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Sample records for functional diffusion maps

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

    PubMed Central

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

    2014-01-01

    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. PMID:25083161

  2. 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.

  3. Corticospinal tract mapping in children with ruptured arteriovenous malformations using functionally guided diffusion-tensor imaging.

    PubMed

    Ellis, Michael J; Rutka, James T; Kulkarni, Abhaya V; Dirks, Peter B; Widjaja, Elysa

    2012-05-01

    Arteriovenous malformations (AVMs) can lead to distortion or reorganization of functional brain anatomy, making localization of eloquent white matter tracts challenging. To improve the accuracy of corticospinal tract (CST) mapping, recent studies have examined the use of functional imaging techniques to help localize cortical motor activations and use these as seed points to reconstruct CSTs using diffusion-tensor imaging (DTI). The authors examined the role of pretreatment functionally guided DTI CST mapping in 3 children with ruptured AVMs. In 2 patients, magnetoencephalography motor activations were adjacent to the nidus and/or hemorrhagic cavity. However, in 1 child, functional MRI motor activations were detected in both hemispheres, suggestive of partial transfer of cortical motor function. In all children, quantitative analysis showed that fractional anisotropy values and fiber density indices were reduced in the CSTs of the hemisphere harboring the AVM compared with the unaffected side. In 2 children, CST caliber was slightly diminished, corresponding to no motor deficit in 1 patient and a temporary motor deficit in the other. In contrast, 1 child demonstrated marked reduction and displacement of the CSTs, correlating with severe motor deficit. Preoperative motor tractography data were loaded onto the intraoperative neuronavigation platform to guide complete resection of the AVM in 2 cases without permanent neurological deficits. These preliminary results confirm the feasibility of CST mapping in children with ruptured AVMs using functionally guided DTI tractography. Prospective studies are needed to assess the full value of this technique in the risk stratification, prognosis, and multimodality management of pediatric AVMs. PMID:22546028

  4. 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. PMID:25673970

  5. 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.

  6. 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.

  7. Diffusion maps and radar data analysis

    NASA Astrophysics Data System (ADS)

    Bhat, Y. S.; Arnold, Gregory

    2007-04-01

    Understanding and organizing data, in particular understanding the key modes of variation in the data, is a first step toward exploiting and evaluating sensor phenomenology. Spectral theory and manifold learning methods have been recently shown to offer sever powerful tools for many parts of the exploitation problem. We will describe the method of diffusion maps and give some examples with radar (backhoe data dome) data. The so-called diffusion coordinates are kernel based dimensionality reduction techniques that can, for example, organize random data and yield explicit insight into the type and relative importance of the data variation. We will provide sufficient background for others to adopt these tools and apply them to other aspects of exploitation and evaluation.

  8. 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

  9. 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.

  10. 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. PMID:25682881

  11. Mapping diffusion in a living cell via the phasor approach.

    PubMed

    Ranjit, Suman; Lanzano, Luca; Gratton, Enrico

    2014-12-16

    Diffusion of a fluorescent protein within a cell has been measured using either fluctuation-based techniques (fluorescence correlation spectroscopy (FCS) or raster-scan image correlation spectroscopy) or particle tracking. However, none of these methods enables us to measure the diffusion of the fluorescent particle at each pixel of the image. Measurement using conventional single-point FCS at every individual pixel results in continuous long exposure of the cell to the laser and eventual bleaching of the sample. To overcome this limitation, we have developed what we believe to be a new method of scanning with simultaneous construction of a fluorescent image of the cell. In this believed new method of modified raster scanning, as it acquires the image, the laser scans each individual line multiple times before moving to the next line. This continues until the entire area is scanned. This is different from the original raster-scan image correlation spectroscopy approach, where data are acquired by scanning each frame once and then scanning the image multiple times. The total time of data acquisition needed for this method is much shorter than the time required for traditional FCS analysis at each pixel. However, at a single pixel, the acquired intensity time sequence is short; requiring nonconventional analysis of the correlation function to extract information about the diffusion. These correlation data have been analyzed using the phasor approach, a fit-free method that was originally developed for analysis of FLIM images. Analysis using this method results in an estimation of the average diffusion coefficient of the fluorescent species at each pixel of an image, and thus, a detailed diffusion map of the cell can be created. PMID:25517145

  12. Usable Functions of Modern Maps

    NASA Astrophysics Data System (ADS)

    Krzywicka-Blum, Ewa

    2012-09-01

    Modem maps created with the application of GIS technology using special techniques and programmes adequate for spatial information systems are. in comparison to their analogue counterparts, of better model qualities, which is obtained by separating their practical functions. The cognitive function of maps is the mam priority. The shape of a map is a result of the applied technology, yet the maps developed using many technical instruments are not always the best ones or graphi- cally correct. There have been many beautiful maps of landscape attempting to show different aspects of landscapes and the results of analyses of multifactorial phenomena and processes. Mapy tworzone w warunkach nowoczesnej techniki komputerowej, technologii i organizacji właściwej systemom informacji przestrzennej, cechuje podwyższenie, w stosunku do analogowych, własności modelowych uzyskuje się to dzięki rozdzieleniu funkcji praktycznych. Walory poznawcze mapy stanowią, w całym rozwoju kartografii wartości prio- rytetowe. Postać mapy jest wynikiem zastosowanej technologii i nie zawsze mapy opracowane w interaktywnym procesie są graficznie poprawne. Pojawiają się nowe ujęcia treści map krajobrazowych i bardzo piękne propozycje ujęć wyników analiz wieloczynnikowych zjawisk i procesów.

  13. 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.

  14. 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

  15. 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.

  16. Granger-causality maps of diffusion processes

    NASA Astrophysics Data System (ADS)

    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.

  17. 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

  18. Minimalism through intraoperative functional mapping.

    PubMed

    Berger, M S

    1996-01-01

    Intraoperative stimulation mapping may be used to avoid unnecessary risk to functional regions subserving language and sensori-motor pathways. Based on the data presented here, language localization is variable in the entire population, with only certainty existing for the inferior frontal region responsible for motor speech. Anatomical landmarks such as the anterior temporal tip for temporal lobe language sites and the posterior aspect of the lateral sphenoid wing for the frontal lobe language zones are unreliable in avoiding postoperative aphasias. Thus, individual mapping to identify essential language sites has the greatest likelihood of avoiding permanent deficits in naming, reading, and motor speech. In a similar approach, motor and sensory pathways from the cortex and underlying white matter may be reliably stimulated and mapped in both awake and asleep patients. Although these techniques require an additional operative time and equipment nominally priced, the result is often gratifying, as postoperative morbidity has been greatly reduced in the process of incorporating these surgical strategies. The patients quality of life is improved in terms of seizure control, with or without antiepileptic drugs. This avoids having to perform a second costly operative procedure, which is routinely done when extraoperative stimulation and recording is done via subdural grids. In addition, an aggressive tumor resection at the initial operation lengthens the time to tumor recurrence and often obviates the need for a subsequent reoperation. Thus, intraoperative functional mapping may be best alluded to as a surgical technique that results in "minimalism in the long term". PMID:9247814

  19. 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

  20. Diffusion-weighted imaging with apparent diffusion coefficient mapping and spectroscopy in prostate cancer.

    PubMed

    Jacobs, Michael A; Ouwerkerk, Ronald; Petrowski, Kyle; Macura, Katarzyna J

    2008-12-01

    Prostate cancer is a major health problem, and the exploration of noninvasive imaging methods that have the potential to improve specificity while maintaining high sensitivity is still critically needed. Tissue changes induced by tumor growth can be visualized by magnetic resonance imaging (MRI) methods. Current MRI methods include conventional T2-weighted imaging, diffusion-weighted imaging (DWI) with apparent diffusion coefficient (ADC) mapping and magnetic resonance spectroscopy (MRS). Techniques such as DWI/ADC provide functional information about the behavior of water molecules in tissue; MRS can provide biochemical information about the presence or absence of certain metabolites, such as choline, creatine, and citrate. Finally, vascular parameters can be investigated using dynamic contrast-enhanced MRI. Moreover, with whole-body MRI and DWI, metastatic disease can be evaluated in 1 session and may provide a way to monitor treatment. Therefore, when combining these various methods, a multiparametric data set can be built to assist in the detection, localization, assessment of prostate cancer aggressiveness, and tumor staging. Such a comprehensive approach offers more power to evaluate prostate disease than any single measure alone. In this article, we focus on the role of DWI/ADC and MRS in the detection and characterization using both in vivo and ex vivo imaging of prostate pathology. PMID:19512848

  1. Apparent diffusion coefficient map of a case of extramedullary plasmacytoma

    PubMed Central

    Ramachandran, Amrutha; Inyang, Alero F; Subhawong, Ty K

    2016-01-01

    Plasmacytomas are rare tumors, which arise from the monoclonal proliferation of malignant plasma cells. They may affect either the bony skeleton or rarely the soft tissues, the latter being referred to as extramedullary or extraosseous. We report a case of an extramedullary plasmacytoma that presented as a soft tissue mass involving the muscles of the left leg, in a patient who was previously treated for multiple myeloma. We describe the MR Imaging characteristics of the tumor and highlight the usefulness of diffusion-weighted imaging with apparent diffusion coefficient mapping. PMID:27200157

  2. 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

  3. The use of map functions in multipoint mapping.

    PubMed Central

    Pascoe, L; Morton, N E

    1987-01-01

    The analysis of multipoint data in humans involves detection of linkage, inferences about order, and estimation of map lengths. In order to calculate likelihoods, it is necessary to have predictive formulas for multiple recombination frequencies. In the present study the Markovian assumption of Morton and MacLean is generalized to give predictive formulas for multiple-region recombination using realistic map functions. The best-fitting map functions have been determined by fitting the nine-locus data of Morgan et al. and the seven-locus data of Weinstein on the Drosophila X chromosome. Two map functions fit the data better than other published functions: that of Rao et al. with a map parameter of P = .33 and a new function suggested in the present paper. The close agreement of the estimate of the mapping parameter with a previous estimate inferred from human male meiosis suggests that the map function is robust. A further improvement in the fit to the data can be obtained by the addition of a second parameter to reduce the expected number of multiple recombinants. By comparison with the map functions recommended in the present paper, the assumption of no interference gives a poor fit to the data. PMID:3565379

  4. Image completion by diffusion maps and spectral relaxation.

    PubMed

    Gepshtein, Shai; Keller, Yosi

    2013-08-01

    We present a framework for image inpainting that utilizes the diffusion framework approach to spectral dimensionality reduction. We show that on formulating the inpainting problem in the embedding domain, the domain to be inpainted is smoother in general, particularly for the textured images. Thus, the textured images can be inpainted through simple exemplar-based and variational methods. We discuss the properties of the induced smoothness and relate it to the underlying assumptions used in contemporary inpainting schemes. As the diffusion embedding is nonlinear and noninvertible, we propose a novel computational approach to approximate the inverse mapping from the inpainted embedding space to the image domain. We formulate the mapping as a discrete optimization problem, solved through spectral relaxation. The effectiveness of the presented method is exemplified by inpainting real images, where it is shown to compare favorably with contemporary state-of-the-art schemes. PMID:23322762

  5. A Mapping Between Structural and Functional Brain Networks.

    PubMed

    Meier, Jil; Tewarie, Prejaas; Hillebrand, Arjan; Douw, Linda; van Dijk, Bob W; Stufflebeam, Steven M; Van Mieghem, Piet

    2016-05-01

    The relationship between structural and functional brain networks is still highly debated. Most previous studies have used a single functional imaging modality to analyze this relationship. In this work, we use multimodal data, from functional MRI, magnetoencephalography, and diffusion tensor imaging, and assume that there exists a mapping between the connectivity matrices of the resting-state functional and structural networks. We investigate this mapping employing group averaged as well as individual data. We indeed find a significantly high goodness of fit level for this structure-function mapping. Our analysis suggests that a functional connection is shaped by all walks up to the diameter in the structural network in both modality cases. When analyzing the inverse mapping, from function to structure, longer walks in the functional network also seem to possess minor influence on the structural connection strengths. Even though similar overall properties for the structure-function mapping are found for different functional modalities, our results indicate that the structure-function relationship is modality dependent. PMID:26860437

  6. 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.

  7. Measuring Psychometric Functions with the Diffusion Model

    PubMed Central

    Ratcliff, Roger

    2014-01-01

    The diffusion decision model (Ratcliff, 1978) was used to examine discrimination for a range of perceptual tasks: numerosity discrimination, number discrimination, brightness discrimination, motion discrimination, speed discrimination, and length discrimination. The model produces a measure of the quality of the information that drives decision processes, a measure termed “drift rate” in the model. As drift rate varies across experimental conditions that differ in difficulty, a psychometric function that plots drift rate against difficulty can be constructed. Psychometric functions for the tasks in this article usually plot accuracy against difficulty, but for some levels of difficulty, accuracy can be at ceiling. The diffusion model extends the range of difficulty that can be evaluated because drift rates depend on response times (RTs) as well as accuracy and when RTs decrease across conditions that are all at ceiling in accuracy, then drift rates will distinguish among the conditions. Signal detection theory assumes that the variable driving performance is the z-transform of the accuracy value and somewhat surprisingly, this closely matches drift rate extracted from the diffusion model when accuracy is not at ceiling, but not sometimes when accuracy is high. Even though the functions are similar in the middle of the range, the interpretations of the variability in the models (e.g., perceptual variability, decision process variability) are incompatible. PMID:24446719

  8. Functional mapping of growth and development.

    PubMed

    Li, Yao; Wu, Rongling

    2010-05-01

    Understanding how an organism develops into a fully functioning adult from a mass of undifferentiated cells may reveal different strategies that allow the organism to survive under limiting conditions. Here, we review an analytical model for characterizing quantitative trait loci (QTLs) that underlie variation in growth trajectories and developmental timing. This model, called functional mapping, incorporates fundamental principles behind biological processes or networks that are bridged with mathematical functions into a statistical mapping framework. Functional mapping estimates parameters that determine the shape and function of a particular biological process, thus providing a flexible platform to test biologically meaningful hypotheses regarding the complex relationships between gene action and development. PMID:19930171

  9. 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.

  10. 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.

  11. 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…

  12. 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

  13. 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

  14. 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.

  15. Multifractal wave functions of simple quantum maps

    NASA Astrophysics Data System (ADS)

    Martin, John; García-Mata, Ignacio; Giraud, Olivier; Georgeot, Bertrand

    2010-10-01

    We study numerically multifractal properties of two models of one-dimensional quantum maps: a map with pseudointegrable dynamics and intermediate spectral statistics and a map with an Anderson-like transition recently implemented with cold atoms. Using extensive numerical simulations, we compute the multifractal exponents of quantum wave functions and study their properties, with the help of two different numerical methods used for classical multifractal systems (box-counting and wavelet methods). We compare the results of the two methods over a wide range of values. We show that the wave functions of the Anderson map display a multifractal behavior similar to eigenfunctions of the three-dimensional Anderson transition but of a weaker type. Wave functions of the intermediate map share some common properties with eigenfunctions at the Anderson transition (two sets of multifractal exponents, with similar asymptotic behavior), but other properties are markedly different (large linear regime for multifractal exponents even for strong multifractality, different distributions of moments of wave functions, and absence of symmetry of the exponents). Our results thus indicate that the intermediate map presents original properties, different from certain characteristics of the Anderson transition derived from the nonlinear sigma model. We also discuss the importance of finite-size effects.

  16. Thickness Mapping of Eleven Retinal Layers Segmented Using the Diffusion Maps Method in Normal Eyes

    PubMed Central

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

    2015-01-01

    This study was conducted to determine the thickness map of eleven retinal layers in normal subjects by spectral domain optical coherence tomography (SD-OCT) and evaluate their association with sex and age. Mean regional retinal thickness of 11 retinal layers was obtained by automatic three-dimensional diffusion map based method in 112 normal eyes of 76 Iranian subjects. We applied our previously reported 3D intraretinal fast layer segmentation which does not require edge-based image information but rather relies on regional image texture. The thickness maps are compared among 9 macular sectors within 3 concentric circles as defined by ETDRS. The thickness map of central foveal area in layers 1, 3, and 4 displayed the minimum thickness. Maximum thickness was observed in nasal to the fovea of layer 1 and in a circular pattern in the parafoveal retinal area of layers 2, 3, and 4 and in central foveal area of layer 6. Temporal and inferior quadrants of the total retinal thickness and most of other quadrants of layer 1 were significantly greater in the men than in the women. Surrounding eight sectors of total retinal thickness and a limited number of sectors in layers 1 and 4 significantly correlated with age. PMID:25960888

  17. Generalized spectral representations of chaotic maps displaying intermittency and anomalous diffusion

    SciTech Connect

    Hasegawa, H.H.; Luschei, E.; Prigogine, I.

    1994-12-31

    Transport processes can be understood in terms of the spectral properties of the Frobenius-Perron operator. For the multi-Bernoulli map we have obtained generalized spectral representations describing diffusion processes. In this paper we consider a chaotic map which leads to intermittency and anomalous diffusion. We calculate the spatio-temporal power spectrum and compare it to numerical simulation.

  18. 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

  19. Soot Volume Fraction Maps for Normal and Reduced Gravity Laminar Acetylene Jet Diffusion Flames

    NASA Technical Reports Server (NTRS)

    Greenberg, Paul S.; Ku, Jerry C.

    1997-01-01

    The study of soot particulate distribution inside gas jet diffusion flames is important to the understanding of fundamental soot particle and thermal radiative transport processes, as well as providing findings relevant to spacecraft fire safety, soot emissions, and radiant heat loads for combustors used in air-breathing propulsion systems. Compared to those under normal gravity (1-g) conditions, the elimination of buoyancy-induced flows is expected to significantly change the flow field in microgravity (O g) flames, resulting in taller and wider flames with longer particle residence times. Work by Bahadori and Edelman demonstrate many previously unreported qualitative and semi-quantitative results, including flame shape and radiation, for sooting laminar zas jet diffusion flames. Work by Ku et al. report soot aggregate size and morphology analyses and data and model predictions of soot volume fraction maps for various gas jet diffusion flames. In this study, we present the first 1-g and 0-g comparisons of soot volume fraction maps for laminar acetylene and nitrogen-diluted acetylene jet diffusion flames. Volume fraction is one of the most useful properties in the study of sooting diffusion flames. The amount of radiation heat transfer depends directly on the volume fraction and this parameter can be measured from line-of-sight extinction measurements. Although most Soot aggregates are submicron in size, the primary particles (20 to 50 nm in diameter) are in the Rayleigh limit, so the extinction absorption) cross section of aggregates can be accurately approximated by the Rayleigh solution as a function of incident wavelength, particles' complex refractive index, and particles' volume fraction.

  20. Functional mapping in biology and medicine

    SciTech Connect

    McEachron, D.L.

    1986-01-01

    This book contains 10 selections. Some of the titles are: Two Views of Functional Mapping and Autoradiography; Quantitative Analysis of Autoradiographs; Hardware and Software Design Considerations in Engineering an Image Processing Workstation: Autoradiographic Analysis with DUMAS and the BRAIN Autoradiograph Analysis Software Package (with 1 color plate); and Quantitative Autoradiography and in vitro Radioligand Binding.

  1. Imaging diffuse clouds: bright and dark gas mapped in CO

    NASA Astrophysics Data System (ADS)

    Liszt, H. S.; Pety, J.

    2012-05-01

    Aims: We wish to relate the degree scale structure of galactic diffuse clouds to sub-arcsecond atomic and molecular absorption spectra obtained against extragalactic continuum background sources. Methods: We used the ARO 12 m telescope to map J = 1-0 CO emission at 1' resolution over 30' fields around the positions of 11 background sources occulted by 20 molecular absorption line components, of which 11 had CO emission counterparts. We compared maps of CO emission to sub-arcsec atomic and molecular absorption spectra and to the large-scale distribution of interstellar reddening. Results: 1) The same clouds, identified by their velocity, were seen in absorption and emission and atomic and molecular phases, not necessarily in the same direction. Sub-arcsecond absorption spectra are a preview of what is seen in CO emission away from the continuum. 2) The CO emission structure was amorphous in 9 cases, quasi-periodic or wave-like around B0528+134 and tangled and filamentary around BL Lac. 3) Strong emission, typically 4-5 K at EB - V ≤ 0.15 mag and up to 10-12 K at EB - V ≲ 0.3 mag was found, much brighter than toward the background targets. Typical covering factors of individual features at the 1 K km s-1 level were 20%. 4) CO-H2 conversion factors as much as 4-5 times below the mean value N(H2)/WCO = 2 × 1020 H2 cm-2 (K km s-1)-1 are required to explain the luminosity of CO emission at/above the level of 1 K km s-1. Small conversion factors and sharp variability of the conversion factor on arcminute scales are due primarily to CO chemistry and need not represent unresolved variations in reddening or total column density. Conclusions: Like Fermi and Planck we see some gas that is dark in CO and other gas in which CO is overluminous per H2. A standard CO-H2 conversion factor applies overall owing to balance between the luminosities per H2 and surface covering factors of bright and dark CO, but with wide variations between sightlines and across the faces of

  2. 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.

  3. Function Based Risk Assessment: Mapping Function to Likelihood

    NASA Technical Reports Server (NTRS)

    Tumer, Irem Y.; Grantham, Katie; Stone, Robert

    2005-01-01

    The concept of function offers a high potential for thinking and reasoning about designs as well as providing a common thread for relating together other design information. This paper focuses specifically on the relation between function and risk by presenting a mathematical mapping from product function to risk likelihood. This risk information is composed of design parameters, failure modes, and likelihood values. A spacecraft orientation subsystem, subsystem used to guide science instruments, and a Bell 206 rotorcraft are used to test the mapping which continues research on these products relating function to failure. Finally, a case study is presented in which the risk element likelihood is calculated for a fuel cell which is in the conceptual design phase at NASA JPL.

  4. Mapping the holes: 3D ISM maps and diffuse X-ray background

    NASA Astrophysics Data System (ADS)

    Lallement, R.; Vergely, J.-L.; Puspitarini, L.; Snowden, S.; Galeazzi, M.; Koutroumpa, D.

    3D maps of Galactic interstellar dust and gas reveal empty regions, including cavities carved by stellar winds and supernovae. Such cavities are often filled with hot gas and are sources of soft X-ray background emission. We discuss the combined analysis of the diffuse soft (0.25 keV) X-ray background and the 3D distribution of nearby (<1 kpc) dust, including studies of shadows cast by nearby clouds in the background. This analysis benefits from recent progress in the estimate of the foreground X-ray emission from the heliosphere. New and past X-ray data are found to be consistent with the maps if the ≃ 100-150 pc wide Local Bubble surrounding the Sun is filled with 106K gas with a pressure 2nT ≃ 10,000 K cm-3. On the other hand, the giant cavity found in the 3rd Galactic quadrant has a weaker volume emission than the LB and is very likely filled to a large extent with warm ionized gas. Its geometry suggests a link with the tilted Gould belt, and a potential mechanism for the formation of the whole structure has been recently proposed. According to it, the local inclination of gas and stars, the velocity pattern and enhanced star formation could have been initiated 60-70 Myr ago when a massive globular cluster crossed the Galactic Plane in the vicinity of the Sun. The destabilization of stellar orbits around the Sun may have generated enhanced asteroid falls of the Cretaceous-Tertiary (KT) extinction events. Additionally, a short gamma ray burst may have occurred in the cluster during the crossing, producing intense ionization and subsequent shock waves leading to the star formations seen today in the form of the giant ionized region and OB associations at its periphery. Gaia measurements of nearby stars and clusters should help shedding light on the local history.

  5. 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.

  6. Sparse Solution of Fiber Orientation Distribution Function by Diffusion Decomposition

    PubMed Central

    Yeh, Fang-Cheng; Tseng, Wen-Yih Isaac

    2013-01-01

    Fiber orientation is the key information in diffusion tractography. Several deconvolution methods have been proposed to obtain fiber orientations by estimating a fiber orientation distribution function (ODF). However, the L2 regularization used in deconvolution often leads to false fibers that compromise the specificity of the results. To address this problem, we propose a method called diffusion decomposition, which obtains a sparse solution of fiber ODF by decomposing the diffusion ODF obtained from q-ball imaging (QBI), diffusion spectrum imaging (DSI), or generalized q-sampling imaging (GQI). A simulation study, a phantom study, and an in-vivo study were conducted to examine the performance of diffusion decomposition. The simulation study showed that diffusion decomposition was more accurate than both constrained spherical deconvolution and ball-and-sticks model. The phantom study showed that the angular error of diffusion decomposition was significantly lower than those of constrained spherical deconvolution at 30° crossing and ball-and-sticks model at 60° crossing. The in-vivo study showed that diffusion decomposition can be applied to QBI, DSI, or GQI, and the resolved fiber orientations were consistent regardless of the diffusion sampling schemes and diffusion reconstruction methods. The performance of diffusion decomposition was further demonstrated by resolving crossing fibers on a 30-direction QBI dataset and a 40-direction DSI dataset. In conclusion, diffusion decomposition can improve angular resolution and resolve crossing fibers in datasets with low SNR and substantially reduced number of diffusion encoding directions. These advantages may be valuable for human connectome studies and clinical research. PMID:24146772

  7. 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.

  8. Cation Diffusion Facilitator family: Structure and function.

    PubMed

    Kolaj-Robin, Olga; Russell, David; Hayes, Kevin A; Pembroke, J Tony; Soulimane, Tewfik

    2015-05-22

    The Cation Diffusion Facilitators (CDFs) form a family of membrane-bound proteins capable of transporting zinc and other heavy metal ions. Involved in metal tolerance/resistance by efflux of ions, CDF proteins share a two-modular architecture consisting of a transmembrane domain (TMD) and C-terminal domain (CTD) that protrudes into the cytoplasm. Discovery of a Zn²⁺ and Cd²⁺ CDF transporter from a marine bacterium Maricaulis maris that does not possess the CTD questions current perceptions regarding this family of proteins. This article describes a new, CTD-lacking subfamily of CDFs and our current knowledge about this family of proteins in the view of these findings. PMID:25896018

  9. Self-organizing maps as an approach to exploring spatiotemporal diffusion patterns

    PubMed Central

    2013-01-01

    Background Self-organizing maps (SOMs) have now been applied for a number of years to identify patterns in large datasets; yet, their application in the spatiotemporal domain has been lagging. Here, we demonstrate how spatialtemporal disease diffusion patterns can be analysed using SOMs and Sammon’s projection. Methods SOMs were applied to identify synchrony between spatial locations, to group epidemic waves based on similarity of diffusion pattern and to construct sequence of maps of synoptic states. The Sammon’s projection was used to created diffusion trajectories from the SOM output. These methods were demonstrated with a dataset that reports Measles outbreaks that took place in Iceland in the period 1946–1970. The dataset reports the number of Measles cases per month in 50 medical districts. Results Both stable and incidental synchronisation between medical districts were identified as well as two distinct groups of epidemic waves, a uniformly structured fast developing group and a multiform slow developing group. Diffusion trajectories for the fast developing group indicate a typical diffusion pattern from Reykjavik to the northern and eastern parts of the island. For the other group, diffusion trajectories are heterogeneous, deviating from the Reykjavik pattern. Conclusions This study demonstrates the applicability of SOMs (combined with Sammon’s Projection and GIS) in spatiotemporal diffusion analyses. It shows how to visualise diffusion patterns to identify (dis)similarity between individual waves and between individual waves and an overall time-series performing integrated analysis of synchrony and diffusion trajectories. PMID:24359538

  10. Effects of Non-Local Diffusion on Structural MRI Preprocessing and Default Network Mapping: Statistical Comparisons with Isotropic/Anisotropic Diffusion

    PubMed Central

    Zuo, Xi-Nian; Xing, Xiu-Xia

    2011-01-01

    Neuroimaging community usually employs spatial smoothing to denoise magnetic resonance imaging (MRI) data, e.g., Gaussian smoothing kernels. Such an isotropic diffusion (ISD) based smoothing is widely adopted for denoising purpose due to its easy implementation and efficient computation. Beyond these advantages, Gaussian smoothing kernels tend to blur the edges, curvature and texture of images. Researchers have proposed anisotropic diffusion (ASD) and non-local diffusion (NLD) kernels. We recently demonstrated the effect of these new filtering paradigms on preprocessing real degraded MRI images from three individual subjects. Here, to further systematically investigate the effects at a group level, we collected both structural and functional MRI data from 23 participants. We first evaluated the three smoothing strategies' impact on brain extraction, segmentation and registration. Finally, we investigated how they affect subsequent mapping of default network based on resting-state functional MRI (R-fMRI) data. Our findings suggest that NLD-based spatial smoothing maybe more effective and reliable at improving the quality of both MRI data preprocessing and default network mapping. We thus recommend NLD may become a promising method of smoothing structural MRI images of R-fMRI pipeline. PMID:22066005

  11. Anisotropy Induced by Macroscopic Boundaries: Surface-Normal Mapping using Diffusion-Weighted Imaging

    PubMed Central

    Özarslan, Evren; Nevo, Uri; Basser, Peter J.

