QMC lattice constants for pure AA graphite agree with experiment. Pure AA-stacked graphite is shown to challenge many van der Waals methods even when they are accurate for conventional AB graphite. Highest overall DFT accuracy, considering pure AA-stacked graphite as well as lithium binding and diffusion, is obtained by the self-consistent van der Waals functional vdW-DF2, although errors in binding energies remain. Empirical approaches based on point charges such as DFT-D are inaccurate unless the local charge transfer is assessed. The results demonstrate that the lithium-carbon system requires a simultaneous highly accurate description of both charge transfer and van der Waals interactions, favoring self-consistent approaches.

  13. A simple regression-based method to map quantitative trait loci underlying function-valued phenotypes.

    PubMed

    Kwak, Il-Youp; Moore, Candace R; Spalding, Edgar P; Broman, Karl W

    2014-08-01

    Most statistical methods for quantitative trait loci (QTL) mapping focus on a single phenotype. However, multiple phenotypes are commonly measured, and recent technological advances have greatly simplified the automated acquisition of numerous phenotypes, including function-valued phenotypes, such as growth measured over time. While methods exist for QTL mapping with function-valued phenotypes, they are generally computationally intensive and focus on single-QTL models. We propose two simple, fast methods that maintain high power and precision and are amenable to extensions with multiple-QTL models using a penalized likelihood approach. After identifying multiple QTL by these approaches, we can view the function-valued QTL effects to provide a deeper understanding of the underlying processes. Our methods have been implemented as a package for R, funqtl. PMID:24931408

  14. A simple regression-based method to map quantitative trait loci underlying function-valued phenotypes.

    PubMed

    Kwak, Il-Youp; Moore, Candace R; Spalding, Edgar P; Broman, Karl W

    2014-08-01

    Most statistical methods for quantitative trait loci (QTL) mapping focus on a single phenotype. However, multiple phenotypes are commonly measured, and recent technological advances have greatly simplified the automated acquisition of numerous phenotypes, including function-valued phenotypes, such as growth measured over time. While methods exist for QTL mapping with function-valued phenotypes, they are generally computationally intensive and focus on single-QTL models. We propose two simple, fast methods that maintain high power and precision and are amenable to extensions with multiple-QTL models using a penalized likelihood approach. After identifying multiple QTL by these approaches, we can view the function-valued QTL effects to provide a deeper understanding of the underlying processes. Our methods have been implemented as a package for R, funqtl.

  15. Mapping SAGE questionnaire to the International Classification of Functioning, Disability and Health (ICF).

    PubMed

    Raggi, Alberto; Quintas, Rui; Russo, Emanuela; Martinuzzi, Andrea; Costardi, Daniela; Frisoni, Giovanni Battista; Franco, Maria Grazia; Andreotti, Alessandra; Ojala, Matti; Peña, Sebastián; Perales, Jaime; Chatterji, Somnath; Miret, Marta; Tobiasz-Adamczyk, Beata; Koskinen, Seppo; Frattura, Lucilla; Leonardi, Matilde

    2014-01-01

    The collaborative research on ageing in Europe protocol was based on that of the World Health Organization Study on global AGEing and adult health (SAGE) project that investigated the relationship between health and well-being and provided a set of instruments that can be used across countries to monitor health and health-related outcomes of older populations as well as the strategies for addressing issues concerning the ageing process. To evaluate the degree to which SAGE protocol covered the spectrum of disability given the scope of the World Health Organization International Classification of Functioning, Disability and Health (ICF), a mapping exercise was performed with SAGE protocol. Results show that the SAGE protocol covers ICF domains in a non-uniform way, with environmental factors categories being underrepresented, whereas mental, cardiovascular, sensory functions and mobility were overrepresented. To overcome this partial coverage of ICF functioning categories, new assessment instruments have been developed. PRACTITIONER MESSAGE: Mapping exercises are valid procedures to understand the extent to which a survey protocol covers the spectrum of functioning. The mapping exercise with SAGE protocol shows that it provides only a partial representation of body functions and activities and participation domains, and the coverage of environmental factors is poor. New instruments are therefore needed for researchers to properly understand the health and disability of ageing populations.

  16. Correlation function analysis of the COBE differential microwave radiometer sky maps

    SciTech Connect

    Lineweaver, C.H. |

    1994-08-01

    The Differential Microwave Radiometer (DMR) aboard the COBE satellite has detected anisotropies in the cosmic microwave background (CMB) radiation. A two-point correlation function analysis which helped lead to this discovery is presented in detail. The results of a correlation function analysis of the two year DMR data set is presented. The first and second year data sets are compared and found to be reasonably consistent. The positive correlation for separation angles less than {approximately}20{degree} is robust to Galactic latitude cuts and is very stable from year to year. The Galactic latitude cut independence of the correlation function is strong evidence that the signal is not Galactic in origin. The statistical significance of the structure seen in the correlation function of the first, second and two year maps is respectively > 9{sigma}, > 10{sigma} and > 18{sigma} above the noise. The noise in the DMR sky maps is correlated at a low level. The structure of the pixel temperature covariance matrix is given. The noise covariance matrix of a DMR sky map is diagonal to an accuracy of better than 1%. For a given sky pixel, the dominant noise covariance occurs with the ring of pixels at an angular separation of 60{degree} due to the 60{degree} separation of the DMR horns. The mean covariance of 60{degree} is 0.45%{sub {minus}0.14}{sup +0.18} of the mean variance. The noise properties of the DMR maps are thus well approximated by the noise properties of maps made by a single-beam experiment. Previously published DMR results are not significantly affected by correlated noise.

  17. Single nanoparticle tracking reveals influence of chemical functionality of nanoparticles on local ordering of liquid crystals and nanoparticle diffusion coefficients.

    PubMed

    Koenig, Gary M; Ong, Rizal; Cortes, Angel D; Moreno-Razo, J Antonio; de Pablo, Juan J; Abbott, Nicholas L

    2009-07-01

    This letter reports that darkfield microscopy can be used to track the trajectories of chemically functionalized gold nanoparticles in nematic liquid crystals (LCs), thus leading to measurements of the diffusion coefficients of the nanoparticles in the LCs. These measurements reveal that the diffusion coefficients of the nanoparticles dispersed in the LC are strongly dependent on the surface chemistry of the nanoparticles. Because the changes in surface chemistry are measured to have negligible influence on the diffusion coefficients of the same nanoparticles dispersed in isotropic solvents, we conclude that surface chemistry-induced changes in the local order of LCs underlie the behavior of the diffusion coefficients of the nanoparticles in the LC. Surface chemistry-dependent ordering of the LCs near the surfaces of the nanoparticles was also found to influence diffusion coefficients measured when the LC was heated above the bulk nematic-to-isotropic transition temperature. These experimental measurements are placed into the context of past theoretical predictions regarding the impact of local ordering of LCs on diffusion coefficients. The results that emerge from this study provide important insights into the mobility of nanoparticles in LCs and suggest new approaches based on measurements of nanoparticle dynamics that can yield information on the ordering of LCs near nanoparticles.

  18. RF-Based Location Using Interpolation Functions to Reduce Fingerprint Mapping.

    PubMed

    Ezpeleta, Santiago; Claver, José M; Pérez-Solano, Juan J; Martí, José V

    2015-10-27

    Indoor RF-based localization using fingerprint mapping requires an initial training step, which represents a time consuming process. This location methodology needs a database conformed with RSSI (Radio Signal Strength Indicator) measures from the communication transceivers taken at specific locations within the localization area. But, the real world localization environment is dynamic and it is necessary to rebuild the fingerprint database when some environmental changes are made. This paper explores the use of different interpolation functions to complete the fingerprint mapping needed to achieve the sought accuracy, thereby reducing the effort in the training step. Also, different distributions of test maps and reference points have been evaluated, showing the validity of this proposal and necessary trade-offs. Results reported show that the same or similar localization accuracy can be achieved even when only 50% of the initial fingerprint reference points are taken.

  19. RF-Based Location Using Interpolation Functions to Reduce Fingerprint Mapping

    PubMed Central

    Ezpeleta, Santiago; Claver, José M.; Pérez-Solano, Juan J.; Martí, José V.

    2015-01-01

    Indoor RF-based localization using fingerprint mapping requires an initial training step, which represents a time consuming process. This location methodology needs a database conformed with RSSI (Radio Signal Strength Indicator) measures from the communication transceivers taken at specific locations within the localization area. But, the real world localization environment is dynamic and it is necessary to rebuild the fingerprint database when some environmental changes are made. This paper explores the use of different interpolation functions to complete the fingerprint mapping needed to achieve the sought accuracy, thereby reducing the effort in the training step. Also, different distributions of test maps and reference points have been evaluated, showing the validity of this proposal and necessary trade-offs. Results reported show that the same or similar localization accuracy can be achieved even when only 50% of the initial fingerprint reference points are taken. PMID:26516862

  20. Wave-function description of conductance mapping for a quantum Hall electron interferometer

    NASA Astrophysics Data System (ADS)

    Kolasiński, K.; Szafran, B.

    2014-04-01

    Scanning gate microscopy of quantum point contacts (QPC) in the integer quantum Hall regime is considered in terms of the scattering wave functions with a finite-difference implementation of the quantum transmitting boundary approach. Conductance (G) maps for a clean QPC as well as for a system including an antidot within the QPC constriction are evaluated. The steplike locally flat G maps for clean QPCs turn into circular resonances that are reentrant in an external magnetic field when the antidot is introduced to the constriction. The current circulation around the antidot and the spacing of the resonances at the magnetic field scale react to the probe approaching the QPC. The calculated G maps with a rigid but soft antidot potential reproduce the features detected recently in the electron interferometer [F. Martins et al., Sci. Rep. 3, 1416 (2013), 10.1038/srep01416].

  1. Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities.

    PubMed

    Venner, Eric; Lisewski, Andreas Martin; Erdin, Serkan; Ward, R Matthew; Amin, Shivas R; Lichtarge, Olivier

    2010-01-01

    High-throughput Structural Genomics yields many new protein structures without known molecular function. This study aims to uncover these missing annotations by globally comparing select functional residues across the structural proteome. First, Evolutionary Trace Annotation, or ETA, identifies which proteins have local evolutionary and structural features in common; next, these proteins are linked together into a proteomic network of ETA similarities; then, starting from proteins with known functions, competing functional labels diffuse link-by-link over the entire network. Every node is thus assigned a likelihood z-score for every function, and the most significant one at each node wins and defines its annotation. In high-throughput controls, this competitive diffusion process recovered enzyme activity annotations with 99% and 97% accuracy at half-coverage for the third and fourth Enzyme Commission (EC) levels, respectively. This corresponds to false positive rates 4-fold lower than nearest-neighbor and 5-fold lower than sequence-based annotations. In practice, experimental validation of the predicted carboxylesterase activity in a protein from Staphylococcus aureus illustrated the effectiveness of this approach in the context of an increasingly drug-resistant microbe. This study further links molecular function to a small number of evolutionarily important residues recognizable by Evolutionary Tracing and it points to the specificity and sensitivity of functional annotation by competitive global network diffusion. A web server is at http://mammoth.bcm.tmc.edu/networks.

  2. Simulation of the radiolysis of water using Green's functions of the diffusion equation.

    PubMed

    Plante, I; Cucinotta, F A

    2015-09-01

    Radiation chemistry is of fundamental importance in the understanding of the effects of ionising radiation, notably with regard to DNA damage by indirect effect (e.g. damage by ·OH radicals created by the radiolysis of water). In the recent years, Green's functions of the diffusion equation (GFDEs) have been used extensively in biochemistry, notably to simulate biochemical networks in time and space. In the present work, an approach based on the GFDE will be used to refine existing models on the indirect effect of ionising radiation on DNA. As a starting point, the code RITRACKS (relativistic ion tracks) will be used to simulate the radiation track structure and calculate the position of all radiolytic species formed during irradiation. The chemical reactions between these radiolytic species and with DNA will be done by using an efficient Monte Carlo sampling algorithm for the GFDE of reversible reactions with an intermediate state that has been developed recently. These simulations should help the understanding of the contribution of the indirect effect in the formation of DNA damage, particularly with regards to the formation of double-strand breaks. PMID:25897139

  3. Masking level differences--a diffusion tensor imaging and functional MRI study.

    PubMed

    Wack, David S; Polak, Paul; Furuyama, Jon; Burkard, Robert F

    2014-01-01

    In our previous study we investigated Masking Level Differences (MLD) using functional Magnetic Resonance Imaging (fMRI), but were unable to confirm neural correlations for the MLD within the auditory cortex and inferior colliculus. Here we have duplicated conditions from our previous study, but have included more participants and changed the study site to a new location with a newer scanner and presentation system. Additionally, Diffusion Tensor Imaging (DTI) is included to allow investigation of fiber tracts that may be involved with MLDs. Twenty participants were included and underwent audiometric testing and MRI scanning. The current study revealed regions of increased and decreased activity within the auditory cortex when comparing the combined noise and signal of the dichotic MLD stimuli (N0Sπ and NπS0) with N0S0. Furthermore, we found evidence of inferior colliculus involvement. Our DTI findings show strong correlations between DTI measures within the brainstem and signal detection threshold levels. Patterns of correlation when the signal was presented only to the right ear showed an extensive network in the left hemisphere; however, the opposite was not true for the signal presented only to the left ear. Our current study was able to confirm what we had previously hypothesized using fMRI, while extending our investigation of MLDs to include the characteristics of connecting neural pathways. PMID:24558392

  4. Simulation of the radiolysis of water using Green's functions of the diffusion equation.

    PubMed

    Plante, I; Cucinotta, F A

    2015-09-01

    Radiation chemistry is of fundamental importance in the understanding of the effects of ionising radiation, notably with regard to DNA damage by indirect effect (e.g. damage by ·OH radicals created by the radiolysis of water). In the recent years, Green's functions of the diffusion equation (GFDEs) have been used extensively in biochemistry, notably to simulate biochemical networks in time and space. In the present work, an approach based on the GFDE will be used to refine existing models on the indirect effect of ionising radiation on DNA. As a starting point, the code RITRACKS (relativistic ion tracks) will be used to simulate the radiation track structure and calculate the position of all radiolytic species formed during irradiation. The chemical reactions between these radiolytic species and with DNA will be done by using an efficient Monte Carlo sampling algorithm for the GFDE of reversible reactions with an intermediate state that has been developed recently. These simulations should help the understanding of the contribution of the indirect effect in the formation of DNA damage, particularly with regards to the formation of double-strand breaks.

  5. Noninvasive functional cardiac electrical source imaging: combining MRI and ECG mapping for imaging electrical function

    NASA Astrophysics Data System (ADS)

    Tilg, Bernhard; Modre, Robert; Fischer, Gerald; Hanser, Friedrich; Messnarz, Bernd; Schocke, Michael F. H.; Kremser, Christian; Roithinger, Franz

    2002-04-01

    Inverse electrocardiography has been developing for several years. By coupling electrocardiographic mapping and 3D+time anatomical data, the electrical excitation sequence can be imaged completely noninvasively in the human heart. In this study, a bidomain theory based surface heart model activation time imaging approach was applied to single beat data of atrial and ventricular depolarization. For sinus and paced rhythms, the sites of early activation and the areas with late activation were estimated with sufficient accuracy. In particular for focal arrhythmias, this model-based imaging approach might allow the guidance and evaluation of antiarrhythmic interventions, for instance, in case of catheter ablation or drug therapy.

  6. What happens inside a fuel cell? Developing an experimental functional map of fuel cell performance.

    PubMed

    Brett, Daniel J L; Kucernak, Anthony R; Aguiar, Patricia; Atkins, Stephen C; Brandon, Nigel P; Clague, Ralph; Cohen, Lesley F; Hinds, Gareth; Kalyvas, Christos; Offer, Gregory J; Ladewig, Bradley; Maher, Robert; Marquis, Andrew; Shearing, Paul; Vasileiadis, Nikos; Vesovic, Velisa

    2010-09-10

    Fuel cell performance is determined by the complex interplay of mass transport, energy transfer and electrochemical processes. The convolution of these processes leads to spatial heterogeneity in the way that fuel cells perform, particularly due to reactant consumption, water management and the design of fluid-flow plates. It is therefore unlikely that any bulk measurement made on a fuel cell will accurately represent performance at all parts of the cell. The ability to make spatially resolved measurements in a fuel cell provides one of the most useful ways in which to monitor and optimise performance. This Minireview explores a range of in situ techniques being used to study fuel cells and describes the use of novel experimental techniques that the authors have used to develop an 'experimental functional map' of fuel cell performance. These techniques include the mapping of current density, electrochemical impedance, electrolyte conductivity, contact resistance and CO poisoning distribution within working PEFCs, as well as mapping the flow of reactant in gas channels using laser Doppler anemometry (LDA). For the high-temperature solid oxide fuel cell (SOFC), temperature mapping, reference electrode placement and the use of Raman spectroscopy are described along with methods to map the microstructural features of electrodes. The combination of these techniques, applied across a range of fuel cell operating conditions, allows a unique picture of the internal workings of fuel cells to be obtained and have been used to validate both numerical and analytical models.

  7. Assembling global maps of cellular function through integrative analysis of physical and genetic networks

    PubMed Central

    Srivas, Rohith; Hannum, Gregory; Ruscheinski, Johannes; Ono, Keiichiro; Wang, Peng-Liang; Smoot, Michael; Ideker, Trey

    2012-01-01

    To take full advantage of high-throughput genetic and physical interaction mapping projects, the raw interactions must first be assembled into models of cell structure and function. PanGIA (for physical and genetic interaction alignment) is a plug-in for the bioinformatics platform Cytoscape, designed to integrate physical and genetic interactions into hierarchical module maps. PanGIA identifies ‘modules’ as sets of proteins whose physical and genetic interaction data matches that of known protein complexes. Higher-order functional cooperativity and redundancy is identified by enrichment for genetic interactions across modules. This protocol begins with importing interaction networks into Cytoscape, followed by filtering and basic network visualization. Next, PanGIA is used to infer a set of modules and their functional inter-relationships. This module map is visualized in a number of intuitive ways, and modules are tested for functional enrichment and overlap with known complexes. The full protocol can be completed between 10 and 30 min, depending on the size of the data set being analyzed. PMID:21886098

  8. Mapping Functional Connectivity between Neuronal Ensembles with Larval Zebrafish Transgenic for a Ratiometric Calcium Indicator

    PubMed Central

    Tao, Louis; Lauderdale, James D.; Sornborger, Andrew T.

    2010-01-01

    The ability to map functional connectivity is necessary for the study of the flow of activity in neuronal circuits. Optical imaging of calcium indicators, including FRET-based genetically encoded indicators and extrinsic dyes, is an important adjunct to electrophysiology and is widely used to visualize neuronal activity. However, techniques for mapping functional connectivities with calcium imaging data have been lacking. We present a procedure to compute reduced functional couplings between neuronal ensembles undergoing seizure activity from ratiometric calcium imaging data in three steps: (1) calculation of calcium concentrations and neuronal firing rates from ratiometric data; (2) identification of putative neuronal populations from spatio-temporal time-series of neural bursting activity; and then, (3) derivation of reduced connectivity matrices that represent neuronal population interactions. We apply our method to the larval zebrafish central nervous system undergoing chemoconvulsant-induced seizures. These seizures generate propagating, central nervous system-wide neural activity from which population connectivities may be calculated. This automatic functional connectivity mapping procedure provides a practical and user-independent means for summarizing the flow of activity between neuronal ensembles. PMID:21373259

  9. The diffuse chemosensory system: exploring the iceberg toward the definition of functional roles.

    PubMed

    Sbarbati, Andrea; Bramanti, Placido; Benati, Donatella; Merigo, Flavia

    2010-05-01

    The diffuse chemosensory system (DCS) is an anatomical structure composed of solitary chemosensory cells (SCCs, also called solitary chemoreceptor cells), which have analogies with taste cells but are not aggregated in buds. The concept of DCS has been advanced, after the discovery that cells similar to gustatory elements are present in several organs. The elements forming the DCS share common morphological and biochemical characteristics with the taste cells located in taste buds of the oro-pharyngeal cavity but they are localized in internal organs. In particular, they may express molecules of the chemoreceptorial cascade (e.g. trans-membrane taste receptors, the G-protein alpha-gustducin, PLCbeta2, TRPM5). This article will focus on the mammalian DCS in apparatuses of endodermic origin (i.e. digestive and respiratory systems), which is composed of an enormous number of sensory elements and presents a multiplicity of morphological aspects. Recent research has provided an adequate description of these elements, but the functional role for the DCS in these apparatuses is unknown. The initial findings led to the definition of a DCS structured like an iceberg, with a mysterious "submerged" portion localized in the distal part of endodermic apparatuses. Recent work has focussed on the discovery of this submerged portion, which now appears less puzzling. However, the functional roles of the different cytotypes belonging to the DCS are not well known. Recent studies linked chemosensation of the intraluminal content to local control of absorptive and secretory (exocrine and endocrine) processes. Control of the microbial population and detection of irritants seem to be other possible functions of the DCS. In the light of these new findings, the DCS might be thought to be involved in a wide range of diseases of both the respiratory (e.g. asthma, chronic obstructive pulmonary disease, cystic fibrosis) and digestive apparatuses (absorptive or secretive diseases, dysmicrobism

  10. Maps of cis-Regulatory Nodes in Megabase Long Genome Segments are an Inevitable Intermediate Step Toward Whole Genome Functional Mapping

    PubMed Central

    Nikolaev, Lev G; Akopov, Sergey B; Chernov, Igor P; Sverdlov, Eugene D

    2007-01-01

    The availability of complete human and other metazoan genome sequences has greatly facilitated positioning and analysis of various genomic functional elements, with initial emphasis on coding sequences. However, complete functional maps of sequenced eukaryotic genomes should include also positions of all non-coding regulatory elements. Unfortunately, experimental data on genomic positions of a multitude of regulatory sequences, such as enhancers, silencers, insulators, transcription terminators, and replication origins are very limited, especially at the whole genome level. Since most genomic regulatory elements (e.g. enhancers) are generally gene-, tissue-, or cell-specific, the prediction of these elements by computational methods is difficult and often ambiguous. Therefore, the development of high-throughput experimental approaches for identifying and mapping genomic functional elements is highly desirable. At the same time, the creation of whole-genome map of hundreds of thousands of regulatory elements in several hundreds of tissue/cell types is presently far beyond our capabilities. A possible alternative for the whole genome approach is to concentrate efforts on individual genomic segments and then to integrate the data obtained into a whole genome functional map. Moreover, the maps of polygenic fragments with functional cis-regulatory elements would provide valuable data on complex regulatory systems, including their variability and evolution. Here, we reviewed experimental approaches to the realization of these ideas, including our own developments of experimental techniques for selection of cis-acting functionally active DNA fragments from large (megabase-sized) segments of mammalian genomes. PMID:18660850

  11. Maps of cis-Regulatory Nodes in Megabase Long Genome Segments are an Inevitable Intermediate Step Toward Whole Genome Functional Mapping.

    PubMed

    Nikolaev, Lev G; Akopov, Sergey B; Chernov, Igor P; Sverdlov, Eugene D

    2007-04-01

    The availability of complete human and other metazoan genome sequences has greatly facilitated positioning and analysis of various genomic functional elements, with initial emphasis on coding sequences. However, complete functional maps of sequenced eukaryotic genomes should include also positions of all non-coding regulatory elements. Unfortunately, experimental data on genomic positions of a multitude of regulatory sequences, such as enhancers, silencers, insulators, transcription terminators, and replication origins are very limited, especially at the whole genome level. Since most genomic regulatory elements (e.g. enhancers) are generally gene-, tissue-, or cell-specific, the prediction of these elements by computational methods is difficult and often ambiguous. Therefore, the development of high-throughput experimental approaches for identifying and mapping genomic functional elements is highly desirable. At the same time, the creation of whole-genome map of hundreds of thousands of regulatory elements in several hundreds of tissue/cell types is presently far beyond our capabilities. A possible alternative for the whole genome approach is to concentrate efforts on individual genomic segments and then to integrate the data obtained into a whole genome functional map. Moreover, the maps of polygenic fragments with functional cis-regulatory elements would provide valuable data on complex regulatory systems, including their variability and evolution. Here, we reviewed experimental approaches to the realization of these ideas, including our own developments of experimental techniques for selection of cis-acting functionally active DNA fragments from large (megabase-sized) segments of mammalian genomes. PMID:18660850

  12. Differentiation of the functional in an optimization problem for diffusion and convective transfer coefficients of elliptic imperfect contact interface problems

    NASA Astrophysics Data System (ADS)

    Manapova, Aigul

    2016-08-01

    We consider optimal control problems for second order elliptic equations with non-self-adjoint operators-convection-diffusion problems. Control processes are described by semi-linear convection-diffusion equation with discontinuous data and solutions (states) subject to the boundary interface conditions of imperfect type (i.e., problems with a jump of the coefficients and the solution on the interface; the jump of the solution is proportional to the normal component of the flux). Controls are involved in the coefficients of diffusion and convective transfer. We prove differentiability and Lipshitz continuity of the cost functional, depending on a state of the system and a control. The calculation of the gradients uses the numerical solutions of direct problems for the state and adjoint problems.

  13. Novel Techniques of Real-time Blood Flow and Functional Mapping: Technical Note

    PubMed Central

    KAMADA, Kyousuke; OGAWA, Hiroshi; SAITO, Masato; TAMURA, Yukie; ANEI, Ryogo; KAPELLER, Christoph; HAYASHI, Hideaki; PRUECKL, Robert; GUGER, Christoph

    2014-01-01

    There are two main approaches to intraoperative monitoring in neurosurgery. One approach is related to fluorescent phenomena and the other is related to oscillatory neuronal activity. We developed novel techniques to visualize blood flow (BF) conditions in real time, based on indocyanine green videography (ICG-VG) and the electrophysiological phenomenon of high gamma activity (HGA). We investigated the use of ICG-VG in four patients with moyamoya disease and two with arteriovenous malformation (AVM), and we investigated the use of real-time HGA mapping in four patients with brain tumors who underwent lesion resection with awake craniotomy. Real-time data processing of ICG-VG was based on perfusion imaging, which generated parameters including arrival time (AT), mean transit time (MTT), and BF of brain surface vessels. During awake craniotomy, we analyzed the frequency components of brain oscillation and performed real-time HGA mapping to identify functional areas. Processed results were projected on a wireless monitor linked to the operating microscope. After revascularization for moyamoya disease, AT and BF were significantly shortened and increased, respectively, suggesting hyperperfusion. Real-time fusion images on the wireless monitor provided anatomical, BF, and functional information simultaneously, and allowed the resection of AVMs under the microscope. Real-time HGA mapping during awake craniotomy rapidly indicated the eloquent areas of motor and language function and significantly shortened the operation time. These novel techniques, which we introduced might improve the reliability of intraoperative monitoring and enable the development of rational and objective surgical strategies. PMID:25263624

  14. Adaptive mapping functions to the azimuthal anisotropy of the neutral atmosphere

    NASA Astrophysics Data System (ADS)

    Gegout, P.; Biancale, R.; Soudarin, L.