    2008-01-01

    In MRI, macroscopic boundaries lead to a diffusion-related increase in signal intensity near them—an effect commonly referred to as edge-enhancement. In diffusion-weighted imaging protocols where the signal attenuation due to diffusion results predominantly from the application of magnetic field gradients, edge-enhancement will depend on the orientation of these diffusion gradients. The resulting diffusion anisotropy can be exploited to map the direction normal to the macroscopic boundary. Simulations suggest that the hypothesized anisotropy may be within observable limits even when the voxel contains no boundary itself—hence, the name remote-anisotropy. Moreover, for certain experimental parameters there may be significant phase cancellations within the voxel that may lead to an edge detraction effect. When this is avoided, the eigenvector corresponding to the smallest eigenvalue of the diffusion tensor obtained from diffusion-tensor imaging can be used to create surface-normal maps conveniently. Experiments performed on simple geometric constructs as well as real tissue demonstrate the feasibility of using the edge-enhancement mechanism to map orientations orthogonal to macroscopic surfaces, which may be used to assess the integrity of tissue and organ boundaries noninvasively. PMID:18065457

  12. 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

  13. 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.

  14. 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.

  15. Mapping the functional yeast ABC transporter interactome.

    PubMed

    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; San Luis, Bryan-Joseph; Shevelev, Igor; Sturley, Stephen L; Boone, Charles; Greenblatt, Jack F; Zhang, Zhaolei; Paumi, Christian M; Babu, Mohan; Park, Hay-Oak; Michaelis, Susan; Stagljar, Igor

    2013-09-01

    ATP-binding cassette (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 technology to map the protein interactome of all of the nonmitochondrial ABC transporters in the model organism Saccharomyces cerevisiae 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 an unexpectedly 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

  16. Computation of diffusion function measures in q-space using magnetic resonance hybrid diffusion imaging.

    PubMed

    Wu, Yu-Chien; Field, Aaron S; Alexander, Andrew L

    2008-06-01

    The distribution of water diffusion in biological tissues may be estimated by a 3-D Fourier transform (FT) of diffusion-weighted measurements in q-space. In this study, methods for estimating diffusion spectrum measures (the zero-displacement probability, the mean-squared displacement, and the orientation distribution function) directly from the q-space signals are described. These methods were evaluated using both computer simulations and hybrid diffusion imaging (HYDI) measurements on a human brain. The HYDI method obtains diffusion-weighted measurements on concentric spheres in q-space. Monte Carlo computer simulations were performed to investigate effects of noise, q-space truncation, and sampling interval on the measures. This new direct computation approach reduces HYDI data processing time and image artifacts arising from 3-D FT and regridding interpolation. In addition, it is less sensitive to the noise and q-space truncation effects than conventional approach. Although this study focused on data using the HYDI scheme, this computation approach may be applied to other diffusion sampling schemes including Cartesian diffusion spectrum imaging. PMID:18541492

  17. Diffusion MRI at 25: Exploring brain tissue structure and function

    PubMed Central

    Bihan, Denis Le; Johansen-Berg, Heidi

    2013-01-01

    Diffusion MRI (or dMRI) came into existence in the mid-1980s. During the last 25 years, diffusion MRI has been extraordinarily successful (with more than 300,000 entries on Google Scholar for diffusion MRI). Its main clinical domain of application has been neurological disorders, especially for the management of patients with acute stroke. It is also rapidly becoming a standard for white matter disorders, as diffusion tensor imaging (DTI) can reveal abnormalities in white matter fiber structure and provide outstanding maps of brain connectivity. The ability to visualize anatomical connections between different parts of the brain, non-invasively and on an individual basis, has emerged as a major breakthrough for neurosciences. The driving force of dMRI is to monitor microscopic, natural displacements of water molecules that occur in brain tissues as part of the physical diffusion process. Water molecules are thus used as a probe that can reveal microscopic details about tissue architecture, either normal or in a diseased state. PMID:22120012

  18. Noninvasive Functional and Structural Connectivity Mapping of the Human Thalamocortical System

    PubMed Central

    Snyder, Abraham Z.; Shimony, Joshua S.; Fox, Michael D.; Raichle, Marcus E.

    2010-01-01

    Relating structural connectivity with functional activity is fundamentally important to understanding the brain's physiology. The thalamocortical system serves as a good model system for exploring structure/function relationships because of its well-documented anatomical connectivity. Here we performed functional and structural magnetic resonance mapping of the human thalamocortical system using intrinsic brain activity and diffusion-weighted imaging. The accuracy of these imaging techniques is tested by comparison with human histology registered to common anatomical space and connectional anatomy derived from nonhuman primates. In general, there is good overall concordance among structural, functional, and histological results which suggests that a simple model of direct anatomical connectivity between the cerebral cortex and the thalamus is capable of explaining much of the observed correlations in neuronal activity. However, important differences between structural and functional mapping results are also manifest which suggests a more complex interpretation and emphasizes the unique contributions from structural and functional mapping. PMID:19729393

  19. 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…

  20. 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.

  1. 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…

  2. 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

  3. Mapping cortical responses to speech using high-density diffuse optical tomography.

    PubMed

    Hassanpour, Mahlega S; Eggebrecht, Adam T; Culver, Joseph P; Peelle, Jonathan E

    2015-08-15

    The functional neuroanatomy of speech processing has been investigated using positron emission tomography (PET) and functional magnetic resonance imaging (fMRI) for more than 20years. However, these approaches have relatively poor temporal resolution and/or challenges of acoustic contamination due to the constraints of echoplanar fMRI. Furthermore, these methods are contraindicated because of safety concerns in longitudinal studies and research with children (PET) or in studies of patients with metal implants (fMRI). High-density diffuse optical tomography (HD-DOT) permits presenting speech in a quiet acoustic environment, has excellent temporal resolution relative to the hemodynamic response, and provides noninvasive and metal-compatible imaging. However, the performance of HD-DOT in imaging the brain regions involved in speech processing is not fully established. In the current study, we use an auditory sentence comprehension task to evaluate the ability of HD-DOT to map the cortical networks supporting speech processing. Using sentences with two levels of linguistic complexity, along with a control condition consisting of unintelligible noise-vocoded speech, we recovered a hierarchically organized speech network that matches the results of previous fMRI studies. Specifically, hearing intelligible speech resulted in increased activity in bilateral temporal cortex and left frontal cortex, with syntactically complex speech leading to additional activity in left posterior temporal cortex and left inferior frontal gyrus. These results demonstrate the feasibility of using HD-DOT to map spatially distributed brain networks supporting higher-order cognitive faculties such as spoken language. PMID:26026816

  4. 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.

  5. 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

  6. Voxel-based cervical spinal cord mapping of diffusion abnormalities in MS-related myelitis

    PubMed Central

    Kou, Nancy; Altmann, Daniel; Wheeler-Kingshott, Claudia A.M.; Thompson, Alan J.; Ciccarelli, Olga

    2014-01-01

    Objective: To apply a novel postprocessing voxel-based analysis for diffusion tensor imaging of the cervical spinal cord in multiple sclerosis (MS) in a prospective cross-sectional study. Methods: Fourteen patients with MS who were within 4 weeks of the onset of cervical myelitis (lesion C1-3) and 11 healthy controls underwent cervical spinal cord diffusion tensor imaging. Cervical spinal cord maps of fractional anisotropy (FA), mean diffusivity, radial diffusivity (RD), and axial diffusivity were registered and compared between patients and controls. Mean FA and RD values from significant thresholded clusters were regressed with clinical scores, after adjusting for cord area and age, to determine associations with physical disability. Results: Cord registrations for subjects were qualitatively assessed (scored out of 5) and those with low scores (1 or 2) were excluded from further analysis. Cord registration was considered good in 11 patients (6 females; mean age = 35.5 years) and 10 controls (6 females; mean age 44 years). Voxel-based comparisons showed patients with MS had lower FA and higher RD at C2-3 levels (left >right mainly in gray matter; p < 0.01, uncorrected). Extracted values of both FA and RD from thresholded clusters were significantly associated with greater disability measured using the Expanded Disability Status Scale and Timed 25-Foot Walk Test in patients with MS. Conclusions: Mapping diffusion abnormalities within the cervical spinal cord using a novel voxel-based approach can localize clinically relevant pathology. PMID:25186861

  7. A simple non-chaotic map generating subdiffusive, diffusive, and superdiffusive dynamics.

    PubMed

    Salari, Lucia; Rondoni, Lamberto; Giberti, Claudio; Klages, Rainer

    2015-07-01

    Analytically tractable dynamical systems exhibiting a whole range of normal and anomalous deterministic diffusion are rare. Here, we introduce a simple non-chaotic model in terms of an interval exchange transformation suitably lifted onto the whole real line which preserves distances except at a countable set of points. This property, which leads to vanishing Lyapunov exponents, is designed to mimic diffusion in non-chaotic polygonal billiards that give rise to normal and anomalous diffusion in a fully deterministic setting. As these billiards are typically too complicated to be analyzed from first principles, simplified models are needed to identify the minimal ingredients generating the different transport regimes. For our model, which we call the slicer map, we calculate all its moments in position analytically under variation of a single control parameter. We show that the slicer map exhibits a transition from subdiffusion over normal diffusion to superdiffusion under parameter variation. Our results may help to understand the delicate parameter dependence of the type of diffusion generated by polygonal billiards. We argue that in different parameter regions the transport properties of our simple model match to different classes of known stochastic processes. This may shed light on difficulties to match diffusion in polygonal billiards to a single anomalous stochastic process. PMID:26232964

  8. The analysis of three typical tropospheric mapping functions

    NASA Astrophysics Data System (ADS)

    Xie, Shaofeng; Jin, Liyang; Zhang, Pengfei

    2015-12-01

    Processing the tropospheric data provided by IGS stations of china with the NMF function,VMF1 function and GMF function. comparing the baseline repetition rate. If the change of IGS station latitude and the cutoff elevation angles can make the height correction become more precision when using this three mapping function. And whether the dynamic mapping function can meet the accuracy requirement with the highly temporal.

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

    PubMed

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

    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

  10. 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.

  11. 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.

  12. 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. PMID:23874733

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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.

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

    PubMed

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

    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. PMID:25240340

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

    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.

  1. 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

  2. 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.

  3. A technology mapping of boolean functions for CPLDs

    NASA Astrophysics Data System (ADS)

    Kania, Dariusz

    2014-10-01

    The effective technology mapping for PAL-based Complex PLDs is presented. The aim of this approach is to cover a multiple-output function by a minimal number of PAL-based logic blocks. Proposed algorithm, implemented within the PALDec system, has been used for synthesizing the benchmarks. The obtained results are compared with the classical technology mapping.

  4. 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.

  5. Functional Imaging of the Developing Brain at the Bedside Using Diffuse Optical Tomography.

    PubMed

    Ferradal, Silvina L; Liao, Steve M; Eggebrecht, Adam T; Shimony, Joshua S; Inder, Terrie E; Culver, Joseph P; Smyser, Christopher D

    2016-04-01

    While histological studies and conventional magnetic resonance imaging (MRI) investigations have elucidated the trajectory of structural changes in the developing brain, less is known regarding early functional cerebral development. Recent investigations have demonstrated that resting-state functional connectivity MRI (fcMRI) can identify networks of functional cerebral connections in infants. However, technical and logistical challenges frequently limit the ability to perform MRI scans early or repeatedly in neonates, particularly in those at greatest risk for adverse neurodevelopmental outcomes. High-density diffuse optical tomography (HD-DOT), a portable imaging modality, potentially enables early continuous and quantitative monitoring of brain function in infants. We introduce an HD-DOT imaging system that combines advancements in cap design, ergonomics, and data analysis methods to allow bedside mapping of functional brain development in infants. In a cohort of healthy, full-term neonates scanned within the first days of life, HD-DOT results demonstrate strong congruence with those obtained using co-registered, subject-matched fcMRI and reflect patterns of typical brain development. These findings represent a transformative advance in functional neuroimaging in infants, and introduce HD-DOT as a powerful and practical method for quantitative mapping of early functional brain development in normal and high-risk neonates. PMID:25595183

  6. 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.

  7. 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.

  8. 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.

  9. Characterizing the Structure of Diffuse Emission in Hi-GAL Maps

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    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.

  10. 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.

  11. Regularization of diffusion-based direction maps for the tracking of brain white matter fascicles.

    PubMed

    Poupon, C; Clark, C A; Frouin, V; Régis, J; Bloch, I; Le Bihan, D; Mangin, J

    2000-08-01

    Magnetic resonance diffusion tensor imaging (DTI) provides information about fiber local directions in brain white matter. This paper addresses inference of the connectivity induced by fascicles made up of numerous fibers from such diffusion data. The usual fascicle tracking idea, which consists of following locally the direction of highest diffusion, is prone to erroneous forks because of problems induced by fiber crossing. In this paper, this difficulty is partly overcomed by the use of a priori knowledge of the low curvature of most of the fascicles. This knowledge is embedded in a model of the bending energy of a spaghetti plate representation of the white matter used to compute a regularized fascicle direction map. A new tracking algorithm is then proposed to highlight putative fascicle trajectories from this direction map. This algorithm takes into account potential fan shaped junctions between fascicles. A study of the tracking behavior according to the influence given to the a priori knowledge is proposed and concrete tracking results obtained with in vivo human brain data are illustrated. These results include putative trajectories of some pyramidal, commissural, and various association fibers. PMID:10913324

  12. 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

  13. Mapping of minority carrier diffusion length and heavy metal contamination with ultimate surface photovoltage method

    NASA Astrophysics Data System (ADS)

    Lagowski, J.; Aleynikov, A.; Savtchouk, A.; Edelman, P.

    2004-07-01

    The Ultimate surface photovoltage method of minority carrier diffusion length measurements reffered to as Ultimate SPV, replaces a sequential “one wavelength at a time” approach with simultaneous illumination with the entire set of wavelengths. In this multiwavelength beam, each monochromatic component is chopped with slightly different frequency. This enables simultaneous monitoring of all component SPV signals corresponding to different wavelengths using multi-frequency signal processing. The amplitude and phase of each component signals are then analyzed and used to calculate the diffusion length and surface lifetime. In-flight Ultimate SPV measurement, whereby the wafer continuously moves under SPV probe, is used for fast whole wafer mapping. In addition to speed advantages, Ultimate SPV offers a fundemental accuracy advantage due to elimination of differences in wafer condition during sequential illumination with individual wavelengths. High-speed measurements make it possible to add additional wafer treatments and perform multi-mapping required for separation of Fe and Cu in the silicon bulk. Wafer mapping in time of 2 minutes realized with Ultimate SPV is critical for monitoring of cobalt in silicon.

  14. A new tropospheric mapping function based on ECMWF models

    NASA Astrophysics Data System (ADS)

    Biancale, Richard; Dupuy, Stephanie; Soudarin, Laurent

    The tropospheric propagation delay of Earth-satellite tracking data (from electromagnetic or optical signals) is generally corrected in two steps: 1) computing the zenithal dry and wet delays at the station, 2) applying a mapping function to pull them down at the elevation needed. Considering that zenithal delays can be well computed from ground pressure, temperature and humidity data through hydrostatic theory, or can be integrated from ECMWF multiple layer models (for instance), or at least can be adjusted in orbit processing, we turned our attention more specifically to the validity of the mapping function. Starting on one hand from a few maps of the ECMWF meteorological model of pressure, temperature and humidity available each 6h in 91 isobaric layers we reconstructed first the dry and wet tropospheric delays at each grid point for several azimuth and elevation angles. On the other hand we computed the same delays from a Marini-type mapping function based on the integrated zenithal delays computed themselves from the same ECMWF models. An adequacy was searched between both approaches which led us to adjust all coefficients of the dry and wet mapping functions. We propose here to describe our approach and to present the dry and wet mapping functions obtained with some tests with real data.

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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.

  20. Parametric Response Mapping of Apparent Diffusion Coefficient (ADC) as an Imaging Biomarker to Distinguish Pseudoprogression from True Tumor Progression In Peptide-Based Vaccine Therapy for Pediatric Diffuse Instrinsic Pontine Glioma

    PubMed Central

    Ceschin, Rafael; Kurland, Brenda F.; Abberbock, Shira R.; Ellingson, Benjamin M.; Okada, Hideho; Jakacki, Regina I.; Pollack, Ian F.; Panigrahy, Ashok

    2015-01-01

    Background and Purpose Immune response to cancer therapy may result in pseudoprogression, which can only be identified retrospectively and which may disrupt an effective therapy. This study assesses whether serial parametric response mapping (PRM, a voxel-by-voxel method of image analysis also known as functional diffusion mapping) analysis of ADC measurements following peptide-based vaccination may help prospectively distinguish progression from pseudoprogression in pediatric patients with diffuse intrinsic pontine gliomas. Materials and Methods From 2009–2012, 21 children age 4–18 with diffuse intrinsic pontine gliomas were enrolled in a serial peptide-based vaccination protocol following radiotherapy. DWI was acquired before immunotherapy and at six week intervals during vaccine treatment. Pseudoprogression was identified retrospectively based on clinical and radiographic findings, excluding DWI. Parametric response mapping was used to analyze 96 scans, comparing ADC measures at multiple time points (from first vaccine to up to 12 weeks after the vaccine was halted) to pre-vaccine baseline values. Log-transformed fractional increased ADC (fiADC), fractional decreased ADC (fdADC), and parametric response mapping ratio (fiADC/fdADC) were compared between patients with and without pseudoprogression, using generalized estimating equations with inverse weighting by cluster size. Results Median survival was 13.1 months from diagnosis (range 6.4–24.9 months). Four of 21 children (19%) were assessed as experiencing pseudoprogression. Patients with pseudoprogression had higher fitted average log-transformed parametric response mapping ratios (p=0.01) and fiADCs (p=0.0004), compared to patients without pseudoprogression. Conclusion Serial parametric response mapping of ADC, performed at multiple time points of therapy, may distinguish pseudoprogression from true progression in patients with diffuse intrinsic pontine gliomas treated with peptide-based vaccination

  1. 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

  2. Testing anatomically specified hypotheses in functional imaging using cytoarchitectonic maps.

    PubMed

    Eickhoff, Simon B; Heim, Stefan; Zilles, Karl; Amunts, Katrin

    2006-08-15

    The statistical inference on functional imaging data is severely complicated by the embedded multiple testing problem. Defining a region of interest (ROI) where the activation is hypothesized a priori helps to circumvent this problem, since in this case the inference is restricted to fewer simultaneous tests, rendering it more sensitive. Cytoarchitectonic maps obtained from postmortem brains provide objective, a priori ROIs that can be used to test anatomically specified hypotheses about the localization of functional activations. We here analyzed three methods for the definition of ROIs based on probabilistic cytoarchitectonic maps. (1) ROIs defined by the volume assigned to a cytoarchitectonic area in the summary map of all areas (maximum probability map, MPM), (2) ROIs based on thresholding the individual probabilistic maps and (3) spherical ROIs build around the cytoarchitectonic center of gravity. The quality with which the thus defined ROIs represented the respective cytoarchitectonic areas as well as their sensitivity for detecting functional activations was subsequently statistically evaluated. Our data showed that the MPM method yields ROIs, which reflect most adequately the underlying anatomical hypotheses. These maps also show a high degree of sensitivity in the statistical analysis. We thus propose the use of MPMs for the definition of ROIs. In combination with thresholding based on the Gaussian random field theory, these ROIs can then be applied to test anatomically specified hypotheses in functional neuroimaging studies. PMID:16781166

  3. 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.

  4. 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…

  5. 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

  6. Functional mapping - how to map and study the genetic architecture of dynamic complex traits.

    PubMed

    Wu, Rongling; Lin, Min

    2006-03-01

    The development of any organism is a complex dynamic process that is controlled by a network of genes as well as by environmental factors. Traditional mapping approaches for analysing phenotypic data measured at a single time point are too simple to reveal the genetic control of developmental processes. A general statistical mapping framework, called functional mapping, has been proposed to characterize, in a single step, the quantitative trait loci (QTLs) or nucleotides (QTNs) that underlie a complex dynamic trait. Functional mapping estimates mathematical parameters that describe the developmental mechanisms of trait formation and expression for each QTL or QTN. The approach provides a useful quantitative and testable framework for assessing the interplay between gene actions or interactions and developmental changes. PMID:16485021

  7. Co-analysis of Brain Structure and Function using fMRI and Diffusion-weighted Imaging

    PubMed Central

    Phillips, Jeffrey S.; Greenberg, Adam S.; Pyles, John A.; Pathak, Sudhir K.; Behrmann, Marlene; Schneider, Walter; Tarr, Michael J.

    2012-01-01

    The study of complex computational systems is facilitated by network maps, such as circuit diagrams. Such mapping is particularly informative when studying the brain, as the functional role that a brain area fulfills may be largely defined by its connections to other brain areas. In this report, we describe a novel, non-invasive approach for relating brain structure and function using magnetic resonance imaging (MRI). This approach, a combination of structural imaging of long-range fiber connections and functional imaging data, is illustrated in two distinct cognitive domains, visual attention and face perception. Structural imaging is performed with diffusion-weighted imaging (DWI) and fiber tractography, which track the diffusion of water molecules along white-matter fiber tracts in the brain (Figure 1). By visualizing these fiber tracts, we are able to investigate the long-range connective architecture of the brain. The results compare favorably with one of the most widely-used techniques in DWI, diffusion tensor imaging (DTI). DTI is unable to resolve complex configurations of fiber tracts, limiting its utility for constructing detailed, anatomically-informed models of brain function. In contrast, our analyses reproduce known neuroanatomy with precision and accuracy. This advantage is partly due to data acquisition procedures: while many DTI protocols measure diffusion in a small number of directions (e.g., 6 or 12), we employ a diffusion spectrum imaging (DSI)1, 2 protocol which assesses diffusion in 257 directions and at a range of magnetic gradient strengths. Moreover, DSI data allow us to use more sophisticated methods for reconstructing acquired data. In two experiments (visual attention and face perception), tractography reveals that co-active areas of the human brain are anatomically connected, supporting extant hypotheses that they form functional networks. DWI allows us to create a "circuit diagram" and reproduce it on an individual-subject basis, for

  8. 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

  9. Rapid Exploration of Configuration Space with Diffusion Map-directed-Molecular Dynamics

    PubMed Central

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

    2013-01-01

    The gap between the timescale of interesting behavior in macromolecular systems and that which our computational resources can afford oftentimes 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 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 300K 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. PMID:23865517

  10. 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.

  11. Localized orbitals from basis sets augmented with diffuse functions

    NASA Astrophysics Data System (ADS)

    Høyvik, Ida-Marie; Jørgensen, Poul

    2013-05-01

    Orbital localization of occupied and virtual Hartree-Fock orbitals generated from basis sets augmented with diffuse functions is performed using the Pipek-Mezey, Boys, powers of the second central moment, and powers of the fourth central moment localizations. The locality of the obtained orbital sets are presented in terms of second and fourth moment orbital spreads. The results show that both local occupied and virtual orbitals may be obtained when using powers of the second central moment and powers of the fourth central moment localizations, while the Pipek-Mezey and Boys localizations fail to produce sets of local virtual orbitals. The locality of the fourth central moment virtual orbitals exhibits a locality similar to the locality of a Boys localization for non-augmented basis sets.

  12. Diffeomorphic Metric Mapping and Probabilistic Atlas Generation of Hybrid Diffusion Imaging based on BFOR Signal Basis

    PubMed Central

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

    2015-01-01

    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. (2012) 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) reconstructure, as well as reduces memory requirement. In addition, since the BFOR signal basis is orthonormal, the L2 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 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. PMID:24972378

  13. Mapping Functions in Health-Related Quality of Life

    PubMed Central

    Young, Tracey A.; Mukuria, Clara; Rowen, Donna; Brazier, John E.; Longworth, Louise

    2015-01-01

    Background. Clinical trials in cancer frequently include cancer-specific measures of health but not preference-based measures such as the EQ-5D that are suitable for economic evaluation. Mapping functions have been developed to predict EQ-5D values from these measures, but there is considerable uncertainty about the most appropriate model to use, and many existing models are poor at predicting EQ-5D values. This study aims to investigate a range of potential models to develop mapping functions from 2 widely used cancer-specific measures (FACT-G and EORTC-QLQ-C30) and to identify the best model. Methods. Mapping models are fitted to predict EQ-5D-3L values using ordinary least squares (OLS), tobit, 2-part models, splining, and to EQ-5D item-level responses using response mapping from the FACT-G and QLQ-C30. A variety of model specifications are estimated. Model performance and predictive ability are compared. Analysis is based on 530 patients with various cancers for the FACT-G and 771 patients with multiple myeloma, breast cancer, and lung cancer for the QLQ-C30. Results. For FACT-G, OLS models most accurately predict mean EQ-5D values with the best predicting model using FACT-G items with similar results using tobit. Response mapping has low predictive ability. In contrast, for the QLQ-C30, response mapping has the most accurate predictions using QLQ-C30 dimensions. The QLQ-C30 has better predicted EQ-5D values across the range of possible values; however, few respondents in the FACT-G data set have low EQ-5D values, which reduces the accuracy at the severe end. Conclusions. OLS and tobit mapping functions perform well for both instruments. Response mapping gives the best model predictions for QLQ-C30. The generalizability of the FACT-G mapping function is limited to populations in moderate to good health. PMID:25997920

  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. 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.

  17. Interstellar medium. Pseudo-three-dimensional maps of the diffuse interstellar band at 862 nm.

    PubMed

    Kos, Janez; Zwitter, Tomaž; Wyse, Rosemary; Bienaymé, Olivier; Binney, James; Bland-Hawthorn, Joss; Freeman, Kenneth; Gibson, Brad K; Gilmore, Gerry; Grebel, Eva K; Helmi, Amina; Kordopatis, Georges; Munari, Ulisse; Navarro, Julio; Parker, Quentin; Reid, Warren A; Seabroke, George; Sharma, Sanjib; Siebert, Arnaud; Siviero, Alessandro; Steinmetz, Matthias; Watson, Fred G; Williams, Mary E K

    2014-08-15

    The diffuse interstellar bands (DIBs) are absorption lines observed in visual and near-infrared spectra of stars. Understanding their origin in the interstellar medium is one of the oldest problems in astronomical spectroscopy, as DIBs have been known since 1922. In a completely new approach to understanding DIBs, we combined information from nearly 500,000 stellar spectra obtained by the massive spectroscopic survey RAVE (Radial Velocity Experiment) to produce the first pseudo-three-dimensional map of the strength of the DIB at 8620 angstroms covering the nearest 3 kiloparsecs from the Sun, and show that it follows our independently constructed spatial distribution of extinction by interstellar dust along the Galactic plane. Despite having a similar distribution in the Galactic plane, the DIB 8620 carrier has a significantly larger vertical scale height than the dust. Even if one DIB may not represent the general DIB population, our observations outline the future direction of DIB research. PMID:25124434

  18. 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

  19. Mapping atomic and diffuse interstellar band absorption across the Magellanic Clouds and the Milky Way

    NASA Astrophysics Data System (ADS)

    Bailey, Mandy; van Loon, Jacco Th.; Sarre, Peter J.; Beckman, John E.

    2015-12-01

    Diffuse interstellar bands (DIBs) trace warm neutral and weakly ionized diffuse interstellar medium (ISM). Here we present a dedicated, high signal-to-noise spectroscopic survey of two of the strongest DIBs, at 5780 and 5797 Å, in optical spectra of 666 early-type stars in the Small and Large Magellanic Clouds, along with measurements of the atomic Na I D and Ca II K lines. The resulting maps show for the first time the distribution of DIB carriers across large swathes of galaxies, as well as the foreground Milky Way ISM. We confirm the association of the 5797 Å DIB with neutral gas, and the 5780 Å DIB with more translucent gas, generally tracing the star-forming regions within the Magellanic Clouds. Likewise, the Na I D line traces the denser ISM whereas the Ca II K line traces the more diffuse, warmer gas. The Ca II K line has an additional component at ˜200-220 km s-1 seen towards both Magellanic Clouds; this may be associated with a pan-Magellanic halo. Both the atomic lines and DIBs show sub-pc-scale structure in the Galactic foreground absorption; the 5780 and 5797 Å DIBs show very little correlation on these small scales, as do the Ca II K and Na I D lines. This suggests that good correlations between the 5780 and 5797 Å DIBs, or between Ca II K and Na I D, arise from the superposition of multiple interstellar structures. Similarity in behaviour between DIBs and Na I in the Small Magellanic Cloud (SMC), Large Magellanic Cloud (LMC) and Milky Way suggests the abundance of DIB carriers scales in proportion to metallicity.

  20. Mapping functional transcription factor networks from gene expression data

    PubMed Central

    Haynes, Brian C.; Maier, Ezekiel J.; Kramer, Michael H.; Wang, Patricia I.; Brown, Holly; Brent, Michael R.

    2013-01-01

    A critical step in understanding how a genome functions is determining which transcription factors (TFs) regulate each gene. Accordingly, extensive effort has been devoted to mapping TF networks. In Saccharomyces cerevisiae, protein–DNA interactions have been identified for most TFs by ChIP-chip, and expression profiling has been done on strains deleted for most TFs. These studies revealed that there is little overlap between the genes whose promoters are bound by a TF and those whose expression changes when the TF is deleted, leaving us without a definitive TF network for any eukaryote and without an efficient method for mapping functional TF networks. This paper describes NetProphet, a novel algorithm that improves the efficiency of network mapping from gene expression data. NetProphet exploits a fundamental observation about the nature of TF networks: The response to disrupting or overexpressing a TF is strongest on its direct targets and dissipates rapidly as it propagates through the network. Using S. cerevisiae data, we show that NetProphet can predict thousands of direct, functional regulatory interactions, using only gene expression data. The targets that NetProphet predicts for a TF are at least as likely to have sites matching the TF's binding specificity as the targets implicated by ChIP. Unlike most ChIP targets, the NetProphet targets also show evidence of functional regulation. This suggests a surprising conclusion: The best way to begin mapping direct, functional TF-promoter interactions may not be by measuring binding. We also show that NetProphet yields new insights into the functions of several yeast TFs, including a well-studied TF, Cbf1, and a completely unstudied TF, Eds1. PMID:23636944

  1. Circulatory function during exercise: integration of convection and diffusion.

    PubMed

    Jones, J H

    1994-01-01

    The cardiovascular system has frequently been hypothesized to be the limiting step for O2 transport that determines VO2 max in many species of mammals. Careful analysis of the factors that determine how O2 is transported by the circulation demonstrate that such a single-step limitation cannot exist. Evaluation of the results of experiments in which circulatory O2 transport capacity was experimentally altered demonstrates no direct or absolute relationship between changes in O2 transport capacity and changes in VO2 max. Furthermore, experimental evidence collected during maximal exercise in hypoxia and hyperoxia supports the concept that multiple components of the O2 transport system contribute to limiting O2 flux at VO2 max. Consideration of the basic equations that describe O2 transport through the respiratory system shows that changes in PO2 at each step of the system required to increase O2 flux through that step conflict with the changes in PO2 required to increase flux through adjacent steps. Changes in convection, capacitance, or conductance at one step affect gas transport through the adjacent steps. Hence, no single-step limitation to O2 transport is possible, because the convective and diffusive gas exchangers are interdependent. Increasing QT at VO2 max always increases O2 flux (although not necessarily in proportion to the increase in QT), unless VO2 max is limited by mitochondrial oxidative capacity, as in goats. Cardiovascular structure and function in mammals reflects allometric, adaptive and induced variation. Maximal heart rate is determined strictly by body size, thus maximal QT/Mb is inevitably lower in larger mammals. Adaptive and induced variation elicit hypertrophy of muscle, capillaries, and mitochondria, increasing circulatory capacity and VO2 max. When selection for maximal respiratory function is weak, as in most species of mammals, any component(s) of the respiratory system may be underdeveloped, relative to other structures in the system

  2. 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.

  3. 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

  4. 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. PMID:23892066

  5. Diffuse fields in open systems and the emergence of the Green's function (L)

    NASA Astrophysics Data System (ADS)

    Weaver, Richard L.; Lobkis, Oleg I.

    2004-11-01

    A definition of a diffuse field applicable to open heterogeneous systems is proposed. The identity between the Green's function of the structure and the diffuse field's correlations is proved. The Green's function that emerges from the correlation is found to be the full Green's function of the medium, symmetrized in time, with all reflections and scatterings and propagation modes. This is in contrast to suggestions that the correlation is the ballistic Green's function only, or the Green's function of a homogeneous effective medium. .

  6. Detailed map of a cis-regulatory input function

    NASA Astrophysics Data System (ADS)

    Setty, Y.; Mayo, A. E.; Surette, M. G.; Alon, U.

    2003-06-01

    Most genes are regulated by multiple transcription factors that bind specific sites in DNA regulatory regions. These cis-regulatory regions perform a computation: the rate of transcription is a function of the active concentrations of each of the input transcription factors. Here, we used accurate gene expression measurements from living cell cultures, bearing GFP reporters, to map in detail the input function of the classic lacZYA operon of Escherichia coli, as a function of about a hundred combinations of its two inducers, cAMP and isopropyl -D-thiogalactoside (IPTG). We found an unexpectedly intricate function with four plateau levels and four thresholds. This result compares well with a mathematical model of the binding of the regulatory proteins cAMP receptor protein (CRP) and LacI to the lac regulatory region. The model is also used to demonstrate that with few mutations, the same region could encode much purer AND-like or even OR-like functions. This possibility means that the wild-type region is selected to perform an elaborate computation in setting the transcription rate. The present approach can be generally used to map the input functions of other genes.

  7. 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. PMID

  8. 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

  9. 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

  10. 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

  11. 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

  12. Mapping Quantitative Trait Loci Underlying Function-Valued Traits Using Functional Principal Component Analysis and Multi-Trait Mapping

    PubMed Central

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

    2015-01-01

    We previously proposed a simple regression-based method to map quantitative trait loci underlying function-valued phenotypes. In order to better handle the case of noisy phenotype measurements and accommodate the correlation structure among time points, we propose an alternative approach that maintains much of the simplicity and speed of the regression-based method. We overcome noisy measurements by replacing the observed data with a smooth approximation. We then apply functional principal component analysis, replacing the smoothed phenotype data with a small number of principal components. Quantitative trait locus mapping is applied to these dimension-reduced data, either with a multi-trait method or by considering the traits individually and then taking the average or maximum LOD score across traits. We apply these approaches to root gravitropism data on Arabidopsis recombinant inbred lines and further investigate their performance in computer simulations. Our methods have been implemented in the R package, funqtl. PMID:26530421

  13. The average pathlength map: a diffusion MRI tractography-derived index for studying brain pathology.

    PubMed

    Pannek, Kerstin; Mathias, Jane L; Bigler, Erin D; Brown, Greg; Taylor, Jamie D; Rose, Stephen E

    2011-03-01

    Magnetic resonance diffusion tractography provides a powerful tool for the assessment of white matter architecture in vivo. Quantitative tractography metrics, such as streamline length, have successfully been used in the study of brain pathology. To date, these studies have relied on a priori knowledge of which tracts are affected by injury or pathology and manual delineation of regions of interest (ROIs) for use as waypoints in tractography. This limits the analyses to specific tracts under investigation and relies on the accurate and consistent placement of ROIs. We present a fully automated technique for the voxel-wise analysis of streamline length within the entire brain, the Average Pathlength Map (APM). We highlight the precision and reproducibility of voxel-wise average streamline length over time, and assess normal variability of pathlength values in a cohort of 43 healthy participants. Additionally, we demonstrate the utility of this approach by performing voxel-wise comparison between pathlength values obtained from a patient with a severe traumatic brain injury (TBI, Glasgow Coma Scale Score=7) and those from control participants. Our analysis shows that voxel-wise average pathlength values are comparable to fractional anisotropy (FA) in terms of reproducibility and variability. For the TBI patient, we observed a significant reduction in streamline pathlength in the genu of the corpus callosum and its projections into the frontal lobe. This study demonstrates that the average pathlength map can be used for voxel-based analysis of a quantitative tractography metric within the whole brain, removing both the dependence on a priori knowledge of affected pathways and time-consuming manual delineation of ROIs. PMID:21147236

  14. 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

  15. 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

  16. 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.

  17. Multi-contrast large deformation diffeomorphic metric mapping for diffusion tensor imaging

    PubMed Central

    Ceritoglu, Can; Oishi, Kenichi; Li, Xin; Chou, Ming-Chung; Younes, Laurent; Albert, Marilyn; Lyketsos, Constantine; van Zijl, Peter C.M.; Miller, Michael I.; Mori, Susumu

    2010-01-01

    Diffusion tensor imaging (DTI) can reveal detailed white matter anatomy and has the potential to detect abnormalities in specific white matter structures. Such detection and quantification are, however, not straightforward. The voxel-based analysis after image normalization is one of the most widely used methods for quantitative image analyses. To apply this approach to DTI, it is important to examine if structures in the white matter are well registered among subjects, which would be highly dependent on employed algorithms for normalization. In this paper, we evaluate the accuracy of normalization of DTI data using a highly elastic transformation algorithm, called large deformation diffeomorphic metric mapping. After simulation-based validation of the algorithm, DTI data from normal subjects were used to measure the registration accuracy. To examine the impact of morphological abnormalities on the accuracy, the algorithm was also tested using data from Alzheimer’s disease (AD) patients with severe brain atrophy. The accuracy level was measured by using manual landmark-based white matter matching and surface-based brain and ventricle matching as gold standard. To improve the accuracy level, cascading and multi-contrast approaches were developed. The accuracy level for the white matter was 1.88 ± 0.55 and 2.19 ± 0.84 mm for the measured locations in the controls and patients, respectively. PMID:19398016

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

    Energy Science and Technology Software Center (ESTSC)

    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 .

  19. 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

  20. 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

  1. 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

  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. Measuring diffusion-relaxation correlation maps using non-uniform field gradients of single-sided NMR devices

    NASA Astrophysics Data System (ADS)

    Nogueira d'Eurydice, Marcel; Galvosas, Petrik

    2014-11-01

    Single-sided NMR systems are becoming a relevant tool in industry and laboratory environments due to their low cost, low maintenance and capacity to evaluate quantity and quality of hydrogen based materials. The performance of such devices has improved significantly over the last decade, providing increased field homogeneity, field strength and even controlled static field gradients. For a class of these devices, the configuration of the permanent magnets provides a linear variation of the magnetic field and can be used in diffusion measurements. However, magnet design depends directly on its application and, according to the purpose, the field homogeneity may significantly be compromised. This may prevent the determination of diffusion properties of fluids based on the natural inhomogeneity of the field using known techniques. This work introduces a new approach that extends the applicability of diffusion-editing CPMG experiments to NMR devices with highly inhomogeneous magnetic fields, which do not vary linearly in space. Herein, we propose a method to determine a custom diffusion kernel based on the gradient distribution, which can be seen as a signature of each NMR device. This new diffusion kernel is then utilised in the 2D inverse Laplace transform (2D ILT) in order to determine diffusion-relaxation correlation maps of homogeneous multi-phasic fluids. The experiments were performed using NMR MObile Lateral Explore (MOLE), which is a single-sided NMR device designed to maximise the volume at the sweet spot with enhanced depth penetration.

  5. 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.

  6. Density probability distribution functions of diffuse gas in the Milky Way

    NASA Astrophysics Data System (ADS)

    Berkhuijsen, E. M.; Fletcher, A.

    2008-10-01

    In a search for the signature of turbulence in the diffuse interstellar medium (ISM) in gas density distributions, we determined the probability distribution functions (PDFs) of the average volume densities of the diffuse gas. The densities were derived from dispersion measures and HI column densities towards pulsars and stars at known distances. The PDFs of the average densities of the diffuse ionized gas (DIG) and the diffuse atomic gas are close to lognormal, especially when lines of sight at |b| < 5° and |b| >= 5° are considered separately. The PDF of at high |b| is twice as wide as that at low |b|. The width of the PDF of the DIG is about 30 per cent smaller than that of the warm HI at the same latitudes. The results reported here provide strong support for the existence of a lognormal density PDF in the diffuse ISM, consistent with a turbulent origin of density structure in the diffuse gas.

  7. Comparison of 3D orientation distribution functions measured with confocal microscopy and diffusion MRI.

    PubMed

    Schilling, Kurt; Janve, Vaibhav; Gao, Yurui; Stepniewska, Iwona; Landman, Bennett A; Anderson, Adam W

    2016-04-01

    The ability of diffusion MRI (dMRI) fiber tractography to non-invasively map three-dimensional (3D) anatomical networks in the human brain has made it a valuable tool in both clinical and research settings. However, there are many assumptions inherent to any tractography algorithm that can limit the accuracy of the reconstructed fiber tracts. Among them is the assumption that the diffusion-weighted images accurately reflect the underlying fiber orientation distribution (FOD) in the MRI voxel. Consequently, validating dMRI's ability to assess the underlying fiber orientation in each voxel is critical for its use as a biomedical tool. Here, using post-mortem histology and confocal microscopy, we present a method to perform histological validation of orientation functions in 3D, which has previously been limited to two-dimensional analysis of tissue sections. We demonstrate the ability to extract the 3D FOD from confocal z-stacks, and quantify the agreement between the MRI estimates of orientation information obtained using constrained spherical deconvolution (CSD) and the true geometry of the fibers. We find an orientation error of approximately 6° in voxels containing nearly parallel fibers, and 10-11° in crossing fiber regions, and note that CSD was unable to resolve fibers crossing at angles below 60° in our dataset. This is the first time that the 3D white matter orientation distribution is calculated from histology and compared to dMRI. Thus, this technique serves as a gold standard for dMRI validation studies - providing the ability to determine the extent to which the dMRI signal is consistent with the histological FOD, and to establish how well different dMRI models can predict the ground truth FOD. PMID:26804781

  8. Universal function for the diffusion coefficient of DNA fragment

    NASA Astrophysics Data System (ADS)

    Mercier, Jean-Francois

    2005-03-01

    The separation of DNA fragments by (gel or capillary) electrophoresis has been studied extensively. To characterize the separation achieved by such systems, one needs to understand the impact (and their dependency upon the experimental quantities) of two physical parameters: the electrophoresis mobility μ and the diffusion coefficient D. Three different regimes have been shown to exist for both μ and D: the Ogston regime, the reptation regime and the reptation-with orientation regime (note that separation is only possible for the first two regimes). Both μ and D are well described by theory for all three regimes. Unfortunatly this results in disjointed scaling regimes and no theory-based general equations can apply to all regimes. Recently, an empirical formula has been proposed that adequately fit the mobility μ of dsDNA fragments across all three regimes and is compatible with accepted theories. In this work we propose a similar formula for the diffusion coefficent D. With those two formulas, one could optimize any separation system quite easily for a wide range of DNA molecular sizes.

  9. Genetic Analyses Reveal Functions for MAP2K3 and MAP2K6 in Mouse Testis Determination.

    PubMed

    Warr, Nick; Siggers, Pam; Carré, Gwenn-Aël; Wells, Sara; Greenfield, Andy

    2016-05-01

    Testis determination in mammals is initiated by expression of SRY in somatic cells of the embryonic gonad. Genetic analyses in the mouse have revealed a requirement for mitogen-activated protein kinase (MAPK) signaling in testis determination: targeted loss of the kinases MAP3K4 and p38 MAPK causes complete XY embryonic gonadal sex reversal. These kinases occupy positions at the top and bottom level, respectively, in the canonical three-tier MAPK-signaling cascade: MAP3K, MAP2K, MAPK. To date, no role in sex determination has been attributed to a MAP2K, although such a function is predicted to exist. Here, we report roles for the kinases MAP2K3 and MAP2K6 in testis determination. C57BL/6J (B6) embryos lacking MAP2K3 exhibited no significant abnormalities of testis development, whilst those lacking MAP2K6 exhibited a minor delay in testis determination. Compound mutants lacking three out of four functional alleles at the two loci also exhibited delayed testis determination and transient ovotestis formation as a consequence, suggestive of partially redundant roles for these kinases in testis determination. Early lethality of double-knockout embryos precludes analysis of sexual development. To reveal their roles in testis determination more clearly, we generated Map2k mutant B6 embryos using a weaker Sry allele (Sry(AKR)). Loss of Map2k3 on this highly sensitized background exacerbates ovotestis development, whilst loss of Map2k6 results in complete XY gonadal sex reversal associated with reduction of Sry expression at 11.25 days postcoitum. Our data suggest that MAP2K6 functions in mouse testis determination, via positive effects on Sry, and also indicate a minor role for MAP2K3. PMID:27009039

  10. Coulomb Green's function and image potential near a cylindrical diffuse interface

    NASA Astrophysics Data System (ADS)

    Xue, Changfeng; Huang, Qiongwei; Deng, Shaozhong

    2015-12-01

    In a preceding paper [Comput. Phys. Commun. 184 (1): 51-59, 2013], we revisited the problem of calculating Coulomb Green's function and image potential near a planar diffuse interface within which the dielectric permittivity of the inhomogeneous medium changes continuously along one Cartesian direction in a transition layer between two dissimilar dielectric materials. In the present paper, we consider a cylindrical diffuse interface within which the dielectric permittivity changes continuously along the radial direction instead. First we propose a specific cylindrical diffuse interface model, termed the quasi-harmonic diffuse interface model, that can admit analytical solution for the Green's function in terms of the modified Bessel functions. Then and more importantly we develop a robust numerical method for building Green's functions for any cylindrical diffuse interface models. The main idea of the numerical method is, after dividing a diffuse interface into multiple sublayers, to approximate the dielectric permittivity profile in each one of the sublayers by one of the quasi-harmonic functional form rather than simply by a constant value as one would normally do. Next we describe how to efficiently compute well-behaved ratios, products, and logarithmic derivatives of the modified Bessel functions so as to avoid direct evaluations of individual modified Bessel functions in our formulations. Finally we conduct numerical experiments to show the effectiveness of the quasi-harmonic diffuse interface model in overcoming the divergence of the image potential, to validate the numerical method in terms of its accuracy and convergence, and to demonstrate its capability for computing Green's functions for any cylindrical diffuse interface models.

  11. 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

  12. 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

  13. 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

  14. 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.

  15. Mapping somatosensory connectivity in adult mice using diffusion MRI tractography and super-resolution track density imaging.

    PubMed

    Richards, Kay; Calamante, Fernando; Tournier, Jacques-Donald; Kurniawan, Nyoman D; Sadeghian, Farnoosh; Retchford, Alexander R; Jones, Gabriel Davis; Reid, Christopher A; Reutens, David C; Ordidge, Roger; Connelly, Alan; Petrou, Steven

    2014-11-15

    In this study we combined ultra-high field diffusion MRI fiber tracking and super-resolution track density imaging (TDI) to map the relay locations and connectivity of the somatosensory pathway in paraformaldehyde fixed, C57Bl/6J mouse brains. Super-resolution TDI was used to achieve 20 μm isotropic resolution to inform the 3D topography of the relay locations including thalamic barreloids and brainstem barrelettes, not described previously using MRI methodology. TDI-guided mapping results for thalamo-cortical connectivity were consistent with thalamo-cortical projections labeled using virus mediated fluorescent protein expression. Trigemino-thalamic TDI connectivity maps were concordant with results obtained using anterograde dye tracing from brainstem to thalamus. Importantly, TDI mapping overcame the constraint of tissue distortion observed in mechanically sectioned tissue, enabling 3D reconstruction and long-range connectivity data. In conclusion, our results showed that diffusion micro-imaging at ultra-high field MRI revealed the stereotypical pattern of somatosensory connectivity and is a valuable tool to complement histologic methods, achieving 3D spatial preservation of whole brain networks for characterization in mouse models of human disease. PMID:25087481

  16. Taking potential probability function maps to the local scale and matching them with land use maps

    NASA Astrophysics Data System (ADS)

    Garg, Saryu; Sinha, Vinayak; Sinha, Baerbel

    2013-04-01

    Source-Receptor models have been developed using different methods. Residence-time weighted concentration back trajectory analysis and Potential Source Contribution Function (PSCF) are the two most popular techniques for identification of potential sources of a substance in a defined geographical area. Both techniques use back trajectories calculated using global models and assign values of probability/concentration to various locations in an area. These values represent the probability of threshold exceedances / the average concentration measured at the receptor in air masses with a certain residence time over a source area. Both techniques, however, have only been applied to regional and long-range transport phenomena due to inherent limitation with respect to both spatial accuracy and temporal resolution of the of back trajectory calculations. Employing the above mentioned concepts of residence time weighted concentration back-trajectory analysis and PSCF, we developed a source-receptor model capable of identifying local and regional sources of air pollutants like Particulate Matter (PM), NOx, SO2 and VOCs. We use 1 to 30 minute averages of concentration values and wind direction and speed from a single receptor site or from multiple receptor sites to trace the air mass back in time. The model code assumes all the atmospheric transport to be Lagrangian and linearly extrapolates air masses reaching the receptor location, backwards in time for a fixed number of steps. We restrict the model run to the lifetime of the chemical species under consideration. For long lived species the model run is limited to < 4 hrs as spatial uncertainty increases the longer an air mass is linearly extrapolated back in time. The final model output is a map, which can be compared with the local land use map to pinpoint sources of different chemical substances and estimate their source strength. Our model has flexible space- time grid extrapolation steps of 1-5 minutes and 1-5 km grid

  17. Novel gas diffusion layer with water management function for PEMFC

    NASA Astrophysics Data System (ADS)

    Chen, Jinhua; Matsuura, Toyoaki; Hori, Michio

    The water management of the membrane electrode assembly (MEA) is a critical technology in developing a polymer electrolyte membrane fuel cell (PEMFC). To maintain the MEA with a satisfactory water content and distribution, a novel gas diffusion layer (GDL) was designed by inserting a water management layer (WML) between the traditional GDL and the catalyst layer of the PEMFC. A simulator was developed for the optimization of the GDL, where the water distribution in the electrode and the profile of the water transport in the polymer membrane could be predicted. For this purpose, the water vapor permeability of the GDL, which was the main variable, was investigated under conditions similar to the PEMFC. Furthermore, the cell performance of the PEMFC with the GDL was tested. The testing results indicated that the water management in the MEA could be significantly improved by using the WML.

  18. 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

  19. Groundwater productivity potential mapping using evidential belief function.

    PubMed

    Park, Inhye; Kim, Yongsung; Lee, Saro

    2014-09-01

    The evidential belief function (EBF) model was applied and validated for analysis of groundwater-productivity potential (GPP) in Boryeong and Pohang cities, agriculture region in Korea using geographic information systems (GIS). Data about related factors, including topography, lineament, geology, forest, soil, and groundwater data were collected and input into a spatial database. Additionally, in the Boryeong area, specific capacity (SPC) data not lower than 4.55 m3 /d/m were collected, corresponding to 300 m3 /d yield from 72 well locations. In the Pohang area, SPC data of ≥ 6.25 m3 /d/m were collected, corresponding to a yield of 500 m3 /d from 44 well locations. By using the constructed spatial database, 19 factors related to groundwater productivity were extracted. The relationships between the well locations and the factors were identified and quantified by using the EBF model. Four relationships were calculated: belief (Bel), disbelief (Dis), uncertainty (Unc), and plausibility (Pls). The relationships were used as factor ratings in the overlay analysis to create GPP indices and maps. The resulting GPP maps showed 83.41% and 77.53% accuracy in Boryeong and Pohang areas, respectively. The EBF model was found to be more effective in terms of prediction accuracy. PMID:24841077

  20. 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)

  1. Diffusion of DNA during gel electrophoresis; a predictive function spanning the relevant regimes

    NASA Astrophysics Data System (ADS)

    McCormick, Laurette; Slater, Gary

    2004-03-01

    Gel electrophoresis is used extensively to separate DNA. Diffusion of the DNA bands during electrophoresis is an important phenomenon which reduces the resolution obtained. As with DNA mobility, the diffusion of DNA can be split into several different regimes, each described by relevant theory. Unfortunately, until recently there was no single formula for DNA mobility or diffusion that could be used in more than one regime. However, Van Winkle and co workers [Van Winkle DH, Beheshti A, Rill RL, ELECTROPHORESIS 23 (1): 15-19 JAN 2002] have successfully developed an analytical function to analyze DNA mobility data, throughout the relevant regimes. We present the development of a complementary function for the analysis of DNA diffusion. This function should be very useful both in analyzing DNA electrophoretic data, and as a predictive tool.

  2. 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

  3. 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

  4. 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

  5. The efficacy of diffusion weighted imaging and apparent diffusion coefficients mapping for liver metastasis of colonic adenocarcinomas

    PubMed Central

    Metin, Melike R.; Aydın, Hasan; Çetin, Hüseyin; Özmen, Evrim; Kayaçetin, Serra

    2016-01-01

    Objectives: To establish retrospectively the relation between the histopathologic grade of colorectal liver metastasis and apparent diffusion coefficient (ADC) values of hepatic metastases of colorectal adenocarcinomas. Methods: The diagnoses of liver metastases were confirmed with biopsy, surgery, and follow-up imaging findings. Twenty-six patients with 94 liver metastasis were included in the study. Of 94 masses, 59 were poorly-differentiated adenocarcinoma, 18 were moderately-differentiated adenocarcinoma, and 17 were well-differentiated regarding the diameters, ADC values, and ratio index (RI) values. Kolmogorov-smirnov normality test, Kruskal-wallis analysis of variance, Mann-Whitney U test with Bonferroni correction, Spearman correlation analysis, and receiver operating characteristics curve methods were applied to evaluate the statistical relations. Results: There was a statistically significant difference in terms of ADC values and RI between poorly-differentiated adenocarcinoma and moderately-differentiated adenocarcinoma plus well-differentiated adenocarcinomas. Poorly-differentiated adenocarcinomas have the lowest ADC values and highest RI values among other groups. Conclusion: Use of ADC values alone can be executed for the diagnosis of focal hepatic masses and also can aid in the differentiation of benign and malignant hepatic lesions. PMID:27052280

  6. 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. PMID:25907410

  7. 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.

  8. A New Adaptive Diffusive Function for Magnetic Resonance Imaging Denoising Based on Pixel Similarity

    PubMed Central

    Heydari, Mostafa; Karami, Mohammad Reza

    2015-01-01

    Although there are many methods for image denoising, but partial differential equation (PDE) based denoising attracted much attention in the field of medical image processing such as magnetic resonance imaging (MRI). The main advantage of PDE-based denoising approach is laid in its ability to smooth image in a nonlinear way, which effectively removes the noise, as well as preserving edge through anisotropic diffusion controlled by the diffusive function. This function was first introduced by Perona and Malik (P-M) in their model. They proposed two functions that are most frequently used in PDE-based methods. Since these functions consider only the gradient information of a diffused pixel, they cannot remove noise in noisy images with low signal-to-noise (SNR). In this paper we propose a modified diffusive function with fractional power that is based on pixel similarity to improve P-M model for low SNR. We also will show that our proposed function will stabilize the P-M method. As experimental results show, our proposed function that is modified version of P-M function effectively improves the SNR and preserves edges more than P-M functions in low SNR. PMID:26955563

  9. Mapping resting-state functional connectivity using perfusion MRI

    PubMed Central

    Chuang, Kai-Hsiang; van Gelderen, Peter; Merkle, Hellmut; Bodurka, Jerzy; Ikonomidou, Vasiliki N.; Koretsky, Alan P.; Duyn, Jeff H.; Talagala, S. Lalith

    2008-01-01

    Resting-state, low frequency (< 0.08 Hz) fluctuations of blood oxygenation level dependent (BOLD) magnetic resonance signal have been shown to exhibit high correlation among functionally connected regions. However, correlations of cerebral blood flow (CBF) fluctuations during the resting state have not been extensively studied. The main challenges of using arterial spin labeling perfusion magnetic resonance imaging to detect CBF fluctuations are low sensitivity, low temporal resolution, and contamination from BOLD. This work demonstrates CBF-based quantitative functional connectivity mapping by combining continuous arterial spin labeling (CASL) with a neck labeling coil and a multi-channel receiver coil to achieve high perfusion sensitivity. In order to reduce BOLD contamination, the CBF signal was extracted from the CASL signal time course by high frequency filtering. This processing strategy is compatible with sinc interpolation for reducing the timing mismatch between control and label images and has the flexibility of choosing an optimal filter cutoff frequency to minimize BOLD fluctuations. Most subjects studied showed high CBF correlation in bilateral sensorimotor areas with good suppression of BOLD contamination. Root-mean-square CBF fluctuation contributing to bilateral correlation was estimated to be 29% ± 19% (N = 13) of the baseline perfusion, while BOLD fluctuation was 0.26% ± 0.14% of the mean intensity (at 3T and 12.5 ms echo time). PMID:18314354

  10. Multi-functional lens based on conformal mapping.

    PubMed

    Lu, Cui; Mei, Zhong Lei

    2015-07-27

    Based on conformal mapping method, a two dimensional, multi-functional lens structure is proposed and designed in this work. The lens is an infinitely-long, gradient-index dielectric cylinder with a semi-elliptic cross-section. The lens can first be considered like a flattened Luneburg lens, which produces highly-directive electromagnetic waves by adjusting the feed position along the line connecting the two foci. It also functions like an Eaton lens. When an incoming beam impinges on the same line but outside the two foci, it will be guided through the lens structure and take a U-turn. Besides, if properly shaped, the structure can also be used as a waveguide bend. The lens can be realized using non-resonant metamaterials with inhomogeneous hole arrays. Simulation results demonstrate excellent performance of the lens and agree well with theoretical prediction. The designed lens can be used in the electromagnetic control. And it is especially useful in the real optical lens system. PMID:26367650

  11. 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.