    2011-10-01

    The anisotropy of propagation of radio waves used by global navigation satellite systems is investigated using high-resolution observational data assimilations produced by the European Centre for Medium-range Weather Forecast. The geometry and the refractivity of the neutral atmosphere are built introducing accurate geodetic heights and continuous formulations of the refractivity and its gradient. Hence the realistic ellipsoidal shape of the refractivity field above the topography is properly represented. Atmospheric delays are obtained by ray-tracing through the refractivity field, integrating the eikonal differential system. Ray-traced delays reveal the anisotropy of the atmosphere. With the aim to preserve the classical mapping function strategy, mapping functions can evolve to adapt to high-frequency atmospheric fluctuations and to account for the anisotropy of propagation by fitting at each site and time the zenith delays and the mapping functions coefficients. Adaptive mapping functions (AMF) are designed with coefficients of the continued fraction form which depend on azimuth. The basic idea is to expand the azimuthal dependency of the coefficients in Fourier series introducing a multi-scale azimuthal decomposition which slightly changes the elevation functions with the azimuth. AMF are used to approximate thousands of atmospheric ray-traced delays using a few tens of coefficients. Generic recursive definitions of the AMF and their partial derivatives lead to observe that the truncation of the continued fraction form at the third term and the truncation of the azimuthal Fourier series at the fourth term are sufficient in usual meteorological conditions. Delays' and elevations' mapping functions allow to store and to retrieve the ray-tracing results to solve the parallax problem at the observation level. AMF are suitable to fit the time-variable isotropic and anisotropic parts of the ray-traced delays at each site at each time step and to provide GPS range

  15. Single cell functional analysis of multiple myeloma cell populations correlates with diffusion profiles in static microfluidic coculture systems.

    PubMed

    Moore, Thomas A; Young, Edmond W K

    2016-07-01

    Microfluidic cell culture systems are becoming increasingly useful for studying biology questions, particularly those involving small cell populations that are cultured within microscale geometries mimicking the complex cellular microenvironment. Depending on the geometry and spatial organization of these cell populations, however, paracrine signaling between cell types can depend critically on spatial concentration profiles of soluble factors generated by diffusive transport. In scenarios where single cell data are acquired to study cell population heterogeneities in functional response, uncertainty associated with concentration profiles can lead to interpretation bias. To address this issue and provide important evidence on how diffusion develops within typical microfluidic cell culture systems, a combination of experimental and computational approaches were applied to measure and predict concentration patterns within microfluidic geometries, and characterize the functional response of culture cells based on single-cell resolution transcription factor activation. Using a model coculture system consisting of multiple myeloma cells (MMCs) and neighboring bone marrow stromal cells (BMSCs), we measured concentrations of three cytokines (IL-6, VEGF, and TNF-α) in conditioned media collected from separate culture compartments using a multiplex ELISA system. A 3D numerical model was developed to predict biomolecular diffusion and resulting concentration profiles within the tested microsystems and compared with experimental diffusion of 20 kDa FITC-Dextran. Finally, diffusion was further characterized by controlling exogenous IL-6 diffusion and the coculture spatial configuration of BMSCs to stimulate STAT3 nuclear translocation in MMCs. Results showed agreement between numerical and experimental results, provided evidence of a shallow concentration gradient across the center well of the microsystem that did not lead to a bias in results, and demonstrated that

  16. Single cell functional analysis of multiple myeloma cell populations correlates with diffusion profiles in static microfluidic coculture systems.

    PubMed

    Moore, Thomas A; Young, Edmond W K

    2016-07-01

    Microfluidic cell culture systems are becoming increasingly useful for studying biology questions, particularly those involving small cell populations that are cultured within microscale geometries mimicking the complex cellular microenvironment. Depending on the geometry and spatial organization of these cell populations, however, paracrine signaling between cell types can depend critically on spatial concentration profiles of soluble factors generated by diffusive transport. In scenarios where single cell data are acquired to study cell population heterogeneities in functional response, uncertainty associated with concentration profiles can lead to interpretation bias. To address this issue and provide important evidence on how diffusion develops within typical microfluidic cell culture systems, a combination of experimental and computational approaches were applied to measure and predict concentration patterns within microfluidic geometries, and characterize the functional response of culture cells based on single-cell resolution transcription factor activation. Using a model coculture system consisting of multiple myeloma cells (MMCs) and neighboring bone marrow stromal cells (BMSCs), we measured concentrations of three cytokines (IL-6, VEGF, and TNF-α) in conditioned media collected from separate culture compartments using a multiplex ELISA system. A 3D numerical model was developed to predict biomolecular diffusion and resulting concentration profiles within the tested microsystems and compared with experimental diffusion of 20 kDa FITC-Dextran. Finally, diffusion was further characterized by controlling exogenous IL-6 diffusion and the coculture spatial configuration of BMSCs to stimulate STAT3 nuclear translocation in MMCs. Results showed agreement between numerical and experimental results, provided evidence of a shallow concentration gradient across the center well of the microsystem that did not lead to a bias in results, and demonstrated that

  17. A Functional Model for Teaching Osmosis-Diffusion to Biology Students

    ERIC Educational Resources Information Center

    Olsen, Richard W.; Petry, Douglas E.

    1976-01-01

    Described is a maternal-fetal model, operated by the student, to teach osmosis-diffusion to biology students. Included are materials needed, assembly instructions, and student operating procedures. (SL)

  18. Probabilistic map of critical functional regions of the human cerebral cortex: Broca's area revisited.

    PubMed

    Tate, Matthew C; Herbet, Guillaume; Moritz-Gasser, Sylvie; Tate, Joseph E; Duffau, Hugues

    2014-10-01

    The organization of basic functions of the human brain, particularly in the right hemisphere, remains poorly understood. Recent advances in functional neuroimaging have improved our understanding of cortical organization but do not allow for direct interrogation or determination of essential (versus participatory) cortical regions. Direct cortical stimulation represents a unique opportunity to provide novel insights into the functional distribution of critical epicentres. Direct cortical stimulation (bipolar, 60 Hz, 1-ms pulse) was performed in 165 consecutive patients undergoing awake mapping for resection of low-grade gliomas. Tasks included motor, sensory, counting, and picture naming. Stimulation sites eliciting positive (sensory/motor) or negative (speech arrest, dysarthria, anomia, phonological and semantic paraphasias) findings were recorded and mapped onto a standard Montreal Neurological Institute brain atlas. Montreal Neurological Institute-space functional data were subjected to cluster analysis algorithms (K-means, partition around medioids, hierarchical Ward) to elucidate crucial network epicentres. Sensorimotor function was observed in the pre/post-central gyri as expected. Articulation epicentres were also found within the pre/post-central gyri. However, speech arrest localized to ventral premotor cortex, not the classical Broca's area. Anomia/paraphasia data demonstrated foci not only within classical Wernicke's area but also within the middle and inferior frontal gyri. We report the first bilateral probabilistic map for crucial cortical epicentres of human brain functions in the right and left hemispheres, including sensory, motor, and language (speech, articulation, phonology and semantics). These data challenge classical theories of brain organization (e.g. Broca's area as speech output region) and provide a distributed framework for future studies of neural networks. PMID:24970097

  19. Probabilistic map of critical functional regions of the human cerebral cortex: Broca's area revisited.

    PubMed

    Tate, Matthew C; Herbet, Guillaume; Moritz-Gasser, Sylvie; Tate, Joseph E; Duffau, Hugues

    2014-10-01

    The organization of basic functions of the human brain, particularly in the right hemisphere, remains poorly understood. Recent advances in functional neuroimaging have improved our understanding of cortical organization but do not allow for direct interrogation or determination of essential (versus participatory) cortical regions. Direct cortical stimulation represents a unique opportunity to provide novel insights into the functional distribution of critical epicentres. Direct cortical stimulation (bipolar, 60 Hz, 1-ms pulse) was performed in 165 consecutive patients undergoing awake mapping for resection of low-grade gliomas. Tasks included motor, sensory, counting, and picture naming. Stimulation sites eliciting positive (sensory/motor) or negative (speech arrest, dysarthria, anomia, phonological and semantic paraphasias) findings were recorded and mapped onto a standard Montreal Neurological Institute brain atlas. Montreal Neurological Institute-space functional data were subjected to cluster analysis algorithms (K-means, partition around medioids, hierarchical Ward) to elucidate crucial network epicentres. Sensorimotor function was observed in the pre/post-central gyri as expected. Articulation epicentres were also found within the pre/post-central gyri. However, speech arrest localized to ventral premotor cortex, not the classical Broca's area. Anomia/paraphasia data demonstrated foci not only within classical Wernicke's area but also within the middle and inferior frontal gyri. We report the first bilateral probabilistic map for crucial cortical epicentres of human brain functions in the right and left hemispheres, including sensory, motor, and language (speech, articulation, phonology and semantics). These data challenge classical theories of brain organization (e.g. Broca's area as speech output region) and provide a distributed framework for future studies of neural networks.

  20. Diffuse reflectance infrared spectroscopic identification of dispersant/particle bonding mechanisms in functional inks.

    PubMed

    Deiner, L Jay; Farjami, Elaheh

    2015-05-08

    In additive manufacturing, or 3D printing, material is deposited drop by drop, to create micron to macroscale layers. A typical inkjet ink is a colloidal dispersion containing approximately ten components including solvent, the nano to micron scale particles which will comprise the printed layer, polymeric dispersants to stabilize the particles, and polymers to tune layer strength, surface tension and viscosity. To rationally and efficiently formulate such an ink, it is crucial to know how the components interact. Specifically, which polymers bond to the particle surfaces and how are they attached? Answering this question requires an experimental procedure that discriminates between polymer adsorbed on the particles and free polymer. Further, the method must provide details about how the functional groups of the polymer interact with the particle. In this protocol, we show how to employ centrifugation to separate particles with adsorbed polymer from the rest of the ink, prepare the separated samples for spectroscopic measurement, and use Diffuse Reflectance Fourier Transform Infrared Spectroscopy (DRIFTS) for accurate determination of dispersant/particle bonding mechanisms. A significant advantage of this methodology is that it provides high level mechanistic detail using only simple, commonly available laboratory equipment. This makes crucial data available to almost any formulation laboratory. The method is most useful for inks composed of metal, ceramic, and metal oxide particles in the range of 100 nm or greater. Because of the density and particle size of these inks, they are readily separable with centrifugation. Further, the spectroscopic signatures of such particles are easy to distinguish from absorbed polymer. The primary limitation of this technique is that the spectroscopy is performed ex-situ on the separated and dried particles as opposed to the particles in dispersion. However, results from attenuated total reflectance spectra of the wet separated

  1. Diffuse reflectance infrared spectroscopic identification of dispersant/particle bonding mechanisms in functional inks.

    PubMed

    Deiner, L Jay; Farjami, Elaheh

    2015-01-01

    In additive manufacturing, or 3D printing, material is deposited drop by drop, to create micron to macroscale layers. A typical inkjet ink is a colloidal dispersion containing approximately ten components including solvent, the nano to micron scale particles which will comprise the printed layer, polymeric dispersants to stabilize the particles, and polymers to tune layer strength, surface tension and viscosity. To rationally and efficiently formulate such an ink, it is crucial to know how the components interact. Specifically, which polymers bond to the particle surfaces and how are they attached? Answering this question requires an experimental procedure that discriminates between polymer adsorbed on the particles and free polymer. Further, the method must provide details about how the functional groups of the polymer interact with the particle. In this protocol, we show how to employ centrifugation to separate particles with adsorbed polymer from the rest of the ink, prepare the separated samples for spectroscopic measurement, and use Diffuse Reflectance Fourier Transform Infrared Spectroscopy (DRIFTS) for accurate determination of dispersant/particle bonding mechanisms. A significant advantage of this methodology is that it provides high level mechanistic detail using only simple, commonly available laboratory equipment. This makes crucial data available to almost any formulation laboratory. The method is most useful for inks composed of metal, ceramic, and metal oxide particles in the range of 100 nm or greater. Because of the density and particle size of these inks, they are readily separable with centrifugation. Further, the spectroscopic signatures of such particles are easy to distinguish from absorbed polymer. The primary limitation of this technique is that the spectroscopy is performed ex-situ on the separated and dried particles as opposed to the particles in dispersion. However, results from attenuated total reflectance spectra of the wet separated

  2. Numerical solution of fractional sub-diffusion and time-fractional diffusion-wave equations via fractional-order Legendre functions

    NASA Astrophysics Data System (ADS)

    Hooshmandasl, M. R.; Heydari, M. H.; Cattani, C.

    2016-08-01

    Fractional calculus has been used to model physical and engineering processes that are best described by fractional differential equations. Therefore designing efficient and reliable techniques for the solution of such equations is an important task. In this paper, we propose an efficient and accurate Galerkin method based on the fractional-order Legendre functions (FLFs) for solving the fractional sub-diffusion equation (FSDE) and the time-fractional diffusion-wave equation (FDWE). The time-fractional derivatives for FSDE are described in the Riemann-Liouville sense, while for FDWE are described in the Caputo sense. To this end, we first derive a new operational matrix of fractional integration (OMFI) in the Riemann-Liouville sense for FLFs. Next, we transform the original FSDE into an equivalent problem with fractional derivatives in the Caputo sense. Then the FLFs and their OMFI together with the Galerkin method are used to transform the problems under consideration into the corresponding linear systems of algebraic equations, which can be simply solved to achieve the numerical solutions of the problems. The proposed method is very convenient for solving such kind of problems, since the initial and boundary conditions are taken into account automatically. Furthermore, the efficiency of the proposed method is shown for some concrete examples. The results reveal that the proposed method is very accurate and efficient.

  3. Detection of prostate cancer by integration of line-scan diffusion, T2-mapping and T2-weighted magnetic resonance imaging; a multichannel statistical classifier.

    PubMed

    Chan, Ian; Wells, William; Mulkern, Robert V; Haker, Steven; Zhang, Jianqing; Zou, Kelly H; Maier, Stephan E; Tempany, Clare M C

    2003-09-01

    A multichannel statistical classifier for detecting prostate cancer was developed and validated by combining information from three different magnetic resonance (MR) methodologies: T2-weighted, T2-mapping, and line scan diffusion imaging (LSDI). From these MR sequences, four different sets of image intensities were obtained: T2-weighted (T2W) from T2-weighted imaging, Apparent Diffusion Coefficient (ADC) from LSDI, and proton density (PD) and T2 (T2 Map) from T2-mapping imaging. Manually segmented tumor labels from a radiologist, which were validated by biopsy results, served as tumor "ground truth." Textural features were extracted from the images using co-occurrence matrix (CM) and discrete cosine transform (DCT). Anatomical location of voxels was described by a cylindrical coordinate system. A statistical jack-knife approach was used to evaluate our classifiers. Single-channel maximum likelihood (ML) classifiers were based on 1 of the 4 basic image intensities. Our multichannel classifiers: support vector machine (SVM) and Fisher linear discriminant (FLD), utilized five different sets of derived features. Each classifier generated a summary statistical map that indicated tumor likelihood in the peripheral zone (PZ) of the prostate gland. To assess classifier accuracy, the average areas under the receiver operator characteristic (ROC) curves over all subjects were compared. Our best FLD classifier achieved an average ROC area of 0.839(+/-0.064), and our best SVM classifier achieved an average ROC area of 0.761(+/-0.043). The T2W ML classifier, our best single-channel classifier, only achieved an average ROC area of 0.599(+/-0.146). Compared to the best single-channel ML classifier, our best multichannel FLD and SVM classifiers have statistically superior ROC performance (P=0.0003 and 0.0017, respectively) from pairwise two-sided t-test. By integrating the information from multiple images and capturing the textural and anatomical features in tumor areas, summary

  4. Mapping plant functional types over broad mountainous regions: A phenological hierarchical time-space classification

    NASA Astrophysics Data System (ADS)

    Cai, Danlu; Guan, Yanning; Guo, Shan; Zhang, Chunyan; Fraedrich, Klaus

    2013-04-01

    Research on global climate change requires plant functional type (PFT) products. Although several PFT mapping procedures for remote sensing imagery are being used (MODIS PFT), none of them appears to be specifically designed to map and evaluate PFTs over broad mountainous areas which are highly relevant regions to identify and analyse the response of natural ecosystems. The limitations of existing methods to generate PFT (uncertainty of accuracy and limited expandability to broad geographic areas) suggest the development of a new method to determine PFT distributions, which is based on a hierarchical strategy by integrating time varying biomass and phenological information with topography: (i) Temporal variability: Fourier transformation of MODIS Normalized Difference Vegetation Index (NDVI) time series (2006 to 2010) to the frequency domain (five year of five half month scenes). (ii) Spatial partitioning: The harmonics are used to partition the study area into four mapping zones using phenological information based on the harmonics and digital elevation data. (iii) Classification: A similarity measure (Euclidean distance) is employed to obtain the phenological hierarchical time-space plant type classification. Applicability and effectiveness is tested for the eastern Tibetan Plateau. Comparing with the MODIS PFT product and evaluation with the Vegetation Map of the People's Republic of China (1:1000000) reveal a gain on overall accuracy (13081 random samples) by about 7% from 64.5% compared to 57.7% by the MODIS PFT product.

  5. dose-response functions and mapping of risk for materials in urban polluted atmosphere

    NASA Astrophysics Data System (ADS)

    Laurans, E.; Ausset, P.; Chabas, A.; Lefevre, R.-A.

    2003-04-01

    The French field test-site of the United-Nations International Co-operative Programme "Influence of Atmospheric Pollution on Materials, including Historic and Cultural Monuments" (ICP-Materials) located at the top of the Saint-Eustache Church in a pedestrian area in the center of Paris allows to expose various materials (stone, glass, metals, polymers...) and to measure simultaneously the atmospheric parameters (gases, particles, rain, temperature, relative humidity, time of wetness...). The dose-response functions are calculated from the doses recorded on the 30 test-sites of the ICP-Materials network and from the responses analyzed on exposed samples. The critical or acceptable levels and loads are then determined and illustrated by means of mapping. The map of risk for Portland limestone, on the entire French territory and only on Ile-de-France are then given. In conclusion, an improvement of the method is proposed for stone: the mapping of the risk has no meaning except for the area of utilization. Nevertheless, the map of risk for entire Europe concerning materials universally used, like Carrara marble, Portland cement based mortars and Si-Ca-Na modern glass are of better utility.

  6. Fast IR laser mapping ellipsometry for the study of functional organic thin films.

    PubMed

    Furchner, Andreas; Sun, Guoguang; Ketelsen, Helge; Rappich, Jörg; Hinrichs, Karsten

    2015-03-21

    Fast infrared mapping with sub-millimeter lateral resolution as well as time-resolved infrared studies of kinetic processes of functional organic thin films require a new generation of infrared ellipsometers. We present a novel laboratory-based infrared (IR) laser mapping ellipsometer, in which a laser is coupled to a variable-angle rotating analyzer ellipsometer. Compared to conventional Fourier-transform infrared (FT-IR) ellipsometers, the IR laser ellipsometer provides ten- to hundredfold shorter measurement times down to 80 ms per measured spot, as well as about tenfold increased lateral resolution of 120 μm, thus enabling mapping of small sample areas with thin-film sensitivity. The ellipsometer, equipped with a HeNe laser emitting at about 2949 cm(-1), was applied for the optical characterization of inhomogeneous poly(3-hexylthiophene) [P3HT] and poly(N-isopropylacrylamide) [PNIPAAm] organic thin films used for opto-electronics and bioapplications. With the constant development of tunable IR laser sources, laser-based infrared ellipsometry is a promising technique for fast in-depth mapping characterization of thin films and blends.

  7. Dynamic topographic mapping of the human bladder during voiding using functional near-infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Macnab, Andrew; Stothers, Lynn; Shadgan, Babak

    2009-03-01

    Functional near-infrared spectroscopy (fNIRS) with multichannel instruments and grids of source-detector pairs can map regional change in oxygenation/hemodynamics. Developed for cortical brain mapping, fNIRS technology has relevance in other organs where pathology affects the microcirculation. We describe fNIRS of the human bladder for evaluation of hemodynamic change during voiding. A 5×5-cm grid with two source-detector pairs is placed on the abdomen suprapubically in an asymptomatic male. In four separate trials, after natural bladder filling NIRS-derived changes in oxyhemoglobin (O2Hb), deoxyhemoglobin (HHb), and total hemoglobin (tHb) concentration are recorded during voiding (measured via uroflow), using four channels of a four wavelength continuous wave instrument. Graphic and video images (topographic mapping software) are generated. Changes in tHb occur following permission to void that predominantly reflected variation in O2Hb; tHb peaks at maximum urine flow then falls to a nadir lasting to uroflow end. Change in fNIRS video color intensity correlates with graphic change in chromophore concentration. Color variations across the mapped area suggest regional hemodynamic variation. fNIRS bladder studies generate reproducible chromophore data consistent with single channel studies, but the dynamic color video and larger tissue area monitored potentially offer new methodology for investigating regional variations in bladder oxygenation and hemodynamics.

  8. Fast IR laser mapping ellipsometry for the study of functional organic thin films.

    PubMed

    Furchner, Andreas; Sun, Guoguang; Ketelsen, Helge; Rappich, Jörg; Hinrichs, Karsten

    2015-03-21

    Fast infrared mapping with sub-millimeter lateral resolution as well as time-resolved infrared studies of kinetic processes of functional organic thin films require a new generation of infrared ellipsometers. We present a novel laboratory-based infrared (IR) laser mapping ellipsometer, in which a laser is coupled to a variable-angle rotating analyzer ellipsometer. Compared to conventional Fourier-transform infrared (FT-IR) ellipsometers, the IR laser ellipsometer provides ten- to hundredfold shorter measurement times down to 80 ms per measured spot, as well as about tenfold increased lateral resolution of 120 μm, thus enabling mapping of small sample areas with thin-film sensitivity. The ellipsometer, equipped with a HeNe laser emitting at about 2949 cm(-1), was applied for the optical characterization of inhomogeneous poly(3-hexylthiophene) [P3HT] and poly(N-isopropylacrylamide) [PNIPAAm] organic thin films used for opto-electronics and bioapplications. With the constant development of tunable IR laser sources, laser-based infrared ellipsometry is a promising technique for fast in-depth mapping characterization of thin films and blends. PMID:25668189

  9. Functional Multi-Locus QTL Mapping of Temporal Trends in Scots Pine Wood Traits

    PubMed Central

    Li, Zitong; Hallingbäck, Henrik R.; Abrahamsson, Sara; Fries, Anders; Gull, Bengt Andersson; Sillanpää, Mikko J.; García-Gil, M. Rosario

    2014-01-01

    Quantitative trait loci (QTL) mapping of wood properties in conifer species has focused on single time point measurements or on trait means based on heterogeneous wood samples (e.g., increment cores), thus ignoring systematic within-tree trends. In this study, functional QTL mapping was performed for a set of important wood properties in increment cores from a 17-yr-old Scots pine (Pinus sylvestris L.) full-sib family with the aim of detecting wood trait QTL for general intercepts (means) and for linear slopes by increasing cambial age. Two multi-locus functional QTL analysis approaches were proposed and their performances were compared on trait datasets comprising 2 to 9 time points, 91 to 455 individual tree measurements and genotype datasets of amplified length polymorphisms (AFLP), and single nucleotide polymorphism (SNP) markers. The first method was a multilevel LASSO analysis whereby trend parameter estimation and QTL mapping were conducted consecutively; the second method was our Bayesian linear mixed model whereby trends and underlying genetic effects were estimated simultaneously. We also compared several different hypothesis testing methods under either the LASSO or the Bayesian framework to perform QTL inference. In total, five and four significant QTL were observed for the intercepts and slopes, respectively, across wood traits such as earlywood percentage, wood density, radial fiberwidth, and spiral grain angle. Four of these QTL were represented by candidate gene SNPs, thus providing promising targets for future research in QTL mapping and molecular function. Bayesian and LASSO methods both detected similar sets of QTL given datasets that comprised large numbers of individuals. PMID:25305041

  10. Activity-dependent regulation of the K/Cl transporter KCC2 membrane diffusion, clustering, and function in hippocampal neurons.

    PubMed

    Chamma, Ingrid; Heubl, Martin; Chevy, Quentin; Renner, Marianne; Moutkine, Imane; Eugène, Emmanuel; Poncer, Jean Christophe; Lévi, Sabine

    2013-09-25

    The neuronal K/Cl transporter KCC2 exports chloride ions and thereby influences the efficacy and polarity of GABA signaling in the brain. KCC2 is also critical for dendritic spine morphogenesis and the maintenance of glutamatergic transmission in cortical neurons. Because KCC2 plays a pivotal role in the function of central synapses, it is of particular importance to understand the cellular and molecular mechanisms underlying its regulation. Here, we studied the impact of membrane diffusion and clustering on KCC2 function. KCC2 forms clusters in the vicinity of both excitatory and inhibitory synapses. Using quantum-dot-based single-particle tracking on rat primary hippocampal neurons, we show that KCC2 is slowed down and confined at excitatory and inhibitory synapses compared with extrasynaptic regions. However, KCC2 escapes inhibitory synapses faster than excitatory synapses, reflecting stronger molecular constraints at the latter. Interfering with KCC2-actin interactions or inhibiting F-actin polymerization releases diffusion constraints on KCC2 at excitatory but not inhibitory synapses. Thus, F-actin constrains KCC2 diffusion at excitatory synapses, whereas KCC2 is confined at inhibitory synapses by a distinct mechanism. Finally, increased neuronal activity rapidly increases the diffusion coefficient and decreases the dwell time of KCC2 at excitatory synapses. This effect involves NMDAR activation, Ca(2+) influx, KCC2 S940 dephosphorylation and calpain protease cleavage of KCC2 and is accompanied by reduced KCC2 clustering and ion transport function. Thus, activity-dependent regulation of KCC2 lateral diffusion and clustering allows for a rapid regulation of chloride homeostasis in neurons.

  11. Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways

    PubMed Central

    Vlasblom, James; Gagarinova, Alla; Phanse, Sadhna; Graham, Chris; Yousif, Fouad; Ding, Huiming; Xiong, Xuejian; Nazarians-Armavil, Anaies; Alamgir, Md; Ali, Mehrab; Pogoutse, Oxana; Pe'er, Asaf; Arnold, Roland; Michaut, Magali; Parkinson, John; Golshani, Ashkan; Whitfield, Chris; Wodak, Shoshana J.; Moreno-Hagelsieb, Gabriel; Greenblatt, Jack F.; Emili, Andrew

    2011-01-01

    As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis genes and pathways have been identified and studied in isolation, how these intersect functionally to ensure envelope integrity during adaptive responses to environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens to generate quantitative functional association maps encompassing virtually the entire cell envelope biosynthetic machinery of Escherichia coli under both auxotrophic (rich medium) and prototrophic (minimal medium) culture conditions. The differential patterns of genetic interactions detected among >235,000 digenic mutant combinations tested reveal unexpected condition-specific functional crosstalk and genetic backup mechanisms that ensure stress-resistant envelope assembly and maintenance. These networks also provide insights into the global systems connectivity and dynamic functional reorganization of a universal bacterial structure that is both broadly conserved among eubacteria (including pathogens) and an important target. PMID:22125496

  12. Application of the lamp mapping technique for overlap function for Raman lidar systems.

    PubMed

    Walker, Monique; Venable, Demetrius; Whiteman, David N; Sakai, Tetsu

    2016-04-01

    Traditionally, the lidar water vapor mixing ratio (WVMR) is corrected for overlap using data from another instrument, such as a radiosonde. Here we introduce a new experimental method to determine the overlap function using the lamp mapping technique (LMT), which relies on the lidar optics and detection system. The LMT discussed here involves a standard halogen lamp being scanned over the aperture of a Raman lidar telescope in synchronization with the lidar detection system [Appl. Opt.50, 4622 (2011)APOPAI0003-693510.1364/AO.50.004622, Appl. Opt.53, 8538 (2014)APOPAI0003-693510.1364/AO.53.008535]. In this paper, we show results for a LMT-determined overlap function for individual channels, as well as a WVMR overlap function. We found that the LMT-determined WVMR overlap functions deviate within 5% of the traditional radiosonde-determined overlap. PMID:27139656

  13. Application of the lamp mapping technique for overlap function for Raman lidar systems.

    PubMed

    Walker, Monique; Venable, Demetrius; Whiteman, David N; Sakai, Tetsu

    2016-04-01

    Traditionally, the lidar water vapor mixing ratio (WVMR) is corrected for overlap using data from another instrument, such as a radiosonde. Here we introduce a new experimental method to determine the overlap function using the lamp mapping technique (LMT), which relies on the lidar optics and detection system. The LMT discussed here involves a standard halogen lamp being scanned over the aperture of a Raman lidar telescope in synchronization with the lidar detection system [Appl. Opt.50, 4622 (2011)APOPAI0003-693510.1364/AO.50.004622, Appl. Opt.53, 8538 (2014)APOPAI0003-693510.1364/AO.53.008535]. In this paper, we show results for a LMT-determined overlap function for individual channels, as well as a WVMR overlap function. We found that the LMT-determined WVMR overlap functions deviate within 5% of the traditional radiosonde-determined overlap.