  12. Structural and functional connectivity mapping of the vestibular circuitry from human brainstem to cortex.

    PubMed

    Kirsch, V; Keeser, D; Hergenroeder, T; Erat, O; Ertl-Wagner, B; Brandt, T; Dieterich, M

    2016-04-01

    Structural and functional interconnections of the bilateral central vestibular network have not yet been completely delineated. This includes both ipsilateral and contralateral pathways and crossing sites on the way from the vestibular nuclei via the thalamic relay stations to multiple "vestibular cortex" areas. This study investigated "vestibular" connectivity in the living human brain in between the vestibular nuclei and the parieto-insular vestibular cortex (PIVC) by combined structural and functional connectivity mapping using diffusion tensor imaging and functional connectivity magnetic resonance imaging in 24 healthy right-handed volunteers. We observed a congruent functional and structural link between the vestibular nuclei and the ipsilateral and contralateral PIVC. Five separate and distinct vestibular pathways were identified: three run ipsilaterally, while the two others cross either in the pons or the midbrain. Two of the ipsilateral projections run through the posterolateral or paramedian thalamic subnuclei, while the third bypasses the thalamus to reach the inferior part of the insular cortex directly. Both contralateral pathways travel through the posterolateral thalamus. At the cortical level, the PIVC regions of both hemispheres with a right hemispherical dominance are interconnected transcallosally through the antero-caudal splenium. The above-described bilateral vestibular circuitry in its entirety takes the form of a structure of a rope ladder extending from the brainstem to the cortex with three crossings in the brainstem (vestibular nuclei, pons, midbrain), none at thalamic level and a fourth cortical crossing through the splenium of the corpus callosum. PMID:25552315

  13. 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

  14. Mapping of the mouse olfactory system with manganese-enhanced magnetic resonance imaging and diffusion tensor imaging.

    PubMed

    Gutman, David A; Magnuson, Matthew; Majeed, Waqas; Keifer, Orion P; Davis, Michael; Ressler, Kerry J; Keilholz, Shella

    2013-03-01

    As the power of studying mouse genetics and behavior advances, research tools to examine systems level connectivity in the mouse are critically needed. In this study, we compared statistical mapping of the olfactory system in adult mice using manganese-enhanced MRI (MEMRI) and diffusion tensor imaging (DTI) with probabilistic tractography. The primary goal was to determine whether these complementary techniques can determine mouse olfactory bulb (OB) connectivity consistent with known anatomical connections. For MEMRI, 3D T1-weighted images were acquired before and after bilateral nasal administration of MnCl(2) solution. Concomitantly, high-resolution diffusion-tensor images were obtained ex vivo from a second group of mice and processed with a probabilistic tractography algorithm originating in the OB. Incidence maps were created by co-registering and overlaying data from the two scan modalities. The resulting maps clearly show pathways between the OB and amygdala, piriform cortex, caudate putamen, and olfactory cortex in both the DTI and MEMRI techniques that are consistent with the known anatomical connections. These data demonstrate that MEMRI and DTI are complementary, high-resolution neuroimaging tools that can be applied to mouse genetic models of olfactory and limbic system connectivity. PMID:22527121

  15. 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.

  16. 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

  17. 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.

  18. Sharp rates of decay of solutions to the nonlinear fast diffusion equation via functional inequalities

    PubMed Central

    Vázquez, J. L.

    2010-01-01

    The goal of this paper is to state the optimal decay rate for solutions of the nonlinear fast diffusion equation and, in self-similar variables, the optimal convergence rates to Barenblatt self-similar profiles and their generalizations. It relies on the identification of the optimal constants in some related Hardy–Poincaré inequalities and concludes a long series of papers devoted to generalized entropies, functional inequalities, and rates for nonlinear diffusion equations. PMID:20823259

  19. 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

  20. Ionospheric mapping functions based on electron density fields

    NASA Astrophysics Data System (ADS)

    Zus, Florian; Deng, Zhiguo; Heise, Stefan; Wickert, Jens

    2016-04-01

    We developed an ionospheric Mapping Function (MF) for the Global Navigation Satellite System (GNSS) which is based on the electron density field of the International Reference Ionosphere (IRI). The station specific MF utilizes a look-up table which contains a set of ray-traced ionospheric delays. Hence, unlike the simple MFs that are currently in use, the developed MF depends on the time, location, elevation and azimuth angle. Ray-bending is taken into account, which implies that the MF depends on the carrier frequency as well. This frequency dependency of the MF can be readily used to examine higher-order ionospheric effects due to ray-bending. We compare the proposed MF with the so-called single layer model MF and find significant differences in particular around the equatorial anomaly. In so-far as the proposed MF is based on a realistic electron density field (IRI) our comparison shows the potential error of the single-layer model MF in practice. We conclude that the developed MF concept might be valuable in the GNSS Total Electron Content estimation. The frequency dependency of the MF can be used to mitigate higher-order ionospheric effects.

  1. Mapping the human blood-retinal barrier function.

    PubMed

    Bernardes, Rui; Dias, Jorge; Cunha-Vaz, José

    2005-01-01

    The aim of the work herein presented is to map blood-retinal barrier function by measuring retinal fluorescein leakage from the blood stream into the human vitreous using a confocal scanning laser ophthalmoscope (CSLO). Existing methods for the assessment of fluorescein leakage into the human vitreous are based on the qualitative evaluation of fluorescein angiographies (FA) and on volume measurements, as performed by the Fluorotron Master. A new procedure is presented capable of measuring fluorescein leakage into the vitreous while simultaneously imaging the retina. The present methodology computes the fluorescein leakage in a fully automated way, based on the three-dimensional fluorescence distribution in the human eye by using a single data acquisition. The processing includes signal filtering, volume alignment and profile deconvolution. The deconvolved profile obeys the established physical model. Representative cases shown are: a healthy eye; an eye with drusen from a nondiabetic person; a photocoagulated eye; and an eye with nonproliferative diabetic retinopathy. The results are in agreement with previous findings and go a step further by making possible its daily usage in a clinical setup based on currently available instrumentation. PMID:15651569

  2. 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.

  3. 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.

  4. 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…

  5. Pulmonary mechanical function and diffusion capacity after deep saturation dives.

    PubMed Central

    Thorsen, E; Segadal, K; Myrseth, E; Påsche, A; Gulsvik, A

    1990-01-01

    To assess the effects of deep saturation dives on pulmonary function, static and dynamic lung volumes, transfer factor for carbon monoxide (T1CO), delta-N2, and closing volume (CV) were measured before and after eight saturation dives to pressures of 3.1-4.6 MPa. The atmospheres were helium-oxygen mixtures with partial pressures of oxygen of 40-60 kPa. The durations of the dives were 14-30 days. Mean rate of decompression was 10.5-13.5 kPa/hour. A total of 43 divers were examined, six of whom took part in two dives, the others in one only. Dynamic lung volumes did not change significantly but total lung capacity (TLC) increased significantly by 4.3% and residual volume (RV) by 14.8% (p less than 0.05). CV was increased by 16.7% (p less than 0.01). The T1CO was reduced from 13.0 +/- 1.6 to 11.8 +/- 1.7 mmol/min/kPa (p less than 0.01) when corrected to a haemoglobin concentration of 146 g/l. Effective alveolar volume was unchanged. The increase in TLC and decrease in T1CO were correlated (r = -0.574, p less than 0.02). A control examination of 38 of the divers four to six weeks after the dives showed a partial normalisation of the changes. The increase in TLC, RV, and CV, and the decrease in T1CO, could be explained by a loss of pulmonary elastic tissue caused by inflammatory reactions induced by oxygen toxicity or venous gas emboli. PMID:2337532

  6. 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.

  7. 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

  8. 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. PMID:27320012

  9. Mapping the Moho in southern California using P receiver functions

    NASA Astrophysics Data System (ADS)

    Zhang, Panxu

    The degree to which faults are localized or distributed within the continental lithosphere has long been a controversial subject. This thesis presents a study of the variation for the crustal thickness in southern California. The goal is to study strain deformation at depth by investigating the variations of the Moho beneath strike-slip faults. The data used in this study are broadband teleseismic waveforms from 2000 to 2011 recorded by the Southern California Seismic Network (SCSN) and USArray. The P Receiver Function (RF) method is used to process the teleseismic events to image the Moho. Synthetic modeling in 3D elastic media using a finite difference algorithm is conducted to constrain the geometry of the Moho. The first part of this thesis presents a map of Moho depth in southern California. The estimated average Moho depth is 30 km but has a range between 18 and 41 km. A shallow Moho of 18-20 km is observed in the Salton Trough and the Inner Continental Borderland. There is a general correlation of a deeper Moho beneath mountains, such as the Peninsular Range, eastern Transverse Ranges and western Transverse Ranges. The deeper Moho beneath these areas is consistent with the presence of the mountain root. Moreover, using a similar broadband seismic data and P receiver function technique as Yan and Clayton (2007), our receiver gather analyses confirm the previous conclusion of a vertical Moho offset beneath the San Gabriel Mountains. The second part of the thesis involves a detailed study of the Moho beneath the San Jacinto fault zone. First, receiver gathers as a function of back azimuth were analyzed. Receiver gathers at certain stations near the San Jacinto fault trace show a strong back azimuthal variation. These back-azimuthal variations of the Moho signal indicate three-dimensional complexity beneath the central San Jacinto fault that may suggest variations of Moho depth. A SW-NE stacking profile across the Elsinore, San Jacinto, and San Andreas faults

  10. 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

  11. Time-resolved diffuse spectroscopy measurements using a hybrid Green's function for the radiative transfer equation

    NASA Astrophysics Data System (ADS)

    Simon, Emanuel; Foschum, Florian; Kienle, Alwin

    2013-06-01

    Time-resolved diffuse optical spectroscopy measurements of phantoms at small source-detector separations yield good results for the retrieved coefficients of reduced scattering and absorption when a hybrid Green's function of the radiative transfer equation for semi-infinite media is used.

  12. Positive solutions of a diffusive Leslie-Gower predator-prey model with Bazykin functional response

    NASA Astrophysics Data System (ADS)

    Zhou, Jun

    2014-02-01

    In this paper, we consider a diffusive Leslie-Gower predator-prey model with Bazykin functional response and zero Dirichlet boundary condition. We show the existence, multiplicity and uniqueness of positive solutions when parameters are in different regions. Results are proved by using bifurcation theory, fixed point index theory, energy estimate and asymptotical behavior analysis.

  13. 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.

  14. Structural and Functional Brain Remodeling during Pregnancy with Diffusion Tensor MRI and Resting-State Functional MRI

    PubMed Central

    Chan, Russell W.; Ho, Leon C.; Zhou, Iris Y.; Gao, Patrick P.; Chan, Kevin C.; Wu, Ed X.

    2015-01-01

    Although pregnancy-induced hormonal changes have been shown to alter the brain at the neuronal level, the exact effects of pregnancy on brain at the tissue level remain unclear. In this study, diffusion tensor imaging (DTI) and resting-state functional MRI (rsfMRI) were employed to investigate and document the effects of pregnancy on the structure and function of the brain tissues. Fifteen Sprague-Dawley female rats were longitudinally studied at three days before mating (baseline) and seventeen days after mating (G17). G17 is equivalent to the early stage of the third trimester in humans. Seven age-matched nulliparous female rats served as non-pregnant controls and were scanned at the same time-points. For DTI, diffusivity was found to generally increase in the whole brain during pregnancy, indicating structural changes at microscopic levels that facilitated water molecular movement. Regionally, mean diffusivity increased more pronouncedly in the dorsal hippocampus while fractional anisotropy in the dorsal dentate gyrus increased significantly during pregnancy. For rsfMRI, bilateral functional connectivity in the hippocampus increased significantly during pregnancy. Moreover, fractional anisotropy increase in the dentate gyrus appeared to correlate with the bilateral functional connectivity increase in the hippocampus. These findings revealed tissue structural modifications in the whole brain during pregnancy, and that the hippocampus was structurally and functionally remodeled in a more marked manner. PMID:26658306

  15. 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.

  16. Power spectra and autocorrelation functions for surface diffusion of lithium on tungsten

    NASA Astrophysics Data System (ADS)

    Gładyszewski, L.

    1989-04-01

    The surface ionization of lithium on polycrystalline tungsten and ionic thermal desorption are studied by a method based on the Li + ion current noise arising from the fluctuation of the work function as a result of random fluctuations of the Li adsorbate density. The activation energy for surface diffusion and energy of desorption for Li atoms have been determined by measuring the time correlation function of the local ion thermoemission current fluctuations.

  17. 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

  18. 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

  19. 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)

  20. 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. PMID:25982658

  1. Phenotyping Mouse Pulmonary Function In Vivo with the Lung Diffusing Capacity

    PubMed Central

    Limjunyawong, Nathachit; Fallica, Jonathan; Ramakrishnan, Amritha; Datta, Kausik; Gabrielson, Matthew; Horton, Maureen; Mitzner, Wayne

    2015-01-01

    The mouse is now the primary animal used to model a variety of lung diseases. To study the mechanisms that underlie such pathologies, phenotypic methods are needed that can quantify the pathologic changes. Furthermore, to provide translational relevance to the mouse models, such measurements should be tests that can easily be done in both humans and mice. Unfortunately, in the present literature few phenotypic measurements of lung function have direct application to humans. One exception is the diffusing capacity for carbon monoxide, which is a measurement that is routinely done in humans. In the present report, we describe a means to quickly and simply measure this diffusing capacity in mice. The procedure involves brief lung inflation with tracer gases in an anesthetized mouse, followed by a 1 min gas analysis time. We have tested the ability of this method to detect several lung pathologies, including emphysema, fibrosis, acute lung injury, and influenza and fungal lung infections, as well as monitoring lung maturation in young pups. Results show significant decreases in all the lung pathologies, as well as an increase in the diffusing capacity with lung maturation. This measurement of lung diffusing capacity thus provides a pulmonary function test that has broad application with its ability to detect phenotypic structural changes with most of the existing pathologic lung models. PMID:25590416

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

    DOEpatents

    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.

  3. Predicting diffuse light-enhancement of GPP from plant functional traits: A multi-site synthesis

    NASA Astrophysics Data System (ADS)

    O'Halloran, T. L.; Barr, J. G.; Cook, B.; Goeckede, M.; Law, B. E.; Kueppers, L. M.; Riley, W. J.

    2013-12-01

    Diffuse light enhances canopy-scale photosynthesis because isotropic diffuse light penetrates deeper into the canopy, involves more leaf area in photosynthesis, and prevents the top of the canopy from becoming light saturated. However, the observational and modeling communities still have little understanding of how the 'Diffuse light Enhancement Effect' (DEE) varies across plant functional types or is constrained by factors such as nitrogen availability and plant structure. So far, variability in the strength of DEE across plant functional types (PFTs) remains poorly constrained, but canopy models indicate leaf area index (LAI) is a primary controller. While the very few existing multi-site, measurement-based syntheses of the DEE have provided valuable information on the variability of the DEE across a few plant functional types, no study has correlated measured metrics of DEE magnitude with direct measurements of canopy physical traits across a wide range of plant functional types. Here we report a new metric that is suitable for quantifying the DEE in both flux measurements and land surface models. We also present, for the first time, an examination of the relationship between the DEE metric and plant functional traits. Results from our 70+ site AmeriFlux and FLUXNET synthesis indicate that LAI is the strongest controller of the DEE across sites and PFTs, with less significant influences from foliar nitrogen, canopy height, and mean annual precipitation. Our results will enable direct evaluation and improvement of remote sensing algorithms and light use efficiency models (e.g. MODIS GPP), which to this point regard diffuse light fraction as a source of noise. Additionally, improving resolution of the DEE in prognostic land surface models, such as the Community Land Model (CLM), will greatly improve our ability to forecast future feedbacks to terrestrial carbon sequestration from changes in cloudiness and aerosol amount.

  4. Network diffusion accurately models the relationship between structural and functional brain connectivity networks

    PubMed Central

    Abdelnour, Farras; Voss, Henning U.; Raj, Ashish

    2014-01-01

    The relationship between anatomic connectivity of large-scale brain networks and their functional connectivity is of immense importance and an area of active research. Previous attempts have required complex simulations which model the dynamics of each cortical region, and explore the coupling between regions as derived by anatomic connections. While much insight is gained from these non-linear simulations, they can be computationally taxing tools for predicting functional from anatomic connectivities. Little attention has been paid to linear models. Here we show that a properly designed linear model appears to be superior to previous non-linear approaches in capturing the brain’s long-range second order correlation structure that governs the relationship between anatomic and functional connectivities. We derive a linear network of brain dynamics based on graph diffusion, whereby the diffusing quantity undergoes a random walk on a graph. We test our model using subjects who underwent diffusion MRI and resting state fMRI. The network diffusion model applied to the structural networks largely predicts the correlation structures derived from their fMRI data, to a greater extent than other approaches. The utility of the proposed approach is that it can routinely be used to infer functional correlation from anatomic connectivity. And since it is linear, anatomic connectivity can also be inferred from functional data. The success of our model confirms the linearity of ensemble average signals in the brain, and implies that their long-range correlation structure may percolate within the brain via purely mechanistic processes enacted on its structural connectivity pathways. PMID:24384152

  5. 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.

  6. 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.

  7. Multi-Sensor Mapping of Diffuse Degassing of C-O-H Compounds in Terrestrial Hydrothermal Systems

    NASA Astrophysics Data System (ADS)

    Schwandner, F. M.; Shock, E. L.

    2004-12-01

    In-situ single-sensor detection and mapping of diffuse degassing phenomena in hydrothermal and volcanic areas can be used to elucidate subsurface tectonic structures, assess emission rates, and to monitor emission variability (Williams 1985; Chiodini et al. 1996, Werner et al., 2003). More than one technique has been deployed to measure several gas species simultaneously (e.g., Crenshaw et al. 1982), and correlations of one gas species (usually CO2) with physical parameters like heat flux (Brombach et al., 2001), or with one other gas species (Rn, He) have been demonstrated (Barberi & Carapezza 1994; Williams-Jones et al., 2000). Recently, correlations of multiple gas species with one another were reported (Schwandner et al., 2004), leading to the possibility of quantitative mapping of subsurface hydrothermal chemical processes by simultaneous measurement of reaction partners and products that continuously and diffusely degas. In the present study, we joined a fully-quantitative multi-sensor instrument (Draeger Multiwarn II) to a modified accumulation-chamber sensing method (Chiodini et al., 1996) and measured diffuse degassing of CH4, H2, CO2, CO, and H2S. In this approach, each batch of gas that is recirculated through the detector is simultaneously analyzed by all sensors. To test this approach we chose two magmatically influenced, hydrothermally active areas at Yellowstone National Park (USA): Sylvan Springs and the Greater Obsidian Pool Area. The area near Obsidian Pool was previously studied during a diffuse CO2 degassing campaign (Werner & Brantley, 2004). Preliminary results show that elevated reduced gas emissions appear to be most prominent near hydrothermal pools, whereas CO2-dominated degassing anomalies highlight subsurface tectonic structures. This multimodal distribution allows us to distinguish deep degassing sources (CO2 anomalies) from shallow localized hydrothermal processes (reduced gas anomalies). The results permit us to positively identify

  8. Estimation of diffusion parameters in functionalized silicas with modulated porosity. Part I: chromatographic studies.

    PubMed

    Armatas, G S; Petrakis, D E; Pomonis, P J

    2005-05-13

    The diffusion parameters of binary gas mixture He (tracer gas)-N2 (carrier gas) in hybrid organic-inorganic SiO2-X porous solids which have suffered gradual functionalization with functional groups X of increasing length (X = psi, [triple bond]Si-H, [triple bond]Si-CH2OH, [triple bond]Si-(CH2)3OH, [triple bond]Si-(CH2)11CH3) are reported. The effective diffusivities Deff, the Henry law constants K as well as the tortuosity factors tau for the examined solids were estimated by a typical pulse gas chromatographic method. Analysis of the experimental results was carried out by the well-known method of linearization of moments. The moments s analysis provides a powerful means for extracting diffusion parameters from the experimental response curves The proposed methodology is simple compared to other similar studies and provides rapidly reliable data. The results of this work indicate that the effective diffusivity Deff in porous networks drops markedly as the initial porosity of the parent SiO2 sample is blocked by the functionalization of the pore surfaces with functional groups of increasing size, [triple bond]Si-H, [triple bond]Si-CH2OH, [triple bond]Si-(CH2)3OH and [triple bond]Si-(CH2)11CH3. The low values of the Henry law constants K found indicate that the adsorption of He on the porous surfaces for all the solids is weak. Also, the tortuosity factor r is proportionally correlated to the pore blocking effects and the percolation phenomena of gases flowing into the porous network. PMID:15941039

  9. On the source function of the soft X-ray diffuse background

    NASA Technical Reports Server (NTRS)

    Burrows, David N.; Kraft, Ralph P.

    1993-01-01

    Radiation transfer theory has been used recently to derive the source function of the soft X-ray diffuse background, resulting in the claim of evidence for 10 exp 6 K gas in the Galactic halo. We show that this analysis has several errors that invalidate its conclusions. We argue that the case for an extensive hot halo remains open, pending further work, but may be settled by the continuing series of Rosat observations of high-latitude soft X-ray shadows.

  10. Multiscale Structured and Functionally Graded Gas Diffusion Electrodes for PEM-Fuel Cells and Electrodialysis

    NASA Astrophysics Data System (ADS)

    Wolf, H.; Franz, M.; Bienhüls, C.; Willert-Porada, M.

    2008-02-01

    In the presented work, different methods of preparation of functionally graded gas diffusion electrodes (GDE) for fuel cell and electrodialysis application were investigated. High electrochemical performance with a low platinum catalyst content of only 0.1 mg/cm2 was achieved. The new GDEs are superior to commercial ones with five times higher platinum content, due to their optimized pore structure and improved distribution of catalyst and ion conductive polymer.

  11. 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

  12. Development of 3-dimensional time-dependent density functional theory and its application to gas diffusion in nanoporous materials.

    PubMed

    Liu, Yu

    2016-05-11

    I developed a novel time-dependent density functional theory (TDDFT) and applied it to complicated 3-dimensional systems for the first time. Superior to conventional TDDFT, the diffusion coefficient is modeled as a function of density profile, which is self-determined by the entropy scaling rule instead using an input parameter. The theory was employed to mimic gas diffusion in a nanoporous material. The TDDFT prediction on the transport diffusivity was reasonable compared to simulations. Moreover, the time-dependent density profiles gave an insight into the microscopic mechanism of the diffusion process. PMID:27121986

  13. Green Functions for Diffuse Photon-Density Waves Generated by a Line Source in Two Nonabsorbing Turbid Media in Contact

    NASA Astrophysics Data System (ADS)

    Shendeleva, Margarita L.

    2004-03-01

    Diffuse photon-density waves generated by an instantaneous line source that is parallel to the interface between two semi-infinite turbid media are studied by use of the diffusion approximation. For two nonabsorbing media the Green functions for diffuse light are obtained based on the Green functions for temperature fields that were derived with the Cagniard-de Hoop method. The boundary conditions for diffuse light take into account the discontinuity in the specific intensity at the interface between two media with different refractive indices. The results of the calculations of the specific intensities and the gradient lines for different sets of parameters are presented.

  14. Rat, ovine and bovine Peyer's patches mounted in horizontal diffusion chambers display sampling function.

    PubMed

    Soni, Jyoti; Baird, Alan W; O'Brien, Leah M; McElroy, Maire; Callanan, John J; Bassett, Hugh F; Campion, Deirdre; Brayden, David J

    2006-09-28

    Freshly excised rat, ovine and bovine ileal Peyer's patch (PP) and non-Peyer's patch tissues (NPP) were mounted in modified horizontal polyethylene diffusion chambers with a range of window areas. Rat tissue was initially used to establish that barrier function and histology were maintained for up to 60 min. Horse-radish peroxidase (HRP) fluxes and S. Typhimurium adherence and invasion were significantly higher in rat PP over NPP. Particle uptake was shown to be a rapid, energy-, time-, and size-dependent process, occurring more readily in PP than NPP tissue in each species. In a kinetic analysis, particles were localized initially in the follicle-associated epithelium and then in the dome region. For NPP uptake, particles were initially localized to villous epithelium, and were then detected in the crypts and lamina propria. Electrophysiological parameters including pharmacologically-stimulated inward short-circuit current responses were determined in isolated PP and NPP from each species mounted under identical conditions in Ussing chambers. In conclusion, comparative functional and histological characteristics of PP from several species were demonstrated in horizontal diffusion chambers. Horizontal diffusion chambers are therefore a useful in vitro model in which a range of functions including transport of particulate formulations by PP may be examined. PMID:16884804

  15. 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.

  16. Mapping cortical haemodynamics during neonatal seizures using diffuse optical tomography: a case study.

    PubMed

    Singh, Harsimrat; Cooper, Robert J; Wai Lee, Chuen; Dempsey, Laura; Edwards, Andrea; Brigadoi, Sabrina; Airantzis, Dimitrios; Everdell, Nick; Michell, Andrew; Holder, David; Hebden, Jeremy C; Austin, Topun

    2014-01-01

    Seizures in the newborn brain represent a major challenge to neonatal medicine. Neonatal seizures are poorly classified, under-diagnosed, difficult to treat and are associated with poor neurodevelopmental outcome. Video-EEG is the current gold-standard approach for seizure detection and monitoring. Interpreting neonatal EEG requires expertise and the impact of seizures on the developing brain remains poorly understood. In this case study we present the first ever images of the haemodynamic impact of seizures on the human infant brain, obtained using simultaneous diffuse optical tomography (DOT) and video-EEG with whole-scalp coverage. Seven discrete periods of ictal electrographic activity were observed during a 60 minute recording of an infant with hypoxic-ischaemic encephalopathy. The resulting DOT images show a remarkably consistent, high-amplitude, biphasic pattern of changes in cortical blood volume and oxygenation in response to each electrographic event. While there is spatial variation across the cortex, the dominant haemodynamic response to seizure activity consists of an initial increase in cortical blood volume prior to a large and extended decrease typically lasting several minutes. This case study demonstrates the wealth of physiologically and clinically relevant information that DOT-EEG techniques can yield. The consistency and scale of the haemodynamic responses observed here also suggest that DOT-EEG has the potential to provide improved detection of neonatal seizures. PMID:25161892

  17. Mapping cortical haemodynamics during neonatal seizures using diffuse optical tomography: A case study

    PubMed Central

    Singh, Harsimrat; Cooper, Robert J.; Wai Lee, Chuen; Dempsey, Laura; Edwards, Andrea; Brigadoi, Sabrina; Airantzis, Dimitrios; Everdell, Nick; Michell, Andrew; Holder, David; Hebden, Jeremy C.; Austin, Topun

    2014-01-01

    Seizures in the newborn brain represent a major challenge to neonatal medicine. Neonatal seizures are poorly classified, under-diagnosed, difficult to treat and are associated with poor neurodevelopmental outcome. Video-EEG is the current gold-standard approach for seizure detection and monitoring. Interpreting neonatal EEG requires expertise and the impact of seizures on the developing brain remains poorly understood. In this case study we present the first ever images of the haemodynamic impact of seizures on the human infant brain, obtained using simultaneous diffuse optical tomography (DOT) and video-EEG with whole-scalp coverage. Seven discrete periods of ictal electrographic activity were observed during a 60 minute recording of an infant with hypoxic–ischaemic encephalopathy. The resulting DOT images show a remarkably consistent, high-amplitude, biphasic pattern of changes in cortical blood volume and oxygenation in response to each electrographic event. While there is spatial variation across the cortex, the dominant haemodynamic response to seizure activity consists of an initial increase in cortical blood volume prior to a large and extended decrease typically lasting several minutes. This case study demonstrates the wealth of physiologically and clinically relevant information that DOT–EEG techniques can yield. The consistency and scale of the haemodynamic responses observed here also suggest that DOT–EEG has the potential to provide improved detection of neonatal seizures. PMID:25161892

  18. Bingham-NODDI: Mapping anisotropic orientation dispersion of neurites using diffusion MRI.

    PubMed

    Tariq, Maira; Schneider, Torben; Alexander, Daniel C; Gandini Wheeler-Kingshott, Claudia A; Zhang, Hui

    2016-06-01

    This paper presents Bingham-NODDI, a clinically-feasible technique for estimating the anisotropic orientation dispersion of neurites. Direct quantification of neurite morphology on clinical scanners was recently realised by a diffusion MRI technique known as neurite orientation dispersion and density imaging (NODDI). However in its current form NODDI cannot estimate anisotropic orientation dispersion, which is widespread in the brain due to common fanning and bending of neurites. This work proposes Bingham-NODDI that extends the NODDI formalism to address this limitation. Bingham-NODDI characterises anisotropic orientation dispersion by utilising the Bingham distribution to model neurite orientation distribution. The new model estimates the extent of dispersion about the dominant orientation, separately along the primary and secondary dispersion orientations. These estimates are subsequently used to estimate the overall dispersion about the dominant orientation and the dispersion anisotropy. We systematically evaluate the ability of the new model to recover these key parameters of anisotropic orientation dispersion with standard NODDI protocol, both in silico and in vivo. The results demonstrate that the parameters of the proposed model can be estimated without additional acquisition requirements over the standard NODDI protocol. Thus anisotropic dispersion can be determined and has the potential to be used as a marker for normal brain development and ageing or in pathology. We additionally find that the original NODDI model is robust to the effects of anisotropic orientation dispersion, when the quantification of anisotropic dispersion is not of interest. PMID:26826512

  19. 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).

  20. 3D mapping of somatotopic reorganization with small animal functional MRI

    PubMed Central

    Yu, Xin; Wang, Shumin; Chen, Der-Yow; Dodd, Stephen; Goloshevsky, Artem; Koretsky, Alan P.

    2009-01-01

    There are few in vivo noninvasive methods to study neuroplasticity in animal brains. Functional MRI (fMRI) has been developed for animal brain mapping, but few fMRI studies have analyzed functional alteration due to plasticity in animal models. One major limitation is that fMRI maps are characterized by statistical parametric mapping making the apparent boundary dependent on the statistical threshold used. Here, we developed a method to characterize the location of center-of-mass in fMRI maps that is shown not to be sensitive to statistical threshold. Utilizing centers-of-mass as anchor points to fit the spatial distribution of the BOLD response enabled quantitative group analysis of altered boundaries of functional somatosensory maps. This approach was used to study cortical reorganization in the rat primary somatosensory cortex (S1) after sensory deprivation to the barrel cortex by follicle ablation (F.A.). FMRI demonstrated an enlarged nose S1 representation in the 3D somatotopic functional maps. This result clearly demonstrates that fMRI enables the spatial mapping of functional changes that can characterize multiple regions of S1 cortex and still be sensitive to changes due to plasticity. PMID:19770051

  1. 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

  2. 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

  3. 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

  4. 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

  5. Connectivity-based structural and functional parcellation of the human cortex using diffusion imaging and tractography

    PubMed Central

    Cloutman, Lauren L.; Lambon Ralph, Matthew A.

    2012-01-01

    The parcellation of the cortex via its anatomical properties has been an important research endeavor for over a century. To date, however, a universally accepted parcellation scheme for the human brain still remains elusive. In the current review, we explore the use of in vivo diffusion imaging and white matter tractography as a non-invasive method for the structural and functional parcellation of the human cerebral cortex, discussing the strengths and limitations of the current approaches. Cortical parcellation via white matter connectivity is based on the premise that, as connectional anatomy determines functional organization, it should be possible to segregate functionally-distinct cortical regions by identifying similarities and differences in connectivity profiles. Recent studies have provided initial evidence in support of the efficacy of this connectional parcellation methodology. Such investigations have identified distinct cortical subregions which correlate strongly with functional regions identified via fMRI and meta-analyses. Furthermore, a strong parallel between the cortical regions defined via tractographic and more traditional cytoarchitectonic parcellation methods has been observed. However, the degree of correspondence and relative functional importance of cytoarchitectonic- versus connectivity-derived parcellations still remains unclear. Diffusion tractography remains one of the only methods capable of visualizing the structural networks of the brain in vivo. As such, it is of vital importance to continue to improve the accuracy of the methodology and to extend its potential applications in the study of cognition in neurological health and disease. PMID:22952459

  6. Subclinical myocardial inflammation and diffuse fibrosis are common in systemic sclerosis – a clinical study using myocardial T1-mapping and extracellular volume quantification

    PubMed Central

    2014-01-01

    Background Systemic sclerosis (SSc) is characterised by multi-organ tissue fibrosis including the myocardium. Diffuse myocardial fibrosis can be detected non-invasively by T1 and extracellular volume (ECV) quantification, while focal myocardial inflammation and fibrosis may be detected by T2-weighted and late gadolinium enhancement (LGE), respectively, using cardiovascular magnetic resonance (CMR). We hypothesised that multiparametric CMR can detect subclinical myocardial involvement in patients with SSc. Methods 19 SSc patients (18 female, mean age 55 ± 10 years) and 20 controls (19 female, mean age 56 ± 8 years) without overt cardiovascular disease underwent CMR at 1.5T, including cine, tagging, T1-mapping, T2-weighted, LGE imaging and ECV quantification. Results Focal fibrosis on LGE was found in 10 SSc patients (53%) but none of controls. SSc patients also had areas of myocardial oedema on T2-weighted imaging (median 13 vs. 0% in controls). SSc patients had significantly higher native myocardial T1 values (1007 ± 29 vs. 958 ± 20 ms, p < 0.001), larger areas of myocardial involvement by native T1 >990 ms (median 52 vs. 3% in controls) and expansion of ECV (35.4 ± 4.8 vs. 27.6 ± 2.5%, p < 0.001), likely representing a combination of low-grade inflammation and diffuse myocardial fibrosis. Regardless of any regional fibrosis, native T1 and ECV were significantly elevated in SSc and correlated with disease activity and severity. Although biventricular size and global function were preserved, there was impairment in the peak systolic circumferential strain (-16.8 ± 1.6 vs. -18.6 ± 1.0, p < 0.001) and peak diastolic strain rate (83 ± 26 vs. 114 ± 16 s-1, p < 0.001) in SSc, which inversely correlated with diffuse myocardial fibrosis indices. Conclusions Cardiac involvement is common in SSc even in the absence of cardiac symptoms, and includes chronic myocardial inflammation as well as focal and diffuse myocardial fibrosis. Myocardial abnormalities detected on

  7. Benchmarking Rapid TLES Simulations of Gas Diffusion in Proteins: Mapping O2 Migration and Escape in Myoglobin as a Case Study.

    PubMed

    Shadrina, Maria S; English, Ann M; Peslherbe, Gilles H

    2016-04-12

    Standard molecular dynamics (MD) simulations of gas diffusion consume considerable computational time and resources even for small proteins. To combat this, temperature-controlled locally enhanced sampling (TLES) examines multiple diffusion trajectories per simulation by accommodating multiple noninteracting copies of a gas molecule that diffuse independently, while the protein and water molecules experience an average interaction from all copies. Furthermore, gas migration within a protein matrix can be accelerated without altering protein dynamics by increasing the effective temperature of the TLES copies. These features of TLES enable rapid simulations of gas diffusion within a protein matrix at significantly reduced (∼98%) computational cost. However, the results of TLES and standard MD simulations have not been systematically compared, which limits the adoption of the TLES approach. We address this drawback here by benchmarking TLES against standard MD in the simulation of O2 diffusion in myoglobin (Mb) as a case study since this model system has been extensively characterized. We find that 2 ns TLES and 108 ns standard simulations map the same network of diffusion tunnels in Mb and uncover the same docking sites, barriers, and escape portals. We further discuss the influence of simulation time as well as the number of independent simulations on the O2 population density within the diffusion tunnels and on the sampling of Mb's conformational space as revealed by principal component analysis. Overall, our comprehensive benchmarking reveals that TLES is an appropriate and robust tool for the rapid mapping of gas diffusion in proteins when the kinetic data provided by standard MD are not required. Furthermore, TLES provides explicit ligand diffusion pathways, unlike most rapid methods. PMID:26938707

  8. 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.

  9. Fitting Chinese syllable-to-character mapping spectrum by the beta rank function

    NASA Astrophysics Data System (ADS)

    Li, Wentian

    2012-02-01

    We define the syllable-to-character mapping spectrum in Chinese as the normalized number of characters per syllable ranked from high to low. This spectrum provides a statistical characterization of the relationship between spoken and written Chinese. We have shown that two functions, the logarithmic function and the beta rank function, fit the syllable-to-character mapping spectrum well. The beta rank function is even better than the logarithmic function judged by two measures of data-fitting performance: the sum of square errors, and Akaike information criterion. We comment on why the beta rank function is a good fitting function for many range-limited ranking data, whereas for range-open data it may be out-performed by other functions, such as a power-law function in the case of Zipf's law.

  10. 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%.

  11. 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.

  12. The AKARI Far-Infrared Surveyor (FIS): all-sky Diffuse Map

    NASA Astrophysics Data System (ADS)

    Komugi, Shinya; Doi, Yasuo; Hattori, Makoto; Kitamura, Yoshimi; Otsubo, Takafumi; Tanaka, Masahiro; Ikeda, Norio; Kato, Daisuke; Nakagawa, Takao

    2011-12-01

    The infrared astronomical satellite AKARI performed an all sky survey at six infrared bands. We report here on the calibration of the all-sky image data, observed in the four long wavelength bands with the FIS instrument (AKARI Far-infrared All Sky Survey : AFASS). The preliminary image attains a calibration uncertainty and sensitivity of better than ~ 30% and ~ 10 MJy str-1, respectively, for all four bands. The point spread function (PSF) is obtained via a stacking technique. The data are shown to be useful for exploring the internal structure and dust spectral energy distributions (SEDs) of nearby galaxies.

  13. Delayed early developmental trajectories of white matter tracts of functional pathways in preterm-born infants: Longitudinal diffusion tensor imaging data

    PubMed Central

    Chang, Linda; Akazawa, Kentaro; Yamakawa, Robyn; Hayama, Sara; Buchthal, Steven; Alicata, Daniel; Andres, Tamara; Castillo, Deborrah; Oishi, Kumiko; Skranes, Jon; Ernst, Thomas; Oishi, Kenichi

    2016-01-01

    Probabilistic maps of white matter pathways related to motor, somatosensory, auditory, visual, and limbic functions, and major white matter tracts (the corpus callosum, the inferior fronto-occipital fasciculus, and the middle cerebellar peduncle) were applied to evaluate the developmental trajectories of these tracts, using longitudinal diffusion tensor imaging (DTI) obtained in term-born and preterm-born healthy infants. Nineteen term-born and 30 preterm-born infants completed MR scans at three time points: Time-point 1, 41.6±2.7 postmenstrual weeks; Time-point 2, 46.0±2.9 postmenstrual weeks; and Time-point 3, 50.8±3.7 postmenstrual weeks. The DTI-derived scalar values (fractional anisotropy, eigenvalues, and radial diffusivity) of the three time points are available in this Data article. PMID:26958632

  14. Prediction of motor outcomes and activities of daily living function using diffusion tensor tractography in acute hemiparetic stroke patients

    PubMed Central

    Imura, Takeshi; Nagasawa, Yuki; Inagawa, Tetsuji; Imada, Naoki; Izumi, Hiroaki; Emoto, Katsuya; Tani, Itaru; Yamasaki, Hiroyuki; Ota, Yuichiro; Oki, Shuichi; Maeda, Tadanori; Araki, Osamu

    2015-01-01

    [Purpose] The efficacy of diffusion tensor imaging in the prediction of motor outcomes and activities of daily living function remains unclear. We evaluated the most appropriate diffusion tensor parameters and methodology to determine whether the region of interest- or tractography-based method was more useful for predicting motor outcomes and activities of daily living function in stroke patients. [Subjects and Methods] Diffusion tensor imaging data within 10 days after stroke onset were collected and analyzed for 25 patients. The corticospinal tract was analyzed. Fractional anisotropy, number of fibers, and apparent diffusion coefficient were used as diffusion tensor parameters. Motor outcomes and activities of daily living function were evaluated on the same day as diffusion tensor imaging and at 1 month post-onset. [Results] The fractional anisotropy value of the affected corticospinal tract significantly correlated with the motor outcome and activities of daily living function within 10 days post-onset and at 1 month post-onset. Tthere were no significant correlations between other diffusion tensor parameters and motor outcomes or activities of daily living function. [Conclusion] The fractional anisotropy value of the affected corticospinal tract obtained using the tractography-based method was useful for predicting motor outcomes and activities of daily living function in stroke patients. PMID:26157225

  15. Localized axial Green's function method for the convection-diffusion equations in arbitrary domains

    NASA Astrophysics Data System (ADS)

    Lee, Wanho; Kim, Do Wan

    2014-10-01

    A localized axial Green's function method (LAGM) is proposed for the convection-diffusion equation. The axial Green's function method (AGM) enables us to calculate the numerical solution of a multi-dimensional problem using only one-dimensional Green's functions for the axially split differential operators. This AGM has been developed not only for the elliptic boundary value problems but also for the steady Stokes flows, however, this paper is concerned with the localization of the AGM. This localization of the method is needed for practical purpose when computing the axial Green's function, specifically for the convection-diffusion equation on a line segment that we call the local axial line. Although our focus is mainly on the convection-dominated cases in arbitrary domains, this method can solve other cases in a unified way. Numerical results show that, despite irregular types of discretization on an arbitrary domain, we can calculate the numerical solutions using the LAGM without loss of accuracy even in cases of large convection. In particular, it is also shown that randomly distributed axial lines are available in our LAGM and complicated domains are not a burden.

  16. 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.

  17. 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

  18. Pulsed Field Gradient NMR with Sigmoid Shape Gradient Sampling To Produce More Detailed Diffusion Ordered Spectroscopy Maps of Real Complex Mixtures: Examples with Medicine Analysis.

    PubMed

    Pagès, Guilhem; Bonny, Alice; Gilard, Véronique; Malet-Martino, Myriam

    2016-03-15

    NMR diffusion measurements are based on signal attenuation. In the case of complex mixtures for which some molecules are diffusing quickly while others are significantly slower, it is challenging to obtain a diffusion ordered spectroscopy (DOSY)-type 2D map giving reliable information on all molecules. In this paper, we propose a new gradient sampling approach based on a sigmoid shape allowing the acquisition of a significant number of points for both the fast and slow diffusing molecules. We applied this new gradient sampling strategy to deformulate two medicines whose composition was known (Esomeprazole) or unknown (Mebendazole). PFG NMR associated with a sigmoid gradient ramp is an exciting strategy to study drugs as a whole, i.e., the active ingredient(s) and excipients. PMID:26905176

  19. Mapping functional groups on oxidised multi-walled carbon nanotubes at the nanometre scale.

    PubMed

    Goode, A E; Hine, N D M; Chen, S; Bergin, S D; Shaffer, M S P; Ryan, M P; Haynes, P D; Porter, A E; McComb, D W

    2014-06-28

    Despite voluminous research on the acid oxidation of carbon nanotubes (CNTs), there is a distinct lack of experimental results showing distributions of functional groups at the nanometre length scale. Here, functional peaks have been mapped across individual multi-walled CNTs with low-dose, monochromated electron energy-loss spectroscopy (EELS) in the scanning transmission electron microscope (STEM). Density functional theory simulations show that the EELS features are consistent with oxygenated functional groups, most likely carboxyl moieties. PMID:24827593

  20. Validation of diffuse correlation spectroscopic measurement of cerebral blood flow using phase-encoded velocity mapping magnetic resonance imaging

    NASA Astrophysics Data System (ADS)

    Buckley, Erin M.; Hance, Dalton; Pawlowski, Thomas; Lynch, Jennifer; Wilson, Felice B.; Mesquita, Rickson C.; Durduran, Turgut; Diaz, Laura K.; Putt, Mary E.; Licht, Daniel J.; Fogel, Mark A.; Yodh, Arjun G.

    2012-03-01

    Diffuse correlation spectroscopy (DCS) is a novel optical technique that appears to be an excellent tool for assessing cerebral blood flow in a continuous and non-invasive manner at the bedside. We present new clinical validation of the DCS methodology by demonstrating strong agreement between DCS indices of relative cerebral blood flow and indices based on phase-encoded velocity mapping magnetic resonance imaging (VENC MRI) of relative blood flow in the jugular veins and superior vena cava. Data were acquired from 46 children with single ventricle cardiac lesions during a hypercapnia intervention. Significant increases in cerebral blood flow, measured both by DCS and by VENC MRI, as well as significant increases in oxyhemoglobin concentration, and total hemoglobin concentration, were observed during hypercapnia. Comparison of blood flow changes measured by VENC MRI in the jugular veins and by DCS revealed a strong linear relationship, R=0.88, p<0.001, slope=0.91+/-0.07. Similar correlations were observed between DCS and VENC MRI in the superior vena cava, R=0.77, slope=0.99+/-0.12, p<0.001. The relationship between VENC MRI in the aorta and DCS, a negative control, was weakly correlated, R=0.46, slope=1.77+/-0.45, p<0.001.

  1. 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.

  2. Pyridine adsorption and diffusion on Pt(111) investigated with density functional theory

    NASA Astrophysics Data System (ADS)

    Kolsbjerg, Esben L.; Groves, Michael N.; Hammer, Bjørk

    2016-04-01

    The adsorption, diffusion, and dissociation of pyridine, C5H5N, on Pt(111) are investigated with van der Waals-corrected density functional theory. An elaborate search for local minima in the adsorption potential energy landscape reveals that the intact pyridine adsorbs with the aromatic ring parallel to the surface. Piecewise interconnections of the local minima in the energy landscape reveal that the most favourable diffusion path for pyridine has a barrier of 0.53 eV. In the preferred path, the pyridine remains parallel to the surface while performing small single rotational steps with a carbon-carbon double bond hinged above a single Pt atom. The origin of the diffusion pathway is discussed in terms of the C2-Pt π-bond being stronger than the corresponding CN-Pt π-bond. The energy barrier and reaction enthalpy for dehydrogenation of adsorbed pyridine into an adsorbed, upright bound α-pyridyl species are calculated to 0.71 eV and 0.18 eV, respectively (both zero-point energy corrected). The calculations are used to rationalize previous experimental observations from the literature for pyridine on Pt(111).

  3. Dynamics of supercooled water in nanotubes: cage correlation function and diffusion coefficient.

    PubMed

    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 220Kdiffusivity 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. PMID:26465407

  4. 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.

  5. Hydration and diffusion dynamics shape microbial community composition and function in soil aggregates.

    NASA Astrophysics Data System (ADS)

    Or, D.; Ebrahimi, A.

    2014-12-01

    Natural variations in soil hydration conditions (rainfall, evaporation, root water uptake) affect gas and nutrient diffusion and soil microbial community composition and function. The conditions in soil aggregates are of particular interest due to limitations to oxygen diffusion into the core often containing organic carbon (as aggregation agent). The constantly varying soil hydration conditions affect the spatial extent of anoxic conditions in aggregates and thus the sized and self-organization of aerobic and anaerobic microbial communities. We developed an artificial soil aggregate composed of 3-D angular pore network combined with individual based models of motile microbial cells that grow, move, intercept nutrients and are inhibited by presence or absence of oxygen. The hydration conditions in the model aggregate affect community size, spatial segregation, and growth rates. The opposing diffusion directions of oxygen and carbon were essential to maintenance of aerobic and anaerobic communities within an aggregate (anaerobes become extinct when carbon sources are external). Cohabited soil aggregates promoted onset of anaerobic conditions by oxygen consumption by peripheral aerobes. Model predictions of CO2 and N2O production rates were in good agreement with experimental data. Results illustrate how aerobic and anaerobic microbial communities are activated by certain hydration conditions that enhance either nitrogen losses or decomposition of organic matter both contributing to GHG emissions.

  6. 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. PMID:21656516

  7. Pyridine adsorption and diffusion on Pt(111) investigated with density functional theory.

    PubMed

    Kolsbjerg, Esben L; Groves, Michael N; Hammer, Bjørk

    2016-04-28

    The adsorption, diffusion, and dissociation of pyridine, C5H5N, on Pt(111) are investigated with van der Waals-corrected density functional theory. An elaborate search for local minima in the adsorption potential energy landscape reveals that the intact pyridine adsorbs with the aromatic ring parallel to the surface. Piecewise interconnections of the local minima in the energy landscape reveal that the most favourable diffusion path for pyridine has a barrier of 0.53 eV. In the preferred path, the pyridine remains parallel to the surface while performing small single rotational steps with a carbon-carbon double bond hinged above a single Pt atom. The origin of the diffusion pathway is discussed in terms of the C2-Pt π-bond being stronger than the corresponding CN-Pt π-bond. The energy barrier and reaction enthalpy for dehydrogenation of adsorbed pyridine into an adsorbed, upright bound α-pyridyl species are calculated to 0.71 eV and 0.18 eV, respectively (both zero-point energy corrected). The calculations are used to rationalize previous experimental observations from the literature for pyridine on Pt(111). PMID:27131536

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

    PubMed

    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

    2016-02-01

    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

  9. 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

  10. 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.

  11. Discrete Fractional Diffusion Equation of Chaotic Order

    NASA Astrophysics Data System (ADS)

    Wu, Guo-Cheng; Baleanu, Dumitru; Xie, He-Ping; Zeng, Sheng-Da

    Discrete fractional calculus is suggested in diffusion modeling in porous media. A variable-order fractional diffusion equation is proposed on discrete time scales. A function of the variable order is constructed by a chaotic map. The model shows some new random behaviors in comparison with other variable-order cases.

  12. 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.

  13. 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…

  14. 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

  15. 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

  16. 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.

  17. Functional mapping of Cre recombinase by pentapeptide insertional mutagenesis.

    PubMed

    Petyuk, Vladislav; McDermott, Jeffrey; Cook, Malcolm; Sauer, Brian

    2004-08-27

    Cre is a site-specific recombinase from bacteriophage P1. It is a member of the tyrosine integrase family and catalyzes reciprocal recombination between specific 34-bp sites called loxP. To analyze the structure-function relationships of this enzyme, we performed large scale pentapeptide insertional mutagenesis to generate insertions of five amino acids at random positions in the protein. The high density of insertion mutations into Cre allowed us to identify an unexpected degree of functional tolerance to insertions into the 4-5 beta-hairpin and into the loop between helices J and K (both of which contact the DNA in the minor groove) and also into helix A. The phenotypes of the majority of inserts allowed us to confirm a variety of predictions made on the basis of sequence conservation, known three-dimensional structure, and proposed catalytic mechanism. In particular, most insertions into conserved regions or secondary structure elements inactivated Cre, and most insertions located in nonconserved, unstructured regions preserved Cre activity. Less expectedly, the non-conserved and poorly structured loops and linkers between helices A-B, E-F, and M-N did not tolerate insertions, thus identifying these as critical regions for recombinase activity. We purified and characterized in vitro several representatives of these "unexpected" Cre insertion mutants. The role of those regions in the recombination process is discussed. PMID:15218019

  18. A systematic review of functional magnetic resonance imaging and diffusion tensor imaging modalities used in presurgical planning of brain tumour resection.

    PubMed

    Dimou, S; Battisti, R A; Hermens, D F; Lagopoulos, J

    2013-04-01

    Historically, brain tumour resection has relied upon standardised anatomical atlases and classical mapping techniques for successful resection. While these have provided adequate results in the past, the emergence of new technologies has heralded a wave of less invasive, patient-specific techniques for the mapping of brain function. Functional magnetic resonance imaging (fMRI) and, more recently, diffusion tensor imaging (DTI) are two such techniques. While fMRI is able to highlight localisation of function within the cortex, DTI represents the only technique able to elucidate white matter structures in vivo. Used in conjunction, both of these techniques provide important presurgical information for thorough preoperative planning, as well as intraoperatively via integration into frameless stereotactic neuronavigational systems. Together, these techniques show great promise for improved neurosurgical outcomes. While further research is required for more widespread clinical validity and acceptance, results from the literature provide a clear road map for future research and development to cement these techniques into the clinical setup of neurosurgical departments globally. PMID:23187966

  19. 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

  20. Functional Mapping of an Oligomeric Autotransporter Adhesin of Aggregatibacter actinomycetemcomitans▿

    PubMed Central

    Yu, Chunxiao; Ruiz, Teresa; Lenox, Christopher; Mintz, Keith P.

    2008-01-01

    Extracellular matrix protein adhesin A (EmaA) is a 202-kDa nonfimbrial adhesin, which mediates the adhesion of the oral pathogen Aggregatibacter actinomycetemcomitans to collagen. EmaA oligomers form surface antenna-like protrusions consisting of a long helical rod with an ellipsoidal ending. The functional analysis of in-frame emaA deletion mutants has located the collagen binding activity to the amino terminus of the protein corresponding to amino acids 70 to 386. The level of collagen binding of this deletion mutant was comparable to the emaA mutant strain. Transmission electron microscopy studies indicate that the first 330 amino acids of the mature protein form the ellipsoidal ending of the EmaA protrusions, where the activity resides. Amino acid substitution analysis within this sequence has identified a critical amino acid, which is essential for the formation of the ellipsoidal ending and for collagen binding activity. PMID:18310342

  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. 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

  3. Physiologic abnormalities of cardiac function in progressive systemic sclerosis with diffuse scleroderma

    SciTech Connect

    Follansbee, W.P.; Curtiss, E.I.; Medsger, T.A. Jr.; Steen, V.D.; Uretsky, B.F.; Owens, G.R.; Rodnan, G.P.

    1984-01-19

    To investigate cardiopulmonary function in progressive systemic sclerosis with diffuse scleroderma, we studied 26 patients with maximal exercise and redistribution thallium scans, rest and exercise radionuclide ventriculography, pulmonary-function testing, and chest roentgenography. Although only 6 patients had clinical evidence of cardiac involvement, 20 had abnormal thallium scans, including 10 with reversible exercise-induced defects and 18 with fixed defects (8 had both). Seven of the 10 patients who had exercise-induced defects and underwent cardiac catheterization had normal coronary angiograms. Mean resting left ventricular ejection fraction and mean resting right ventricular ejection fraction were lower in patients with post-exercise left ventricular thallium defect scores above the median (59 +/- 13 per cent vs. 69 +/- 6 per cent, and 36 +/- 12 per cent vs. 47 +/- 7 per cent, respectively). The authors conclude that in progressive systemic sclerosis with diffuse scleroderma, abnormalities of myocardial perfusion are common and appear to be due to a disturbance of the myocardial microcirculation. Both right and left ventricular dysfunction appear to be related to this circulatory disturbance, suggesting ischemically mediated injury.

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

    PubMed

    Karalunas, Sarah L; Huang-Pollock, Cynthia L

    2013-07-01

    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 = 91, [Formula: see text] age = 10.2 years, 67 % male) and without ADHD (n = 62, [Formula: see text] 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

  5. 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

  6. Plant functional type mapping for earth system models

    NASA Astrophysics Data System (ADS)

    Poulter, B.; Ciais, P.; Hodson, E.; Lischke, H.; Maignan, F.; Plummer, S.; Zimmermann, N. E.