  14. Vacuum ultraviolet photolysis of hydrogenated amorphous carbons. III. Diffusion of photo-produced H2 as a function of temperature

    NASA Astrophysics Data System (ADS)

    Martín-Doménech, R.; Dartois, E.; Muñoz Caro, G. M.

    2016-06-01

    Context. Hydrogenated amorphous carbon (a-C:H) has been proposed as one of the carbonaceous solids detected in the interstellar medium. Energetic processing of the a-C:H particles leads to the dissociation of the C-H bonds and the formation of hydrogen molecules and small hydrocarbons. Photo-produced H2 molecules in the bulk of the dust particles can diffuse out to the gas phase and contribute to the total H2 abundance. Aims: We have simulated this process in the laboratory with plasma-produced a-C:H and a-C:D analogs under astrophysically relevant conditions to investigate the dependence of the diffusion as a function of temperature. Methods: Experimental simulations were performed in a high-vacuum chamber, with complementary experiments carried out in an ultra-high-vacuum chamber. Plasma-produced a-C:H and a-C:D analogs were UV-irradiated using a microwave-discharged hydrogen flow lamp. Molecules diffusing to the gas-phase were detected by a quadrupole mass spectrometer, providing a measurement of the outgoing H2 or D2 flux. By comparing the experimental measurements with the expected flux from a one-dimensional diffusion model, a diffusion coefficient D could be derived for experiments carried out at different temperatures. Results: Dependence on the diffusion coefficient D with the temperature followed an Arrhenius-type equation. The activation energy for the diffusion process was estimated (ED(H2) = 1660 ± 110 K, ED(D2) = 2090 ± 90 K), as well as the pre-exponential factor (D0(H2) = 0.0007 cm2 s-1, D0(D2) = 0.0045 cm2 s-1). Conclusions: The strong decrease of the diffusion coefficient at low dust particle temperatures exponentially increases the diffusion times in astrophysical environments. Therefore, transient dust heating by cosmic rays needs to be invoked for the release of the photo-produced H2 molecules in cold photon-dominated regions, where destruction of the aliphatic component in hydrogenated amorphous carbons most probably takes place.

  15. A differential equation model for functional mapping of a virus-cell dynamic system.

    PubMed

    Luo, Jiangtao; Hager, William W; Wu, Rongling

    2010-07-01

    The dynamic pattern of viral load in a patient's body critically depends on the host's genes. For this reason, the identification of those genes responsible for virus dynamics, although difficult, is of fundamental importance to design an optimal drug therapy based on patients' genetic makeup. Here, we present a differential equation (DE) model for characterizing specific genes or quantitative trait loci (QTLs) that affect viral load trajectories within the framework of a dynamic system. The model is formulated with the principle of functional mapping, originally derived to map dynamic QTLs, and implemented with a Markov chain process. The DE-integrated model enhances the mathematical robustness of functional mapping, its quantitative prediction about the temporal pattern of genetic expression, and therefore its practical utilization and effectiveness for gene discovery in clinical settings. The model was used to analyze simulated data for viral dynamics, aimed to investigate its statistical properties and validate its usefulness. With an increasing availability of genetic polymorphic data, the model will have great implications for probing the molecular genetic mechanism of virus dynamics and disease progression. PMID:19685244

  16. Functional genomics platform for pooled screening and mammalian genetic interaction maps

    PubMed Central

    Kampmann, Martin; Bassik, Michael C.; Weissman, Jonathan S.

    2014-01-01

    Systematic genetic interaction maps in microorganisms are powerful tools for identifying functional relationships between genes and defining the function of uncharacterized genes. We have recently implemented this strategy in mammalian cells as a two-stage approach. First, genes of interest are robustly identified in a pooled genome-wide screen using complex shRNA libraries. Second, phenotypes for all pairwise combinations of hit genes are measured in a double-shRNA screen and used to construct a genetic interaction map. Our protocol allows for rapid pooled screening under various conditions without a requirement for robotics, in contrast to arrayed approaches. Each stage of the protocol can be implemented in ~2 weeks, with additional time for analysis and generation of reagents. We discuss considerations for screen design, and present complete experimental procedures as well as a full computational analysis suite for identification of hits in pooled screens and generation of genetic interaction maps. While the protocols outlined here were developed for our original shRNA-based approach, they can be applied more generally, including to CRISPR-based approaches. PMID:24992097

  17. Finding zeros of nonlinear functions using the hybrid parallel cell mapping method

    NASA Astrophysics Data System (ADS)

    Xiong, Fu-Rui; Schütze, Oliver; Ding, Qian; Sun, Jian-Qiao

    2016-05-01

    Analysis of nonlinear dynamical systems including finding equilibrium states and stability boundaries often leads to a problem of finding zeros of vector functions. However, finding all the zeros of a set of vector functions in the domain of interest is quite a challenging task. This paper proposes a zero finding algorithm that combines the cell mapping methods and the subdivision techniques. Both the simple cell mapping (SCM) and generalized cell mapping (GCM) methods are used to identify a covering set of zeros. The subdivision technique is applied to enhance the solution resolution. The parallel implementation of the proposed method is discussed extensively. Several examples are presented to demonstrate the application and effectiveness of the proposed method. We then extend the study of finding zeros to the problem of finding stability boundaries of potential fields. Examples of two and three dimensional potential fields are studied. In addition to the effectiveness in finding the stability boundaries, the proposed method can handle several millions of cells in just a few seconds with the help of parallel computing in graphics processing units (GPUs).

  18. Loss of MAP function leads to hippocampal synapse loss and deficits in the Morris Water Maze with aging.

    PubMed

    Ma, Qiu-Lan; Zuo, Xiaohong; Yang, Fusheng; Ubeda, Oliver J; Gant, Dana J; Alaverdyan, Mher; Kiosea, Nicolae C; Nazari, Sean; Chen, Ping Ping; Nothias, Fatiha; Chan, Piu; Teng, Edmond; Frautschy, Sally A; Cole, Greg M

    2014-05-21

    Hyperphosphorylation and accumulation of tau aggregates are prominent features in tauopathies, including Alzheimer's disease, but the impact of loss of tau function on synaptic and cognitive deficits remains poorly understood. We report that old (19-20 months; OKO) but not middle-aged (8-9 months; MKO) tau knock-out mice develop Morris Water Maze (MWM) deficits and loss of hippocampal acetylated α-tubulin and excitatory synaptic proteins. Mild motor deficits and reduction in tyrosine hydroxylase (TH) in the substantia nigra were present by middle age, but did not affect MWM performance, whereas OKO mice showed MWM deficits paralleling hippocampal deficits. Deletion of tau, a microtubule-associated protein (MAP), resulted in increased levels of MAP1A, MAP1B, and MAP2 in MKO, followed by loss of MAP2 and MAP1B in OKO. Hippocampal synaptic deficits in OKO mice were partially corrected with dietary supplementation with docosahexaenoic acid (DHA) and both MWM and synaptic deficits were fully corrected by combining DHA with α-lipoic acid (ALA), which also prevented TH loss. DHA or DHA/ALA restored phosphorylated and total GSK3β and attenuated hyperactivation of the tau C-Jun N-terminal kinases (JNKs) while increasing MAP1B, dephosphorylated (active) MAP2, and acetylated α-tubulin, suggesting improved microtubule stability and maintenance of active compensatory MAPs. Our results implicate the loss of MAP function in age-associated hippocampal deficits and identify a safe dietary intervention, rescuing both MAP function and TH in OKO mice. Therefore, in addition to microtubule-stabilizing therapeutic drugs, preserving or restoring compensatory MAP function may be a useful new prevention strategy.

  19. Lateral diffusion in substrate-supported lipid monolayers as a function of ambient relative humidity.

    PubMed Central

    Baumgart, Tobias; Offenhäusser, Andreas

    2002-01-01

    We analyzed the influence of water activity on the lateral self-diffusion of supported phospholipid monolayers. Lipid monolayer membranes were supported by polysaccharide cushions (chitosan and agarose), or glass. A simple diffusion model was derived, based on activated diffusion with an activation energy, E(a), which depends on the hydration state of the lipid headgroup. A crucial assumption of the derived model is that E(a) can be calculated assuming an exponential decay of the humidity-dependent disjoining pressure in the monolayer/substrate interface with respect to the equilibrium separation distance. A plot of ln(D) against ln(p(0)/p), where D is the measured diffusion coefficient and p(0) and p are the partial water pressures at saturation and at a particular relative humidity, respectively, was observed to be linear in all cases (i.e., for differing lipids, lateral monolayer pressures, temperatures, and substrates), in accordance with the above-mentioned diffusion model. No indications for humidity-induced first-order phase transitions in the supported phospholipid monolayers were found. Many biological processes such as vesicle fusion and recognition processes involve dehydration/hydration cycles, and it can be expected that the water activity significantly affects the kinetics of these processes in a manner similar to that examined in the present work. PMID:12202374

  20. Structural and functional evaluation of the palindromic alanine-rich antimicrobial peptide Pa-MAP2.

    PubMed

    Migliolo, Ludovico; Felício, Mário R; Cardoso, Marlon H; Silva, Osmar N; Xavier, Mary-Ann E; Nolasco, Diego O; de Oliveira, Adeliana Silva; Roca-Subira, Ignasi; Vila Estape, Jordi; Teixeira, Leandro D; Freitas, Sonia M; Otero-Gonzalez, Anselmo J; Gonçalves, Sónia; Santos, Nuno C; Franco, Octavio L

    2016-07-01

    Recently, several peptides have been studied regarding the defence process against pathogenic microorganisms, which are able to act against different targets, with the purpose of developing novel bioactive compounds. The present work focuses on the structural and functional evaluation of the palindromic antimicrobial peptide Pa-MAP2, designed based on the peptide Pa-MAP from Pleuronectes americanus. For a better structural understanding, molecular modelling analyses were carried out, together with molecular dynamics and circular dichroism, in different media. Antibacterial activity against Gram-negative and positive bacteria was evaluated, as well as cytotoxicity against human erythrocytes, RAW 264.7, Vero and L6 cells. In silico docking experiments, lipid vesicle studies, and atomic force microscopy (AFM) imaging were carried out to explore the activity of the peptide. In vivo studies on infected mice were also done. The palindromic primary sequence favoured an α-helix structure that was pH dependent, only present on alkaline environment, with dynamic N- and C-terminals that are stabilized in anionic media. Pa-MAP2 only showed activity against Gram-negative bacteria, with a MIC of 3.2 μM, and without any cytotoxic effect. In silico, lipid vesicles and AFM studies confirm the preference for anionic lipids (POPG, POPS, DPPE, DPPG and LPS), with the positively charged lysine residues being essential for the initial electrostatic interaction. In vivo studies showed that Pa-MAP2 increases to 100% the survival rate of mice infected with Escherichia coli. Data here reported indicated that palindromic Pa-MAP2 could be an alternative candidate for use in therapeutics against Gram-negative bacterial infections.

  1. Structural and functional evaluation of the palindromic alanine-rich antimicrobial peptide Pa-MAP2.

    PubMed

    Migliolo, Ludovico; Felício, Mário R; Cardoso, Marlon H; Silva, Osmar N; Xavier, Mary-Ann E; Nolasco, Diego O; de Oliveira, Adeliana Silva; Roca-Subira, Ignasi; Vila Estape, Jordi; Teixeira, Leandro D; Freitas, Sonia M; Otero-Gonzalez, Anselmo J; Gonçalves, Sónia; Santos, Nuno C; Franco, Octavio L

    2016-07-01

    Recently, several peptides have been studied regarding the defence process against pathogenic microorganisms, which are able to act against different targets, with the purpose of developing novel bioactive compounds. The present work focuses on the structural and functional evaluation of the palindromic antimicrobial peptide Pa-MAP2, designed based on the peptide Pa-MAP from Pleuronectes americanus. For a better structural understanding, molecular modelling analyses were carried out, together with molecular dynamics and circular dichroism, in different media. Antibacterial activity against Gram-negative and positive bacteria was evaluated, as well as cytotoxicity against human erythrocytes, RAW 264.7, Vero and L6 cells. In silico docking experiments, lipid vesicle studies, and atomic force microscopy (AFM) imaging were carried out to explore the activity of the peptide. In vivo studies on infected mice were also done. The palindromic primary sequence favoured an α-helix structure that was pH dependent, only present on alkaline environment, with dynamic N- and C-terminals that are stabilized in anionic media. Pa-MAP2 only showed activity against Gram-negative bacteria, with a MIC of 3.2 μM, and without any cytotoxic effect. In silico, lipid vesicles and AFM studies confirm the preference for anionic lipids (POPG, POPS, DPPE, DPPG and LPS), with the positively charged lysine residues being essential for the initial electrostatic interaction. In vivo studies showed that Pa-MAP2 increases to 100% the survival rate of mice infected with Escherichia coli. Data here reported indicated that palindromic Pa-MAP2 could be an alternative candidate for use in therapeutics against Gram-negative bacterial infections. PMID:27063608

  2. MAPping the eukaryotic tree of life: structure, function, and evolution of the MAP215/Dis1 family of microtubule-associated proteins.

    PubMed

    Gard, David L; Becker, Bret E; Josh Romney, S

    2004-01-01

    The MAP215/Dis1 family of proteins is an evolutionarily ancient family of microtubule-associated proteins, with characterized members in all major kingdoms of eukaryotes, including fungi (Stu2 in S. cerevisiae, Dis1 and Alp14 in S. pombe), Dictyostelium (DdCP224), plants (Mor1 in A. thaliana and TMBP200 in N. tabaccum), and animals (Zyg9 in C. elegans, Msps in Drosophila, XMAP215 in Xenopus, and ch-TOG in humans). All MAP215/Dis1 proteins (with the exception of those in plants) localize to microtubule-organizing centers (MTOCs), including spindle pole bodies in yeast and centrosomes in animals, and all bind to microtubules in vitro and?or in vivo. Diverse roles in regulating microtubule assembly and organization have been proposed for individual family members, and a substantial body of evidence suggests that MAP215/Dis1-related proteins play critical roles in the assembly and function of the meiotic/mitotic spindles and/or cell division. An extensive search of public databases (including both EST and genome databases) identified partial sequences predicted to encode more than three dozen new members of the MAP215/Dis1 family, including putative MAP215/Dis1-related proteins in Giardia lamblia and four other protists, sixteen additional species of fungi, six plants, and twelve animals. The structure and function of MAP215/Dis1 proteins are discussed in relation to the evolution of this ancient family of microtubule-associated proteins.

  3. New Angle on the Parton Distribution Functions: Self-Organizing Maps

    SciTech Connect

    Honkanen, H.; Liuti, S.

    2009-08-04

    Neural network (NN) algorithms have been recently applied to construct Parton Distribution Function (PDF) parametrizations, providing an alternative to standard global fitting procedures. Here we explore a novel technique using Self-Organizing Maps (SOMs). SOMs are a class of clustering algorithms based on competitive learning among spatially-ordered neurons. We train our SOMs with stochastically generated PDF samples. On every optimization iteration the PDFs are clustered on the SOM according to a user-defined feature and the most promising candidates are used as a seed for the subsequent iteration using the topology of the map to guide the PDF generating process. Our goal is a fitting procedure that, at variance with the standard neural network approaches, will allow for an increased control of the systematic bias by enabling user interaction in the various stages of the process.

  4. The paradigm compiler: Mapping a functional language for the connection machine

    NASA Technical Reports Server (NTRS)

    Dennis, Jack B.

    1989-01-01

    The Paradigm Compiler implements a new approach to compiling programs written in high level languages for execution on highly parallel computers. The general approach is to identify the principal data structures constructed by the program and to map these structures onto the processing elements of the target machine. The mapping is chosen to maximize performance as determined through compile time global analysis of the source program. The source language is Sisal, a functional language designed for scientific computations, and the target language is Paris, the published low level interface to the Connection Machine. The data structures considered are multidimensional arrays whose dimensions are known at compile time. Computations that build such arrays usually offer opportunities for highly parallel execution; they are data parallel. The Connection Machine is an attractive target for these computations, and the parallel for construct of the Sisal language is a convenient high level notation for data parallel algorithms. The principles and organization of the Paradigm Compiler are discussed.

  5. Physical mapping of a functional cluster of epidermal differentiation genes on chromosome 1q21

    SciTech Connect

    Volz, A.; Ziegler, A.; Mischke, D. ); Korge, B.P.; Compton, J.G.; Steinert, P.M. )

    1993-10-01

    Genes of three protein families, which are in part specifically expressed in the course of terminal differentiation of human epidermis, have previously been mapped to chromosome 1q21. Here, the authors show that these genes are physically linked within 2.05 Mb of DNA. The order is calpactin I light chain, trichohyalin, profilaggrin, involucrin/small proline-rich protein, loricrin, and calcyclin. The colocalization in the 1q21 region together with their functional interdependence during epidermal differentiation raises the question whether these genes share regulatory elements which control their transcriptional activities. As several of them are potential candidate genes for dyskeratotic skin diseases, this physical map should be of great value for genetic linkage analyses. 55 refs., 3 figs., 1 tab.

  6. New Angle on the Parton Distribution Functions: Self-Organizing Maps

    NASA Astrophysics Data System (ADS)

    Honkanen, H.; Liuti, S.

    2009-08-01

    Neural network (NN) algorithms have been recently applied to construct Parton Distribution Function (PDF) parametrizations, providing an alternative to standard global fitting procedures. Here we explore a novel technique using Self-Organizing Maps (SOMs). SOMs are a class of clustering algorithms based on competitive learning among spatially-ordered neurons. We train our SOMs with stochastically generated PDF samples. On every optimization iteration the PDFs are clustered on the SOM according to a user-defined feature and the most promising candidates are used as a seed for the subsequent iteration using the topology of the map to guide the PDF generating process. Our goal is a fitting procedure that, at variance with the standard neural network approaches, will allow for an increased control of the systematic bias by enabling user interaction in the various stages of the process.

  7. Mapping of healthy oral mucosal tissue using diffuse reflectance spectroscopy: ratiometric-based total hemoglobin comparative study.

    PubMed

    Hafez, Razan; Hamadah, Omar; Bachir, Wesam

    2015-11-01

    The objective of this study is to clinically evaluate the diffuse reflectance spectroscopy (DRS) ratiometric method for differentiation of normal oral mucosal tissues with different histological natures and vascularizations in the oral cavity. Twenty-one healthy patients aged 20-44 years were diagnosed as healthy and probed with a portable DRS system. Diffuse reflectance spectra were recorded in vivo in the range (450-650 nm). In this study, the following three oral mucosal tissues were considered: masticatory mucosa, lining mucosa, and specialized mucosa. Spectral features based on spectral intensity ratios were determined at five specific wavelengths (512, 540, 558, 575, and 620 nm). Total hemoglobin based on spectral ratios for the three anatomical regions have also been evaluated. The three studied groups representing different anatomical regions in the oral cavity were compared using analysis of variance and post hoc least significant difference tests. Statistical analysis showed a significant difference in the mean of diffuse spectral ratios between the groups (P < 0.05). Post hoc test detected significant difference between masticatory mucosa group and lining mucosa group (P < 0.05) and between masticatory mucosa group and specialized mucosa group (P = 0.000, at ratio 558/620 and P = 0.000, at ratio 575/620). Significant difference was also found between the lining mucosa group and specialized mucosa group (P = 0.000, at ratio 512/558 and P = 0.000, at ratio 512/575). It has also been shown that spectral ratios at wavelengths 558, 575, and 620 nm reveal the greatest difference among the main oral sites in terms of total hemoglobin content. Diffuse reflectance spectroscopy might be used for creating a DRS databank of normal oral mucosal tissue with specific spectral ratios featuring the total hemoglobin concentrations. That would further enhance the discrimination of oral tissue for examining the histological nature of oral mucosa

  8. Mapping of healthy oral mucosal tissue using diffuse reflectance spectroscopy: ratiometric-based total hemoglobin comparative study.

    PubMed

    Hafez, Razan; Hamadah, Omar; Bachir, Wesam

    2015-11-01

    The objective of this study is to clinically evaluate the diffuse reflectance spectroscopy (DRS) ratiometric method for differentiation of normal oral mucosal tissues with different histological natures and vascularizations in the oral cavity. Twenty-one healthy patients aged 20-44 years were diagnosed as healthy and probed with a portable DRS system. Diffuse reflectance spectra were recorded in vivo in the range (450-650 nm). In this study, the following three oral mucosal tissues were considered: masticatory mucosa, lining mucosa, and specialized mucosa. Spectral features based on spectral intensity ratios were determined at five specific wavelengths (512, 540, 558, 575, and 620 nm). Total hemoglobin based on spectral ratios for the three anatomical regions have also been evaluated. The three studied groups representing different anatomical regions in the oral cavity were compared using analysis of variance and post hoc least significant difference tests. Statistical analysis showed a significant difference in the mean of diffuse spectral ratios between the groups (P < 0.05). Post hoc test detected significant difference between masticatory mucosa group and lining mucosa group (P < 0.05) and between masticatory mucosa group and specialized mucosa group (P = 0.000, at ratio 558/620 and P = 0.000, at ratio 575/620). Significant difference was also found between the lining mucosa group and specialized mucosa group (P = 0.000, at ratio 512/558 and P = 0.000, at ratio 512/575). It has also been shown that spectral ratios at wavelengths 558, 575, and 620 nm reveal the greatest difference among the main oral sites in terms of total hemoglobin content. Diffuse reflectance spectroscopy might be used for creating a DRS databank of normal oral mucosal tissue with specific spectral ratios featuring the total hemoglobin concentrations. That would further enhance the discrimination of oral tissue for examining the histological nature of oral mucosa

  9. Vacancy diffusion in colloidal crystals as determined by dynamical density-functional theory and the phase-field-crystal model.

    PubMed

    van Teeffelen, Sven; Achim, Cristian Vasile; Löwen, Hartmut

    2013-02-01

    A two-dimensional crystal of repulsive dipolar particles is studied in the vicinity of its melting transition by using Brownian dynamics computer simulation, dynamical density-functional theory, and phase-field-crystal modeling. A vacancy is created by taking out a particle from an equilibrated crystal, and the relaxation dynamics of the vacancy is followed by monitoring the time-dependent one-particle density. We find that the vacancy is quickly filled up by diffusive hopping of neighboring particles towards the vacancy center. We examine the temperature dependence of the diffusion constant and find that it decreases with decreasing temperature in the simulations. This trend is reproduced by the dynamical density-functional theory. Conversely, the phase-field-crystal calculations predict the opposite trend. Therefore, the phase-field model needs a temperature-dependent expression for the mobility to predict trends correctly.

  10. Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants.

    PubMed

    Du, Mengmeng; Jiao, Shuo; Bien, Stephanie A; Gala, Manish; Abecasis, Goncalo; Bezieau, Stephane; Brenner, Hermann; Butterbach, Katja; Caan, Bette J; Carlson, Christopher S; Casey, Graham; Chang-Claude, Jenny; Conti, David V; Curtis, Keith R; Duggan, David; Gallinger, Steven; Haile, Robert W; Harrison, Tabitha A; Hayes, Richard B; Hoffmeister, Michael; Hopper, John L; Hudson, Thomas J; Jenkins, Mark A; Küry, Sébastien; Le Marchand, Loic; Leal, Suzanne M; Newcomb, Polly A; Nickerson, Deborah A; Potter, John D; Schoen, Robert E; Schumacher, Fredrick R; Seminara, Daniela; Slattery, Martha L; Hsu, Li; Chan, Andrew T; White, Emily; Berndt, Sonja I; Peters, Ulrike

    2016-01-01

    Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs). We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33). We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s).

  11. Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants.

    PubMed

    Du, Mengmeng; Jiao, Shuo; Bien, Stephanie A; Gala, Manish; Abecasis, Goncalo; Bezieau, Stephane; Brenner, Hermann; Butterbach, Katja; Caan, Bette J; Carlson, Christopher S; Casey, Graham; Chang-Claude, Jenny; Conti, David V; Curtis, Keith R; Duggan, David; Gallinger, Steven; Haile, Robert W; Harrison, Tabitha A; Hayes, Richard B; Hoffmeister, Michael; Hopper, John L; Hudson, Thomas J; Jenkins, Mark A; Küry, Sébastien; Le Marchand, Loic; Leal, Suzanne M; Newcomb, Polly A; Nickerson, Deborah A; Potter, John D; Schoen, Robert E; Schumacher, Fredrick R; Seminara, Daniela; Slattery, Martha L; Hsu, Li; Chan, Andrew T; White, Emily; Berndt, Sonja I; Peters, Ulrike

    2016-01-01

    Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs). We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33). We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s). PMID:27379672

  12. Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants

    PubMed Central

    Gala, Manish; Abecasis, Goncalo; Bezieau, Stephane; Brenner, Hermann; Butterbach, Katja; Caan, Bette J.; Carlson, Christopher S.; Casey, Graham; Chang-Claude, Jenny; Conti, David V.; Curtis, Keith R.; Duggan, David; Gallinger, Steven; Haile, Robert W.; Harrison, Tabitha A.; Hayes, Richard B.; Hoffmeister, Michael; Hopper, John L.; Hudson, Thomas J.; Jenkins, Mark A.; Küry, Sébastien; Le Marchand, Loic; Leal, Suzanne M.; Newcomb, Polly A.; Nickerson, Deborah A.; Potter, John D.; Schoen, Robert E.; Schumacher, Fredrick R.; Seminara, Daniela; Slattery, Martha L.; Hsu, Li; Chan, Andrew T.; White, Emily; Berndt, Sonja I.; Peters, Ulrike

    2016-01-01

    Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs). We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33). We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s). PMID:27379672

  13. Using Catalytic Atom Maps to Predict the Catalytic Functions Present in Enzyme Active Sites

    PubMed Central

    Nosrati, Geoffrey R.; Houk, K. N.

    2012-01-01

    Catalytic Atom Maps (CAMs) are minimal models of enzyme active sites. The structures in the Protein Data Bank (PDB) were examined to determine if proteins with CAM-like geometries in their active sites all share the same catalytic function. We combined the CAM-based search protocol with a filter based on the weighted contact number (WCN) of the catalytic residues, a measure of the “crowdedness” of the microenvironment around a protein residue. Using this technique, a CAM based on the Ser-His-Asp catalytic triad of trypsin was able to correctly identify catalytic triads in other enzymes within 0.5 Å RMSD of the Catalytic Atom Map with 96% accuracy. A CAM based on the Cys-Arg-(Asp/Glu) active site residues from the tyrosine phosphatase active site achieved 89% accuracy in identifying this type of catalytic functionality. Both of these Catalytic Atom Maps were able to identify active sites across different fold types. Finally, the PDB was searched to locate proteins with catalytic functionality similar to that present in the active site of orotidine 5′-monophosphate decarboxylase (ODCase), whose mechanism is not known with certainty. A CAM, based on the conserved Lys-Asp-Lys-Asp tetrad in the ODCase active site, was used to search the PDB for enzymes with similar active sites. The ODCase active site has a geometry similar to that of Schiff base-forming Class I aldolases, with lowest aldolase RMSD to the ODCase CAM at 0.48 Å. The similarity between this CAM and the aldolase active site suggests that ODCase has the correct catalytic functionality present in its active site for the generation of a nucleophilic lysine. PMID:22909276

  14. Investigation of the diffusion of atomic fission products in UC by density functional calculations

    NASA Astrophysics Data System (ADS)

    Bévillon, Émile; Ducher, Roland; Barrachin, Marc; Dubourg, Roland

    2013-03-01

    Activation energies of U and C atoms self-diffusion in UC, as well as activation energies of hetero-diffusion of fission products (FPs) are investigated by first-principles calculations. According to a previous study which showed a likely U site occupation was favoured for all the FPs, their diffusion is restricted to the uranium sublattice of UC in the present study. In this framework, long-range displacements are only possible through a concerted mechanism with a surrounding uranium vacancy. Using the apparent formation energies of the uranium vacancy defect calculated in our previous study and the classical approach used in UO2 by Andersson et al., the activation energies of the main fission products in the various stoichiometric domains have been calculated. The results are compared to those obtained with the five frequency model applied to two representative fission products, Xe and Zr. Interestingly, despite strong differences of formalism, both models provided similar activation energies.