    2011-08-01

    The sensitivity of global carbon and water cycling to climate variability is coupled directly to land cover and the distribution of vegetation. To investigate biogeochemistry-climate interactions, earth system models require a representation of vegetation distributions that are either prescribed from remote sensing data or simulated via biogeography models. However, the abstraction of earth system state variables in models means that data products derived from remote sensing need to be post-processed for model-data assimilation. Dynamic global vegetation models (DGVM) rely on the concept of plant functional types (PFT) to group shared traits of thousands of plant species into just several classes. Available databases of observed PFT distributions must be relevant to existing satellite sensors and their derived products, and to the present day distribution of managed lands. Here, we develop four PFT datasets based on land-cover information from three satellite sensors (EOS-MODIS 1 km and 0.5 km, SPOT4-VEGETATION 1 km, and ENVISAT-MERIS 0.3 km spatial resolution) that are merged with spatially-consistent Köppen-Geiger climate zones. Using a beta (β) diversity metric to assess reclassification similarity, we find that the greatest uncertainty in PFT classifications occur most frequently between cropland and grassland categories, and in dryland systems between shrubland, grassland and forest categories because of differences in the minimum threshold required for forest cover. The biogeography-biogeochemistry DGVM, LPJmL, is used in diagnostic mode with the four PFT datasets prescribed to quantify the effect of land-cover uncertainty on climatic sensitivity of gross primary productivity (GPP) and transpiration fluxes. Our results show that land-cover uncertainty has large effects in arid regions, contributing up to 30 % (20 %) uncertainty in the sensitivity of GPP (transpiration) to precipitation. The availability of plant functional type datasets that are consistent

  7. THE EFFECT OF MAGNETIC FIELDS AND AMBIPOLAR DIFFUSION ON CORE MASS FUNCTIONS

    SciTech Connect

    Bailey, Nicole D.; Basu, Shantanu E-mail: basu@uwo.ca

    2013-03-20

    Linear analysis of the formation of protostellar cores in planar magnetic interstellar clouds yields information about length scales involved in star formation. Combining these length scales with various distributions of other environmental variables (i.e., column density and mass-to-flux ratio) and applying Monte Carlo methods allow us to produce synthetic core mass functions (CMFs) for different environmental conditions. Our analysis shows that the shape of the CMF is directly dependent on the physical conditions of the cloud. Specifically, magnetic fields act to broaden the mass function and develop a high-mass tail while ambipolar diffusion will truncate this high-mass tail. In addition, we analyze the effect of small number statistics on the shape and high-mass slope of the synthetic CMFs. We find that observed CMFs are severely statistically limited, which has a profound effect on the derived slope for the high-mass tail.

  8. 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

  9. Time domain functional NIRS imaging for human brain mapping.

    PubMed

    Torricelli, Alessandro; Contini, Davide; Pifferi, Antonio; Caffini, Matteo; Re, Rebecca; Zucchelli, Lucia; Spinelli, Lorenzo

    2014-01-15

    This review is aimed at presenting the state-of-the-art of time domain (TD) functional near-infrared spectroscopy (fNIRS). We first introduce the physical principles, the basics of modeling and data analysis. Basic instrumentation components (light sources, detection techniques, and delivery and collection systems) of a TD fNIRS system are described. A survey of past, existing and next generation TD fNIRS systems used for research and clinical studies is presented. Performance assessment of TD fNIRS systems and standardization issues are also discussed. Main strengths and weakness of TD fNIRS are highlighted, also in comparison with continuous wave (CW) fNIRS. Issues like quantification of the hemodynamic response, penetration depth, depth selectivity, spatial resolution and contrast-to-noise ratio are critically examined, with the help of experimental results performed on phantoms or in vivo. Finally we give an account on the technological developments that would pave the way for a broader use of TD fNIRS in the neuroimaging community. PMID:23747285

  10. 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

  11. 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.

  12. A survey of biofilms on wastewater aeration diffusers suggests bacterial community composition and function vary by substrate type and time.

    PubMed

    Noble, Peter A; Park, Hee-Deung; Olson, Betty H; Asvapathanagul, Pitiporn; Hunter, M Colby; Garrido-Baserba, Manel; Lee, Sang-Hoon; Rosso, Diego

    2016-07-01

    Aeration diffusers in wastewater treatment plants generate air bubbles that promote mixing, distribution of dissolved oxygen, and microbial processing of dissolved and suspended matter in bulk solution. Biofouling of diffusers represents a significant problem to wastewater treatment plants because biofilms decrease oxygen transfer efficiency and increase backpressure on the blower. To better understand biofouling, we conducted a pilot study to survey the bacterial community composition and function of biofilms on different diffuser substrates and compare them to those in the bulk solution. DNA was extracted from the surface of ethylene-propylene-diene monomer (EPDM), polyurethane, and silicone diffusers operated for 15 months in a municipal treatment plant and sampled at 3 and 9 months. The bacterial community composition and function of the biofilms and bulk solution were determined by amplifying the 16S rRNA genes and pyrosequencing the amplicons and raw metagenomic DNA. The ordination plots and dendrograms of the 16S rRNA and functional genes showed that while the bacterial community composition and function of the bulk solution was independent of sampling time, the composition and function of the biofilms differed by diffuser type and testing time. For the EPDM and silicone diffusers, the biofilm communities were more similar in composition to the bulk solution at 3 months than 9 months. In contrast, the bacteria on the polyurethane diffusers were more dissimilar to the bulk solution at 3 months than 9 months. Taken together, the survey showed that the community composition and function of bacterial biofilms depend on the diffuser substrate and testing time, which warrants further elucidation. PMID:27294381

  13. Fiber tract-driven topographical mapping (FTTM) reveals microstructural relevance for interhemispheric visuomotor function in the aging brain

    PubMed Central

    Schulte, Tilman; Maddah, Mahnaz; Müller-Oehring, Eva M.; Rohlfing, Torsten; Pfefferbaum, Adolf; Sullivan, Edith V.

    2013-01-01

    We present a novel approach – DTI-based fiber tract-driven topographical mapping (FTTM) – to map and measure the influence of age on the integrity of interhemispheric fibers and challenge their selective functions with measures of interhemispheric integration of lateralized information. This approach enabled identification of spatially specific topographical maps of scalar diffusion measures and their relation to measures of visuomotor performance. Relative to younger adults, older adults showed lower fiber integrity indices in anterior than posterior callosal fibers. FTTM analysis identified a dissociation in the microstructural – function associates between age groups: in younger adults, genu fiber integrity correlated with interhemispheric transfer time, whereas in older adults, body fiber integrity was correlated with interhemispheric transfer time with topographical specificity along left-lateralized callosal fiber trajectories. Neural co-activation from redundant targets was evidenced by fMRI-derived bilateral extrastriate cortex activation in both groups, and a group difference emerged for a pontine activation cluster that was differently modulated by response hand in older than younger adults. Bilateral processing advantages in older but not younger adults further correlated with fiber integrity in transverse pontine fibers that branch into the right cerebellar cortex, thereby supporting a role for the pons in interhemispheric facilitation. In conclusion, in the face of compromised anterior callosal fibers, older adults appear to use alternative pathways to accomplish visuomotor interhemispheric information transfer and integration for lateralized processing. This shift from youthful associations may indicate recruitment of compensatory mechanisms involving medial corpus callosum fibers and subcortical pathways. PMID:23567886

  14. Atypically diffuse functional connectivity between caudate nuclei and cerebral cortex in autism

    PubMed Central

    Turner, Katherine C; Frost, Leonard; Linsenbardt, David; McIlroy, John R; Müller, Ralph-Axel

    2006-01-01

    Background Autism is a neurodevelopmental disorder affecting sociocommunicative behavior, but also sensorimotor skill learning, oculomotor control, and executive functioning. Some of these impairments may be related to abnormalities of the caudate nuclei, which have been reported for autism. Methods Our sample was comprised of 8 high-functioning males with autism and 8 handedness, sex, and age-matched controls. Subjects underwent functional MRI scanning during performance on simple visuomotor coordination tasks. Functional connectivity MRI (fcMRI) effects were identified as interregional blood oxygenation level dependent (BOLD) signal cross-correlation, using the caudate nuclei as seed volumes. Results In the control group, fcMRI effects were found in circuits with known participation of the caudate nuclei (associative, orbitofrontal, oculomotor, motor circuits). Although in the autism group fcMRI effects within these circuits were less pronounced or absent, autistic subjects showed diffusely increased connectivity mostly in pericentral regions, but also in brain areas outside expected anatomical circuits (such as visual cortex). Conclusion These atypical connectivity patterns may be linked to developmental brain growth disturbances recently reported in autism and suggest inefficiently organized functional connectivity between caudate nuclei and cerebral cortex, potentially accounting for stereotypic behaviors and executive impairments. PMID:17042953

  15. 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

  16. Plant functional type mapping for earth system models

    NASA Astrophysics Data System (ADS)

    Poulter, B.; Ciais, P.; Hodson, E.; Lischke, H.; Maignan, F.; Plummer, S.; Zimmermann, N. E.

    2011-11-01

    The sensitivity of global carbon and water cycling to climate variability is coupled directly to land cover and the distribution of vegetation. To investigate biogeochemistry-climate interactions, earth system models require a representation of vegetation distributions that are either prescribed from remote sensing data or simulated via biogeography models. However, the abstraction of earth system state variables in models means that data products derived from remote sensing need to be post-processed for model-data assimilation. Dynamic global vegetation models (DGVM) rely on the concept of plant functional types (PFT) to group shared traits of thousands of plant species into usually only 10-20 classes. Available databases of observed PFT distributions must be relevant to existing satellite sensors and their derived products, and to the present day distribution of managed lands. Here, we develop four PFT datasets based on land-cover information from three satellite sensors (EOS-MODIS 1 km and 0.5 km, SPOT4-VEGETATION 1 km, and ENVISAT-MERIS 0.3 km spatial resolution) that are merged with spatially-consistent Köppen-Geiger climate zones. Using a beta (ß) diversity metric to assess reclassification similarity, we find that the greatest uncertainty in PFT classifications occur most frequently between cropland and grassland categories, and in dryland systems between shrubland, grassland and forest categories because of differences in the minimum threshold required for forest cover. The biogeography-biogeochemistry DGVM, LPJmL, is used in diagnostic mode with the four PFT datasets prescribed to quantify the effect of land-cover uncertainty on climatic sensitivity of gross primary productivity (GPP) and transpiration fluxes. Our results show that land-cover uncertainty has large effects in arid regions, contributing up to 30% (20%) uncertainty in the sensitivity of GPP (transpiration) to precipitation. The availability of PFT datasets that are consistent with current

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

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

    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.

  18. 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.

  19. 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

  20. Construction of fuzzy membership functions using interactive self-organizing maps

    NASA Astrophysics Data System (ADS)

    Sandidge, Thomas E., Jr.; Dagli, Cihan H.

    1998-03-01

    This paper presents a Kohonen-like mapping that eliminates or reduces four limitations of the Kohonen maps. The described network is invariant to scale, very resistant to 'automatic selection of feature dimensions,' results in strictly ordered clusters of ascending/descending magnitude, and may allow a greater amount of information to be gleaned from high dimensional data sets. The network treats each input component separately but each map is influenced via inter-map connections. Unfortunately, processing time increases combinatorially as the number of input components and number of neurons per component increases. As a demonstration, membership functions are constructed for a four variable data set with minimal parameter setting, the most crucial being the number of classes per input component.

  1. 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.

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

    PubMed Central

    Kichaev, Gleb; Pasaniuc, Bogdan

    2015-01-01

    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. PMID:26189819

  3. Anomalous kinetics in diffusion limited reactions linked to non-Gaussian concentration probability distribution function.

    PubMed

    de Anna, Pietro; Le Borgne, Tanguy; Dentz, Marco; Bolster, Diogo; Davy, Philippe

    2011-11-01

    We investigate anomalous reaction kinetics related to segregation in the one-dimensional reaction-diffusion system A + B → C. It is well known that spatial fluctuations in the species concentrations cause a breakdown of the mean-field behavior at low concentration values. The scaling of the average concentration with time changes from the mean-field t(-1) to the anomalous t(-1/4) behavior. Using a stochastic modeling approach, the reaction-diffusion system can be fully characterized by the multi-point probability distribution function (PDF) of the species concentrations. Its evolution is governed by a Fokker-Planck equation with moving boundaries, which are determined by the positivity of the species concentrations. The concentration PDF is in general non-Gaussian. As long as the concentration fluctuations are small compared to the mean, the PDF can be approximated by a Gaussian distribution. This behavior breaks down in the fluctuation dominated regime, for which anomalous reaction kinetics are observed. We show that the transition from mean field to anomalous reaction kinetics is intimately linked to the evolution of the concentration PDF from a Gaussian to non-Gaussian shape. This establishes a direct relationship between anomalous reaction kinetics, incomplete mixing and the non-Gaussian nature of the concentration PDF. PMID:22070289

  4. Learning one-to-many mapping functions for audio-visual integrated perception

    NASA Astrophysics Data System (ADS)

    Lim, Jung-Hui; Oh, Do-Kwan; Lee, Soo-Young

    2010-04-01

    In noisy environment the human speech perception utilizes visual lip-reading as well as audio phonetic classification. This audio-visual integration may be done by combining the two sensory features at the early stage. Also, the top-down attention may integrate the two modalities. For the sensory feature fusion we introduce mapping functions between the audio and visual manifolds. Especially, we present an algorithm to provide one-to-many mapping function for the videoto- audio mapping. The top-down attention is also presented to integrate both the sensory features and classification results of both modalities, which is able to explain McGurk effect. Each classifier is separately implemented by the Hidden-Markov Model (HMM), but the two classifiers are combined at the top level and interact by the top-down attention.

  5. 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.

  6. 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

  7. Electron distribution functions in the diffusion region of asymmetric magnetic reconnection

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    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. 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.

  9. Enhanced anisotropic ionic diffusion in layered electrolyte structures from density functional theory

    NASA Astrophysics Data System (ADS)

    Hirschfeld, J. A.; Lustfeld, H.

    2014-01-01

    Electrolytes with high ionic diffusivity at temperatures distinctively lower than the presently used ones are the prerequisite for the success of, e.g., solid oxide fuel cells. We have found a promising structure having an asymmetric but superior ionic mobility in the direction of the oxygen-ion current. Using a layering of zirconium and yttrium in the fluorite structure of zirconia, a high vacancy concentration and a low migration barrier in two dimensions are obtained, while the mobility in the third direction is basically sacrificed. According to our density functional theory calculations an electrolyte made of this structure could operate at a temperature reduced by ≈200∘C. Thus a window to a different class of electrolytes has been flung open. In our structure the price paid is a more complicated manufacturing method.

  10. 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…

  11. 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

  12. Statistical maps of geomagnetic perturbations as a function of the interplanetary magnetic field

    NASA Astrophysics Data System (ADS)

    Weimer, D. R.; Clauer, C. R.; Engebretson, M. J.; Hansen, T. L.; Gleisner, H.; Mann, I.; Yumoto, K.

    2010-10-01

    Mappings of geomagnetic perturbations are shown for different combinations of the solar wind velocity, interplanetary magnetic field (IMF), and dipole tilt angle (season). Average maps were derived separately for the northward, eastward, and vertical (downward) components of the geomagnetic disturbances, using spherical cap harmonics in least error fits of sorted measurements. The source data are obtained from 104 ground-based magnetometer stations in the Northern Hemisphere at geomagnetic latitudes over 40° during the years 1998 through 2001. Contour maps of statistical fits are shown along-side scatter plots of individual measurements in corrected geomagnetic apex coordinates. The patterns are consistent with previous mappings of ionospheric electric potential. Interestingly, the vertical component of the magnetic perturbations closely resembles maps of the overhead, field-aligned currents, including the Northward IMF configuration. The maximum and minimum values from the statistical mappings are graphed to show their changes as a function of southward IMF magnitude, solar wind velocity, and seasons. It is expected that this work will lead to better advance predictions of the geomagnetic perturbations that are based on real-time IMF measurements.

  13. 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

  14. 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). PMID:26379489

  15. 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.

  16. Prognostic and Functional Significance of MAP4K5 in Pancreatic Cancer

    PubMed Central

    Wang, Oliver H.; Azizian, Nancy; Guo, Ming; Capello, Michela; Deng, Defeng; Zang, Fenglin; Fry, Jason; Katz, Matthew H.; Fleming, Jason B.; Lee, Jeffrey E.; Wolff, Robert A.; Hanash, Samir; Wang, Huamin; Maitra, Anirban

    2016-01-01

    Objectives MAP4K5 plays an important role in regulating a range of cellular responses and is involved in Wnt signaling in hematopoietic cells. However, its functions in human malignancies have not been studied. The major objectives of this study are to examine the expression, functions and clinical significance of MAP4K5 in pancreatic ductal adenocarcinoma (PDAC). Materials and Methods The expression levels of MAP4K5, E-cadherin, vimentin, and carboxylesterase 2 (CES2) were examined by immunohistochemistry in 105 PDAC and matched non-neoplastic pancreas samples from our institution. The RNA sequencing data of 112 PDAC patients were downloaded from the TCGA data portal. Immunoblotting and RNA sequencing analysis were used to examine the expression of MAP4K5 and E-cadherin in pancreatic cancer cell lines. The effect of knockdown MAP4K5 using siRNA on the expression of CDH1 and vimentin were examined by Real-time RT-PCR in Panc-1 and AsPC-1 cells. Statistical analyses were performed using IBM SPSS Statistics. Results MAP4K5 protein is expressed at high levels specifically in the pancreatic ductal cells of 100% non-neoplastic pancreas samples, but is decreased or lost in 77.1% (81/105) of PDAC samples. MAP4K5-low correlated with the loss of E-cadherin (P = 0.001) and reduced CES2 expression (P = 0.002) in our patient populations. The expression levels of MAP4K5 mRNA directly correlated with the expression levels of CDH1 mRNA (R = 0.2490, P = 0.008) in the second cohort of 112 PDAC patients from The Cancer Genome Atlas (TCGA) RNA-seq dataset. Similar correlations between the expression of MAP4K5 and E-cadherin were observed both at protein and mRNA levels in multiple pancreatic cancer cell lines. Knockdown MAP4K5 led to decreased CDH1 mRNA expression in Panc-1 and AsPC-1 cells. MAP4K5-low correlated significantly with reduced overall survival and was an independent prognosticator in patients with stage II PDAC. Conclusions MAP4K5 expression is decreased or lost in

  17. Radial distribution function imaging by STEM diffraction: Phase mapping and analysis of heterogeneous nanostructured glasses.

    PubMed

    Mu, Xiaoke; Wang, Di; Feng, Tao; Kübel, Christian

    2016-09-01

    Characterizing heterogeneous nanostructured amorphous materials is a challenging topic, because of difficulty to solve disordered atomic arrangement in nanometer scale. We developed a new transmission electron microscopy (TEM) method to enable phase analysis and mapping of heterogeneous amorphous structures. That is to combine scanning TEM (STEM) diffraction mapping, radial distribution function (RDF) analysis, and hyperspectral analysis. This method was applied to an amorphous zirconium oxide and zirconium iron multilayer system, and showed extreme sensitivity to small atomic packing variations. This approach helps to understand local structure variations in glassy composite materials and provides new insights to correlate structure and properties of glasses. PMID:27236215

  18. 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.

  19. Brain Maps on the Go: Functional Imaging During Motor Challenge in Animals

    PubMed Central

    Holschneider, DP; Maarek, J-M I

    2008-01-01

    Brain mapping in the freely-moving animal is useful for studying motor circuits, not only because it avoids the potential confound of sedation or restraints, but because activated brain states may serve to accentuate differences that only manifest partially while a subject is in the resting state. Perfusion or metabolic mapping using autoradiography allows one to examine changes in brain function at the circuit level across the entire brain with a spatial resolution (∼100 microns) appropriate for the rat or mouse brain, and a temporal resolution (seconds – minutes) sufficient for capturing acute brain changes. Here we summarize the application of these methods to the functional brain mapping of behaviors involving locomotion of small animals, methods for the three dimensional reconstruction of the brain from autoradiographic sections, voxel based analysis of the whole brain, and generation of maps of the flattened rat cortex. Application of these methods in animal models promises utility in improving our understanding of motor function in the normal brain, and of the effects of neuropathology and treatment interventions such as exercise have on the reorganization of motor circuits. PMID:18554522

  20. 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.

  1. Real-time functional mapping: potential tool for improving language outcome in pediatric epilepsy surgery

    PubMed Central

    Korostenskaja, Milena; Chen, Po-Ching; Salinas, Christine M.; Westerveld, Michael; Brunner, Peter; Schalk, Gerwin; Cook, Jane C.; Baumgartner, James; Lee, Ki H.

    2015-01-01

    Accurate language localization expands surgical treatment options for epilepsy patients and reduces the risk of postsurgery language deficits. Electrical cortical stimulation mapping (ESM) is considered to be the clinical gold standard for language localization. While ESM affords clinically valuable results, it can be poorly tolerated by children, requires active participation and compliance, carries a risk of inducing seizures, is highly time consuming, and is labor intensive. Given these limitations, alternative and/or complementary functional localization methods such as analysis of electrocorticographic (ECoG) activity in high gamma frequency band in real time are needed to precisely identify eloquent cortex in children. In this case report, the authors examined 1) the use of real-time functional mapping (RTFM) for language localization in a high gamma frequency band derived from ECoG to guide surgery in an epileptic pediatric patient and 2) the relationship of RTFM mapping results to postsurgical language outcomes. The authors found that RTFM demonstrated relatively high sensitivity (75%) and high specificity (90%) when compared with ESM in a “next-neighbor” analysis. While overlapping with ESM in the superior temporal region, RTFM showed a few other areas of activation related to expressive language function, areas that were eventually resected during the surgery. The authors speculate that this resection may be associated with observed postsurgical expressive language deficits. With additional validation in more subjects, this finding would suggest that surgical planning and associated assessment of the risk/benefit ratio would benefit from information provided by RTFM mapping. PMID:24995815

  2. The lap-counting and zeta functions of the tent map

    NASA Astrophysics Data System (ADS)

    Flatto, Leopold; Lagarias, Jeffrey C.

    2000-07-01

    The tent map tβ:[0,1]→[0,1] with parameter 1 < β≤2 is defined by t_{\\beta }(x) = \\cases{\\beta x & $0 \\leq x \\leq \\case{1}{2}$\\\\ \\beta (1- x) & $\\case{1}{2} \\leq x \\leq 1$. } This paper derives formulae for its dynamical zeta and lap-counting <span class=functions which exhibit the renormalization structure of such maps. It relates these functions to the centrally symmetric linear mod 1 transformation f_ {\\beta }(x) = \\beta x + 1- \\case{1}{2} \\beta\\quad (\\mathop{\\rm mod} 1). The singularities of these functions on the circle |z| = 1/β are determined explicitly.

  3. 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

  4. Mutational interference mapping experiment (MIME) for studying RNA structure and function.

    PubMed

    Smyth, Redmond P; Despons, Laurence; Huili, Gong; Bernacchi, Serena; Hijnen, Marcel; Mak, Johnson; Jossinet, Fabrice; Weixi, Li; Paillart, Jean-Christophe; von Kleist, Max; Marquet, Roland

    2015-09-01

    RNA regulates many biological processes; however, identifying functional RNA sequences and structures is complex and time-consuming. We introduce a method, mutational interference mapping experiment (MIME), to identify, at single-nucleotide resolution, the primary sequence and secondary structures of an RNA molecule that are crucial for its function. MIME is based on random mutagenesis of the RNA target followed by functional selection and next-generation sequencing. Our analytical approach allows the recovery of quantitative binding parameters and permits the identification of base-pairing partners directly from the sequencing data. We used this method to map the binding site of the human immunodeficiency virus-1 (HIV-1) Pr55(Gag) protein on the viral genomic RNA in vitro, and showed that, by analyzing permitted base-pairing patterns, we could model RNA structure motifs that are crucial for protein binding. PMID:26237229

  5. Clinical Team Functioning and IT Innovation: A Study of the Diffusion of a Point-of-care Online Evidence System

    PubMed Central

    Gosling, A. Sophie; Westbrook, Johanna I.; Braithwaite, Jeffrey

    2003-01-01

    Objectives: To investigate the association between clinical team functioning and diffusion (awareness, use, and impact) of a 24-hour online evidence retrieval system. To examine the relationships between clinical team characteristics and the adoption of the online evidence system. Design: 18 clinical teams, consisting of 180 clinicians from three Australian hospitals, were identified and studied. Teams were categorized as small (≤ 15 members) or large (> 15). Measurements: Clinical team functioning was assessed using the Team Climate Inventory (TCI). Awareness, use, and impact of an online evidence retrieval system were measured using a self-administered questionnaire. The relationships between TCI scores and awareness, use, and impact were examined using t-tests and one-way ANOVAs. Chi square analyses were used to examine differences between small and large teams. Results were interpreted within a diffusion of innovations framework. Results: Clinical team functioning was not related to awareness or use of the online evidence retrieval system. However, clinical team functioning was significantly associated with the impact of online evidence in terms of reported experience of improved patient care following system use. Clinicians in small teams (≤ 15 members) had higher levels of system awareness compared to large (> 15) teams. Conclusions: Team functioning had the greatest impact on the fourth stage of innovation diffusion, the effective use of online evidence for clinical care. This supports Rogers’ diffusion of innovation theory, to the effect that different types of communication about an innovation are important at different stages in the diffusion process. Members of small teams were more aware of the system than members of large teams. Team functioning is amenable to improvement through interventions. The findings suggest that the role of team climate in the diffusion of information systems is a promising area for future research. PMID:12626379

  6. 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.

  7. DIFFUSIVE PARTICLE ACCELERATION IN SHOCKED, VISCOUS ACCRETION DISKS: GREEN'S FUNCTION ENERGY DISTRIBUTION

    SciTech Connect

    Becker, Peter A.; Das, Santabrata; Le, Truong E-mail: sbdas@iitg.ernet.in

    2011-12-10

    The acceleration of relativistic particles in a viscous accretion disk containing a standing shock is investigated as a possible explanation for the energetic outflows observed around radio-loud black holes. The energy/space distribution of the accelerated particles is computed by solving a transport equation that includes the effects of first-order Fermi acceleration, bulk advection, spatial diffusion, and particle escape. The velocity profile of the accreting gas is described using a model for shocked viscous disks recently developed by the authors, and the corresponding Green's function distribution for the accelerated particles in the disk and the outflow is obtained using a classical method based on eigenfunction analysis. The accretion-driven, diffusive shock acceleration scenario explored here is conceptually similar to the standard model for the acceleration of cosmic rays at supernova-driven shocks. However, in the disk application, the distribution of the accelerated particles is much harder than would be expected for a plane-parallel shock with the same compression ratio. Hence the disk environment plays a key role in enhancing the efficiency of the shock acceleration process. The presence of the shock helps to stabilize the disk by reducing the Bernoulli parameter, while channeling the excess binding energy into the escaping relativistic particles. In applications to M87 and Sgr A*, we find that the kinetic power in the jet is {approx}0.01 M-dot c{sup 2}, and the outflowing relativistic particles have a mean energy {approx}300 times larger than that of the thermal gas in the disk at the shock radius. Our results suggest that a standing shock may be an essential ingredient in accretion onto underfed black holes, helping to resolve the long-standing problem of the stability of advection-dominated accretion disks.

  8. RF-Based Location Using Interpolation Functions to Reduce Fingerprint Mapping.

    PubMed

    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

  9. 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

  10. 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.

  11. 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.

  12. Absorption and diffusion of hydrogen in palladium-silver alloys by density functional theory

    NASA Astrophysics Data System (ADS)

    Ke, Xuezhi; Kramer, Gert Jan

    2002-11-01

    The vibrational states, absorption energies, and diffusions of H in Pd and Pd1-xAgx(0<~x<~1) have been studied by first-principle calculations. All results compare favorably to experiment. The zero-point motion of H is important in the determination of the H site occupation, in the estimation of the diffusion barrier, and in the explanation of the reversed isotope effect. The interesting anomalous isotope effect is explored, and a diffusion mechanism is proposed for tritium. The preferred diffusion paths of H in Pd and Pd1-xAgx are “indirect” paths. According to the absorption energies and diffusion barriers, H diffusion in Pd-Ag alloys should avoid the Ag-rich areas.

  13. Functional organization of glomerular maps in the mouse accessory olfactory bulb

    PubMed Central

    Hammen, Gary F.; Turaga, Diwakar; Holy, Timothy E.; Meeks, Julian P.

    2014-01-01

    Summary The mammalian accessory olfactory system (AOS) extracts information about species, sex, and individual identity from social odors, but its functional organization remains unclear. We imaged presynaptic Ca2+ signals in vomeronasal inputs to the accessory olfactory bulb (AOB) during peripheral stimulation using light sheet microscopy. Urine- and steroid-responsive glomeruli densely innervated the anterior AOB. Glomerular activity maps for sexually mature female mouse urine overlapped maps for juvenile and/or gonadectomized urine of both sexes, whereas maps for sexually mature male urine were highly distinct. Further spatial analysis revealed a complicated organization involving selective juxtaposition and dispersal of functionally-grouped glomerular classes. Glomeruli that were similarly tuned to urines were often closely associated, whereas more disparately tuned glomeruli were selectively dispersed. Maps to a panel of sulfated steroid odorants identified tightly-juxtaposed groups that were disparately tuned and dispersed groups that were similarly tuned. These results reveal a modular, non-chemotopic spatial organization in the AOB. PMID:24880215

  14. Functional cluster analysis of CT perfusion maps: a new tool for diagnosis of acute stroke?

    PubMed

    Baumgartner, Christian; Gautsch, Kurt; Böhm, Christian; Felber, Stephan

    2005-09-01

    CT perfusion imaging constitutes an important contribution to the early diagnosis of acute stroke. Cerebral blood flow (CBF), cerebral blood volume (CBV) and time-to-peak (TTP) maps are used to estimate the severity of cerebral damage after acute ischemia. We introduce functional cluster analysis as a new tool to evaluate CT perfusion in order to identify normal brain, ischemic tissue and large vessels. CBF, CBV and TTP maps represent the basis for cluster analysis applying a partitioning (k-means) and density-based (density-based spatial clustering of applications with noise, DBSCAN) paradigm. In patients with transient ischemic attack and stroke, cluster analysis identified brain areas with distinct hemodynamic properties (gray and white matter) and segmented territorial ischemia. CBF, CBV and TTP values of each detected cluster were displayed. Our preliminary results indicate that functional cluster analysis of CT perfusion maps may become a helpful tool for the interpretation of perfusion maps and provide a rapid means for the segmentation of ischemic tissue. PMID:15827821

  15. 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.

  16. 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

  17. 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

  18. 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

  19. A functional PCA model for the study of time series of pressure maps.

    PubMed

    Chicote, Juan C; Durá, Juan V; Belda, Juan M; Poveda, Rakel

    2013-04-01

    Principal component analysis and functional regression are combined in a model to analyze a time series of pressure maps. The model is tested measuring the pressures over a chair seat while a subject performs a combination of simple movements. A sampling rate of 3 Hz is adequate for applying the model in sitting postures. The model is able to detect patterns of movement over time, although more variables are necessary if the movements produce similar pressure distributions. PMID:23645485

  20. Stimulation mapping of white matter tracts to study brain functional connectivity.

    PubMed

    Duffau, Hugues

    2015-05-01

    Despite advances in the new science of connectomics, which aims to comprehensively map neural connections at both structural and functional levels, techniques to directly study the function of white matter tracts in vivo in humans have proved elusive. Direct electrical stimulation (DES) mapping of the subcortical fibres offers a unique opportunity to investigate the functional connectivity of the brain. This original method permits real-time anatomo-functional correlations, especially with regard to neural pathways, in awake patients undergoing brain surgery. In this article, the goal is to review new insights, gained from axonal DES, into the functional connectivity underlying the sensorimotor, visuospatial, language and sociocognitive systems. Interactions between these neural networks and multimodal systems, such as working memory, attention, executive functions and consciousness, can also be investigated by axonal stimulation. In this networking model of conation and cognition, brain processing is not conceived as the sum of several subfunctions, but results from the integration and potentiation of parallel-though partially overlapping-subnetworks. This hodotopical account, supported by axonal DES, improves our understanding of neuroplasticity and its limitations. The clinical implications of this paradigmatic shift from localizationism to hodotopy, in the context of brain surgery, neurology, neurorehabilitation and psychiatry, are discussed. PMID:25848923

  1. 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

  2. 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

  3. Minkowski functionals used in the morphological analysis of cosmic microwave background anisotropy maps

    NASA Astrophysics Data System (ADS)

    Schmalzing, Jens; Gorski, Krzysztof M.

    1998-06-01

    We present a novel approach to quantifying the morphology of cosmic microwave background (CMB) anisotropy maps. As morphological descriptors, we use shape parameters known as Minkowski functionals. Using the mathematical framework provided by the theory of integral geometry on arbitrary curved supports, we point out the differences in their characterization and interpretation in the case of flat space. With the restrictions of real data - such as pixelization and incomplete sky coverage, to mention just a few - in mind, we derive and test unbiased estimators for all Minkowski functionals. Various examples, among them the analysis of the four-year COBE DMR data, illustrate the application of our method.

  4. Exact Green's function of the reversible diffusion-influenced reaction for an isolated pair in two dimensions

    NASA Astrophysics Data System (ADS)

    Prüstel, Thorsten; Meier-Schellersheim, Martin

    2012-08-01

    We derive an exact Green's function of the diffusion equation for a pair of disk-shaped interacting particles in two dimensions subject to a backreaction boundary condition. Furthermore, we use the obtained function to calculate exact expressions for the survival probability and the time-dependent rate coefficient for the initially unbound pair and the survival probability of the bound state. The derived expressions will be of particular utility for the description of reversible membrane-bound reactions in cell biology.

  5. Explicitly correlated wave functions for atoms and singly charged ions from Li through Sr: Variational and Diffusion Monte Carlo results

    NASA Astrophysics Data System (ADS)

    Buendía, E.; Gálvez, F. J.; Maldonado, P.; Sarsa, A.

    2014-11-01

    Total energies calculated from explicitly correlated wave functions for the ground state of the atoms Li to Sr and their singly charged anions and cations are obtained. Accurate all electron, non-relativistic Variational and Diffusion Monte Carlo energies are reported. The quality of the results, when comparing with exact estimations and experimental electron affinities and ionization potential is similar for all of the atoms studied. The parameterization of the explicitly correlated wave functions for all of the atomic systems studied is provided.

  6. Dynamic topographic mapping of the human bladder during voiding using functional near-infrared spectroscopy.

    PubMed

    Macnab, Andrew; Stothers, Lynn; Shadgan, Babak

    2009-01-01

    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 5x5-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 (O(2)Hb), 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 O(2)Hb; 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. PMID:19405712

  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. 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

  9. Rapid and low-invasive functional brain mapping by realtime visualization of high gamma activity for awake craniotomy.

    PubMed

    Kamada, K; Ogawa, H; Kapeller, C; Prueckl, R; Guger, C

    2014-01-01

    For neurosurgery with an awake craniotomy, the critical issue is to set aside enough time to identify eloquent cortices by electrocortical stimulation (ECS). High gamma activity (HGA) ranging between 80 and 120 Hz on electrocorticogram (ECoG) is assumed to reflect localized cortical processing. In this report, we used realtime HGA mapping and functional magnetic resonance imaging (fMRI) for rapid and reliable identification of motor and language functions. Three patients with intra-axial tumors in their dominant hemisphere underwent preoperative fMRI and lesion resection with an awake craniotomy. All patients showed significant fMRI activation evoked by motor and language tasks. After the craniotomy, we recorded ECoG activity by placing subdural grids directly on the exposed brain surface. Each patient performed motor and language tasks and demonstrated realtime HGA dynamics in hand motor areas and parts of the inferior frontal gyrus. Sensitivity and specificity of HGA mapping were 100% compared to ECS mapping in the frontal lobe, which suggested HGA mapping precisely indicated eloquent cortices. The investigation times of HGA mapping was significantly shorter than that of ECS mapping. Specificities of the motor and language-fMRI, however, did not reach 85%. The results of HGA mapping was mostly consistent with those of ECS mapping, although fMRI tended to overestimate functional areas. This novel technique enables rapid and accurate functional mapping. PMID:25571558

  10. Spatiotemporal Dynamics of a Diffusive Leslie-Gower Predator-Prey Model with Ratio-Dependent Functional Response

    NASA Astrophysics Data System (ADS)

    Shi, Hong-Bo; Ruan, Shigui; Su, Ying; Zhang, Jia-Fang

    This paper is devoted to the study of spatiotemporal dynamics of a diffusive Leslie-Gower predator-prey system with ratio-dependent Holling type III functional response under homogeneous Neumann boundary conditions. It is shown that the model exhibits spatial patterns via Turing (diffusion-driven) instability and temporal patterns via Hopf bifurcation. Moreover, the existence of spatiotemporal patterns is established via Turing-Hopf bifurcation at the degenerate points where the Turing instability curve and the Hopf bifurcation curve intersect. Various numerical simulations are also presented to illustrate the theoretical results.

  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. Mapping the current-current correlation function near a quantum critical point

    NASA Astrophysics Data System (ADS)

    Prodan, Emil; Bellissard, Jean

    2016-05-01

    The current-current correlation function is a useful concept in the theory of electron transport in homogeneous solids. The finite-temperature conductivity tensor as well as Anderson's localization length can be computed entirely from this correlation function. Based on the critical behavior of these two physical quantities near the plateau-insulator or plateau-plateau transitions in the integer quantum Hall effect, we derive an asymptotic formula for the current-current correlation function, which enables us to make several theoretical predictions about its generic behavior. For the disordered Hofstadter model, we employ numerical simulations to map the current-current correlation function, obtain its asymptotic form near a critical point and confirm the theoretical predictions.

  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. PMID:27139656

  14. Brownian motion in a rotating fluid: Diffusivity is a function of the rotation rate

    NASA Astrophysics Data System (ADS)

    Ryskin, Gregory

    1988-09-01

    The phenomenological relations between thermodynamic fluxes and forces are normally assumed to be invariant with respect to arbitrary motion of the frame of reference. We describe a breakdown of this invariance strong enough to be observable. It is shown that the diffusivity in a rotating fluid is anisotropic and also smaller in magnitude than in a fluid at rest in an inertial frame, giving rise to a diffusion analog of the Hall effect. For large Brownian particles (e.g., biological macromolecules) the diffusivity may decrease by 50% at the rotation speeds achievable in ultracentrifuges.

  15. Comprehensive language mapping in children, using functional magnetic resonance imaging: what's missing counts.

    PubMed

    Wilke, Marko; Lidzba, Karen; Staudt, Martin; Buchenau, Karin; Grodd, Wolfgang; Krägeloh-Mann, Ingeborg

    2005-06-21

    Noninvasive language mapping is a frequently used application of functional magnetic resonance imaging. The examination of children, however, poses both practical and technical challenges. To this effect, we have developed two new paradigms mainly requiring passive listening to stories from which several key words were removed. Results were compared with a standard active verb-generation task, particularly with regard to hemispheric dominance in frontal brain areas. Fifteen healthy children (seven boys, eight girls, 6-14 years) were scanned. Distinct frontal activation was seen in our new tasks, which was stronger when the tasks were analyzed specifically with regard to the missing words. This confirms the hypothesis that the removal of these words is the key in inducing frontal activation. Frontal lateralization was consistent and strong in all three paradigms. Additionally, receptive language areas are also mapped by our new tasks. We conclude that our two new, child-friendly functional magnetic resonance imaging paradigms are useful in determining hemispheric dominance for language in children too young or too impaired to execute an active task. They also allow robust mapping of receptive language areas. PMID:15931061

  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. An improved simulation of the deep Pacific Ocean using optimally estimated vertical diffusivity based on the Green's function method

    NASA Astrophysics Data System (ADS)

    Toyoda, Takahiro; Sugiura, Nozomi; Masuda, Shuhei; Sasaki, Yuji; Igarashi, Hiromichi; Ishikawa, Yoichi; Hatayama, Takaki; Kawano, Takeshi; Kawai, Yoshimi; Kouketsu, Shinya; Katsumata, Katsuro; Uchida, Hiroshi; Doi, Toshimasa; Fukasawa, Masao; Awaji, Toshiyuki

    2015-11-01

    An improved vertical diffusivity scheme is introduced into an ocean general circulation model to better reproduce the observed features of water property distribution inherent in the deep Pacific Ocean structure. The scheme incorporates (a) a horizontally uniform background profile, (b) a parameterization depending on the local static stability, and (c) a parameterization depending on the bottom topography. Weighting factors for these parameterizations are optimally estimated based on the Green's function method. The optimized values indicate an important role of both the intense vertical diffusivity near rough topography and the background vertical diffusivity. This is consistent with recent reports that indicate the presence of significant vertical mixing associated with finite-amplitude internal wave breaking along the bottom slope and its remote effect. The robust simulation with less artificial trend of water properties in the deep Pacific Ocean illustrates that our approach offers a better modeling analysis for the deep ocean variability.

  19. 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.

  20. 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. PMID:24849348

  1. Intraoperative mapping during repeat awake craniotomy reveals the functional plasticity of adult cortex.

    PubMed

    Southwell, Derek G; Hervey-Jumper, Shawn L; Perry, David W; Berger, Mitchel S

    2016-05-01

    OBJECT To avoid iatrogenic injury during the removal of intrinsic cerebral neoplasms such as gliomas, direct electrical stimulation (DES) is used to identify cortical and subcortical white matter pathways critical for language, motor, and sensory function. When a patient undergoes more than 1 brain tumor resection as in the case of tumor recurrence, the use of DES provides an unusual opportunity to examine brain plasticity in the setting of neurological disease. METHODS The authors examined 561 consecutive cases in which patients underwent DES mapping during surgery forglioma resection. "Positive" and "negative" sites-discrete cortical regions where electrical stimulation did (positive) or did not (negative) produce transient sensory, motor, or language disturbance-were identified prior to tumor resection and documented by intraoperative photography for categorization into functional maps. In this group of 561 patients, 18 were identified who underwent repeat surgery in which 1 or more stimulation sites overlapped with those tested during the initial surgery. The authors compared intraoperative sensory, motor, or language mapping results between initial and repeat surgeries, and evaluated the clinical outcomes for these patients. RESULTS A total of 117 sites were tested for sensory (7 sites, 6.0%), motor (9 sites, 7.7%), or language (101 sites, 86.3%) function during both initial and repeat surgeries. The mean interval between surgical procedures was 4.1 years. During initial surgeries, 95 (81.2%) of 117 sites were found to be negative and 22 (18.8%) of 117 sites were found to be positive. During repeat surgeries, 103 (88.0%) of 117 sites were negative and 14 (12.0%) of 117 were positive. Of the 95 sites that were negative at the initial surgery, 94 (98.9%) were also negative at the repeat surgery, while 1 (1.1%) site was found to be positive. Of the 22 sites that were initially positive, 13 (59.1%) remained positive at repeat surgery, while 9 (40.9%) had become

  2. High resolution Moho topography map beneath Iberia and Northern Morocco from receiver function analysis

    NASA Astrophysics Data System (ADS)

    Mancilla, Flor de Lis; Diaz, Jordi

    2015-11-01

    Crustal thickness maps at regional scales are typically compiled using estimations inferred from different geophysical datasets providing a variable coverage of the investigated area. Consequently, spurious effects related to changes in data resolution or artifacts in grid interpolation may affect significant zones of those maps. The TopoIberia-IberArray broad-band seismic network, covering the Iberian Peninsula and Northern Morocco with stations distributed on a regular 60 × 60 km grid provides a unique opportunity to avoid such technical problems and to obtain a crustal thickness map derived from a same method sampling evenly all the region. Data from more than 340 stations has been gathered and analyzed using the P-to-S conversion phases at the Moho discontinuity (receiver functions). The crustal thickness has been inferred applying the classical H-κ stacking technique, though in regions of complex crustal structure, we have preferred to estimate the thickness directly from the arrival time of the converted phase at some sites. The topography of the Moho discontinuity is strongly correlated with tectonic processes. The investigated area, extending from the Sahara platform to the Bay of Biscay, has a great geodynamic diversity, including, North to South, crustal imbrication in the Pyrenean and Cantabrian range, a large and relatively undisturbed Variscan Massif in the center of Iberia and areas of complex and still not completely understood geodynamics in the Alboran crust domain and the Atlas range. The crustal thickness map reflects this diversity, showing variations reaching 30 km between the thickest and thinnest zones of continental crust. The final map has an overall similarity with previous estimations of the crustal thickness using independent data, as those coming from more sparse deep seismic sounding profiles, but provides further constraints at regional scale.

  3. 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

  4. [Interest of EEG recording during direct electrical stimulation for brain mapping function in surgery].

    PubMed

    Trebuchon, A; Guye, M; Tcherniack, V; Tramoni, E; Bruder, N; Metellus, P

    2012-06-01

    Brain tumor surgery is at risk when lesions are located in eloquent areas. The interindividual anatomo-functional variability of the central nervous system implies that brain surgery within eloquent regions may induce neurological sequelae. Brain mapping using intraoperative direct electrical stimulation in awake patients has been for long validated as the standard for functional brain mapping. Direct electrical stimulation inducing a local transient electrical and functional disorganization is considered positive if the task performed by the patient is disturbed. The brain area stimulated is then considered as essential for the function tested. However, the exactitude of the information provided by this technique is cautious because the actual impact of cortical direct electrical stimulation is not known. Indeed, the possibility of false negative (insufficient intensity of the stimulation due to the heterogeneity of excitability threshold of different cortical areas) or false positive (current spread, interregional signal propagation responsible for remote effects, which make difficult the interpretation of positive or negative behavioural effects) constitute a limitation of this technique. To improve the sensitivity and specificity of this technique, we used an electrocorticographic recording system allowing a real time visualization of the local. We provide here evidence that direct cortical stimulation combined with electrocorticographic recording could be useful to detect remote after discharge and to adjust stimulation parameters. In addition this technique offers new perspective to better assess connectivity of cerebral networks. PMID:22683402

  5. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.

    PubMed

    Jin, Jinpu; He, Kun; Tang, Xing; Li, Zhe; Lv, Le; Zhao, Yi; Luo, Jingchu; Gao, Ge

    2015-07-01

    Transcription factors (TFs) play key roles in both development and stress responses. By integrating into and rewiring original systems, novel TFs contribute significantly to the evolution of transcriptional regulatory networks. Here, we report a high-confidence transcriptional regulatory map covering 388 TFs from 47 families in Arabidopsis. Systematic analysis of this map revealed the architectural heterogeneity of developmental and stress response subnetworks and identified three types of novel network motifs that are absent from unicellular organisms and essential for multicellular development. Moreover, TFs of novel families that emerged during plant landing present higher binding specificities and are preferentially wired into developmental processes and these novel network motifs. Further unveiled connection between the binding specificity and wiring preference of TFs explains the wiring preferences of novel-family TFs. These results reveal distinct functional and evolutionary features of novel TFs, suggesting a plausible mechanism for their contribution to the evolution of multicellular organisms. PMID:25750178

  6. 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.

  7. 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.

  8. 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)

  9. 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

  10. Combining Diffusion Tensor Imaging and Gray Matter Volumetry to Investigate Motor Functioning in Chronic Stroke

    PubMed Central

    Yang, Ming; Yang, Ya-ru; Li, Hui-jun; Lu, Xue-song; Shi, Yong-mei; Liu, Bin; Chen, Hua-jun; Teng, Gao-jun; Chen, Rong; Herskovits, Edward H.

    2015-01-01

    Motor impairment after stroke is related to the integrity of the corticospinal tract (CST). However, considerable variability in motor impairment remains unexplained. To increase the accuracy in evaluating long-term motor function after ischemic stroke, we tested the hypothesis that combining diffusion tensor imaging (DTI) and gray matter (GM) volumetry can better characterize long-term motor deficit than either method alone in patients with chronic stroke. We recruited 31 patients whose Medical Research Council strength grade was ≤ 3/5 in the extensor muscles of the affected upper extremity in the acute phase. We used the Upper Extremity Fugl-Meyer (UE-FM) assessment to evaluate motor impairment, and as the primary outcome variable. We computed the fractional anisotropy ratio of the entire CST (CSTratio) and the volume of interest ratio (VOIratio), between ipsilesional and contralesional hemispheres, to explain long-term motor impairment. The results showed that CSTratio, VOIratio of motor-related brain regions, and VOIratio in the temporal lobe were correlated with UE-FM. A multiple regression model including CSTratio and VOIratio of the caudate nucleus explained 40.7% of the variability in UE-FM. The adjusted R2 of the regression model with CSTratio as an independent variable was 29.4%, and that of using VOIratio of the caudate nucleus as an independent variable was 23.1%. These results suggest that combining DTI and GM volumetry may achieve better explanation of long-term motor deficit in stroke patients, than using either measure individually. This finding may provide guidance in determining optimal neurorehabilitative interventions. PMID:25965398

  11. 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

  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. 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

  14. 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

  15. 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.

  16. 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.…

  17. Effects of a Story Map on Accelerated Reader Postreading Test Scores in Students with High-Functioning Autism

    ERIC Educational Resources Information Center

    Stringfield, Suzanne Griggs; Luscre, Deanna; Gast, David L.

    2011-01-01

    In this study, three elementary-aged boys with high-functioning autism (HFA) were taught to use a graphic organizer called a Story Map as a postreading tool during language arts instruction. Students learned to accurately complete the Story Map. The effect of the intervention on story recall was assessed within the context of a multiple-baseline…

  18. 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

  19. 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

  20. In-depth mapping of human testicular and epididymal proteins and their functional association with spermatozoa

    PubMed Central

    LIU, XUEXIA; LIU, FUJUN

    2015-01-01

    The mammalian testis and epididymis are responsible for spermatozoa production and maturation, which contributes to male fertility. Predominantly expressed proteins in the testis and epididymis were suggested to be involved in the key functions or pathways in spermatogenesis and sperm maturation. To further investigate these proteins and their associations with sperm, large protein profiles of human testis and epididymis were mapped. Predominantly-expressed testicular (173) and epididymal (244) secreted proteins were further screened and functionally characterized. Differential expression levels of solute carrier family 2 (facilitated glucose transporter), member 3, solute carrier family 25 (carnitine/acylcarnitine translocase), member 20, WAP-type four-disulfide core domain protein 8 and prostate and testis expressed 1 were validated using western blot and immunohistochemical analyses. The results may provide novel insight into the understanding of testicular and epididymal physiology and function, and facilitate sperm maturation research. PMID:25760095

  1. 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

  2. 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'. PMID:26448908

  3. 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.

  4. The impact of functional connectivity changes on support vector machines mapping of fMRI data.

    PubMed

    Sato, João Ricardo; Mourão-Miranda, Janaina; Morais Martin, Maria da Graça; Amaro, Edson; Morettin, Pedro Alberto; Brammer, Michael John

    2008-07-15

    Functional magnetic resonance imaging (fMRI) is currently one of the most widely used methods for studying human brain function in vivo. Although many different approaches to fMRI analysis are available, the most widely used methods employ so called "mass-univariate" modeling of responses in a voxel-by-voxel fashion to construct activation maps. However, it is well known that many brain processes involve networks of interacting regions and for this reason multivariate analyses might seem to be attractive alternatives to univariate approaches. The current paper focuses on one multivariate application of statistical learning theory: the statistical discrimination maps (SDM) based on support vector machine, and seeks to establish some possible interpretations when the results differ from univariate approaches. In fact, when there are changes not only on the activation level of two conditions but also on functional connectivity, SDM seems more informative. We addressed this question using both simulations and applications to real data. We have shown that the combined use of univariate approaches and SDM yields significant new insights into brain activations not available using univariate methods alone. In the application to a visual working memory fMRI data, we demonstrated that the interaction among brain regions play a role in SDM's power to detect discriminative voxels. PMID:18499266

  5. 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

  6. 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).

  7. Effect of yoga regimen on lung functions including diffusion capacity in coronary artery disease patients: A randomized controlled study

    PubMed Central

    Yadav, Asha; Singh, Savita; Singh, KP; Pai, Preeti

    2015-01-01

    Background: Lung functions are found to be impaired in coronary artery disease (CAD), congestive heart failure, left ventricular dysfunction, and after cardiac surgery. Diffusion capacity progressively worsens as the severity of CAD increases due to reduction in lung tissue participating in gas exchange. Aims and Objectives: Pranayama breathing exercises and yogic postures may play an impressive role in improving cardio-respiratory efficiency and facilitating gas diffusion at the alveolo-capillary membrane. This study was done to see the effect of yoga regimen on lung functions particularly diffusion capacity in CAD patients. Materials and Methods: A total of 80 stable CAD patients below 65 years of age of both sexes were selected and randomized into two groups of 40 each. Group I CAD patients were given yoga regimen for 3 months which consisted of yogic postures, pranayama breathing exercises, dietary modification, and holistic teaching along with their conventional medicine while Group II CAD patients were put only on conventional medicine. Lung functions including diffusion capacity were recorded thrice in both the groups: 0 day as baseline, 22nd day and on 90th day by using computerized MS medisoft Cardio-respiratory Instrument, HYP’AIR Compact model of cardio-respiratory testing machine was manufactured by P K Morgan, India. The recorded parameters were statistically analyzed by repeated measures ANOVA followed by Tukey's test in both the groups. Cardiovascular parameters were also compared before and after intervention in both the groups. Results: Statistically significant improvements were seen in slow vital capacity, forced vital capacity, peak expiratory flow rate, maximum voluntary ventilation, and diffusion factor/ transfer factor of lung for carbon monoxide after 3 months of yoga regimen in Group I. Forced expiratory volume in 1st sec (FEV1), and FEV1 % also showed a trend toward improvement although not statistically significant. HR, SBP and DBP also

  8. 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

  9. 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

  10. 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

  11. 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.

  12. Instantaneous, parallel mapping of protein electronic function with angle-resolved coherent wave-mixing

    NASA Astrophysics Data System (ADS)

    Mercer, Ian

    2010-03-01

    We present a novel laser method, angle-resolved coherent (ARC) wave-mixing, that separates out coherent electronic couplings from energy transfers in an instantaneous two-dimensional mapping (Ian P. Mercer et.al., Phys. Rev. Lett. 102, 57402, 2009). For this we use an ultra-broadband hollow fibre laser source. The power of the new method is demonstrated with the light harvesting complex II (LH2) of purple bacteria at ambient temperature. We observe signaturs of a coherent quantum electronic beating, a correlation between excitation and emission energies in the protein and a coherent component to the energy transfer between molecular rings. We are interested in exploring avenues for high throughput fingerprinting of molecular structure and function. Massively parallel maps, rich in detail, can be taken from solutions, surface films or solids of between 1 and 1000 microL. Each ARC map is generated instantaneously, with high throughput (currently up to 1kHz frame rate) and is noninvasive.

  13. Glial and neuronal Semaphorin signaling instruct the development of a functional myotopic map for Drosophila walking.

    PubMed

    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. PMID:26926907

  14. 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

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. Diffuse reflectance spectroscopic mapping imaging applied to art objects materials determination from 200 up to 5000 nm

    NASA Astrophysics Data System (ADS)

    Karagiannis, G.; Alexiadis, D.; Damtsios, A.; Sergiadis, G.; Salpistis, C.

    2010-11-01

    The microsampling destructions caused by the sampling of analytical spectroscopic methods are generally not permitted to art objects. Consequently, the development of nondestructive analysis techniques is a necessity. In this work we present a set of signal processing and artificial intelligence techniques which support the operation of a novel device developed for the nondestructive identification of art objects. The proposed device combines ultraviolet, visible, near infrared, and midinfrared spectroscopy in diffuse reflectance mode to identify the materials that exist in each paint layer of an artwork.