  15. Mapping biological soil crusts for understanding their functional relevance in dryland ecosystems

    NASA Astrophysics Data System (ADS)

    Rodriguez-Caballero, E.; Escribano, P.; Chamizo, S.; Canton, Y.

    2012-04-01

    Biological soil crusts (BSCs) are considered a key element in the functioning of arid and semiarid ecosystems as they modify numerous soil surface properties involved in primary ecosystem processes such as hydrological and erosion processes, and nutrient cycling.. It is known that arid and semiarid ecosystems are conformed by a complex matrix of vegetated and open ground patches usually covered by BSCs. Geomorphic evolution of drylands depends on the individual response of patches and also on the interactions and feedback-processes among patches. These interactions are controlled by patch spatial distribution. On this account, to understand the role of BSCs in the system, it is necessary to introduce their effect at coarser scales, and to have accurate and spatially continuous information of BSC distribution. The inherent complexity and the spatial heterogeneity of drylands make field survey methods very limited for BSC mapping. Images reported by remote sensors are presented as a powerful tool for mapping BSC spatial distribution. Remote sensors provide synoptic and spatially continuous information of the territory. Different indices for mapping BSCs have been published. These indices are based on distinctive spectral characteristic of BSCs and differ in nature and objectives. The aim of this work was to analyze the feasibility of some of these indices in a semiarid area characterized by sparse vegetation cover usually mixed at subpixel level with elements characterized by very similar spectral response (bare soil, BSCs and dry vegetation). These indices were: i) CRCIA, index applied for mapping BSCs from hyperspectral images. ii) CI, index developed for mapping of cyanobacteria-dominated BSCs and iii) BSCI, index for mapping of lichen-dominated BSCs. The multispectral indices (CI and BSCI) classified as BSCs 50% of the pixels dominated by BSCs. The CRCIA hyperspectral index, showed better results than those obtained with multispectral indices. This index

  16. Mapping Long-Term Functional Changes in Cerebral Blood Flow by Arterial Spin Labeling

    PubMed Central

    Ssali, Tracy; Anazodo, Udunna C.; Bureau, Yves; MacIntosh, Bradley J.; Günther, Matthias; St. Lawrence, Keith

    2016-01-01

    Although arterial spin labeling (ASL) is appealing for mapping long-term changes in functional activity, inter-sessional variations in basal blood flow, arterial transit times (ATTs), and alignment errors, can result in significant false activation when comparing images from separate sessions. By taking steps to reduce these sources of noise, this study assessed the ability of ASL to detect functional CBF changes between sessions. ASL data were collected in three sessions to image ATT, resting CBF and CBF changes associated with motor activation (7 participants). Activation maps were generated using rest and task images acquired in the same session and from sessions separated by up to a month. Good agreement was found when comparing between-session activation maps to within-session activation maps with only a 16% decrease in precision (within-session: 90 ± 7%) and a 13% decrease in the Dice similarity (within-session: 0.75 ± 0.07) coefficient after a month. In addition, voxel-wise reproducibility (within-session: 4.7 ± 4.5%) and reliability (within-session: 0.89 ± 0.20) of resting grey-matter CBF decreased by less than 18% for the between-session analysis relative to within-session values. ATT variability between sessions (5.0 ± 2.7%) was roughly half the between-subject variability, indicating that its effects on longitudinal CBF were minimal. These results demonstrate that conducting voxel-wise analysis on CBF images acquired on different days is feasible with only modest loss in precision, highlighting the potential of ASL for longitudinal studies. PMID:27706218

  17. Global and regional functional connectivity maps of neural oscillations in focal epilepsy.

    PubMed

    Englot, Dario J; Hinkley, Leighton B; Kort, Naomi S; Imber, Brandon S; Mizuiri, Danielle; Honma, Susanne M; Findlay, Anne M; Garrett, Coleman; Cheung, Paige L; Mantle, Mary; Tarapore, Phiroz E; Knowlton, Robert C; Chang, Edward F; Kirsch, Heidi E; Nagarajan, Srikantan S

    2015-08-01

    Intractable focal epilepsy is a devastating disorder with profound effects on cognition and quality of life. Epilepsy surgery can lead to seizure freedom in patients with focal epilepsy; however, sometimes it fails due to an incomplete delineation of the epileptogenic zone. Brain networks in epilepsy can be studied with resting-state functional connectivity analysis, yet previous investigations using functional magnetic resonance imaging or electrocorticography have produced inconsistent results. Magnetoencephalography allows non-invasive whole-brain recordings, and can be used to study both long-range network disturbances in focal epilepsy and regional connectivity at the epileptogenic zone. In magnetoencephalography recordings from presurgical epilepsy patients, we examined: (i) global functional connectivity maps in patients versus controls; and (ii) regional functional connectivity maps at the region of resection, compared to the homotopic non-epileptogenic region in the contralateral hemisphere. Sixty-one patients were studied, including 30 with mesial temporal lobe epilepsy and 31 with focal neocortical epilepsy. Compared with a group of 31 controls, patients with epilepsy had decreased resting-state functional connectivity in widespread regions, including perisylvian, posterior temporo-parietal, and orbitofrontal cortices (P < 0.01, t-test). Decreased mean global connectivity was related to longer duration of epilepsy and higher frequency of consciousness-impairing seizures (P < 0.01, linear regression). Furthermore, patients with increased regional connectivity within the resection site (n = 24) were more likely to achieve seizure postoperative seizure freedom (87.5% with Engel I outcome) than those with neutral (n = 15, 64.3% seizure free) or decreased (n = 23, 47.8% seizure free) regional connectivity (P < 0.02, chi-square). Widespread global decreases in functional connectivity are observed in patients with focal epilepsy, and may reflect deleterious

  18. Time Dependent Density Functional Theory Calculations of Large Compact PAH Cations: Implications for the Diffuse Interstellar Bands

    NASA Technical Reports Server (NTRS)

    Weisman, Jennifer L.; Lee, Timothy J.; Salama, Farid; Gordon-Head, Martin; Kwak, Dochan (Technical Monitor)

    2002-01-01

    We investigate the electronic absorption spectra of several maximally pericondensed polycyclic aromatic hydrocarbon radical cations with time dependent density functional theory calculations. We find interesting trends in the vertical excitation energies and oscillator strengths for this series containing pyrene through circumcoronene, the largest species containing more than 50 carbon atoms. We discuss the implications of these new results for the size and structure distribution of the diffuse interstellar band carriers.

  19. Exact free energy functional for a driven diffusive open stationary nonequilibrium system.

    PubMed

    Derrida, B; Lebowitz, J L; Speer, E R

    2002-07-15

    We obtain the exact probability exp[-LF([rho(x)])] of finding a macroscopic density profile rho(x) in the stationary nonequilibrium state of an open driven diffusive system, when the size of the system L-->infinity. F, which plays the role of a nonequilibrium free energy, has a very different structure from that found in the purely diffusive case. As there, F is nonlocal, but the shocks and dynamic phase transitions of the driven system are reflected in nonconvexity of F, in discontinuities in its second derivatives, and in non-Gaussian fluctuations in the steady state. PMID:12144382

  20. Si grain-boundary diffusion in forsterite as a function of pressure, temperature and water content

    NASA Astrophysics Data System (ADS)

    Katsura, T.; Fei, H.; Koizumi, S.; Hiraga, T.; Sakamoto, N.; Hashiguchi, M.; Yurimoto, H.; Yamazaki, D.

    2013-12-01

    In order to estimate the rate of Coble creep of olivine under various regions in the upper mantle, we have measured Si grain-boundary diffusion coefficients of forsterite aggregates. The grain sizes of the aggregates were 0.6 μm in most runs, and 2 μm in some runs to confirm that the Si diffusion occurs in grain boundaries. Measurement for samples without detectable amount of water by FT-IR spectroscopy was conducted at temperatures of 1200 to 1600 K at a pressure of 8 GPa and at pressures of 0 to 13 GPa at a temperature of 1300 K, which gives the activation energy and volume of 240×10 kJ/mol and 1.8×0.2 cm3/mol, respectively. Thus, the activation energy of the grain-boundary diffusion is much smaller than that of the lattice diffusion (415×10 kJ/mol), although its activation volume is identical to that of the lattice diffusion (1.7×0.2 cm3/mol). Measurement for hydrous samples was also conducted at temperatures of 1200 to 1600 K at a pressure of 8 GPa. The water contents in grain boundaries were estimated by subtracting the contribution of the lattice water from the bulk water in FT-IR spectra and normalizing them by the area of grain boundaries. The range of grain-boundary water was up to 130 wt.ppm μm. In this range of grain-boundary water, grain growth during diffusion annealing was very limited, whereas it became prominent above this range, suggesting that the system with the present range of the grain-boundary water content should be free from fluid phases. It was found that the water-content exponent of the Si grain-boundary diffusion is 0.22×0.05, which is even smaller than that of the lattice diffusion (0.32×0.07). These results suggest that the Coble creep rate will have 1) negligible pressure dependence, 2) much smaller temperature dependence than the grain-interior creep (Nabarro-Herring and dislocation creep), and 3) even smaller water content dependence than the grain-interior creep.

  1. BANK1 functional variants are associated with susceptibility to diffuse systemic sclerosis in Caucasians

    PubMed Central

    Rueda, B; Gourh, P; Broen, J; Agarwal, S K; Simeon, C; Ortego-Centeno, N; Vonk, M C; Coenen, M; Riemekasten, G; Hunzelmann, N; Hesselstrand, R; Tan, F K; Reveille, J D; Assassi, S; Garcia-Hernandez, F J; Carreira, P; Camps, M; Fernandez-Nebro, A; de la Peña, P Garcia; Nearney, T; Hilda, D; Gónzalez-Gay, M A; Airo, P; Beretta, L; Scorza, R; Radstake, T R D J; Mayes, M D; Arnett, F C; Martin, J

    2010-01-01

    Objective To investigate the possible association of the BANK1 gene with genetic susceptibility to systemic sclerosis (SSc) and its subphenotypes. Methods A large multicentre case–control association study including 2380 patients with SSc and 3270 healthy controls from six independent case–control sets of Caucasian ancestry (American, Spanish, Dutch, German, Swedish and Italian) was conducted. Three putative functional BANK1 polymorphisms (rs17266594 T/C, rs10516487 G/A, rs3733197 G/A) were selected as genetic markers and genotyped by Taqman 5´ allelic discrimination assay. Results A significant association of the rs10516487 G and rs17266594 T alleles with SSc susceptibility was observed (pooled OR=1.12, 95% CI 1.03 to 1.22; p=0.01 and pooled OR=1.14, 95% CI 1.05 to 1.25; p=0.003, respectively), whereas the rs3733197 genetic variant showed no statistically significant deviation. Stratification for cutaneous SSc phenotype showed that the BANK1 rs10516487 G, rs17266594 T and rs3733197 G alleles were strongly associated with susceptibility to diffuse SSc (dcSSc) (pooled OR=1.20, 95% CI 1.05 to 1.37, p=0.005; pooled OR=1.23, 95% CI 1.08 to 1.41, p=0.001; pooled OR=1.15, 95% CI 1.02 to 1.31, p=0.02, respectively). Similarly, stratification for specific SSc autoantibodies showed that the association of BANK1 rs10516487, rs17266594 and rs3733197 polymorphisms was restricted to the subgroup of patients carrying anti-topoisomerase I antibodies (pooled OR=1.20, 95% CI 1.02 to 1.41, p=0.03; pooled OR=1.24, 95% CI 1.05 to 1.46, p=0.01; pooled OR=1.26, 95% CI 1.07 to 1.47, p=0.004, respectively). Conclusion The results suggest that the BANK1 gene confers susceptibility to SSc in general, and specifically to the dcSSc and anti-topoisomerase I antibody subsets. PMID:19815934

  2. Mapping the energy density of shaped waves in scattering media onto a complete set of diffusion modes.

    PubMed

    Ojambati, Oluwafemi S; Mosk, Allard P; Vellekoop, Ivo M; Lagendijk, Ad; Vos, Willem L

    2016-08-01

    We study the energy density of shaped waves inside a quasi-1D disordered waveguide. We find that the spatial energy density of optimally shaped waves, when expanded in the complete set of eigenfunctions of the diffusion equation, is well described by considering only a few of the lowest eigenfunctions. Taking into account only the fundamental eigenfunction, the total internal energy inside the sample is underestimated by only 2%. The spatial distribution of the shaped energy density is very similar to the fundamental eigenfunction, up to a cosine distance of about 0.01. We obtain the energy density of transmission eigenchannels inside the sample by numerical simulation of the scattering matrix. Computing the transmission-averaged energy density over all transmission channels yields the ensemble averaged energy density of shaped waves. From the averaged energy density, we reconstruct its spatial distribution using the eigenfunctions of the diffusion equation. The results of our study have exciting applications in controlled biomedical imaging, efficient light harvesting in solar cells, enhanced energy conversion in solid-state lighting, and low threshold random lasers. PMID:27505816

  3. Mapping the energy density of shaped waves in scattering media onto a complete set of diffusion modes.

    PubMed

    Ojambati, Oluwafemi S; Mosk, Allard P; Vellekoop, Ivo M; Lagendijk, Ad; Vos, Willem L

    2016-08-01

    We study the energy density of shaped waves inside a quasi-1D disordered waveguide. We find that the spatial energy density of optimally shaped waves, when expanded in the complete set of eigenfunctions of the diffusion equation, is well described by considering only a few of the lowest eigenfunctions. Taking into account only the fundamental eigenfunction, the total internal energy inside the sample is underestimated by only 2%. The spatial distribution of the shaped energy density is very similar to the fundamental eigenfunction, up to a cosine distance of about 0.01. We obtain the energy density of transmission eigenchannels inside the sample by numerical simulation of the scattering matrix. Computing the transmission-averaged energy density over all transmission channels yields the ensemble averaged energy density of shaped waves. From the averaged energy density, we reconstruct its spatial distribution using the eigenfunctions of the diffusion equation. The results of our study have exciting applications in controlled biomedical imaging, efficient light harvesting in solar cells, enhanced energy conversion in solid-state lighting, and low threshold random lasers.

  4. Seventh Graders' Academic Achievement, Creativity, and Ability to Construct a Cross-Domain Concept Map--A Brain Function Perspective

    ERIC Educational Resources Information Center

    Yeh, Yu-Chu

    2004-01-01

    This study proposes an interactive model of "cross-domain" concept mapping with an emphasis on brain functions, and it further investigates the relationships between academic achievement, creative thinking, and cross-domain concept mapping. Sixty-nine seventh graders participated in this study which employed two 50-minute instructional sessions.…

  5. Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics.

    PubMed

    Urich, Tim; Lanzén, Anders; Stokke, Runar; Pedersen, Rolf B; Bayer, Christoph; Thorseth, Ingunn H; Schleper, Christa; Steen, Ida H; Ovreas, Lise

    2014-09-01

    Deep-sea hydrothermal vents are unique environments on Earth, as they host chemosynthetic ecosystems fuelled by geochemical energy with chemolithoautotrophic microorganisms at the basis of the food webs. Whereas discrete high-temperature venting systems have been studied extensively, the microbiotas associated with low-temperature diffuse venting are not well understood. We analysed the structure and functioning of microbial communities in two diffuse venting sediments from the Jan Mayen vent fields in the Norwegian-Greenland Sea, applying an integrated 'omics' approach combining metatranscriptomics, metaproteomics and metagenomics. Polymerase chain reaction-independent three-domain community profiling showed that the two sediments hosted highly similar communities dominated by Epsilonproteobacteria, Deltaproteobacteria and Gammaproteobacteria, besides ciliates, nematodes and various archaeal taxa. Active metabolic pathways were identified through transcripts and peptides, with genes of sulphur and methane oxidation, and carbon fixation pathways highly expressed, in addition to genes of aerobic and anaerobic (nitrate and sulphate) respiratory chains. High expression of chemotaxis and flagella genes reflected a lifestyle in a dynamic habitat rich in physico-chemical gradients. The major metabolic pathways could be assigned to distinct taxonomic groups, thus enabling hypotheses about the function of the different prokaryotic and eukaryotic taxa. This study advances our understanding of the functioning of microbial communities in diffuse hydrothermal venting sediments.

  6. Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics.

    PubMed

    Urich, Tim; Lanzén, Anders; Stokke, Runar; Pedersen, Rolf B; Bayer, Christoph; Thorseth, Ingunn H; Schleper, Christa; Steen, Ida H; Ovreas, Lise

    2014-09-01

    Deep-sea hydrothermal vents are unique environments on Earth, as they host chemosynthetic ecosystems fuelled by geochemical energy with chemolithoautotrophic microorganisms at the basis of the food webs. Whereas discrete high-temperature venting systems have been studied extensively, the microbiotas associated with low-temperature diffuse venting are not well understood. We analysed the structure and functioning of microbial communities in two diffuse venting sediments from the Jan Mayen vent fields in the Norwegian-Greenland Sea, applying an integrated 'omics' approach combining metatranscriptomics, metaproteomics and metagenomics. Polymerase chain reaction-independent three-domain community profiling showed that the two sediments hosted highly similar communities dominated by Epsilonproteobacteria, Deltaproteobacteria and Gammaproteobacteria, besides ciliates, nematodes and various archaeal taxa. Active metabolic pathways were identified through transcripts and peptides, with genes of sulphur and methane oxidation, and carbon fixation pathways highly expressed, in addition to genes of aerobic and anaerobic (nitrate and sulphate) respiratory chains. High expression of chemotaxis and flagella genes reflected a lifestyle in a dynamic habitat rich in physico-chemical gradients. The major metabolic pathways could be assigned to distinct taxonomic groups, thus enabling hypotheses about the function of the different prokaryotic and eukaryotic taxa. This study advances our understanding of the functioning of microbial communities in diffuse hydrothermal venting sediments. PMID:24112684

  7. HAM-5 Functions As a MAP Kinase Scaffold during Cell Fusion in Neurospora crassa

    PubMed Central

    Jonkers, Wilfried; Leeder, Abigail C.; Ansong, Charles; Wang, Yuexi; Yang, Feng; Starr, Trevor L.; Camp, David G.; Smith, Richard D.; Glass, N. Louise

    2014-01-01

    Cell fusion in genetically identical Neurospora crassa germlings and in hyphae is a highly regulated process involving the activation of a conserved MAP kinase cascade that includes NRC-1, MEK-2 and MAK-2. During chemotrophic growth in germlings, the MAP kinase cascade members localize to conidial anastomosis tube (CAT) tips every ∼8 minutes, perfectly out of phase with another protein that is recruited to the tip: SOFT, a recently identified scaffold for the MAK-1 MAP kinase pathway in Sordaria macrospora. How the MAK-2 oscillation process is initiated, maintained and what proteins regulate the MAP kinase cascade is currently unclear. A global phosphoproteomics approach using an allele of mak-2 (mak-2Q100G) that can be specifically inhibited by the ATP analog 1NM-PP1 was utilized to identify MAK-2 kinase targets in germlings that were potentially involved in this process. One such putative target was HAM-5, a protein of unknown biochemical function. Previously, Δham-5 mutants were shown to be deficient for hyphal fusion. Here we show that HAM-5-GFP co-localized with NRC-1, MEK-2 and MAK-2 and oscillated with identical dynamics from the cytoplasm to CAT tips during chemotropic interactions. In the Δmak-2 strain, HAM-5-GFP localized to punctate complexes that did not oscillate, but still localized to the germling tip, suggesting that MAK-2 activity influences HAM-5 function/localization. However, MAK-2-GFP showed cytoplasmic and nuclear localization in a Δham-5 strain and did not localize to puncta. Via co-immunoprecipitation experiments, HAM-5 was shown to physically interact with NRC-1, MEK-2 and MAK-2, suggesting that it functions as a scaffold/transport hub for the MAP kinase cascade members for oscillation and chemotropic interactions during germling and hyphal fusion in N. crassa. The identification of HAM-5 as a scaffold-like protein will help to link the activation of MAK-2 cascade to upstream factors and proteins involved in this intriguing process of

  8. Velocity correlation functions, Fickian and higher order diffusion coefficients for ions in electrostatic fields via molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Koutselos, Andreas D.

    1996-06-01

    The dynamic and transport properties of swarms of ions in a uniform electrostatic field are studied by using a molecular dynamics method. For a representative system, K+ in Ar, using a universal interaction model potential, second and third order ion-velocity correlation functions are determined at various field strengths. From them, Fickian diffusion coefficients parallel and perpendicular to the field, as well as higher order diffusion coefficients, Qzzz, are obtained within estimated overall accuracy 5% and 7%, respectively. Comparisons of the Fickian diffusion coefficients against results of the moment solution of Boltzmann kinetic equation and a Monte Carlo simulation method using the same interaction potential as well as against experimental data, reveal consistency among all calculation procedures and in addition agreement with drift tube measurements. These comparisons provide new tests for the accuracy of the employed interaction potential. The method has been applied for up to third order velocity correlations and diffusion coefficients but it is extendible to higher order dynamic and transport properties.

  9. Non-Invasive Functional Mapping of the Brain Using Magnetoencephalography and Functional Magnetic Resonance Imaging.

    NASA Astrophysics Data System (ADS)

    Wang, Jihong

    Magnetoencephalography (MEG) and Functional Magnetic Resonance Imaging (FMRI) are two non-invasive techniques that can be used to study brain function. The first part of this dissertation discusses experimental factors that affect the accuracy of MEG source localization. These factors include measurement error, signal to noise ratio, number of measurement points and the local curvature of the head. A skull phantom and computer simulation were used to study the accuracy of MEG localization. It was found that the MEG dipole localization error was approximately 5-10 mm in the temporal region. This localization error was directly proportional to the digitization error. An empirical formula is given for the dependence of the MEG localization accuracy on the signal to noise ratio. The dependence of the MEG localization accuracy on the number of measurement points was also studied. Adequate coverage of extrema is necessary for accurate dipole localizations. The local curvature of the head does not affect localization accuracy as long as the center of the best fit sphere to this local surface is within 4 cm of the center of the best fit sphere to the whole head. The second part of the dissertation presents MEG and FMRI results of motor and auditory stimulation. It was found that the locations of auditory and motor activities as identified by MEG were in agreement with those identified by FMRI within 1-2 cm. The reasons for this discrepancy are discussed. The successful FMRI during auditory stimulation is reported. The fundamental aspects of the MEG inverse solution are discussed and a new spatiotemporal inverse solution algorithm is proposed.

  10. Mapping causal functional contributions derived from the clinical assessment of brain damage after stroke.

    PubMed

    Zavaglia, Melissa; Forkert, Nils D; Cheng, Bastian; Gerloff, Christian; Thomalla, Götz; Hilgetag, Claus C

    2015-01-01

    Lesion analysis reveals causal contributions of brain regions to mental functions, aiding the understanding of normal brain function as well as rehabilitation of brain-damaged patients. We applied a novel lesion inference technique based on game theory, Multi-perturbation Shapley value Analysis (MSA), to a large clinical lesion dataset. We used MSA to analyze the lesion patterns of 148 acute stroke patients together with their neurological deficits, as assessed by the National Institutes of Health Stroke Scale (NIHSS). The results revealed regional functional contributions to essential behavioral and cognitive functions as reflected in the NIHSS, particularly by subcortical structures. There were also side specific differences of functional contributions between the right and left hemispheric brain regions which may reflect the dominance of the left hemispheric syndrome aphasia in the NIHSS. Comparison of MSA to established lesion inference methods demonstrated the feasibility of the approach for analyzing clinical data and indicated its capability for objectively inferring functional contributions from multiple injured, potentially interacting sites, at the cost of having to predict the outcome of unknown lesion configurations. The analysis of regional functional contributions to neurological symptoms measured by the NIHSS contributes to the interpretation of this widely used standardized stroke scale in clinical practice as well as clinical trials and provides a first approximation of a 'map of stroke'.

  11. Mapping causal functional contributions derived from the clinical assessment of brain damage after stroke

    PubMed Central

    Zavaglia, Melissa; Forkert, Nils D.; Cheng, Bastian; Gerloff, Christian; Thomalla, Götz; Hilgetag, Claus C.

    2015-01-01

    Lesion analysis reveals causal contributions of brain regions to mental functions, aiding the understanding of normal brain function as well as rehabilitation of brain-damaged patients. We applied a novel lesion inference technique based on game theory, Multi-perturbation Shapley value Analysis (MSA), to a large clinical lesion dataset. We used MSA to analyze the lesion patterns of 148 acute stroke patients together with their neurological deficits, as assessed by the National Institutes of Health Stroke Scale (NIHSS). The results revealed regional functional contributions to essential behavioral and cognitive functions as reflected in the NIHSS, particularly by subcortical structures. There were also side specific differences of functional contributions between the right and left hemispheric brain regions which may reflect the dominance of the left hemispheric syndrome aphasia in the NIHSS. Comparison of MSA to established lesion inference methods demonstrated the feasibility of the approach for analyzing clinical data and indicated its capability for objectively inferring functional contributions from multiple injured, potentially interacting sites, at the cost of having to predict the outcome of unknown lesion configurations. The analysis of regional functional contributions to neurological symptoms measured by the NIHSS contributes to the interpretation of this widely used standardized stroke scale in clinical practice as well as clinical trials and provides a first approximation of a ‘map of stroke’. PMID:26448908

  12. Response Properties of Human Amygdala Subregions: Evidence Based on Functional MRI Combined with Probabilistic Anatomical Maps

    PubMed Central

    Rahm, Benjamin; Eickhoff, Simon B.; Schulze-Bonhage, Andreas; Speck, Oliver

    2007-01-01

    The human amygdala is thought to play a pivotal role in the processing of emotionally significant sensory information. The major subdivisions of the human amygdala—the laterobasal group (LB), the superficial group (SF), and the centromedial group (CM)—have been anatomically delineated, but the functional response properties of these amygdala subregions in humans are still unclear. We combined functional MRI with cyto-architectonically defined probabilistic maps to analyze the response characteristics of amygdala subregions in subjects presented with auditory stimuli. We found positive auditory stimulation-related signal changes predominantly in probabilistically defined LB, and negative responses predominantly in SF and CM. In the left amygdala, mean response magnitude in the core area of LB with 90–100% assignment probability was significantly larger than in the core areas of SF and CM. These differences were observed for pleasant and unpleasant stimuli. Our findings reveal that the probabilistically defined anatomical subregions of the human amygdala show distinctive fMRI response patterns. The stronger auditory responses in LB as compared with SF and CM may reflect a predominance of auditory inputs to human LB, similar to many animal species in which the majority of sensory, including auditory, afferents project to this subdivision of the amygdala. Our study indicates that the intrinsic functional differentiation of the human amygdala may be probed using fMRI combined with probabilistic anatomical maps. PMID:17375193

  13. Fine mapping of the celiac disease-associated LPP locus reveals a potential functional variant

    PubMed Central

    Almeida, Rodrigo; Ricaño-Ponce, Isis; Kumar, Vinod; Deelen, Patrick; Szperl, Agata; Trynka, Gosia; Gutierrez-Achury, Javier; Kanterakis, Alexandros; Westra, Harm-Jan; Franke, Lude; Swertz, Morris A.; Platteel, Mathieu; Bilbao, Jose Ramon; Barisani, Donatella; Greco, Luigi; Mearin, Luisa; Wolters, Victorien M.; Mulder, Chris; Mazzilli, Maria Cristina; Sood, Ajit; Cukrowska, Bozena; Núñez, Concepción; Pratesi, Riccardo; Withoff, Sebo; Wijmenga, Cisca

    2014-01-01

    Using the Immunochip for genotyping, we identified 39 non-human leukocyte antigen (non-HLA) loci associated to celiac disease (CeD), an immune-mediated disease with a worldwide frequency of ∼1%. The most significant non-HLA signal mapped to the intronic region of 70 kb in the LPP gene. Our aim was to fine map and identify possible functional variants in the LPP locus. We performed a meta-analysis in a cohort of 25 169 individuals from six different populations previously genotyped using Immunochip. Imputation using data from the Genome of the Netherlands and 1000 Genomes projects, followed by meta-analysis, confirmed the strong association signal on the LPP locus (rs2030519, P = 1.79 × 10−49), without any novel associations. The conditional analysis on this top SNP-indicated association to a single common haplotype. By performing haplotype analyses in each population separately, as well as in a combined group of the four populations that reach the significant threshold after correction (P < 0.008), we narrowed down the CeD-associated region from 70 to 2.8 kb (P = 1.35 × 10−44). By intersecting regulatory data from the ENCODE project, we found a functional SNP, rs4686484 (P = 3.12 × 10−49), that maps to several B-cell enhancer elements and a highly conserved region. This SNP was also predicted to change the binding motif of the transcription factors IRF4, IRF11, Nkx2.7 and Nkx2.9, suggesting its role in transcriptional regulation. We later found significantly low levels of LPP mRNA in CeD biopsies compared with controls, thus our results suggest that rs4686484 is the functional variant in this locus, while LPP expression is decreased in CeD. PMID:24334606

  14. Impact of different NWM-derived mapping functions on VLBI and GNSS analysis

    NASA Astrophysics Data System (ADS)

    Nikolaidou, Thalia; Balidakis, Kyriakos; Nievinski, Felipe; Mendonça, Marco; Santos, Marcelo; Schuh, Harald

    2016-04-01

    In this study, the issue of the tropospheric mapping functions (MF) employed for VLBI and GNSS data analysis is addressed. IERS Conventions (2010) recommend for standard operational solutions, the use of MF based on numerical weather models (NWM) to improve troposphere modeling. The Vienna Mapping Functions 1 (VMF1) map the atmospheric delay from zenith to the line of sight as an elevation dependent function and are capable of better accounting for real weather phenomena compared to MF without NWM input data. However, the spatial resolution of the NWM itself, directly impacts the ability to model atmospheric conditions effectively. Therefore, we employ the UNB-VMF1 which utilize the high resolution model from the Canadian Meteorological Centre based on the Global Deterministic Prediction System (CMC GDPS). The latter, as a modern operational model, contains the latest application of atmospheric physics and parameterizations and is relieved from spatially based systematic effects. For our investigations, we analyze all rapid turnaround VLBI experiments spanning a five year period using the VieVS@GFZ software, as well as the entire data set from IGS sites that observed at the same interval using GAPS: UNB Precise Point Positioning software. Using the independent UNB ray-tracing algorithm we derive hydrostatic and wet "a" coefficients of MF as well as zenith delays from ray-tracing in CMC NWM. The solutions we produced differ only in the choice of the MF. The VLBI and GNSS analysis are fully consistent. The comparison is conducted on both global and local parameters (station positions and velocities, Earth rotation parameters, zenith wet delays and first order tropospheric gradients) between VLBI and GNSS derived products as well as between employing VMF1 (ECMWF operational analysis) and UNB-VMF1 (CMC).

  15. New Magnetic Resonance Imaging Index for Renal Fibrosis Assessment: A Comparison between Diffusion-Weighted Imaging and T1 Mapping with Histological Validation.

    PubMed

    Friedli, I; Crowe, L A; Berchtold, L; Moll, S; Hadaya, K; de Perrot, T; Vesin, C; Martin, P-Y; de Seigneux, S; Vallée, J-P

    2016-01-01

    A need exists to noninvasively assess renal interstitial fibrosis, a common process to all kidney diseases and predictive of renal prognosis. In this translational study, Magnetic Resonance Imaging (MRI) T1 mapping and a new segmented Diffusion-Weighted Imaging (DWI) technique, for Apparent Diffusion Coefficient (ADC), were first compared to renal fibrosis in two well-controlled animal models to assess detection limits. Validation against biopsy was then performed in 33 kidney allograft recipients (KARs). Predictive MRI indices, ΔT1 and ΔADC (defined as the cortico-medullary differences), were compared to histology. In rats, both T1 and ADC correlated well with fibrosis and inflammation showing a difference between normal and diseased kidneys. In KARs, MRI indices were not sensitive to interstitial inflammation. By contrast, ΔADC outperformed ΔT1 with a stronger negative correlation to fibrosis (R(2) = 0.64 against R(2) = 0.29 p < 0.001). ΔADC tends to negative values in KARs harboring cortical fibrosis of more than 40%. Using a discriminant analysis method, the ΔADC, as a marker to detect such level of fibrosis or higher, led to a specificity and sensitivity of 100% and 71%, respectively. This new index has potential for noninvasive assessment of fibrosis in the clinical setting. PMID:27439482

  16. New Magnetic Resonance Imaging Index for Renal Fibrosis Assessment: A Comparison between Diffusion-Weighted Imaging and T1 Mapping with Histological Validation

    PubMed Central

    Friedli, I.; Crowe, L. A.; Berchtold, L.; Moll, S.; Hadaya, K.; de Perrot, T.; Vesin, C.; Martin, P.-Y.; de Seigneux, S.; Vallée, J.-P.

    2016-01-01

    A need exists to noninvasively assess renal interstitial fibrosis, a common process to all kidney diseases and predictive of renal prognosis. In this translational study, Magnetic Resonance Imaging (MRI) T1 mapping and a new segmented Diffusion-Weighted Imaging (DWI) technique, for Apparent Diffusion Coefficient (ADC), were first compared to renal fibrosis in two well-controlled animal models to assess detection limits. Validation against biopsy was then performed in 33 kidney allograft recipients (KARs). Predictive MRI indices, ΔT1 and ΔADC (defined as the cortico-medullary differences), were compared to histology. In rats, both T1 and ADC correlated well with fibrosis and inflammation showing a difference between normal and diseased kidneys. In KARs, MRI indices were not sensitive to interstitial inflammation. By contrast, ΔADC outperformed ΔT1 with a stronger negative correlation to fibrosis (R2 = 0.64 against R2 = 0.29 p < 0.001). ΔADC tends to negative values in KARs harboring cortical fibrosis of more than 40%. Using a discriminant analysis method, the ΔADC, as a marker to detect such level of fibrosis or higher, led to a specificity and sensitivity of 100% and 71%, respectively. This new index has potential for noninvasive assessment of fibrosis in the clinical setting. PMID:27439482

  17. Analysis of the human brain in primary progressive multiple sclerosis with mapping of the spatial distributions using 1H MR spectroscopy and diffusion tensor imaging.

    PubMed

    Sijens, Paul E; Irwan, Roy; Potze, Jan Hendrik; Mostert, Jop P; De Keyser, Jacques; Oudkerk, Matthijs

    2005-08-01

    Primary progressive multiple sclerosis (ppMS; n=4) patients and controls (n=4) were examined by 1H magnetic resonance spectroscopy (MRS) and diffusion tensor imaging (DTI) in order to map choline (Cho), creatine and N-acetylaspartate (NAA), the fractional anisotropy (FA) and the apparent diffusion constant (ADC). After chemical shift imaging (point-resolved spectroscopy, repetition time/echo time 1,500 ms/135 ms) of a supraventricular volume of interest of 8x8x2 cm3 (64 voxels) MRS peak areas were matched to the results of DTI for the corresponding volume elements. Mean FA and NAA values were reduced in the ppMS patients (P<0.01, both) and the ADC increased (P<0.02). The spatial distribution of NAA showed strong correlation to ADC in both ppMS patients and controls (r =-0.74 and r= -0.70; P<0.00001, both), and weaker correlations to FA (r=0.49 and r=0.41; P<0.00001, all). FA and ADC also correlated significantly with Cho in patients and controls (P<0.00001, all). The relationship of Cho and NAA to the ADC and the FA and thus to the content of neuronal structures suggests that these metabolite signals essentially originate from axons (NAA) and the myelin sheath (Cho). This is of interest in view of previous reports in which Cho increases were associated with demyelination and the subsequent breakdown of neurons.

  18. HAM-5 functions as a MAP kinase scaffold during cell fusion in Neurospora crassa

    DOE PAGESBeta

    Jonkers, Wilfried; Leeder, Abigail C.; Ansong, Charles; Wang, Yuexi; Yang, Feng; Starr, Trevor L.; Camp, II, David G.; Smith, Richard D.; Glass, N. Louise; Heitman, Joseph

    2014-11-20

    Cell fusion in genetically identical Neurospora crassa germlings and in hyphae is a highly regulated process involving the activation of a conserved MAP kinase cascade that includes NRC1, MEK2 and MAK2. During chemotrophic growth in germlings, the MAP kinase cascade members localize to conidial anastomosis tube (CAT) tips every 4 minutes, perfectly out of phase with another protein that is recruited to the tip: SOFT, a protein of unknown biochemical function. How this oscillation process is initiated, maintained and what proteins regulate the MAP kinase cascade is currently unclear. A global phosphoproteomics approach using an allele of mak-2 (mak-2Q100G) thatmore » can be specifically inhibited by the ATP analog 1NM-PP1 was utilized to identify MAK2 kinase targets in germlings that were potentially involved in this process. One such putative target was HAM5, a protein of unknown biochemical function. Previously, Δham-5 mutants were shown to be deficient for hyphal fusion. Here we show that HAM5-GFP co-localized with NRC1, MEK2 and MAK2 and oscillated with identical dynamics from the cytoplasm to CAT tips during chemotropic interactions. In the Δmak-2 strain, HAM5-GFP localized to punctate complexes that did not oscillate, but still localized to the germling tip, suggesting that MAK2 activity influences HAM5 function/localization. However, MAK2-GFP showed only cytoplasmic and nuclear localization in a Δham-5 strain and did not localize to puncta, as observed in wild type germlings. Via co-immunoprecipitation experiments, HAM5 was shown to physically interact with MAK2, MEK2 and NRC1, suggesting that it functions as a scaffold/transport hub for the MAP kinase cascade members during oscillation and chemotropic interactions during both germling and hyphal fusion in N. crassa. The identification of HAM5 as a scaffold-like protein will help to link the activation of MAK2 to upstream factors and other proteins involved in this intriguing process of fungal

  19. Nanometric resolution magnetic resonance imaging methods for mapping functional activity in neuronal networks

    PubMed Central

    Boretti, Albert; Castelletto, Stefania

    2016-01-01

    This contribution highlights and compares some recent achievements in the use of k-space and real space imaging (scanning probe and wide-filed microscope techniques), when applied to a luminescent color center in diamond, known as nitrogen vacancy (NV) center. These techniques combined with the optically detected magnetic resonance of NV, provide a unique platform to achieve nanometric magnetic resonance imaging (MRI) resolution of nearby nuclear spins (known as nanoMRI), and nanometric NV real space localization. • Atomic size optically detectable spin probe. • High magnetic field sensitivity and nanometric resolution. • Non-invasive mapping of functional activity in neuronal networks. PMID:27144128

  20. Algorithm To Architecture Mapping Model (ATAMM) multicomputer operating system functional specification

    NASA Technical Reports Server (NTRS)

    Mielke, R.; Stoughton, J.; Som, S.; Obando, R.; Malekpour, M.; Mandala, B.

    1990-01-01

    A functional description of the ATAMM Multicomputer Operating System is presented. ATAMM (Algorithm to Architecture Mapping Model) is a marked graph model which describes the implementation of large grained, decomposed algorithms on data flow architectures. AMOS, the ATAMM Multicomputer Operating System, is an operating system which implements the ATAMM rules. A first generation version of AMOS which was developed for the Advanced Development Module (ADM) is described. A second generation version of AMOS being developed for the Generic VHSIC Spaceborne Computer (GVSC) is also presented.

  1. Nanometric resolution magnetic resonance imaging methods for mapping functional activity in neuronal networks.

    PubMed

    Boretti, Albert; Castelletto, Stefania

    2016-01-01

    This contribution highlights and compares some recent achievements in the use of k-space and real space imaging (scanning probe and wide-filed microscope techniques), when applied to a luminescent color center in diamond, known as nitrogen vacancy (NV) center. These techniques combined with the optically detected magnetic resonance of NV, provide a unique platform to achieve nanometric magnetic resonance imaging (MRI) resolution of nearby nuclear spins (known as nanoMRI), and nanometric NV real space localization. •Atomic size optically detectable spin probe.•High magnetic field sensitivity and nanometric resolution.•Non-invasive mapping of functional activity in neuronal networks. PMID:27144128

  2. Nanometric resolution magnetic resonance imaging methods for mapping functional activity in neuronal networks.

    PubMed

    Boretti, Albert; Castelletto, Stefania

    2016-01-01

    This contribution highlights and compares some recent achievements in the use of k-space and real space imaging (scanning probe and wide-filed microscope techniques), when applied to a luminescent color center in diamond, known as nitrogen vacancy (NV) center. These techniques combined with the optically detected magnetic resonance of NV, provide a unique platform to achieve nanometric magnetic resonance imaging (MRI) resolution of nearby nuclear spins (known as nanoMRI), and nanometric NV real space localization. •Atomic size optically detectable spin probe.•High magnetic field sensitivity and nanometric resolution.•Non-invasive mapping of functional activity in neuronal networks.

  3. Quantitative NumART2* mapping in functional MRI studies at 1.5 T.

    PubMed

    Hagberg, Gisela E; Bianciardi, Marta; Patria, Fabiana; Indovina, Iole

    2003-12-01

    Quantitative mapping of the effective transverse relaxation time, T2* and proton density was performed in a motor activation functional MRI (fMRI) study using multi-echo, echo planar imaging (EPI) and NumART2* (Numerical Algorithm for Real time T2*). Comparisons between NumART2* and conventional single echo EPI with an echo time of 64 ms were performed for five healthy participants examined twice. Simulations were also performed to address specific issues associated with the two techniques, such as echo time-dependent signal variation. While the single echo contrast varied with the baseline T2* value, relative changes in T2* remained unaffected. Statistical analysis of the T2* maps yielded fMRI activation patterns with an improved statistical detection relative to conventional EPI but with less activated voxels, suggesting that NumART2* has superior spatial specificity. Two effects, inflow and dephasing, that may explain this finding were investigated. Particularly, a statistically significant increase in proton density was found in a brain area that was detected as activated by conventional EPI but not by NumART2* while no such changes were observed in brain areas that showed stimulus correlated signal changes on T2* maps.

  4. The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function.

    PubMed

    Noel, Jeffrey K; Whitford, Paul C; Onuchic, José N

    2012-07-26

    Structure-based models (SBMs) are simplified models of the biomolecular dynamics that arise from funneled energy landscapes. We recently introduced an all-atom SBM that explicitly represents the atomic geometry of a biomolecule. While this initial study showed the robustness of the all-atom SBM Hamiltonian to changes in many of the energetic parameters, an important aspect, which has not been explored previously, is the definition of native interactions. In this study, we propose a general definition for generating atomically grained contact maps called "Shadow". The Shadow algorithm initially considers all atoms within a cutoff distance and then, controlled by a screening parameter, discards the occluded contacts. We show that this choice of contact map is not only well behaved for protein folding, since it produces consistently cooperative folding behavior in SBMs but also desirable for exploring the dynamics of macromolecular assemblies since, it distributes energy similarly between RNAs and proteins despite their disparate internal packing. All-atom structure-based models employing Shadow contact maps provide a general framework for exploring the geometrical features of biomolecules, especially the connections between folding and function.

  5. Glial and neuronal Semaphorin signaling instruct the development of a functional myotopic map for Drosophila walking

    PubMed Central

    Syed, Durafshan Sakeena; Gowda, Swetha B.M.; Reddy, O Venkateswara; Reichert, Heinrich; VijayRaghavan, K

    2016-01-01

    Motoneurons developmentally acquire appropriate cellular architectures that ensure connections with postsynaptic muscles and presynaptic neurons. In Drosophila, leg motoneurons are organized as a myotopic map, where their dendritic domains represent the muscle field. Here, we investigate mechanisms underlying development of aspects of this myotopic map, required for walking. A behavioral screen identified roles for Semaphorins (Sema) and Plexins (Plex) in walking behavior. Deciphering this phenotype, we show that PlexA/Sema1a mediates motoneuron axon branching in ways that differ in the proximal femur and distal tibia, based on motoneuronal birth order. Importantly, we show a novel role for glia in positioning dendrites of specific motoneurons; PlexB/Sema2a is required for dendritic positioning of late-born motoneurons but not early-born motoneurons. These findings indicate that communication within motoneurons and between glia and motoneurons, mediated by the combined action of different Plexin/Semaphorin signaling systems, are required for the formation of a functional myotopic map. DOI: http://dx.doi.org/10.7554/eLife.11572.001 PMID:26926907

  6. Determination of tracer diffusion coefficients of 22NaCl as function of magnesium chloride concentration in water at 25°C

    NASA Astrophysics Data System (ADS)

    Ahl, J.; Liukkonen, S.

    1999-01-01

    The tracer diffusion coefficients of sodium-22-chloride were determined as function of magnesium chloride concentrations in aqueous solutions (10-4...1 mol dm-3) at 25°C. Closed capillary method was used in experiments. The most accurate method to calculate the tracer diffusion coefficient from an infinite series solution was further developed. The Onsager limiting law was verified to the tracer diffusion of 22NaCl in aqueous magnesium chloride in low concentration region.

  7. Structural relaxation and diffusion in a model colloid-polymer mixture: dynamical density functional theory and simulation

    NASA Astrophysics Data System (ADS)

    Stopper, Daniel; Roth, Roland; Hansen-Goos, Hendrik

    2016-11-01

    Within the Asakura-Oosawa model, we study structural relaxation in mixtures of colloids and polymers subject to Brownian motion in the overdamped limit. We obtain the time evolution of the self and distinct parts of the van Hove distribution function G(r,t) by means of dynamical density functional theory (DDFT) using an accurate free-energy functional based on Rosenfeld’s fundamental measure theory. In order to remove unphysical interactions within the self part, we extend the recently proposed quenched functional framework (Stopper et al 2015 J. Chem. Phys. 143 181105) toward mixtures. In addition, we obtain results for the long-time self diffusion coefficients of colloids and polymers from dynamic Monte Carlo simulations, which we incorporate into the DDFT. From the resulting DDFT equations we calculate G(r, t), which we find to agree very well with our simulations. In particular, we examine the influence of polymers which are slow relative to the colloids—a scenario for which both DDFT and simulation show a significant peak forming at r  =  0 in the colloid-colloid distribution function, akin to experimental findings involving gelation of colloidal suspensions. Moreover, we observe that, in the presence of slow polymers, the long-time self diffusivity of the colloids displays a maximum at an intermediate colloid packing fraction. This behavior is captured by a simple semi-empirical formula, which provides an excellent description of the data.

  8. Structural relaxation and diffusion in a model colloid-polymer mixture: dynamical density functional theory and simulation.

    PubMed

    Stopper, Daniel; Roth, Roland; Hansen-Goos, Hendrik

    2016-11-16

    Within the Asakura-Oosawa model, we study structural relaxation in mixtures of colloids and polymers subject to Brownian motion in the overdamped limit. We obtain the time evolution of the self and distinct parts of the van Hove distribution function G(r,t) by means of dynamical density functional theory (DDFT) using an accurate free-energy functional based on Rosenfeld's fundamental measure theory. In order to remove unphysical interactions within the self part, we extend the recently proposed quenched functional framework (Stopper et al 2015 J. Chem. Phys. 143 181105) toward mixtures. In addition, we obtain results for the long-time self diffusion coefficients of colloids and polymers from dynamic Monte Carlo simulations, which we incorporate into the DDFT. From the resulting DDFT equations we calculate G(r, t), which we find to agree very well with our simulations. In particular, we examine the influence of polymers which are slow relative to the colloids-a scenario for which both DDFT and simulation show a significant peak forming at r  =  0 in the colloid-colloid distribution function, akin to experimental findings involving gelation of colloidal suspensions. Moreover, we observe that, in the presence of slow polymers, the long-time self diffusivity of the colloids displays a maximum at an intermediate colloid packing fraction. This behavior is captured by a simple semi-empirical formula, which provides an excellent description of the data. PMID:27608916

  9. Mapping of functionally characterized cell classes onto canonical circuit operations in primate prefrontal cortex.

    PubMed

    Ardid, Salva; Vinck, Martin; Kaping, Daniel; Marquez, Susanna; Everling, Stefan; Womelsdorf, Thilo

    2015-02-18

    Microcircuits are composed of multiple cell classes that likely serve unique circuit operations. But how cell classes map onto circuit functions is largely unknown, particularly for primate prefrontal cortex during actual goal-directed behavior. One difficulty in this quest is to reliably distinguish cell classes in extracellular recordings of action potentials. Here we surmount this issue and report that spike shape and neural firing variability provide reliable markers to segregate seven functional classes of prefrontal cells in macaques engaged in an attention task. We delineate an unbiased clustering protocol that identifies four broad spiking (BS) putative pyramidal cell classes and three narrow spiking (NS) putative inhibitory cell classes dissociated by how sparse, bursty, or regular they fire. We speculate that these functional classes map onto canonical circuit functions. First, two BS classes show sparse, bursty firing, and phase synchronize their spiking to 3-7 Hz (theta) and 12-20 Hz (beta) frequency bands of the local field potential (LFP). These properties make cells flexibly responsive to network activation at varying frequencies. Second, one NS and two BS cell classes show regular firing and higher rate with only marginal synchronization preference. These properties are akin to setting tonically the excitation and inhibition balance. Finally, two NS classes fired irregularly and synchronized to either theta or beta LFP fluctuations, tuning them potentially to frequency-specific subnetworks. These results suggest that a limited set of functional cell classes emerges in macaque prefrontal cortex (PFC) during attentional engagement to not only represent information, but to subserve basic circuit operations. PMID:25698735

  10. Radiomic Texture Analysis Mapping Predicts Areas of True Functional MRI Activity.

    PubMed

    Hassan, Islam; Kotrotsou, Aikaterini; Bakhtiari, Ali Shojaee; Thomas, Ginu A; Weinberg, Jeffrey S; Kumar, Ashok J; Sawaya, Raymond; Luedi, Markus M; Zinn, Pascal O; Colen, Rivka R

    2016-01-01

    Individual analysis of functional Magnetic Resonance Imaging (fMRI) scans requires user-adjustment of the statistical threshold in order to maximize true functional activity and eliminate false positives. In this study, we propose a novel technique that uses radiomic texture analysis (TA) features associated with heterogeneity to predict areas of true functional activity. Scans of 15 right-handed healthy volunteers were analyzed using SPM8. The resulting functional maps were thresholded to optimize visualization of language areas, resulting in 116 regions of interests (ROIs). A board-certified neuroradiologist classified different ROIs into Expected (E) and Non-Expected (NE) based on their anatomical locations. TA was performed using the mean Echo-Planner Imaging (EPI) volume, and 20 rotation-invariant texture features were obtained for each ROI. Using forward stepwise logistic regression, we built a predictive model that discriminated between E and NE areas of functional activity, with a cross-validation AUC and success rate of 79.84% and 80.19% respectively (specificity/sensitivity of 78.34%/82.61%). This study found that radiomic TA of fMRI scans may allow for determination of areas of true functional activity, and thus eliminate clinician bias. PMID:27151623

  11. Radiomic Texture Analysis Mapping Predicts Areas of True Functional MRI Activity

    PubMed Central

    Hassan, Islam; Kotrotsou, Aikaterini; Bakhtiari, Ali Shojaee; Thomas, Ginu A.; Weinberg, Jeffrey S.; Kumar, Ashok J.; Sawaya, Raymond; Luedi, Markus M.; Zinn, Pascal O.; Colen, Rivka R.

    2016-01-01

    Individual analysis of functional Magnetic Resonance Imaging (fMRI) scans requires user-adjustment of the statistical threshold in order to maximize true functional activity and eliminate false positives. In this study, we propose a novel technique that uses radiomic texture analysis (TA) features associated with heterogeneity to predict areas of true functional activity. Scans of 15 right-handed healthy volunteers were analyzed using SPM8. The resulting functional maps were thresholded to optimize visualization of language areas, resulting in 116 regions of interests (ROIs). A board-certified neuroradiologist classified different ROIs into Expected (E) and Non-Expected (NE) based on their anatomical locations. TA was performed using the mean Echo-Planner Imaging (EPI) volume, and 20 rotation-invariant texture features were obtained for each ROI. Using forward stepwise logistic regression, we built a predictive model that discriminated between E and NE areas of functional activity, with a cross-validation AUC and success rate of 79.84% and 80.19% respectively (specificity/sensitivity of 78.34%/82.61%). This study found that radiomic TA of fMRI scans may allow for determination of areas of true functional activity, and thus eliminate clinician bias. PMID:27151623

  12. An integrative architecture for general intelligence and executive function revealed by lesion mapping

    PubMed Central

    Colom, Roberto; Solomon, Jeffrey; Krueger, Frank; Forbes, Chad; Grafman, Jordan

    2012-01-01

    Although cognitive neuroscience has made remarkable progress in understanding the involvement of the prefrontal cortex in executive control, the broader functional networks that support high-level cognition and give rise to general intelligence remain to be well characterized. Here, we investigated the neural substrates of the general factor of intelligence (g) and executive function in 182 patients with focal brain damage using voxel-based lesion–symptom mapping. The Wechsler Adult Intelligence Scale and Delis–Kaplan Executive Function System were used to derive measures of g and executive function, respectively. Impaired performance on these measures was associated with damage to a distributed network of left lateralized brain areas, including regions of frontal and parietal cortex and white matter association tracts, which bind these areas into a coordinated system. The observed findings support an integrative framework for understanding the architecture of general intelligence and executive function, supporting their reliance upon a shared fronto-parietal network for the integration and control of cognitive representations and making specific recommendations for the application of the Wechsler Adult Intelligence Scale and Delis–Kaplan Executive Function System to the study of high-level cognition in health and disease. PMID:22396393

  13. Binding and Diffusion of Lithium in Graphite: Quantum Monte Carlo Benchmarks and Validation of van der Waals Density Functional Methods

    DOE PAGESBeta

    Ganesh, P.; Kim, Jeongnim; Park, Changwon; Yoon, Mina; Reboredo, Fernando A.; Kent, Paul R. C.

    2014-11-03

    In highly accurate diffusion quantum Monte Carlo (QMC) studies of the adsorption and diffusion of atomic lithium in AA-stacked graphite are compared with van der Waals-including density functional theory (DFT) calculations. Predicted QMC lattice constants for pure AA graphite agree with experiment. Pure AA-stacked graphite is shown to challenge many van der Waals methods even when they are accurate for conventional AB graphite. Moreover, the highest overall DFT accuracy, considering pure AA-stacked graphite as well as lithium binding and diffusion, is obtained by the self-consistent van der Waals functional vdW-DF2, although errors in binding energies remain. Empirical approaches based onmore » point charges such as DFT-D are inaccurate unless the local charge transfer is assessed. Our results demonstrate that the lithium carbon system requires a simultaneous highly accurate description of both charge transfer and van der Waals interactions, favoring self-consistent approaches.« less

  14. The MapCHECK Measurement Uncertainty function and its effect on planar dose pass rates.

    PubMed

    Bailey, Daniel W; Spaans, Jason D; Kumaraswamy, Lalith K; Podgorsak, Matthew B

    2016-03-08

    Our study aimed to quantify the effect of the Measurement Uncertainty function on planar dosimetry pass rates, as measured and analyzed with the Sun Nuclear Corporation MapCHECK 2 array and its associated software. This optional function is toggled in the program preferences of the software (though turned on by default upon installation), and automatically increases the dose difference tolerance defined by the user for each planar dose comparison. Dose planes from 109 static-gantry IMRT fields and 40 VMAT arcs, of varying modulation complexity, were measured at 5 cm water-equivalent depth in the MapCHECK 2 diode array, and respective calculated dose planes were exported from a commercial treatment planning system. Planar dose comparison pass rates were calculated within the Sun Nuclear Corporation analytic software using a number of calculation parameters, including Measurement Uncertainty on and off. By varying the percent difference (%Diff) criterion for similar analyses performed with Measurement Uncertainty turned off, an effective %Diff criterion was defined for each field/arc corresponding to the pass rate achieved with Measurement Uncertainty turned on. On average, the Measurement Uncertainty function increases the user-defined %Diff criterion by 0.8%-1.1% for 3%/3 mm analysis, depending on plan type and calculation technique (corresponding to an average change in pass rate of 1.0%-3.5%, and a maximum change of 8.7%). At the 2%/2 mm level, the Measurement Uncertainty function increases the user-defined %Diff criterion by 0.7%-1.2% on average, again depending on plan type and calculation technique (corresponding to an average change in pass rate of 3.5%-8.1%, and a maximum change of 14.2%). The largest increases in pass rate due to the Measurement Uncertainty function are generally seen with poorly matched planar dose comparisons, while the function has a notably smaller effect as pass rates approach 100%. The Measurement Uncertainty function, then, may

  15. Diffusion-Based Density-Equalizing Maps: an Interdisciplinary Approach to Visualizing Homicide Rates and Other Georeferenced Statistical Data

    NASA Astrophysics Data System (ADS)

    Mazzitello, Karina I.; Candia, Julián

    2012-12-01

    In every country, public and private agencies allocate extensive funding to collect large-scale statistical data, which in turn are studied and analyzed in order to determine local, regional, national, and international policies regarding all aspects relevant to the welfare of society. One important aspect of that process is the visualization of statistical data with embedded geographical information, which most often relies on archaic methods such as maps colored according to graded scales. In this work, we apply nonstandard visualization techniques based on physical principles. We illustrate the method with recent statistics on homicide rates in Brazil and their correlation to other publicly available data. This physics-based approach provides a novel tool that can be used by interdisciplinary teams investigating statistics and model projections in a variety of fields such as economics and gross domestic product research, public health and epidemiology, sociodemographics, political science, business and marketing, and many others.

  16. Quantitative diffusion-weighted magnetic resonance imaging in the assessment of myocardial fibrosis in hypertrophic cardiomyopathy compared with T1 mapping.

    PubMed

    Wu, Lian-Ming; Chen, Bing-Hua; Yao, Qiu-Ying; Ou, Yang-Rongzheng; Wu, Rui; Jiang, Meng; Hu, Jiani; An, Dong-Aolei; Xu, Jian-Rong

    2016-08-01

    To identify myocardial fibrosis in hypertrophic cardiomyopathy (HCM) subjects using quantitative cardiac diffusion-weighted imaging (DWI) and to compare its performance with native T1 mapping and extracellular volume (ECV). Thirty-eight HCM subjects (mean age, 53 ± 9 years) and 14 normal controls (mean age, 51 ± 8 years) underwent cardiac magnetic resonance imaging (CMRI) on a 3.0T magnetic resonance (MR) machine with DWI, T1 mapping and late gadolinium enhancement (LGE) imaging as the reference standard. The mean apparent diffusion coefficient (ADC), native T1 value and ECV were determined for each subject. Overall, the HCM subjects exhibited an increased native T1 value (1241.04 ± 78.50 ms), ECV (0.31 ± 0.03) and ADC (2.36 ± 0.34 s/mm(2)) compared with the normal controls (1114.60 ± 37.99 ms, 0.24 ± 0.04, and 1.62 ± 0.38 s/mm(2), respectively) (p < 0.05). DWI differentiated healthy and fibrotic myocardia with an area under the curve (AUC) of 0.93, while the AUCs of the native T1 values (0.93), (p > 0.05) and ECV (0.94), (p > 0.05) exhibited an equal differentiation ability. Both HCM LGE+ and HCM LGE- subjects had an increased native T1 value, ECV and ADC compared to the normal controls (p < 0.05). HCM LGE+ subjects exhibited an increased ECV (0.31 ± 0.04) and ADC (2.43 ± 0.36 s/mm(2)) compared to HCM LGE- subjects (p < 0.05). HCM LGE+ and HCM LGE- subjects had similar native T1 values (1250 ± 76.36 ms vs. 1213.98 ± 92.30 ms, respectively) (p > 0.05). ADC values were linearly associated with increased ECV (R(2) = 0.36) and native T1 values (R(2) = 0.40) among all subjects. DWI is a feasible alternative to native T1 mapping and ECV for the identification of myocardial fibrosis in patients with HCM. DWI and ECV can quantitatively characterize the extent of fibrosis in HCM LGE+ and HCM LGE- patients. PMID:27198892

  17. Computing diffuse reflection from particulate planetary surface with a new function.

    PubMed

    Wolff, M

    1981-07-15

    An equation is derived to compute the amount of diffuse light reflected by a particulate surface such as on Mars or an asteroid. The method traces the paths of rays within an ensemble of randomly shaped grains and finds the eventual probability of emission. The amount of diffuse, unpolarized emitted light is obtained in terms of the real index of refraction, the imaginary index, and the average diameter of particles making up the surface. The equation is used to compute the empirical rule for obtaining the planetary albedo from the slope of its polarization curve. Accuracy of the equation, estimated at +/-4%, seems justified because of quantitative agreement with experimental measures of the empirical rule. It is also shown that the equation can be applied to bubble-enclosing surfaces such as volcanic foams. Results for the indices of the moon, Mars, Io, and Europa are obtained and compared with other data.

  18. Dispersion in Rectangular Networks: Effective Diffusivity and Large-Deviation Rate Function

    NASA Astrophysics Data System (ADS)

    Tzella, Alexandra; Vanneste, Jacques

    2016-09-01

    The dispersion of a diffusive scalar in a fluid flowing through a network has many applications including to biological flows, porous media, water supply, and urban pollution. Motivated by this, we develop a large-deviation theory that predicts the evolution of the concentration of a scalar released in a rectangular network in the limit of large time t ≫1 . This theory provides an approximation for the concentration that remains valid for large distances from the center of mass, specifically for distances up to O (t ) and thus much beyond the O (t1 /2) range where a standard Gaussian approximation holds. A byproduct of the approach is a closed-form expression for the effective diffusivity tensor that governs this Gaussian approximation. Monte Carlo simulations of Brownian particles confirm the large-deviation results and demonstrate their effectiveness in describing the scalar distribution when t is only moderately large.

  19. Dispersion in Rectangular Networks: Effective Diffusivity and Large-Deviation Rate Function.

    PubMed

    Tzella, Alexandra; Vanneste, Jacques

    2016-09-01

    The dispersion of a diffusive scalar in a fluid flowing through a network has many applications including to biological flows, porous media, water supply, and urban pollution. Motivated by this, we develop a large-deviation theory that predicts the evolution of the concentration of a scalar released in a rectangular network in the limit of large time t≫1. This theory provides an approximation for the concentration that remains valid for large distances from the center of mass, specifically for distances up to O(t) and thus much beyond the O(t^{1/2}) range where a standard Gaussian approximation holds. A byproduct of the approach is a closed-form expression for the effective diffusivity tensor that governs this Gaussian approximation. Monte Carlo simulations of Brownian particles confirm the large-deviation results and demonstrate their effectiveness in describing the scalar distribution when t is only moderately large. PMID:27661692

  20. Sub-diffuse optical biomarkers characterize localized microstructure and function of cortex and malignant tumor.

    PubMed

    Bravo, Jaime J; Paulsen, Keith D; Roberts, David W; Kanick, Stephen C

    2016-02-15

    This study uses a sub-diffusive light transport model to analyze fiber-optic measurements of reflectance spectra to recover endogenous tissue biomarkers and to correct raw fluorescence emissions for distortions from background optical properties. Measurements in tissue-simulating phantoms validated accurate recovery of the reduced scattering coefficient [(0.3-3.4  mm-1), error 10%], blood volume fraction [(1-3 vol%), error 7%], and a dimensionless metric of anisotropic scattering, γ, that is sensitive to submillimeter tissue ultrastructure [(1.29-2.06), error 11%]. In vivo sub-diffusive optical data acquired during clinical neurosurgeries characterize differences in microstructure (γ), perfusion (blood volume), and metabolism (PpIX fluorescence) between normal cortex and malignant tumor. PMID:26872187

  1. Dispersion in Rectangular Networks: Effective Diffusivity and Large-Deviation Rate Function.

    PubMed

    Tzella, Alexandra; Vanneste, Jacques

    2016-09-01

    The dispersion of a diffusive scalar in a fluid flowing through a network has many applications including to biological flows, porous media, water supply, and urban pollution. Motivated by this, we develop a large-deviation theory that predicts the evolution of the concentration of a scalar released in a rectangular network in the limit of large time t≫1. This theory provides an approximation for the concentration that remains valid for large distances from the center of mass, specifically for distances up to O(t) and thus much beyond the O(t^{1/2}) range where a standard Gaussian approximation holds. A byproduct of the approach is a closed-form expression for the effective diffusivity tensor that governs this Gaussian approximation. Monte Carlo simulations of Brownian particles confirm the large-deviation results and demonstrate their effectiveness in describing the scalar distribution when t is only moderately large.

  2. Chondroitinase enhances cortical map plasticity and increases functionally active sprouting axons after brain injury.

    PubMed

    Harris, Neil G; Nogueira, Marcia S M; Verley, Derek R; Sutton, Richard L

    2013-07-15

    The beneficial effect of interventions with chondroitinase ABC enzyme to reduce axon growth-inhibitory chondroitin sulphate side chains after central nervous system injuries has been mainly attributed to enhanced axonal sprouting. After traumatic brain injury (TBI), it is unknown whether newly sprouting axons that occur as a result of interventional strategies are able to functionally contribute to existing circuitry, and it is uncertain whether maladaptive sprouting occurs to increase the well-known risk for seizure activity after TBI. Here, we show that after a controlled cortical impact injury in rats, chondroitinase infusion into injured cortex at 30 min and 3 days reduced c-Fos⁺ cell staining resulting from the injury alone at 1 week postinjury, indicating that at baseline, abnormal spontaneous activity is likely to be reduced, not increased, with this type of intervention. c-Fos⁺ cell staining elicited by neural activity from stimulation of the affected forelimb 1 week after injury was significantly enhanced by chondroitinase, indicating a widespread effect on cortical map plasticity. Underlying this map plasticity was a larger contribution of neuronal, rather than glial cells and an absence of c-Fos⁺ cells surrounded by perineuronal nets that were normally present in stimulated naïve rats. After injury, chondroitin sulfate proteoglycan digestion produced the expected increase in growth-associated protein 43-positive axons and perikarya, of which a significantly greater number were double labeled for c-Fos after intervention with chondroitinase, compared to vehicle. These data indicate that chondroitinase produces significant gains in cortical map plasticity after TBI, and that either axonal sprouting and/or changes in perineuronal nets may underlie this effect. Chondroitinase dampens, rather than increases nonspecific c-Fos activity after brain injury, and induction of axonal sprouting is not maladaptive because greater numbers are functionally

  3. Testing of global pressure/temperature (GPT) model and global mapping function (GMF) in GPS analyses

    NASA Astrophysics Data System (ADS)

    Kouba, J.

    2009-03-01

    Several sources of a priori meteorological data have been compared for their effects on geodetic results from GPS precise point positioning (PPP). The new global pressure and temperature model (GPT), available at the IERS Conventions web site, provides pressure values that have been used to compute a priori hydrostatic (dry) zenith path delay z h estimates. Both the GPT-derived and a simple height-dependent a priori constant z h performed well for low- and mid-latitude stations. However, due to the actual variations not accounted for by the seasonal GPT model pressure values or the a priori constant z h, GPS height solution errors can sometimes exceed 10 mm, particularly in Polar Regions or with elevation cutoff angles less than 10 degrees. Such height errors are nearly perfectly correlated with local pressure variations so that for most stations they partly (and for solutions with 5-degree elevation angle cutoff almost fully) compensate for the atmospheric loading displacements. Consequently, unlike PPP solutions utilizing a numerical weather model (NWM) or locally measured pressure data for a priori z h, the GPT-based PPP height repeatabilities are better for most stations before rather than after correcting for atmospheric loading. At 5 of the 11 studied stations, for which measured local meteorological data were available, the PPP height errors caused by a priori z h interpolated from gridded Vienna Mapping Function-1 (VMF1) data (from a NWM) were less than 0.5 mm. Height errors due to the global mapping function (GMF) are even larger than those caused by the GPT a priori pressure errors. The GMF height errors are mainly due to the hydrostatic mapping and for the solutions with 10-degree elevation cutoff they are about 50% larger than the GPT a priori errors.

  4. Functional fiber mats with tunable diffuse reflectance composed of electrospun VO2/PVP composite fibers.

    PubMed

    Li, Shaotang; Li, Yamei; Qian, Kun; Ji, Shidong; Luo, Hongjie; Gao, Yanfeng; Jin, Ping

    2014-01-01

    Thermochromic VO2 nanoparticles have been dispersed into polyvinyl pyrrolidone (PVP) fibers by electrospinning of a VO2-PVP blend solution. The structure and optical properties of the obtained composite fiber mat were studied by X-ray diffraction (XRD), scanning electron microscopy (SEM), ultraviolet-visible (UV-Vis) spectrophotometry, and Fourier transform infrared (FT-IR) spectroscopy. The fiber mat revealed two diffuse reflectance states in infrared spectral region at temperatures under and above the phase transition temperature of VO2 and its IR reflectance is smaller in high temperature. The difference of diffuse reflectance between the two states (ΔRdif) was obvious to be more than 25% in the wavelengths from 1.5 μm to 6 μm. The diffuse reflectance of the fiber mat could be controlled by adjusting the diameter of the fiber or the content of VO2 in the fibers and this particular optical property was explained by a multiple scattering-absorbing process.

  5. Charged particle velocity map image reconstruction with one-dimensional projections of spherical functions

    SciTech Connect

    Gerber, Thomas; Liu Yuzhu; Knopp, Gregor; Hemberger, Patrick; Bodi, Andras; Radi, Peter; Sych, Yaroslav

    2013-03-15

    Velocity map imaging (VMI) is used in mass spectrometry and in angle resolved photo-electron spectroscopy to determine the lateral momentum distributions of charged particles accelerated towards a detector. VM-images are composed of projected Newton spheres with a common centre. The 2D images are usually evaluated by a decomposition into base vectors each representing the 2D projection of a set of particles starting from a centre with a specific velocity distribution. We propose to evaluate 1D projections of VM-images in terms of 1D projections of spherical functions, instead. The proposed evaluation algorithm shows that all distribution information can be retrieved from an adequately chosen set of 1D projections, alleviating the numerical effort for the interpretation of VM-images considerably. The obtained results produce directly the coefficients of the involved spherical functions, making the reconstruction of sliced Newton spheres obsolete.

  6. Charged particle velocity map image reconstruction with one-dimensional projections of spherical functions.

    PubMed

    Gerber, Thomas; Liu, Yuzhu; Knopp, Gregor; Hemberger, Patrick; Bodi, Andras; Radi, Peter; Sych, Yaroslav

    2013-03-01

    Velocity map imaging (VMI) is used in mass spectrometry and in angle resolved photo-electron spectroscopy to determine the lateral momentum distributions of charged particles accelerated towards a detector. VM-images are composed of projected Newton spheres with a common centre. The 2D images are usually evaluated by a decomposition into base vectors each representing the 2D projection of a set of particles starting from a centre with a specific velocity distribution. We propose to evaluate 1D projections of VM-images in terms of 1D projections of spherical functions, instead. The proposed evaluation algorithm shows that all distribution information can be retrieved from an adequately chosen set of 1D projections, alleviating the numerical effort for the interpretation of VM-images considerably. The obtained results produce directly the coefficients of the involved spherical functions, making the reconstruction of sliced Newton spheres obsolete.

  7. Neurotransmitter Specific, Cellular-Resolution Functional Brain Mapping Using Receptor Coated Nanoparticles: Assessment of the Possibility

    PubMed Central

    Forati, Ebrahim; Sabouni, Abas; Ray, Supriyo; Head, Brian; Schoen, Christian; Sievenpiper, Dan

    2015-01-01

    Receptor coated resonant nanoparticles and quantum dots are proposed to provide a cellular-level resolution image of neural activities inside the brain. The functionalized nanoparticles and quantum dots in this approach will selectively bind to different neurotransmitters in the extra-synaptic regions of neurons. This allows us to detect neural activities in real time by monitoring the nanoparticles and quantum dots optically. Gold nanoparticles (GNPs) with two different geometries (sphere and rod) and quantum dots (QDs) with different sizes were studied along with three different neurotransmitters: dopamine, gamma-Aminobutyric acid (GABA), and glycine. The absorption/emission spectra of GNPs and QDs before and after binding of neurotransmitters and their corresponding receptors are reported. The results using QDs and nanorods with diameter 25nm and aspect rations larger than three were promising for the development of the proposed functional brain mapping approach. PMID:26717196

  8. MAP kinases with distinct inhibitory functions impart signaling specificity during yeast differentiation.

    PubMed

    Madhani, H D; Styles, C A; Fink, G R

    1997-11-28

    Filamentous invasive growth of S. cerevisiae requires multiple elements of the mitogen-activated protein kinase (MAPK) signaling cascade that are also components of the mating pheromone response pathway. Here we show that, despite sharing several constituents, the two pathways use different MAP kinases. The Fus3 MAPK regulates mating, whereas the Kss1 MAPK regulates filamentation and invasion. Remarkably, in addition to their kinase-dependent activation functions, Kss1 and Fus3 each have a distinct kinase-independent inhibitory function. Kss1 inhibits the filamentation pathway by interacting with its target transcription factor Ste12. Fus3 has a different inhibitory activity that prevents the inappropriate activation of invasion by the pheromone response pathway. In the absence of Fus3, there is erroneous crosstalk in which mating pheromone now activates filamentation-specific gene expression using the Kss1 MAPK. PMID:9393860

  9. 3D mapping of stellar populations in galaxies as a function of environment

    NASA Astrophysics Data System (ADS)

    Thomas, Daniel

    2015-08-01

    MaNGA (Mapping Nearby Galaxies at Apache Point Observatory) is a6-year SDSS-IV survey that will obtain resolved spectroscopy from 3600A to 10300 A for a representative sample of 10,000 nearby galaxies. MaNGA will allow the internal kinematics and spatially-resolved properties of stellar populations and gas inside galaxies to be studied as a function of local environment and halo mass for the very first time. I will present results from our analysis of the first year MaNGA data. The main focus is on the 3-dimensional distribution of stellar population properties in galaxies - formation age, element abundance, IMF slope - studying how these vary spatially in galaxies as a function of galaxy environment and dark matter halo mass.

  10. Charged particle velocity map image reconstruction with one-dimensional projections of spherical functions

    NASA Astrophysics Data System (ADS)

    Gerber, Thomas; Liu, Yuzhu; Knopp, Gregor; Hemberger, Patrick; Bodi, Andras; Radi, Peter; Sych, Yaroslav

    2013-03-01

    Velocity map imaging (VMI) is used in mass spectrometry and in angle resolved photo-electron spectroscopy to determine the lateral momentum distributions of charged particles accelerated towards a detector. VM-images are composed of projected Newton spheres with a common centre. The 2D images are usually evaluated by a decomposition into base vectors each representing the 2D projection of a set of particles starting from a centre with a specific velocity distribution. We propose to evaluate 1D projections of VM-images in terms of 1D projections of spherical functions, instead. The proposed evaluation algorithm shows that all distribution information can be retrieved from an adequately chosen set of 1D projections, alleviating the numerical effort for the interpretation of VM-images considerably. The obtained results produce directly the coefficients of the involved spherical functions, making the reconstruction of sliced Newton spheres obsolete.

  11. High-resolution magnetoencephalographic functional mapping of the cortical network mediating intentional movement.

    PubMed

    Amo, Carlos; Boyajian, Robert A; Romine, John S; Otis, Shirley M

    2007-04-01

    Magnetoencephalography (MEG) is a sensitive technique that can detect and map cortical electrophysiologic activations with high spatial (mm) and temporal (msecs) resolutions. We used 148-channel whole-head MEG to record the activation sequence for the somatosensory and motor cortical network during cued hand movements in a healthy 39-yr-old subject. The complex sequence and topography of cortical activations were superimposed onto the subject's brain magnetic resonance images. Frontal premotor and supplementary motor and cingulate areas activated well before the primary motor area and again repetitively from 200 msecs onward with activations alternating repeatedly between frontal and parietal areas. The network's very close functional integration of supplementary motor areas suggests how brain injury that is localized to these regions, but not to the primary motor area itself, can disrupt integrity of movement, and why preservation of functional integrity of some areas traditionally viewed as extramotor may be necessary for recovery from neurologic disability.

  12. Nanoscale structural and functional mapping of nacre by scanning probe microscopy techniques

    NASA Astrophysics Data System (ADS)

    Zhou, Xilong; Miao, Hongchen; Li, Faxin

    2013-11-01

    Nacre has received great attention due to its nanoscale hierarchical structure and extraordinary mechanical properties. Meanwhile, the nanoscale piezoelectric properties of nacre have also been investigated but the structure-function relationship has never been addressed. In this work, firstly we realized quantitative nanomechanical mapping of nacre of a green abalone using atomic force acoustic microscopy (AFAM). The modulus of the mineral tablets is determined to be ~80 GPa and that of the organic biopolymer no more than 23 GPa, and the organic-inorganic interface width is determined to be about 34 +/- 9 nm. Then, we conducted both AFAM and piezoresponse force microscopy (PFM) mapping in the same scanning area to explore the correlations between the nanomechanical and piezoelectric properties. The PFM testing shows that the organic biopolymer exhibits a significantly stronger piezoresponse than the mineral tablets, and they permeate each other, which is very difficult to reproduce in artificial materials. Finally, the phase hysteresis loops and amplitude butterfly loops were also observed using switching spectroscopy PFM, implying that nacre may also be a bio-ferroelectric material. The obtained nanoscale structural and functional properties of nacre could be very helpful in understanding its deformation mechanism and designing biomimetic materials of extraordinary properties.

  13. A polynomial approach for extracting the extrema of a spherical function and its application in diffusion MRI.

    PubMed

    Ghosh, Aurobrata; Tsigaridas, Elias; Mourrain, Bernard; Deriche, Rachid

    2013-07-01

    Antipodally symmetric spherical functions play a pivotal role in diffusion MRI in representing sub-voxel-resolution microstructural information of the underlying tissue. This information is described by the geometry of the spherical function. In this paper we propose a method to automatically compute all the extrema of a spherical function. We then classify the extrema as maxima, minima and saddle-points to identify the maxima. We take advantage of the fact that a spherical function can be described equivalently in the spherical harmonic (SH) basis, in the symmetric tensor (ST) basis constrained to the sphere, and in the homogeneous polynomial (HP) basis constrained to the sphere. We extract the extrema of the spherical function by computing the stationary points of its constrained HP representation. Instead of using traditional optimization approaches, which are inherently local and require exhaustive search or re-initializations to locate multiple extrema, we use a novel polynomial system solver which analytically brackets all the extrema and refines them numerically, thus missing none and achieving high precision. To illustrate our approach we consider the Orientation Distribution Function (ODF). In diffusion MRI the ODF is a spherical function which represents a state-of-the-art reconstruction algorithm whose maxima are aligned with the dominant fiber bundles. It is, therefore, vital to correctly compute these maxima to detect the fiber bundle directions. To demonstrate the potential of the proposed polynomial approach we compute the extrema of the ODF to extract all its maxima. This polynomial approach is, however, not dependent on the ODF and the framework presented in this paper can be applied to any spherical function described in either the SH basis, ST basis or the HP basis.

  14. Gold Nanorods Based Air Scanning Electron Microscopy and Diffusion Reflection Imaging for Mapping Tumor Margins in Squamous Cell Carcinoma.

    PubMed

    Ankri, Rinat; Ashkenazy, Ariel; Milstein, Yonat; Brami, Yaniv; Olshinka, Asaf; Goldenberg-Cohen, Nitza; Popovtzer, Aron; Fixler, Dror; Hirshberg, Abraham

    2016-02-23

    A critical challenge arising during a surgical procedure for tumor removal is the determination of tumor margins. Gold nanorods (GNRs) conjugated to epidermal growth factor receptors (EGFR) (GNRs-EGFR) have long been used in the detection of cancerous cells as the expression of EGFR dramatically increases once the tissue becomes cancerous. Optical techniques for the identification of these GNRs-EGFR in tumor are intensively developed based on the unique scattering and absorption properties of the GNRs. In this study, we investigate the distribution of the GNRs in tissue sections presenting squamous cell carcinoma (SCC) to evaluate the SCC margins. Air scanning electron microscopy (airSEM), a novel, high resolution microscopy is used, enabling to localize and actually visualize nanoparticles on the tissue. The airSEM pictures presented a gradient of GNRs from the tumor to normal epithelium, spread in an area of 1 mm, suggesting tumor margins of 1 mm. Diffusion reflection (DR) measurements, performed in a resolution of 1 mm, of human oral SCC have shown a clear difference between the DR profiles of the healthy epithelium and the tumor itself. PMID:26759920

  15. Trans-ethnic Fine Mapping Highlights Kidney-Function Genes Linked to Salt Sensitivity.

    PubMed

    Mahajan, Anubha; Rodan, Aylin R; Le, Thu H; Gaulton, Kyle J; Haessler, Jeffrey; Stilp, Adrienne M; Kamatani, Yoichiro; Zhu, Gu; Sofer, Tamar; Puri, Sanjana; Schellinger, Jeffrey N; Chu, Pei-Lun; Cechova, Sylvia; van Zuydam, Natalie; Arnlov, Johan; Flessner, Michael F; Giedraitis, Vilmantas; Heath, Andrew C; Kubo, Michiaki; Larsson, Anders; Lindgren, Cecilia M; Madden, Pamela A F; Montgomery, Grant W; Papanicolaou, George J; Reiner, Alex P; Sundström, Johan; Thornton, Timothy A; Lind, Lars; Ingelsson, Erik; Cai, Jianwen; Martin, Nicholas G; Kooperberg, Charles; Matsuda, Koichi; Whitfield, John B; Okada, Yukinori; Laurie, Cathy C; Morris, Andrew P; Franceschini, Nora

    2016-09-01

    We analyzed genome-wide association studies (GWASs), including data from 71,638 individuals from four ancestries, for estimated glomerular filtration rate (eGFR), a measure of kidney function used to define chronic kidney disease (CKD). We identified 20 loci attaining genome-wide-significant evidence of association (p < 5 × 10(-8)) with kidney function and highlighted that allelic effects on eGFR at lead SNPs are homogeneous across ancestries. We leveraged differences in the pattern of linkage disequilibrium between diverse populations to fine-map the 20 loci through construction of "credible sets" of variants driving eGFR association signals. Credible variants at the 20 eGFR loci were enriched for DNase I hypersensitivity sites (DHSs) in human kidney cells. DHS credible variants were expression quantitative trait loci for NFATC1 and RGS14 (at the SLC34A1 locus) in multiple tissues. Loss-of-function mutations in ancestral orthologs of both genes in Drosophila melanogaster were associated with altered sensitivity to salt stress. Renal mRNA expression of Nfatc1 and Rgs14 in a salt-sensitive mouse model was also reduced after exposure to a high-salt diet or induced CKD. Our study (1) demonstrates the utility of trans-ethnic fine mapping through integration of GWASs involving diverse populations with genomic annotation from relevant tissues to define molecular mechanisms by which association signals exert their effect and (2) suggests that salt sensitivity might be an important marker for biological processes that affect kidney function and CKD in humans. PMID:27588450

  16. Mapping Shear Zones, Faults, and Crustal Deformation Fabric With Receiver Functions

    NASA Astrophysics Data System (ADS)

    Schulte-Pelkum, V.; Mahan, K. H.

    2014-12-01

    Dipping faults, shear zones, and pervasive anisotropic crustal fabric due to deformation are all capable of generating strong near-station mode conversions of teleseismic body waves, even for weak (a few percent) velocity anisotropy. These conversions can be found using the receiver function technique. Dipping foliation and dipping isotropic velocity contrasts can occur in isolation or together in deformed crust. Both generate receiver function arrivals that have a characteristic periodicity with azimuth. Different fixed azimuthal phase shifts between radial and tangential component receiver functions distinguish dipping or tilted structure and fabric from horizontal axis anisotropy. We demonstrate a method that uses these characteristics to map geologically relevant information such as strike and depth of foliation of dipping isotropic velocity contrasts and of horizontal symmetry axis anisotropy contrasts. The method uses waveforms without matching them via forward modeling, which makes choices such as slow versus fast axis symmetry and isotropic dip versus anisotropic axis tilt unnecessary. It also does not use shear wave splitting of the converted waves, which is more difficult to isolate. We show results from the continental U.S. and Canada and from the collision zones in the Himalaya and Tibetan Plateau and Taiwan. We discuss interpretation of our results in the light of recent laboratory measurements of deformed crustal rocks and contributions to the seismic signal from individual minerals such as micas, amphiboles, and quartz. Our observations are connected to geological ground truth by using structural maps and sample anisotropy determined using electron backscatter diffraction from exhumed deep crust in the Athabasca granulite province to predict the seismic signal from present-day deep crust. We also discuss the reconciliation of measurements from anisotropic receiver functions, surface waves, and split shear waves.

  17. Combining anatomical, diffusion, and resting state functional magnetic resonance imaging for individual classification of mild and moderate Alzheimer's disease.

    PubMed

    Schouten, Tijn M; Koini, Marisa; de Vos, Frank; Seiler, Stephan; van der Grond, Jeroen; Lechner, Anita; Hafkemeijer, Anne; Möller, Christiane; Schmidt, Reinhold; de Rooij, Mark; Rombouts, Serge A R B

    2016-01-01

    Magnetic resonance imaging (MRI) is sensitive to structural and functional changes in the brain caused by Alzheimer's disease (AD), and can therefore be used to help in diagnosing the disease. Improving classification of AD patients based on MRI scans might help to identify AD earlier in the disease's progress, which may be key in developing treatments for AD. In this study we used an elastic net classifier based on several measures derived from the MRI scans of mild to moderate AD patients (N = 77) from the prospective registry on dementia study and controls (N = 173) from the Austrian Stroke Prevention Family Study. We based our classification on measures from anatomical MRI, diffusion weighted MRI and resting state functional MRI. Our unimodal classification performance ranged from an area under the curve (AUC) of 0.760 (full correlations between functional networks) to 0.909 (grey matter density). When combining measures from multiple modalities in a stepwise manner, the classification performance improved to an AUC of 0.952. This optimal combination consisted of grey matter density, white matter density, fractional anisotropy, mean diffusivity, and sparse partial correlations between functional networks. Classification performance for mild AD as well as moderate AD also improved when using this multimodal combination. We conclude that different MRI modalities provide complementary information for classifying AD. Moreover, combining multiple modalities can substantially improve classification performance over unimodal classification. PMID:26909327

  18. Combining anatomical, diffusion, and resting state functional magnetic resonance imaging for individual classification of mild and moderate Alzheimer's disease

    PubMed Central

    Schouten, Tijn M.; Koini, Marisa; de Vos, Frank; Seiler, Stephan; van der Grond, Jeroen; Lechner, Anita; Hafkemeijer, Anne; Möller, Christiane; Schmidt, Reinhold; de Rooij, Mark; Rombouts, Serge A.R.B.

    2016-01-01

    Magnetic resonance imaging (MRI) is sensitive to structural and functional changes in the brain caused by Alzheimer's disease (AD), and can therefore be used to help in diagnosing the disease. Improving classification of AD patients based on MRI scans might help to identify AD earlier in the disease's progress, which may be key in developing treatments for AD. In this study we used an elastic net classifier based on several measures derived from the MRI scans of mild to moderate AD patients (N = 77) from the prospective registry on dementia study and controls (N = 173) from the Austrian Stroke Prevention Family Study. We based our classification on measures from anatomical MRI, diffusion weighted MRI and resting state functional MRI. Our unimodal classification performance ranged from an area under the curve (AUC) of 0.760 (full correlations between functional networks) to 0.909 (grey matter density). When combining measures from multiple modalities in a stepwise manner, the classification performance improved to an AUC of 0.952. This optimal combination consisted of grey matter density, white matter density, fractional anisotropy, mean diffusivity, and sparse partial correlations between functional networks. Classification performance for mild AD as well as moderate AD also improved when using this multimodal combination. We conclude that different MRI modalities provide complementary information for classifying AD. Moreover, combining multiple modalities can substantially improve classification performance over unimodal classification. PMID:26909327

  19. Mapping the Pareto Optimal Design Space for a Functionally Deimmunized Biotherapeutic Candidate

    PubMed Central

    Salvat, Regina S.; Parker, Andrew S.; Choi, Yoonjoo; Bailey-Kellogg, Chris; Griswold, Karl E.

    2015-01-01

    The immunogenicity of biotherapeutics can bottleneck development pipelines and poses a barrier to widespread clinical application. As a result, there is a growing need for improved deimmunization technologies. We have recently described algorithms that simultaneously optimize proteins for both reduced T cell epitope content and high-level function. In silico analysis of this dual objective design space reveals that there is no single global optimum with respect to protein deimmunization. Instead, mutagenic epitope deletion yields a spectrum of designs that exhibit tradeoffs between immunogenic potential and molecular function. The leading edge of this design space is the Pareto frontier, i.e. the undominated variants for which no other single design exhibits better performance in both criteria. Here, the Pareto frontier of a therapeutic enzyme has been designed, constructed, and evaluated experimentally. Various measures of protein performance were found to map a functional sequence space that correlated well with computational predictions. These results represent the first systematic and rigorous assessment of the functional penalty that must be paid for pursuing progressively more deimmunized biotherapeutic candidates. Given this capacity to rapidly assess and design for tradeoffs between protein immunogenicity and functionality, these algorithms may prove useful in augmenting, accelerating, and de-risking experimental deimmunization efforts. PMID:25568954

  20. Mapping the Pareto optimal design space for a functionally deimmunized biotherapeutic candidate.

    PubMed

    Salvat, Regina S; Parker, Andrew S; Choi, Yoonjoo; Bailey-Kellogg, Chris; Griswold, Karl E

    2015-01-01

    The immunogenicity of biotherapeutics can bottleneck development pipelines and poses a barrier to widespread clinical application. As a result, there is a growing need for improved deimmunization technologies. We have recently described algorithms that simultaneously optimize proteins for both reduced T cell epitope content and high-level function. In silico analysis of this dual objective design space reveals that there is no single global optimum with respect to protein deimmunization. Instead, mutagenic epitope deletion yields a spectrum of designs that exhibit tradeoffs between immunogenic potential and molecular function. The leading edge of this design space is the Pareto frontier, i.e. the undominated variants for which no other single design exhibits better performance in both criteria. Here, the Pareto frontier of a therapeutic enzyme has been designed, constructed, and evaluated experimentally. Various measures of protein performance were found to map a functional sequence space that correlated well with computational predictions. These results represent the first systematic and rigorous assessment of the functional penalty that must be paid for pursuing progressively more deimmunized biotherapeutic candidates. Given this capacity to rapidly assess and design for tradeoffs between protein immunogenicity and functionality, these algorithms may prove useful in augmenting, accelerating, and de-risking experimental deimmunization efforts.

  1. Fine-grained mapping of mouse brain functional connectivity with resting-state fMRI.

    PubMed

    Mechling, Anna E; Hübner, Neele S; Lee, Hsu-Lei; Hennig, Jürgen; von Elverfeldt, Dominik; Harsan, Laura-Adela

    2014-08-01

    Understanding the intrinsic circuit-level functional organization of the brain has benefited tremendously from the advent of resting-state fMRI (rsfMRI). In humans, resting-state functional network has been consistently mapped and its alterations have been shown to correlate with symptomatology of various neurological or psychiatric disorders. To date, deciphering the mouse brain functional connectivity (MBFC) with rsfMRI remains a largely underexplored research area, despite the plethora of human brain disorders that can be modeled in this specie. To pave the way from pre-clinical to clinical investigations we characterized here the intrinsic architecture of mouse brain functional circuitry, based on rsfMRI data acquired at 7T using the Cryoprobe technology. High-dimensional spatial group independent component analysis demonstrated fine-grained segregation of cortical and subcortical networks into functional clusters, overlapping with high specificity onto anatomical structures, down to single gray matter nuclei. These clusters, showing a high level of stability and reliability in their patterning, formed the input elements for computing the MBFC network using partial correlation and graph theory. Its topological architecture conserved the fundamental characteristics described for the human and rat brain, such as small-worldness and partitioning into functional modules. Our results additionally showed inter-modular interactions via "network hubs". Each major functional system (motor, somatosensory, limbic, visual, autonomic) was found to have representative hubs that might play an important input/output role and form a functional core for information integration. Moreover, the rostro-dorsal hippocampus formed the highest number of relevant connections with other brain areas, highlighting its importance as core structure for MBFC.

  2. Application of Polynomial and Radial Basis Function Maps to Signal Masking

    SciTech Connect

    Damiano, B.

    1998-01-01

    The objective of this research was to develop and demonstrate a technique for encrypting information by using a masking signal that closely approximates local ambient noise. Signal masking techniques developed to date have used nonlinear differential equations, spread spectrum, and various modulation schemes to encode information. While these techniques can effectively hide a signal, the resulting masks may not appear as ambient noise to an observer. The advantage of the proposed technique over commonly used masking methods is that the transmitted signal will appear as normal background noise, thus greatly reducing the probability of detection and exploitation. A promising near-term application of this technology presents itself in the area of clandestine minefield reconnaissance in shallow water areas. Shallow water mine-counter-mine (SWMCM) activity is essential for minefield avoidance, efficient minefield clearance, and effective selection of transit lanes within minefields. A key technology area for SWMCM is the development of special sonar waveforms with low probability of exploitation/intercept (LPE/LPI) attributes. In addition to LPE/LPI sonar, this technology has the potential to enable significant improvements in underwater acoustic communications. For SWMCM, the chaotic waveform research provides a mechanism for encrypted communications between a submarine (SSN) and an unmanned underwater vehicle (UUV) via an acoustic channel. Acoustic SSN/UUV communications would eliminate the need for a fiberoptic link between the two vessels, thus increasing the robustness of SWMCM. Similar applications may exist in the areas of radar masking and secure communications. The original approach called for the use of polynomial maps to generate a masking signal. Because polynomial maps were found to have highly restrictive stability criteria, the approach was modified to use radial basis function (RBF) maps. they have shown that stable RBF maps that closely approximate an

  3. Mapping Physician Twitter Networks: Describing How They Work as a First Step in Understanding Connectivity, Information Flow, and Message Diffusion

    PubMed Central

    2014-01-01

    Background Twitter is becoming an important tool in medicine, but there is little information on Twitter metrics. In order to recommend best practices for information dissemination and diffusion, it is important to first study and analyze the networks. Objective This study describes the characteristics of four medical networks, analyzes their theoretical dissemination potential, their actual dissemination, and the propagation and distribution of tweets. Methods Open Twitter data was used to characterize four networks: the American Medical Association (AMA), the American Academy of Family Physicians (AAFP), the American Academy of Pediatrics (AAP), and the American College of Physicians (ACP). Data were collected between July 2012 and September 2012. Visualization was used to understand the follower overlap between the groups. Actual flow of the tweets for each group was assessed. Tweets were examined using Topsy, a Twitter data aggregator. Results The theoretical information dissemination potential for the groups is large. A collective community is emerging, where large percentages of individuals are following more than one of the groups. The overlap across groups is small, indicating a limited amount of community cohesion and cross-fertilization. The AMA followers’ network is not as active as the other networks. The AMA posted the largest number of tweets while the AAP posted the fewest. The number of retweets for each organization was low indicating dissemination that is far below its potential. Conclusions To increase the dissemination potential, medical groups should develop a more cohesive community of shared followers. Tweet content must be engaging to provide a hook for retweeting and reaching potential audience. Next steps call for content analysis, assessment of the behavior and actions of the messengers and the recipients, and a larger-scale study that considers other medical groups using Twitter. PMID:24733146

  4. Equivalent Dynamic Stiffness Mapping technique for identifying nonlinear structural elements from frequency response functions

    NASA Astrophysics Data System (ADS)

    Wang, X.; Zheng, G. T.

    2016-02-01

    A simple and general Equivalent Dynamic Stiffness Mapping technique is proposed for identifying the parameters or the mathematical model of a nonlinear structural element with steady-state primary harmonic frequency response functions (FRFs). The Equivalent Dynamic Stiffness is defined as the complex ratio between the internal force and the displacement response of unknown element. Obtained with the test data of responses' frequencies and amplitudes, the real and imaginary part of Equivalent Dynamic Stiffness are plotted as discrete points in a three dimensional space over the displacement amplitude and the frequency, which are called the real and the imaginary Equivalent Dynamic Stiffness map, respectively. These points will form a repeatable surface as the Equivalent Dynamic stiffness is only a function of the corresponding data as derived in the paper. The mathematical model of the unknown element can then be obtained by surface-fitting these points with special functions selected by priori knowledge of the nonlinear type or with ordinary polynomials if the type of nonlinearity is not pre-known. An important merit of this technique is its capability of dealing with strong nonlinearities owning complicated frequency response behaviors such as jumps and breaks in resonance curves. In addition, this technique could also greatly simplify the test procedure. Besides there is no need to pre-identify the underlying linear parameters, the method uses the measured data of excitation forces and responses without requiring a strict control of the excitation force during the test. The proposed technique is demonstrated and validated with four classical single-degree-of-freedom (SDOF) numerical examples and one experimental example. An application of this technique for identification of nonlinearity from multiple-degree-of-freedom (MDOF) systems is also illustrated.

  5. Functional MRI mapping of dynamic visual features during natural viewing in the macaque

    PubMed Central

    Russ, Brian E.; Leopold, David A.

    2015-01-01

    The ventral visual pathway of the primate brain is specialized to respond to stimuli in certain categories, such as the well-studied face selective patches in the macaque inferotemporal cortex. To what extent does response selectivity determined using brief presentations of isolated stimuli predict activity during the free viewing of a natural, dynamic scene, where features are superimposed in space and time? To approach this question, we obtained fMRI activity from the brains of three macaques viewing extended video clips containing a range of social and nonsocial content and compared the fMRI time courses to a family of feature models derived from the movie content. Starting with more than two dozen feature models extracted from each movie, we created functional maps based on features whose time courses were nearly orthogonal, focusing primarily on faces, motion content, and contrast level. Activity mapping using the face feature model readily yielded functional regions closely resembling face patches obtained using a block design in the same animals. Overall, the motion feature model dominated responses in nearly all visually driven areas, including the face patches as well as ventral visual areas V4, TEO, and TE. Control experiments presenting dynamic movies, whose content was free of animals, demonstrated that biological movement critically contributed to the predominance of motion in fMRI responses. These results highlight the value of natural viewing paradigms for studying the brain’s functional organization and also underscore the paramount contribution of magnocellular input to the ventral visual pathway during natural vision. PMID:25579448

  6. Functional MRI mapping of dynamic visual features during natural viewing in the macaque.

    PubMed

    Russ, Brian E; Leopold, David A

    2015-04-01

    The ventral visual pathway of the primate brain is specialized to respond to stimuli in certain categories, such as the well-studied face selective patches in the macaque inferotemporal cortex. To what extent does response selectivity determined using brief presentations of isolated stimuli predict activity during the free viewing of a natural, dynamic scene, where features are superimposed in space and time? To approach this question, we obtained fMRI activity from the brains of three macaques viewing extended video clips containing a range of social and nonsocial content and compared the fMRI time courses to a family of feature models derived from the movie content. Starting with more than two dozen feature models extracted from each movie, we created functional maps based on features whose time courses were nearly orthogonal, focusing primarily on faces, motion content, and contrast level. Activity mapping using the face feature model readily yielded functional regions closely resembling face patches obtained using a block design in the same animals. Overall, the motion feature model dominated responses in nearly all visually driven areas, including the face patches as well as ventral visual areas V4, TEO, and TE. Control experiments presenting dynamic movies, whose content was free of animals, demonstrated that biological movement critically contributed to the predominance of motion in fMRI responses. These results highlight the value of natural viewing paradigms for studying the brain's functional organization and also underscore the paramount contribution of magnocellular input to the ventral visual pathway during natural vision. PMID:25579448

  7. A simple way to improve anatomical mapping of functional brain imaging

    PubMed Central

    Villain, Nicolas; Landeau, Brigitte; Groussard, Mathilde; Mevel, Katell; Fouquet, Marine; Dayan, Jacques; Eustache, Francis; Desgranges, Béatrice; Chételat, Gaël

    2010-01-01

    Background and purpose Advances in functional neuroimaging studies have led to the need for improved anatomical precision to face with more and more specific challenges. Nevertheless, functional MRI (fMRI) suffers from geometrical distortions which limit the matching between functional and anatomical data necessary to interpret fMRI results. The ‘FieldMap’ method is the most widely used technique to correct for geometrical distortions but in some cases cannot be applied or provides unsatisfactory results. The objective of the present study is thus to provide a very simple alternative method for distortion correction and to demonstrate its efficiency. Methods This correction relies on the non-linear registration of Echo-Planar-Imaging (EPI) acquisitions onto their corresponding undistorted non-EPI T2Star volume, and was tested on two independent groups of subjects undertaking the same paradigm but scanned with distinct EPI sequences. Results This procedure was found to considerably decrease the mismatch between functional and anatomical data in both groups, as revealed through several quantitative and qualitative measures on both EPI volumes and activation maps. Conclusion The present study describes a simple, rapid, and easily implementable method to significantly improve neuroanatomical accuracy of fMRI results localization, which may be relevant for future neuroimaging studies. PMID:20331499

  8. Bioinformatics Knowledge Map for Analysis of Beta-Catenin Function in Cancer.

    PubMed

    Çelen, İrem; Ross, Karen E; Arighi, Cecilia N; Wu, Cathy H

    2015-01-01

    Given the wealth of bioinformatics resources and the growing complexity of biological information, it is valuable to integrate data from disparate sources to gain insight into the role of genes/proteins in health and disease. We have developed a bioinformatics framework that combines literature mining with information from biomedical ontologies and curated databases to create knowledge "maps" of genes/proteins of interest. We applied this approach to the study of beta-catenin, a cell adhesion molecule and transcriptional regulator implicated in cancer. The knowledge map includes post-translational modifications (PTMs), protein-protein interactions, disease-associated mutations, and transcription factors co-activated by beta-catenin and their targets and captures the major processes in which beta-catenin is known to participate. Using the map, we generated testable hypotheses about beta-catenin biology in normal and cancer cells. By focusing on proteins participating in multiple relation types, we identified proteins that may participate in feedback loops regulating beta-catenin transcriptional activity. By combining multiple network relations with PTM proteoform-specific functional information, we proposed a mechanism to explain the observation that the cyclin dependent kinase CDK5 positively regulates beta-catenin co-activator activity. Finally, by overlaying cancer-associated mutation data with sequence features, we observed mutation patterns in several beta-catenin PTM sites and PTM enzyme binding sites that varied by tissue type, suggesting multiple mechanisms by which beta-catenin mutations can contribute to cancer. The approach described, which captures rich information for molecular species from genes and proteins to PTM proteoforms, is extensible to other proteins and their involvement in disease. PMID:26509276

  9. Step-by-Step Simulation of Radiation of Radiation Chemistry Using Green Functions for Diffusion-Influenced Reactions

    NASA Technical Reports Server (NTRS)

    Plante, Ianik; Cucinotta, Francis A.

    2011-01-01

    The irradiation of biological systems leads to the formation of radiolytic species such as H(raised dot), (raised dot)OH, H2, H2O2, e(sup -)(sub aq), etc.[1]. These species react with neighboring molecules, which result in damage in biological molecules such as DNA. Radiation chemistry is there for every important to understand the radiobiological consequences of radiation[2]. In this work, we discuss an approach based on the exact Green Functions for diffusion-influenced reactions which may be used to simulate radiation chemistry and eventually extended to study more complex systems, including DNA.

  10. Probabilistic maps of the white matter tracts with known associated functions on the neonatal brain atlas: Application to evaluate longitudinal developmental trajectories in term-born and preterm-born infants.

    PubMed

    Akazawa, Kentaro; Chang, Linda; Yamakawa, Robyn; Hayama, Sara; Buchthal, Steven; Alicata, Daniel; Andres, Tamara; Castillo, Deborrah; Oishi, Kumiko; Skranes, Jon; Ernst, Thomas; Oishi, Kenichi

    2016-03-01

    Diffusion tensor imaging (DTI) has been widely used to investigate the development of the neonatal and infant brain, and deviations related to various diseases or medical conditions like preterm birth. In this study, we created a probabilistic map of fiber pathways with known associated functions, on a published neonatal multimodal atlas. The pathways-of-interest include the superficial white matter (SWM) fibers just beneath the specific cytoarchitectonically defined cortical areas, which were difficult to evaluate with existing DTI analysis methods. The Jülich cytoarchitectonic atlas was applied to define cortical areas related to specific brain functions, and the Dynamic Programming (DP) method was applied to delineate the white matter pathways traversing through the SWM. Probabilistic maps were created for pathways related to motor, somatosensory, auditory, visual, and limbic functions, as well as major white matter tracts, such as the corpus callosum, the inferior fronto-occipital fasciculus, and the middle cerebellar peduncle, by delineating these structures in eleven healthy term-born neonates. In order to characterize maturation-related changes in diffusivity measures of these pathways, the probabilistic maps were then applied to DTIs of 49 healthy infants who were longitudinally scanned at three time-points, approximately five weeks apart. First, we investigated the normal developmental pattern based on 19 term-born infants. Next, we analyzed 30 preterm-born infants to identify developmental patterns related to preterm birth. Last, we investigated the difference in diffusion measures between these groups to evaluate the effects of preterm birth on the development of these functional pathways. Term-born and preterm-born infants both demonstrated a time-dependent decrease in diffusivity, indicating postnatal maturation in these pathways, with laterality seen in the corticospinal tract and the optic radiation. The comparison between term- and preterm

  11. Towards an automated selection of spontaneous co-activity maps in functional magnetic resonance imaging

    NASA Astrophysics Data System (ADS)

    Sourty, Marion; Thoraval, Laurent; Roquet, Daniel; Armspach, Jean-Paul; Foucher, Jack

    2015-03-01

    Functional magnetic resonance imaging allows to assess large scale functional integration of the brain. One of the leading techniques to extract functionally relevant networks is spatial independent component analysis (ICA). Spatial ICA separates independent spatial sources, many of whom are noise or imaging artifacts, whereas some do correspond to functionally relevant Spontaneous co-Activity Maps (SAMs). For research purposes, ICA is generally performed on group data. This strategy is well adapted to uncover commonly shared networks, e.g. resting-state networks, but fails to capture idiosyncratic functional networks which may be related to pathological activity, e.g. epilepsy, hallucinations. To capture these subject specific networks, ICA has to be applied to single subjects using a large number of components, from which a tenth are SAMs. Up to now, SAMs have to be selected manually by an expert based on predefined criteria. We aim to semi-automate the selection process in order to save time. To this end, some approaches have been proposed but none with the near 100 % sensitivity required for clinical purposes. In this paper, we propose a computerized version of the SAM's criteria used by experts, based on frequential and spatial characteristics of functional networks. Here we present a pre-selection method and its results at different resolutions, with different scanners or imaging sequences. While preserving a near 100 % sensitivity, it allows an average of 70 % reduction of components to be classified which save 55% of experts' time. In comparison, group ICA fails to detect about 25% of the SAMs.

  12. Cross-Population Joint Analysis of eQTLs: Fine Mapping and Functional Annotation

    PubMed Central

    Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

    2015-01-01

    Mapping expression quantitative trait loci (eQTLs) has been shown as a powerful tool to uncover the genetic underpinnings of many complex traits at molecular level. In this paper, we present an integrative analysis approach that leverages eQTL data collected from multiple population groups. In particular, our approach effectively identifies multiple independent cis-eQTL signals that are consistent across populations, accounting for population heterogeneity in allele frequencies and linkage disequilibrium patterns. Furthermore, by integrating genomic annotations, our analysis framework enables high-resolution functional analysis of eQTLs. We applied our statistical approach to analyze the GEUVADIS data consisting of samples from five population groups. From this analysis, we concluded that i) jointly analysis across population groups greatly improves the power of eQTL discovery and the resolution of fine mapping of causal eQTL ii) many genes harbor multiple independent eQTLs in their cis regions iii) genetic variants that disrupt transcription factor binding are significantly enriched in eQTLs (p-value = 4.93 × 10-22). PMID:25906321

  13. Quantitative mapping of functional MAO-A in the brain with radioiodinated clorgyline derivative

    SciTech Connect

    Magata, Y.; Konishi, J.; Hirata, M.

    1994-05-01

    The alteration of monoamine oxidase (MAO) activity in the brain may be associated with a number of neurological and psychiatric disorders. C-11 labeled clorgyline and deprenyl have been reported as imaging agents for MAO in the human brain. In order to expand this imaging technique to SPECT, the authors have reported the synthesis and biological evaluation of a number of iodinated clorgyline derivatives. On this basis, 2,4-dichloro-6-iodo-clorgyline analog (SIC) was selected as the most potential agent for mapping MAO-A with SPECT. In this paper, quantitative mapping of functional MAO-A in the brain with this compound was estimated. Pretreatment study with clorgyline showed the selective binding to MAO-A in the brain at 24 hr post injection of I-125-SIC. Good linear correlation between the enzyme activity and the brain up-take of I-125-SIC was observed in the pretreated study with several dose of clorgyline. Furthermore, local MAO-A activity was estimated by the autoradiographic method. High MAO-A activities were observed in midbrain and pons. This result was well agreed with another reported value obtained in vitro assay. In conclusion, this compound is indicated to be variable for quantitative analysis of MAO-A in the brain with SPECT.

  14. Towards DIB mapping in galaxies beyond 100 Mpc. A radial profile of the λ5780.5 diffuse interstellar band in AM 1353-272 B

    NASA Astrophysics Data System (ADS)

    Monreal-Ibero, A.; Weilbacher, P. M.; Wendt, M.; Selman, F.; Lallement, R.; Brinchmann, J.; Kamann, S.; Sandin, C.

    2015-04-01

    Context. Diffuse interstellar bands (DIBs) are non-stellar weak absorption features of unknown origin found in the spectra of stars viewed through one or several clouds of the interstellar medium (ISM). Research of DIBs outside the Milky Way is currently very limited. In particular, spatially resolved investigations of DIBs outside of the Local Group are, to our knowledge, inexistent. Aims: In this contribution, we explore the capability of the high-sensitivity integral field spectrograph, MUSE, as a tool for mapping diffuse interstellar bands at distances larger than 100 Mpc. Methods: We used MUSE commissioning data for AM 1353-272 B, the member with the highest extinction of the Dentist's Chair, an interacting system of two spiral galaxies. High signal-to-noise spectra were created by co-adding the signal of many spatial elements distributed in a geometry of concentric elliptical half-rings. Results: We derived decreasing radial profiles for the equivalent width of the λ5780.5 DIB both in the receding and approaching side of the companion galaxy up to distances of ~4.6 kpc from the centre of the galaxy. The interstellar extinction as derived from the Hα/Hβ line ratio displays a similar trend, with decreasing values towards the external parts. This translates into an intrinsic correlation between the strength of the DIB and the extinction within AM 1353-272 B, consistent with the currently existing global trend between these quantities when using measurements for Galactic and extragalactic sightlines. Conclusions: It seems feasible to map the DIB strength in the Local Universe, which has up to now only been performed for the Milky Way. This offers a new approach to studying the relationship between DIBs and other characteristics and species of the ISM in addition to using galaxies in the Local Group or sightlines towards very bright targets outside the Local Group. Based on observations made with ESO telescopes at the La Silla Paranal Observatory under program

  15. Three-Dimensional Mapping of Soil Organic Carbon by Combining Kriging Method with Profile Depth Function.

    PubMed

    Chen, Chong; Hu, Kelin; Li, Hong; Yun, Anping; Li, Baoguo

    2015-01-01

    Understanding spatial variation of soil organic carbon (SOC) in three-dimensional direction is helpful for land use management. Due to the effect of profile depths and soil texture on vertical distribution of SOC, the stationary assumption for SOC cannot be met in the vertical direction. Therefore the three-dimensional (3D) ordinary kriging technique cannot be directly used to map the distribution of SOC at a regional scale. The objectives of this study were to map the 3D distribution of SOC at a regional scale by combining kriging method with the profile depth function of SOC (KPDF), and to explore the effects of soil texture and land use type on vertical distribution of SOC in a fluvial plain. A total of 605 samples were collected from 121 soil profiles (0.0 to 1.0 m, 0.20 m increment) in Quzhou County, China and SOC contents were determined for each soil sample. The KPDF method was used to obtain the 3D map of SOC at the county scale. The results showed that the exponential equation well described the vertical distribution of mean values of the SOC contents. The coefficients of determination, root mean squared error and mean prediction error between the measured and the predicted SOC contents were 0.52, 1.82 and -0.24 g kg(-1) respectively, suggesting that the KPDF method could be used to produce a 3D map of SOC content. The surface SOC contents were high in the mid-west and south regions, and low values lay in the southeast corner. The SOC contents showed significant positive correlations between the five different depths and the correlations of SOC contents were larger in adjacent layers than in non-adjacent layers. Soil texture and land use type had significant effects on the spatial distribution of SOC. The influence of land use type was more important than that of soil texture in the surface soil, and soil texture played a more important role in influencing the SOC levels for 0.2-0.4 m layer.

  16. Three-Dimensional Mapping of Soil Organic Carbon by Combining Kriging Method with Profile Depth Function

    PubMed Central

    Chen, Chong; Hu, Kelin; Li, Hong; Yun, Anping; Li, Baoguo

    2015-01-01

    Understanding spatial variation of soil organic carbon (SOC) in three-dimensional direction is helpful for land use management. Due to the effect of profile depths and soil texture on vertical distribution of SOC, the stationary assumption for SOC cannot be met in the vertical direction. Therefore the three-dimensional (3D) ordinary kriging technique cannot be directly used to map the distribution of SOC at a regional scale. The objectives of this study were to map the 3D distribution of SOC at a regional scale by combining kriging method with the profile depth function of SOC (KPDF), and to explore the effects of soil texture and land use type on vertical distribution of SOC in a fluvial plain. A total of 605 samples were collected from 121 soil profiles (0.0 to 1.0 m, 0.20 m increment) in Quzhou County, China and SOC contents were determined for each soil sample. The KPDF method was used to obtain the 3D map of SOC at the county scale. The results showed that the exponential equation well described the vertical distribution of mean values of the SOC contents. The coefficients of determination, root mean squared error and mean prediction error between the measured and the predicted SOC contents were 0.52, 1.82 and -0.24 g kg-1 respectively, suggesting that the KPDF method could be used to produce a 3D map of SOC content. The surface SOC contents were high in the mid-west and south regions, and low values lay in the southeast corner. The SOC contents showed significant positive correlations between the five different depths and the correlations of SOC contents were larger in adjacent layers than in non-adjacent layers. Soil texture and land use type had significant effects on the spatial distribution of SOC. The influence of land use type was more important than that of soil texture in the surface soil, and soil texture played a more important role in influencing the SOC levels for 0.2-0.4 m layer. PMID:26047012

  17. Arterial Input Function Placement for Accurate CT Perfusion Map Construction in Acute Stroke

    PubMed Central

    Ferreira, Rafael M.; Lev, Michael H.; Goldmakher, Gregory V.; Kamalian, Shahmir; Schaefer, Pamela W.; Furie, Karen L.; Gonzalez, R. Gilberto; Sanelli, Pina C.

    2013-01-01

    OBJECTIVE The objective of our study was to evaluate the effect of varying arterial input function (AIF) placement on the qualitative and quantitative CT perfusion parameters. MATERIALS AND METHODS Retrospective analysis of CT perfusion data was performed on 14 acute stroke patients with a proximal middle cerebral artery (MCA) clot. Cerebral blood flow (CBF), cerebral blood volume (CBV), and mean transit time (MTT) maps were constructed using a systematic method by varying only the AIF placement in four positions relative to the MCA clot including proximal and distal to the clot in the ipsilateral and contralateral hemispheres. Two postprocessing software programs were used to evaluate the effect of AIF placement on perfusion parameters using a delay-insensitive deconvolution method compared with a standard deconvolution method. RESULTS One hundred sixty-eight CT perfusion maps were constructed for each software package. Both software programs generated a mean CBF at the infarct core of < 12 mL/100 g/min and a mean CBV of < 2 mL/100 g for AIF placement proximal to the clot in the ipsilateral hemisphere and proximal and distal to the clot in the contralateral hemisphere. For AIF placement distal to the clot in the ipsilateral hemisphere, the mean CBF significantly increased to 17.3 mL/100 g/min with delay-insensitive software and to 19.4 mL/100 g/min with standard software (p < 0.05). The mean MTT was significantly decreased for this AIF position. Furthermore, this AIF position yielded qualitatively different parametric maps, being most pronounced with MTT and CBF. Overall, CBV was least affected by AIF location. CONCLUSION For postprocessing of accurate quantitative CT perfusion maps, laterality of the AIF location is less important than avoiding AIF placement distal to the clot as detected on CT angiography. This pitfall is less severe with deconvolution-based software programs using a delay-insensitive technique than with those using a standard deconvolution

  18. An indicator to map diffuse chemical river pollution considering buffer capacity of riparian vegetation--a pan-European case study on pesticides.

    PubMed

    Weissteiner, Christof J; Pistocchi, Alberto; Marinov, Dimitar; Bouraoui, Fayçal; Sala, Serenella

    2014-06-15

    Vegetated riparian areas alongside streams are thought to be effective at intercepting and controlling chemical loads from diffuse agricultural sources entering water bodies. Based on a recently compiled European map of riparian zones and a simplified soil chemical balance model, we propose a new indicator at a continental scale. QuBES (Qualitative indicator of Buffered Emissions to Streams) allows a qualitative assessment of European rivers exposed to pesticide input. The indicator consists of normalised pesticide loads to streams computed through a simplified steady-state fate model that distinguishes various chemical groups according to physico-chemical behaviour (solubility and persistence). The retention of pollutants in the buffer zone is modelled according to buffer width and sorption properties. While the indicator may be applied for the study of a generic emission pattern and for a chemical of generic properties, we demonstrate it to the case of agricultural emissions of pesticides. Due to missing geo-spatial data of pesticide emissions, a total pesticide emission scenario is assumed. The QuBES indicator is easy to calculate and requires far less input data and parameterisation than typical chemical-specific models. At the same time, it allows mapping of (i) riparian buffer permeability, (ii) chemical runoff from soils, and (iii) the buffered load of chemicals to the stream network. When the purpose of modelling is limited to identifying chemical pollution patterns and understanding the relative importance of emissions and natural attenuation in soils and stream buffer strips, the indicator may be suggested as a screening level, cost-effective alternative to spatially distributed models of higher complexity.

  19. Mapping quantal touch using 7 Tesla functional magnetic resonance imaging and single-unit intraneural microstimulation.

    PubMed

    Sanchez Panchuelo, Rosa Maria; Ackerley, Rochelle; Glover, Paul M; Bowtell, Richard W; Wessberg, Johan; Francis, Susan T; McGlone, Francis

    2016-05-07

    Using ultra-high field 7 Tesla (7T) functional magnetic resonance imaging (fMRI), we map the cortical and perceptual responses elicited by intraneural microstimulation (INMS) of single mechanoreceptive afferent units in the median nerve, in humans. Activations are compared to those produced by applying vibrotactile stimulation to the unit's receptive field, and unit-type perceptual reports are analyzed. We show that INMS and vibrotactile stimulation engage overlapping areas within the topographically appropriate digit representation in the primary somatosensory cortex. Additional brain regions in bilateral secondary somatosensory cortex, premotor cortex, primary motor cortex, insula and posterior parietal cortex, as well as in contralateral prefrontal cortex are also shown to be activated in response to INMS. The combination of INMS and 7T fMRI opens up an unprecedented opportunity to bridge the gap between first-order mechanoreceptive afferent input codes and their spatial, dynamic and perceptual representations in human cortex.

  20. Strategy of Surgical Resection for Glioma Based on Intraoperative Functional Mapping and Monitoring

    PubMed Central

    TAMURA, Manabu; MURAGAKI, Yoshihiro; SAITO, Taiichi; MARUYAMA, Takashi; NITTA, Masayuki; TSUZUKI, Shunsuke; ISEKI, Hiroshi; OKADA, Yoshikazu

    2015-01-01

    A growing number of papers have pointed out the relationship between aggressive resection of gliomas and survival prognosis. For maximum resection, the current concept of surgical decision-making is in “information-guided surgery” using multimodal intraoperative information. With this, anatomical information from intraoperative magnetic resonance imaging (MRI) and navigation, functional information from brain mapping and monitoring, and histopathological information must all be taken into account in the new perspective for innovative minimally invasive surgical treatment of glioma. Intraoperative neurofunctional information such as neurophysiological functional monitoring takes the most important part in the process to acquire objective visual data during tumor removal and to integrate these findings as digitized data for intraoperative surgical decision-making. Moreover, the analysis of qualitative data and threshold-setting for quantitative data raise difficult issues in the interpretation and processing of each data type, such as determination of motor evoked potential (MEP) decline, underestimation in tractography, and judgments of patient response for neurofunctional mapping and monitoring during awake craniotomy. Neurofunctional diagnosis of false-positives in these situations may affect the extent of resection, while false-negatives influence intra- and postoperative complication rates. Additionally, even though the various intraoperative visualized data from multiple sources contribute significantly to the reliability of surgical decisions when the information is integrated and provided, it is not uncommon for individual pieces of information to convey opposing suggestions. Such conflicting pieces of information facilitate higher-order decision-making that is dependent on the policies of the facility and the priorities of the patient, as well as the availability of the histopathological characteristics from resected tissue. PMID:26185825

  1. An Intracranial Electroencephalography (iEEG) Brain Function Mapping Tool with an Application to Epilepsy Surgery Evaluation

    PubMed Central

    Wang, Yinghua; Yan, Jiaqing; Wen, Jianbin; Yu, Tao; Li, Xiaoli

    2016-01-01

    Objects: Before epilepsy surgeries, intracranial electroencephalography (iEEG) is often employed in function mapping and epileptogenic foci localization. Although the implanted electrodes provide crucial information for epileptogenic zone resection, a convenient clinical tool for electrode position registration and Brain Function Mapping (BFM) visualization is still lacking. In this study, we developed a BFM Tool, which facilitates electrode position registration and BFM visualization, with an application to epilepsy surgeries. Methods: The BFM Tool mainly utilizes electrode location registration and function mapping based on pre-defined brain models from other software. In addition, the electrode node and mapping properties, such as the node size/color, edge color/thickness, mapping method, can be adjusted easily using the setting panel. Moreover, users may manually import/export location and connectivity data to generate figures for further application. The role of this software is demonstrated by a clinical study of language area localization. Results: The BFM Tool helps clinical doctors and researchers visualize implanted electrodes and brain functions in an easy, quick and flexible manner. Conclusions: Our tool provides convenient electrode registration, easy brain function visualization, and has good performance. It is clinical-oriented and is easy to deploy and use. The BFM tool is suitable for epilepsy and other clinical iEEG applications. PMID:27199729

  2. Coordinate-independent mapping of structural and functional data by objective relational transformation (ORT).

    PubMed Central

    Stephan, K E; Zilles, K; Kötter, R

    2000-01-01

    Neuroscience has produced an enormous amount of structural and functional data. Powerful database systems are required to make these data accessible for computational approaches such as higher-order analyses and simulations. Available databases for key data such as anatomical and functional connectivity between cortical areas, however, are still hampered by methodological problems. These problems arise predominantly from the parcellation problem, the use of incongruent parcellation schemes by different authors. We here present a coordinate-independent mathematical method to overcome this problem: objective relational transformation (ORT). Based on new classifications for brain data and on methods from theoretical computer science, ORT represents a formally defined, transparent transformation method for reproducible, coordinate-independent mapping of brain data to freely chosen parcellation schemes. We describe the methodology of ORT and discuss its strengths and limitations. Using two practical examples, we show that ORT in conjunction with connectivity databases like CoCoMac (http://www.cocomac.org) is an important tool for analyses of cortical organization and structure-function relationships. PMID:10703043

  3. Functional region identification in proteins by accumulative-quantitative peptide mapping using RP-HPLC-MS.

    PubMed

    Kuipers, Bas J H; Bakx, E J; Gruppen, Harry

    2007-11-14

    A new method was developed to identify regions in proteins from which peptides are derived with specific functional properties. This method is applicable for systems in which peptides of a hydrolyzed protein possess specific functional properties, but are too large to be sequenced directly and/or the peptide mixture is too complex to purify and characterize each peptide individually. In the present work, aggregating peptides obtained by proteolytic hydrolysis of soy glycinin were used as a case study. The aggregating peptides are isolated and subsequently further degraded with trypsin to result in peptides with a mass <5000 Da to enable sequence identification using RP-HPLC-MS in combination with MS/MS. Prior to RP-HPLC the peptides are fractionated using anion and cation exchange chromatography. The fractions obtained are analyzed with RP-HPLC-MS. The peptides, with identified sequences, were quantified using the peak areas of the RP-HPLC chromatograms measured at 214 nm. Next, the peak areas were corrected for the molar extinction coefficient of the individual peptides, followed by accumulative-quantitative peptide mapping. The results show that in complex systems, based on the method described, the regions in the parental protein from which the functional peptides originate can be properly identified.

  4. Quantitative interaction mapping reveals an extended UBX domain in ASPL that disrupts functional p97 hexamers

    PubMed Central

    Arumughan, Anup; Roske, Yvette; Barth, Carolin; Forero, Laura Lleras; Bravo-Rodriguez, Kenny; Redel, Alexandra; Kostova, Simona; McShane, Erik; Opitz, Robert; Faelber, Katja; Rau, Kirstin; Mielke, Thorsten; Daumke, Oliver; Selbach, Matthias; Sanchez-Garcia, Elsa; Rocks, Oliver; Panáková, Daniela; Heinemann, Udo; Wanker, Erich E.

    2016-01-01

    Interaction mapping is a powerful strategy to elucidate the biological function of protein assemblies and their regulators. Here, we report the generation of a quantitative interaction network, directly linking 14 human proteins to the AAA+ ATPase p97, an essential hexameric protein with multiple cellular functions. We show that the high-affinity interacting protein ASPL efficiently promotes p97 hexamer disassembly, resulting in the formation of stable p97:ASPL heterotetramers. High-resolution structural and biochemical studies indicate that an extended UBX domain (eUBX) in ASPL is critical for p97 hexamer disassembly and facilitates the assembly of p97:ASPL heterotetramers. This spontaneous process is accompanied by a reorientation of the D2 ATPase domain in p97 and a loss of its activity. Finally, we demonstrate that overproduction of ASPL disrupts p97 hexamer function in ERAD and that engineered eUBX polypeptides can induce cell death, providing a rationale for developing anti-cancer polypeptide inhibitors that may target p97 activity. PMID:27762274

  5. Functional heterogeneity of inferior parietal cortex during mathematical cognition assessed with cytoarchitectonic probability maps.

    PubMed

    Wu, S S; Chang, T T; Majid, A; Caspers, S; Eickhoff, S B; Menon, V

    2009-12-01

    Although the inferior parietal cortex (IPC) has been consistently implicated in mathematical cognition, the functional roles of its subdivisions are poorly understood. We address this problem using probabilistic cytoarchitectonic maps of IPC subdivisions intraparietal sulcus (IPS), angular gyrus (AG), and supramarginal gyrus. We quantified IPC responses relative to task difficulty and individual differences in task proficiency during mental arithmetic (MA) tasks performed with Arabic (MA-A) and Roman (MA-R) numerals. The 2 tasks showed similar levels of activation in 3 distinct IPS areas, hIP1, hIP2, and hIP3, suggesting their obligatory role in MA. Both AG areas, PGa and PGp, were strongly deactivated in both tasks, with stronger deactivations in posterior area PGp. Compared with the more difficult MA-R task, the MA-A task showed greater responses in both AG areas, but this effect was driven by less deactivation in the MA-A task. AG deactivations showed prominent overlap with lateral parietal nodes of the default mode network, suggesting a nonspecific role in MA. In both tasks, greater bilateral AG deactivation was associated with poorer performance. Our findings suggest a close link between IPC structure and function and they provide new evidence for behaviorally salient functional heterogeneity within the IPC during mathematical cognition. PMID:19406903

  6. Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins

    PubMed Central

    Schirò, Giorgio; Fichou, Yann; Gallat, Francois-Xavier; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Härtlein, Michael; Heyden, Matthias; Colletier, Jacques-Philippe; Orecchini, Andrea; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J.; Weik, Martin

    2015-01-01

    Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240 K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity. PMID:25774711

  7. Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins.

    PubMed

    Schirò, Giorgio; Fichou, Yann; Gallat, Francois-Xavier; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Härtlein, Michael; Heyden, Matthias; Colletier, Jacques-Philippe; Orecchini, Andrea; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J; Weik, Martin

    2015-01-01

    Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240 K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity.

  8. CSF1R mutations in hereditary diffuse leukoencephalopathy with spheroids are loss of function.

    PubMed

    Pridans, Clare; Sauter, Kristin A; Baer, Kristin; Kissel, Holger; Hume, David A

    2013-10-22

    Hereditary diffuse leukoencephalopathy with spheroids (HDLS) in humans is a rare autosomal dominant disease characterized by giant neuroaxonal swellings (spheroids) within the CNS white matter. Symptoms are variable and can include personality and behavioural changes. Patients with this disease have mutations in the protein kinase domain of the colony-stimulating factor 1 receptor (CSF1R) which is a tyrosine kinase receptor essential for microglia development. We investigated the effects of these mutations on Csf1r signalling using a factor dependent cell line. Corresponding mutant forms of murine Csf1r were expressed on the cell surface at normal levels, and bound CSF1, but were not able to sustain cell proliferation. Since Csf1r signaling requires receptor dimerization initiated by CSF1 binding, the data suggest a mechanism for phenotypic dominance of the mutant allele in HDLS.

  9. Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins

    NASA Astrophysics Data System (ADS)

    Schirò, Giorgio; Fichou, Yann; Gallat, Francois-Xavier; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Härtlein, Michael; Heyden, Matthias; Colletier, Jacques-Philippe; Orecchini, Andrea; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J.; Weik, Martin

    2015-03-01

    Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240 K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity.

  10. CSF1R mutations in hereditary diffuse leukoencephalopathy with spheroids are loss of function

    NASA Astrophysics Data System (ADS)

    Pridans, Clare; Sauter, Kristin A.; Baer, Kristin; Kissel, Holger; Hume, David A.

    2013-10-01

    Hereditary diffuse leukoencephalopathy with spheroids (HDLS) in humans is a rare autosomal dominant disease characterized by giant neuroaxonal swellings (spheroids) within the CNS white matter. Symptoms are variable and can include personality and behavioural changes. Patients with this disease have mutations in the protein kinase domain of the colony-stimulating factor 1 receptor (CSF1R) which is a tyrosine kinase receptor essential for microglia development. We investigated the effects of these mutations on Csf1r signalling using a factor dependent cell line. Corresponding mutant forms of murine Csf1r were expressed on the cell surface at normal levels, and bound CSF1, but were not able to sustain cell proliferation. Since Csf1r signaling requires receptor dimerization initiated by CSF1 binding, the data suggest a mechanism for phenotypic dominance of the mutant allele in HDLS.

  11. Function of the mitochondrial outer membrane as a diffusion barrier in health and diseases.

    PubMed

    Gellerich, F N; Trumbeckaite, S; Opalka, J R; Seppet, E; Rasmussen, H N; Neuhoff, C; Zierz, S

    2000-02-01

    The mitochondrial outer membrane separates the intermembrane space from the cytosol. The whole exchange of metabolites, cations and information between mitochondria and the cell occurs through the outer membrane. Experimental evidence is reviewed supporting the hypothesis of dynamic ADP compartmentation within the intermembrane space. The outer membrane creates a diffusion barrier for small molecules (adenine nucleotides, creatine phosphate, creatine etc.) causing rate-dependent concentration gradients as a prerequisite for the action of ADP shuttles via creatine kinases or adenylate kinases. If the outer membrane becomes leaky, cytochrome c and apoptosis-inducing factor can be released, leading to apoptosis, and as a bioenergetic consequence the cytosolic phosphorylation potential decreases. Leaky outer membranes can be detected in saponin-skinned fibres with spectrophotometric and oxygraphic methods. This is of special interest in respect to acute impairment of mitochondria during ischaemia/reperfusion.

  12. Regional MRI Diffusion, White-Matter Hyperintensities, and Cognitive Function in Alzheimer's Disease and Vascular Dementia

    PubMed Central

    Scrascia, Federica; Quattrocchi, Carlo Cosimo; Errante, Yuri; Gangemi, Emma; Curcio, Giuseppe; Ursini, Francesca; Silvestrini, Mauro; Maggio, Paola; Beomonte Zobel, Bruno; Rossini, Paolo Maria; Pasqualetti, Patrizio; Falsetti, Lorenzo; Vernieri, Fabrizio

    2016-01-01

    Background and Purpose An increase in brain water diffusivity as measured using magnetic resonance imaging (MRI) has been recently reported in normal-appearing white matter (NAWM) in patients affected by cognitive impairment. However, it remains to be clarified if this reflects an overt neuronal tissue disruption that leads to degenerative or microvascular lesions. This question was addressed by comparing the regional MRI apparent diffusion coefficients (ADCs) of NAWM in patients affected by Alzheimer's disease (AD) or vascular dementia (VaD). The relationships of ADCs with the white-matter hyperintensity (WMH) burden, carotid atherosclerosis, and cognitive performance were also investigated. Methods Forty-nine AD and 31 VaD patients underwent brain MRI to assess the WMH volume and regional NAWM ADCs, neuropsychological evaluations, and carotid ultrasound to assess the plaque severity and intima-media thickness (IMT). Results Regional ADCs in NAWM did not differ between VaD and AD patients, while the WMH volume was greater in VaD than in AD patients. The ADC in the anterior corpus callosum was related to the WMH volume, while a greater carotid IMT was positively correlated with the temporal ADC and WMH volume. The memory performance was worse in patients with higher temporal ADCs. Constructional praxis scores were related to ADCs in the frontal, and occipital lobes, in the anterior and posterior corpus callosum as well as to the WMH volume. Abstract reasoning was related to frontal, parietal, and temporal ADCs. Conclusions Our data show that higher regional ADCs in NAWM are associated with microcirculatory impairment, as depicted by the WMH volume. Moreover, regional ADCs in NAWM are differently associated with the neuropsychological performances in memory, constructional praxia, and abstract reasoning domains. PMID:27074295

  13. NEREC, an effective brain mapping protocol for combined language and long-term memory functions.

    PubMed

    Perrone-Bertolotti, Marcela; Girard, Cléa; Cousin, Emilie; Vidal, Juan Ricardo; Pichat, Cédric; Kahane, Philippe; Baciu, Monica

    2015-12-01

    Temporal lobe epilepsy can induce functional plasticity in temporoparietal networks involved in language and long-term memory processing. Previous studies in healthy subjects have revealed the relative difficulty for this network to respond effectively across different experimental designs, as compared to more reactive regions such as frontal lobes. For a protocol to be optimal for clinical use, it has to first show robust effects in a healthy cohort. In this study, we developed a novel experimental paradigm entitled NEREC, which is able to reveal the robust participation of temporoparietal networks in a uniquely combined language and memory task, validated in an fMRI study with healthy subjects. Concretely, NEREC is composed of two runs: (a) an intermixed language-memory task (confrontation naming associated with encoding in nonverbal items, NE) to map language (i.e., word retrieval and lexico-semantic processes) combined with simultaneous long-term verbal memory encoding (NE items named but also explicitly memorized) and (b) a memory retrieval task of items encoded during NE (word recognition, REC) intermixed with new items. Word recognition is based on both perceptual-semantic familiarity (feeling of 'know') and accessing stored memory representations (remembering). In order to maximize the remembering and recruitment of medial temporal lobe structures, we increased REC difficulty by changing the modality of stimulus presentation (from nonverbal during NE to verbal during REC). We report that (a) temporoparietal activation during NE was attributable to both lexico-semantic (language) and memory (episodic encoding and semantic retrieval) processes; that (b) encoding activated the left hippocampus, bilateral fusiform, and bilateral inferior temporal gyri; and that (c) task recognition (recollection) activated the right hippocampus and bilateral but predominant left fusiform gyrus. The novelty of this protocol consists of (a) combining two tasks in one (language

  14. NEREC, an effective brain mapping protocol for combined language and long-term memory functions.

    PubMed

    Perrone-Bertolotti, Marcela; Girard, Cléa; Cousin, Emilie; Vidal, Juan Ricardo; Pichat, Cédric; Kahane, Philippe; Baciu, Monica

    2015-12-01

    Temporal lobe epilepsy can induce functional plasticity in temporoparietal networks involved in language and long-term memory processing. Previous studies in healthy subjects have revealed the relative difficulty for this network to respond effectively across different experimental designs, as compared to more reactive regions such as frontal lobes. For a protocol to be optimal for clinical use, it has to first show robust effects in a healthy cohort. In this study, we developed a novel experimental paradigm entitled NEREC, which is able to reveal the robust participation of temporoparietal networks in a uniquely combined language and memory task, validated in an fMRI study with healthy subjects. Concretely, NEREC is composed of two runs: (a) an intermixed language-memory task (confrontation naming associated with encoding in nonverbal items, NE) to map language (i.e., word retrieval and lexico-semantic processes) combined with simultaneous long-term verbal memory encoding (NE items named but also explicitly memorized) and (b) a memory retrieval task of items encoded during NE (word recognition, REC) intermixed with new items. Word recognition is based on both perceptual-semantic familiarity (feeling of 'know') and accessing stored memory representations (remembering). In order to maximize the remembering and recruitment of medial temporal lobe structures, we increased REC difficulty by changing the modality of