  20. 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

  1. 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

    2016-01-01

    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 func-tion is toggled in the program preferences of the software (though turned on by default upon installation), and automatically increases the dose difference toler-ance 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 func-tion, then, may

  2. 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

  3. BrainKnowledge: a human brain function mapping knowledge-base system.

    PubMed

    Hsiao, Mei-Yu; Chen, Chien-Chung; Chen, Jyh-Horng

    2011-03-01

    Associating fMRI image datasets with the available literature is crucial for the analysis and interpretation of fMRI data. Here, we present a human brain function mapping knowledge-base system (BrainKnowledge) that associates fMRI data analysis and literature search functions. BrainKnowledge not only contains indexed literature, but also provides the ability to compare experimental data with those derived from the literature. BrainKnowledge provides three major functions: (1) to search for brain activation models by selecting a particular brain function; (2) to query functions by brain structure; (3) to compare the fMRI data with data extracted from the literature. All these functions are based on our literature extraction and mining module developed earlier (Hsiao, Chen, Chen. Journal of Biomedical Informatics 42, 912-922, 2009), which automatically downloads and extracts information from a vast amount of fMRI literature and generates co-occurrence models and brain association patterns to illustrate the relevance of brain structures and functions. BrainKnowledge currently provides three co-occurrence models: (1) a structure-to-function co-occurrence model; (2) a function-to-structure co-occurrence model; and (3) a brain structure co-occurrence model. Each model has been generated from over 15,000 extracted Medline abstracts. In this study, we illustrate the capabilities of BrainKnowledge and provide an application example with the studies of affect. BrainKnowledge, which combines fMRI experimental results with Medline abstracts, may be of great assistance to scientists not only by freeing up resources and valuable time, but also by providing a powerful tool that collects and organizes over ten thousand abstracts into readily usable and relevant sources of information for researchers. PMID:20857233

  4. Statistical mapping of functional olfactory connections of the rat brain in vivo.

    PubMed

    Cross, Donna J; Minoshima, Satoshi; Anzai, Yoshimi; Flexman, Jennifer A; Keogh, Bartholomew P; Kim, Yongmin; Maravilla, Kenneth R

    2004-12-01

    The olfactory pathway is a unique route into the brain. To better characterize this system in vivo, rat olfactory functional connections were mapped using magnetic resonance (MR) imaging and manganese ion (Mn2+) as a transport-mediated tracer combined with newly developed statistical brain image analysis. Six rats underwent imaging on a 1.5-T MR scanner at pre-administration, and 6, 12, 24, 36, 48, and 72 h and 5.5, 7.5, 10.5, and 13.5 days post-administration of manganese chloride (MnCl2) into the right nasal cavity. Images were coregistered, pixel-intensity normalized, and stereotactically transformed to the Paxinos and Watson rat brain atlas, then averaged across subjects using automated image analysis software (NEUROSTAT). Images at each time point were compared to pre-administration using a one-sample t statistic on a pixel-by-pixel basis in 3-D and converted to Z statistic maps. Statistical mapping and group averaging improved signal to noise ratios and signal detection sensitivity. Significant transport of Mn2+ was observed in olfactory structures ipsilateral to site of Mn2+ administration including the bulb, lateral olfactory tract (lo) by 12 h and in the tubercle, piriform cortex, ventral pallidum, amygdala, and in smaller structures such as the anterior commissure after 24 h post-administration. MR imaging with group-wise statistical analysis clearly demonstrated bilateral transsynaptic Mn2+ transport to secondary and tertiary neurons of the olfactory system. The method permits in vivo investigations of functional neuronal connections within the brain. PMID:15589097

  5. 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

  6. Functional magnetic resonance imaging of category-specific cortical activation: evidence for semantic maps.

    PubMed

    Spitzer, M; Kischka, U; Gückel, F; Bellemann, M E; Kammer, T; Seyyedi, S; Weisbrod, M; Schwartz, A; Brix, G

    1998-04-01

    Functional magnetic resonance imaging (fMRI) was used to examine the pattern of cortical activity during a picture naming task. Subjects (n=12) had to covertly name either animals or furniture items. Functional scanning was performed using a conventional 1.5-Tesla whole-body MRI system. Images obtained during naming the two categories were compared using a non-parametric test. The study revealed evidence for domain-specific lexical regions in left middle, right middle and inferior frontal areas, as well as in superior and middle temporal areas. The results corroborate neuropsychological data and demonstrate directly and non-invasively in human volunteers that semantic representations in frontal and temporal areas are, to some degree, localized and possibly implemented as multiple maps. A completely distributed storage of semantic information is rendered unlikely. PMID:9593960

  7. Mapping of functional activity in brain with /sup 18/F-fluoro-deoxyglucose

    SciTech Connect

    Alavi, A.; Reivich, M.; Greenberg, J.; Hand, P.; Rosenquist, A.; Rintelmann, W.; Christman, D.; Fowler, J.; Goldman, A.; MacGregor, R.; Wolf, A.

    1981-01-01

    The efficacy of using the /sup 18/F-fluoro-deoxyglucose (/sup 18/F-DG) for measuring regional cerebral glucose utilization in man during functional activation is demonstrated. Normal male volunteers subjected to sensory stimuli (visual, auditory, tactile) exhibited focal increases in glucose metabolism in response to the stimulus. Unilateral visual hemifield stimulation caused the contralateral striate cortex to become more active metabolically than the striate cortex ipsilateral to the stimulated hemifield. Similarly, stroking of the fingers and hand of one arm with a brush produced an increase in metabolism in the contralateral postcentral gyrus compared to the homologous ipsilateral region. The auditory stimulus, which consisted of monaural listening to either a meaningful or nonmeaningful story, caused an increase in glucose metabolism in the right temporal cortex independent of which ear was stimulated. These results demonstrate that the /sup 18/F-DG technique is capable of providing functional maps in vivo in the human brain.

  8. 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.

  9. Quantitative full-colour transmitted light microscopy and dyes for concentration mapping and measurement of diffusion coefficients in microfluidic architectures.

    PubMed

    Werts, Martinus H V; Raimbault, Vincent; Texier-Picard, Rozenn; Poizat, Rémi; Français, Olivier; Griscom, Laurent; Navarro, Julien R G

    2012-02-21

    A simple and versatile methodology has been developed for the simultaneous measurement of multiple concentration profiles of colourants in transparent microfluidic systems, using a conventional transmitted light microscope, a digital colour (RGB) camera and numerical image processing combined with multicomponent analysis. Rigorous application of the Beer-Lambert law would require monochromatic probe conditions, but in spite of the broad spectral bandwidths of the three colour channels of the camera, a linear relation between the measured optical density and dye concentration is established under certain conditions. An optimised collection of dye solutions for the quantitative optical microscopic characterisation of microfluidic devices is proposed. Using the methodology for optical concentration measurement we then implement and validate a simplified and robust method for the microfluidic measurement of diffusion coefficients using an H-filter architecture. It consists of measuring the ratio of the concentrations of the two output channels of the H-filter. It enables facile determination of the diffusion coefficient, even for non-fluorescent molecules and nanoparticles, and is compatible with non-optical detection of the analyte. PMID:22228225

  10. 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

  11. Mapping dynamical properties of cortical microcircuits using robotized TMS and EEG: Towards functional cytoarchitectonics.

    PubMed

    Harquel, Sylvain; Bacle, Thibault; Beynel, Lysianne; Marendaz, Christian; Chauvin, Alan; David, Olivier

    2016-07-15

    Brain dynamics at rest depend on the large-scale interactions between oscillating cortical microcircuits arranged into macrocolumns. Cytoarchitectonic studies have shown that the structure of those microcircuits differs between cortical regions, but very little is known about interregional differences of their intrinsic dynamics at a macro-scale in human. We developed here a new method aiming at mapping the dynamical properties of cortical microcircuits non-invasively using the coupling between robotized transcranial magnetic stimulation and electroencephalography. We recorded the responses evoked by the stimulation of 18 cortical targets largely covering the accessible neocortex in 22 healthy volunteers. Specific data processing methods were developed to map the local source activity of each cortical target, which showed inter-regional differences with very good interhemispheric reproducibility. Functional signatures of cortical microcircuits were further studied using spatio-temporal decomposition of local source activities in order to highlight principal brain modes. The identified brain modes revealed that cortical areas with similar intrinsic dynamical properties could be distributed either locally or not, with a spatial signature that was somewhat reminiscent of resting state networks. Our results provide the proof of concept of "functional cytoarchitectonics", that would guide the parcellation of the human cortex using not only its cytoarchitecture but also its intrinsic responses to local perturbations. This opens new avenues for brain modelling and physiopathology readouts. PMID:27153976

  12. Photoreflectance characterization of functionally graded materials. Application to diffusion process analysis

    NASA Astrophysics Data System (ADS)

    Jumel, J.; Rochais, D.; Lepoutre, F.

    2005-06-01

    Samples made of two slabs respectively of Cu and Zn are heat treated to create concentration gradient, and consequently a thermal properties gradient. Photoreflectance microscopy is used to image these samples with a microscopic resolution. The observed thermal contrast is used to evaluate the distribution of thermal diffusivity.

  13. 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

  14. 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

  15. Density Functional Theory Investigation of Proton Diffusion in Tungsten Oxide And Its Hydrates

    NASA Astrophysics Data System (ADS)

    Lin, Hao

    Fast proton conduction mechanism is of key importance for achieving high performance in fuel cell membranes, batteries, supercapacitors, and electrochromic materials. Enhanced proton diffusion is often observed in hydrated materials where it is thought to occur via the famous Grotthuss mechanism through pathways formed by structural water. Using first-principles calculations, we demonstrate that proton diffusion in tungsten oxide dihydrate (WO3·2H 2O), a known good proton conductor, takes place within the layers of corner-sharing WO6 octahedra without direct involvement of structural water. The calculated proton migration barrier in WO3·2H 2O is in good agreement with the experimental value inferred from the temperature dependence of conductivity. The preferred proton diffusion path in WO3·2H2O is essentially the same as in gamma-WO 3. In contrast to the small intercalation voltages calculated for WO 3 and WO3·2H2O, we find that proton absorption in the monohydrate WO3·H2O is energetically highly favorable. However, strong proton-proton repulsion limits the equilibrium H content at zero voltage. We find a fast one-dimensional diffusion channel in WO3·H2O at dilute proton concentrations, but much higher barriers are expected at near-equilibrium concentrations due to strong repulsive interactions with other protons. Our results illustrate that low proton diffusion barriers and low insertion voltages both contribute to fast proton transport in bulk WO3·2H2O and gamma-WO 3.

  16. 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

  17. Functional Nature of Electrogram Fractionation Demonstrated by Left Atrial High Density Mapping

    PubMed Central

    Jadidi, Amir S.; Duncan, Edward; Miyazaki, Shinsuke; Lellouche, Nicolas; Shah, Ashok J.; Forclaz, Andrei; Nault, Isabelle; Wright, Matthew; Rivard, Lena; Liu, Xingpeng; Scherr, Daniel; Wilton, Stephen; Sacher, Frédéric; Derval, Nicolas; Knecht, Sebastien; Kim, Steven J.; Hocini, Mélèze; Narayan, Sanjiv; Haïssaguerre, Michel; Jaïs, Pierre

    2012-01-01

    Background Complex fractionated electrograms (CFAE) are targets of atrial fibrillation (AF) ablation. Serial high density maps were evaluated to understand the impact of activation direction and rate on electrogram (EGM) fractionation. Methods and Results 18 patients (9 persistent) underwent high density, 3D, left atrial mapping (>400 points/map) during AF, Sinus (SR) and CS-paced (CSp) rhythms. In SR and CSp, fractionation was defined as EGM with ≥4 deflections, while in AF CFEmean <80ms was considered as continuous CFAE. The anatomic distribution of CFAE sites was assessed, quantified and correlated between rhythms. Mechanisms underlying fractionation were investigated by analysis of voltage, activation and propagation maps. A minority of continuous CFAE sites displayed EGM fractionation in SR (15+/−4%) and CSp (12+/(12+/−8%). EGM fractionation did not match between SR and CSp at 70+/−10% sites. Activation maps in SR and CSp showed that wave collision (71%) and regional slow conduction (24%) caused EGM fractionation. EGM voltage during AF (0.59+/−0.58mV) was lower than during SR and CSp (>1.0mV) at all sites. During AF, the EGM voltage was higher at continuous CFAE sites than at non-CFAE sites (0.53mV (Q1, Q3: 0.33–0.83) vs. 0.30 mV (Q1, Q3: 0.18–0.515), p<0.00001). Global LA voltage in AF was lower in persistent vs. paroxysmal AF patients (0.6+/−0.59mV vs. 1.12+/−1.32mV, p<0.01). Conclusions The distribution of fractionated EGMs is highly variable, depending on direction and rate of activation (SR vs. CSp vs. AF). Fractionation in sinus and CSp rhythms mostly resulted from wave collision. All sites with continuous fractionation in AF displayed normal voltage in SR suggesting absence of structural scar. Thus, many fractionated EGMs are functional in nature and their sites dynamic. PMID:22215849

  18. What, if anything, are topological maps for?

    PubMed

    Wilson, Stuart P; Bednar, James A

    2015-06-01

    What, if anything, is the functional significance of spatial patterning in cortical feature maps? We ask this question of four major theories of cortical map formation: self-organizing maps, wiring optimization, place coding, and reaction-diffusion. We argue that (i) self-organizing maps yield spatial patterning only as a by-product of efficient mechanisms for developing environmentally appropriate distributions of feature preferences, (ii) wiring optimization assumes rather than explains a map-like organization, (iii) place-coding mechanisms can at best explain only a subset of maps in functional terms, and (iv) reaction-diffusion models suggest two factors in the evolution of maps, the first based on efficient development of feature distributions, and the second based on generating feature-specific long-range recurrent cortical circuitry. None of these explanations for the existence of topological maps requires spatial patterning in maps to be useful. Thus despite these useful frameworks for understanding how maps form and how they are wired, the possibility that patterns are merely epiphenomena in the evolution of mammalian neocortex cannot be rejected. The article is intended as a nontechnical introduction to the assumptions and predictions of these four important classes of models, along with other possible functional explanations for maps. PMID:25683193

  19. 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

  20. 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

  1. Multi-scale functional mapping of tidal marsh vegetation for restoration monitoring

    NASA Astrophysics Data System (ADS)

    Tuxen Bettman, Karin

    2007-12-01

    Nearly half of the world's natural wetlands have been destroyed or degraded, and in recent years, there have been significant endeavors to restore wetland habitat throughout the world. Detailed mapping of restoring wetlands can offer valuable information about changes in vegetation and geomorphology, which can inform the restoration process and ultimately help to improve chances of restoration success. I studied six tidal marshes in the San Francisco Estuary, CA, US, between 2003 and 2004 in order to develop techniques for mapping tidal marshes at multiple scales by incorporating specific restoration objectives for improved longer term monitoring. I explored a "pixel-based" remote sensing image analysis method for mapping vegetation in restored and natural tidal marshes, describing the benefits and limitations of this type of approach (Chapter 2). I also performed a multi-scale analysis of vegetation pattern metrics for a recently restored tidal marsh in order to target the metrics that are consistent across scales and will be robust measures of marsh vegetation change (Chapter 3). Finally, I performed an "object-based" image analysis using the same remotely sensed imagery, which maps vegetation type and specific wetland functions at multiple scales (Chapter 4). The combined results of my work highlight important trends and management implications for monitoring wetland restoration using remote sensing, and will better enable restoration ecologists to use remote sensing for tidal marsh monitoring. Several findings important for tidal marsh restoration monitoring were made. Overall results showed that pixel-based methods are effective at quantifying landscape changes in composition and diversity in recently restored marshes, but are limited in their use for quantifying smaller, more fine-scale changes. While pattern metrics can highlight small but important changes in vegetation composition and configuration across years, scientists should exercise caution when

  2. 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

  3. 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

  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. NOTCH1, TP53, and MAP2K1 Mutations in Splenic Diffuse Red Pulp Small B-cell Lymphoma Are Associated With Progressive Disease.

    PubMed

    Martinez, Daniel; Navarro, Alba; Martinez-Trillos, Alejandra; Molina-Urra, Ricardo; Gonzalez-Farre, Blanca; Salaverria, Itziar; Nadeu, Ferran; Enjuanes, Anna; Clot, Guillem; Costa, Dolors; Carrio, Ana; Villamor, Neus; Colomer, Dolors; Martinez, Antonio; Bens, Susanne; Siebert, Reiner; Wotherspoon, Andrew; Beà, Sílvia; Matutes, Estella; Campo, Elias

    2016-02-01

    Splenic diffuse red pulp small B-cell lymphoma (SDRPL) is considered an indolent neoplasm and its pathogenesis is not well known. We investigated the molecular characteristics of 19 SDRPL patients, 5 of them with progressive disease. IGHV genes were mutated in 9/13 (69%). Cytogenetic and molecular studies identified complex karyotypes in 2 cases, and IGH rearrangements in 3, with PAX5 and potentially TCL1 as partners in each one of them. Copy number arrays showed aberrations in 69% of the tumors, including recurrent losses of 10q23, 14q31-q32, and 17p13 in 3, and 9p21 in 2 cases. Deletion of 7q31.3-q32.3 was present in only 1 case and no trisomies 3 or 18 were detected. NOTCH1 and MAP2K1 were mutated in 2 cases each, whereas BRAF, TP53, and SF3B1 were mutated each in single cases. No mutations were found in NOTCH2 or MYD88. Four of the 5 patients with aggressive disease had mutations in NOTCH1 (2 cases), TP53 (1 case), and MAP2K1 (1 case). The progression-free survival of patients with mutated genes was significantly shorter than in the unmutated (P=0.011). These findings show that SDRPL share some mutated genes but not chromosomal alterations, with other splenic lymphomas, that may confer a more aggressive behavior. PMID:26426381

  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. Structure and diffusion of intrinsic defect complexes in LiNbO₃ from density functional theory calculations.

    PubMed

    Xu, Haixuan; Lee, Donghwa; Sinnott, Susan B; Dierolf, Volkmar; Gopalan, Venkatraman; Phillpot, Simon R

    2010-04-01

    Organized defect clusters in non-stoichiometric LiNbO₃ are known to dominate macroscale ferroelectric properties; yet the detailed nature of these defects is currently unknown. Here, the relative stabilities of various defect cluster arrangements of lithium vacancies around a niobium antisite in LiNbO₃ are determined using density functional theory combined with thermodynamic calculations. Their effects on the ferroelectricity of the system are also discussed. It is found that at room temperature the non-uniaxial dipole moments associated with the defect clusters could affect the properties of the system locally. The diffusion mechanism is predicted to be through first nearest neighbor jumps on the Li sublattice. The diffusivity of the lithium vacancy is found to be extremely low at room temperature, which indicates that the defect complexes should be rather stable. PMID:21389505

  9. Mapping 3-D functional capillary geometry in rat skeletal muscle in vivo

    PubMed Central

    Milkovich, Stephanie; Goldman, Daniel; Ellis, Christopher G.

    2012-01-01

    We have developed a novel mapping software package to reconstruct microvascular networks in three dimensions (3-D) from in vivo video images for use in blood flow and O2 transport modeling. An intravital optical imaging system was used to collect video sequences of blood flow in microvessels at different depths in the tissue. Functional images of vessels were produced from the video sequences and were processed using automated edge tracking software to yield location and geometry data for construction of the 3-D network. The same video sequences were analyzed for hemodynamic and O2 saturation data from individual capillaries in the network. Simple user-driven commands allowed the connection of vessel segments at bifurcations, and semiautomated registration enabled the tracking of vessels across multiple focal planes and fields of view. The reconstructed networks can be rotated and manipulated in 3-D to verify vessel connections and continuity. Hemodynamic and O2 saturation measurements made in vivo can be indexed to corresponding vessels and visualized using colorized maps of the vascular geometry. Vessels in each reconstruction are saved as text-based files that can be easily imported into flow or O2 transport models with complete geometry, hemodynamic, and O2 transport conditions. The results of digital morphometric analysis of seven microvascular networks showed mean capillary diameters and overall capillary density consistent with previous findings using histology and corrosion cast techniques. The described mapping software is a valuable tool for the quantification of in vivo microvascular geometry, hemodynamics, and oxygenation, thus providing rich data sets for experiment-based computational models. PMID:22140042

  10. 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.

  11. Linking Brain Connectivity Across Different Time Scales with Electroencephalogram, Functional Magnetic Resonance Imaging, and Diffusion Tensor Imaging

    PubMed Central

    Federspiel, Andrea; Giezendanner, Stéphanie; Andreotti, Jennifer; Kottlow, Mara; Dierks, Thomas; Koenig, Thomas

    2012-01-01

    Abstract Structural and functional connectivity are intrinsic properties of the human brain and represent the amount of cognitive capacities of individual subjects. These connections are modulated due to development, learning, and disease. Momentary adaptations in functional connectivity alter the structural connections, which in turn affect the functional connectivity. Thus, structural and functional connectivity interact on a broad timescale. In this study, we aimed to explore distinct measures of connectivity assessed by functional magnetic resonance imaging and diffusion tensor imaging and their association to the dominant electroencephalogram oscillatory property at rest: the individual alpha frequency (IAF). We found that in 21 healthy young subjects, small intraindividual temporal IAF fluctuations were correlated to increased blood oxygenation level-dependent signal in brain areas associated to working memory functions and to the modulation of attention. These areas colocalized with functionally connected networks supporting the respective functions. Furthermore, subjects with higher IAF show increased fractional anisotropy values in fascicles connecting the above-mentioned areas and networks. Hence, due to a multimodal approach a consistent functionally and structurally connected network related to IAF was observed. PMID:22574926

  12. 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

  13. Dependence of Mos-induced Cdc2 activation on MAP kinase function in a cell-free system.

    PubMed Central

    Huang, C Y; Ferrell, J E

    1996-01-01

    The progression of G2-arrested Xenopus laevis oocytes into meiotic M-phase is accompanied by the nearly simultaneous activation of p42 MAP kinase and Cdc2/cyclin B. This timing raises the possibility that the activation of one kinase might depend upon the other. Here we have examined whether Cdc2 activation requires p42 MAP kinase function. We have reconstituted Mos-induced Cdc2 activation in cell-free Xenopus oocyte extracts, and have found that Mos-induced Cdc2 activation requires active p42 MAP kinase, is inhibited by a MAP kinase phosphatase and is independent of protein synthesis. These findings indicate that p42 MAP kinase is an essential component of the M phase trigger in this system. Images PMID:8641282

  14. Myocardial function and perfusion in the CREST syndrome variant of progressive systemic sclerosis. Exercise radionuclide evaluation and comparison with diffuse scleroderma

    SciTech Connect

    Follansbee, W.P.; Curtiss, E.I.; Medsger, T.A. Jr.; Owens, G.R.; Steen, V.D.; Rodnan, G.P.

    1984-09-01

    Myocardial function and perfusion were evaluated in 22 patients with progressive systemic sclerosis with the CREST syndrome using exercise and radionuclide techniques, pulmonary function testing, and chest roentgenography. The results were compared with a similar study of 26 patients with progressive systemic sclerosis with diffuse scleroderma. The prevalence of thallium perfusion abnormalities was similar in the groups with CREST syndrome and diffuse scleroderma, (64 percent versus 77 percent), but the defects were significantly smaller in the CREST syndrome (p less than 0.01). Reperfusion thallium defects in the absence of extramural coronary artery disease were seen in 38 percent of patients with diffuse scleroderma. This finding was not seen in any of the patients with the CREST syndrome. In diffuse scleroderma, abnormalities of both right and left ventricular function were related to larger thallium perfusion defects. In the CREST syndrome, abnormalities of left ventricular function were minor, were seen only during exercise, and were unrelated to thallium perfusion defects. Abnormal resting right ventricular function was seen in 36 percent of the patients with the CREST syndrome and was associated with an isolated decrease in diffusing capacity of carbon monoxide. It is concluded that the cardiac manifestations of the CREST syndrome are distinct from those found in diffuse scleroderma. Unlike diffuse scleroderma, abnormalities of left ventricular function in the CREST syndrome are minor and are unrelated to abnormalities of coronary perfusion. Right ventricular dysfunction in the CREST syndrome appears to be primarily related to pulmonary vascular disease.

  15. 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

  16. 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.

  17. 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.

  18. Parameterization of Parton Distributions Functions Based on Self-Organizing Maps

    NASA Astrophysics Data System (ADS)

    Loitiere, Y.; Honkanen, H.; Liuti, S.

    2006-11-01

    Neural network algorithms have been recently applied to construct Parton Distribution Functions (PDFs) parametrizations which provide an alternative to standard global fitting procedures [1]. In this contribution we propose a different technique, namely an interactive neural network algorithm using Self-Organizing Maps (SOMs) [2]. SOMs generate a nonuniform projection from a high dimensional data space onto a low dimensional one (usually 1 or 2 dimensions) by clustering similar PDF representations together. Our SOMs are trained on progressively narrower selections of data samples. The selection criterion is that of convergence towards a neighborhood of the experimental data. Our procedure utilizes all available data on deep inelastic scattering in the kinematical region of 0.001 <=x <= 0.75, and 1 <=Q^2 <= 100 GeV^2, with a cut on the final state invariant mass, W^2 >= 10 GeV^2. Our main goal is to provide a fitting procedure that, at variance with standard neural network approaches, allows for an increased control of the systematic bias. SOMs, in fact, enable the user to directly control the data selection procedure at various stages of the process. [1] L. Del Debbio, S. Forte, J. I. Latorre, A. Piccione and J. Rojo, [NNPDF Collaboration], JHEP 0503, 080 (2005). [2] T. Kohonen, ``Self Organizing Maps,'' Springer-Verlag, 1997.

  19. Structure–function mapping of a heptameric module in the nuclear pore complex

    PubMed Central

    Fernandez-Martinez, Javier; Phillips, Jeremy; Sekedat, Matthew D.; Diaz-Avalos, Ruben; Velazquez-Muriel, Javier; Franke, Josef D.; Williams, Rosemary; Stokes, David L.; Chait, Brian T.

    2012-01-01

    The nuclear pore complex (NPC) is a multiprotein assembly that serves as the sole mediator of nucleocytoplasmic exchange in eukaryotic cells. In this paper, we use an integrative approach to determine the structure of an essential component of the yeast NPC, the ∼600-kD heptameric Nup84 complex, to a precision of ∼1.5 nm. The configuration of the subunit structures was determined by satisfaction of spatial restraints derived from a diverse set of negative-stain electron microscopy and protein domain–mapping data. Phenotypic data were mapped onto the complex, allowing us to identify regions that stabilize the NPC’s interaction with the nuclear envelope membrane and connect the complex to the rest of the NPC. Our data allow us to suggest how the Nup84 complex is assembled into the NPC and propose a scenario for the evolution of the Nup84 complex through a series of gene duplication and loss events. This work demonstrates that integrative approaches based on low-resolution data of sufficient quality can generate functionally informative structures at intermediate resolution. PMID:22331846

  20. Automated cortical projection of head-surface locations for transcranial functional brain mapping.

    PubMed

    Okamoto, Masako; Dan, Ippeita

    2005-05-15

    Recent advancements in two noninvasive transcranial neuroimaging techniques, near-infrared spectroscopy (NIRS) and transcranial magnetic stimulation (TMS), signify the increasing importance of establishing structural compatibility between transcranial methods and conventional tomographic methods, such as functional magnetic resonance imaging (fMRI) and positron emission tomography (PET). The transcranial data obtained from the head surface should be projected onto the cortical surface to present the transcranial brain-mapping data on the same platform as tomographic methods. Thus, we developed two transcranial projection algorithms that project given head-surface points onto the cortical surface in structural images, and computer programs based on them. The convex-hull algorithm features geometric handling of the cortical surface, while the balloon-inflation algorithm is faster, and better reflects the local cortical structure. The automatic cortical projection methods proved to be as effective as the manual projection method described in our previous study. These methods achieved perfect correspondence between any given point on the head surface or a related nearby point in space, and its cortical projection point. Moreover, we developed a neighbor-reference method that enables transcranial cortical projection of a given head-surface point in reference to three neighboring points and one additional standard point, even when no structural image of the subject is available. We also calculated an error factor associated with these probabilistic estimations. The current study presents a close topological link between transcranial and tomographic brain-mapping modalities, which could contribute to inter-modal data standardization. PMID:15862201

  1. 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

  2. American Clinical Magnetoencephalography Society Clinical Practice Guideline 2: Presurgical Functional Brain Mapping Using Magnetic Evoked Fields*

    PubMed Central

    Burgess, Richard C.; Funke, Michael E.; Bowyer, Susan M.; Lewine, Jeffrey D.; Kirsch, Heidi E.; Bagić, Anto I.

    2012-01-01

    The following are “minimum standards” for the routine clinical recording of magnetic evoked fields (MEFs) in all age-groups. Practicing at minimum standards should not be the goal of a magnetoencephalography (MEG) center but rather a starting level for continued improvement. Minimum standards meet only the most basic responsibilities to the patient and the referring physician. These minimum standards have been put forth to improve standardization of procedures, to facilitate interchange of recordings and reports among laboratories in the United States, and to confirm the expectations of referring physicians. Recommendations regarding Laboratory (Center) Environment and Preparation for MEG Recordings are detailed in the American Clinical Magnetoencephalography Society Clinical Practice Guideline (CPG) 1 : Recording and Analysis of Spontaneous Cerebral Activity, except for its EEG aspect that is not considered necessary (although may be helpful in trained hands) for MEFs (presurgical functional brain mapping). PMID:21811122

  3. 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

    2016-01-01

    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. PMID:27154626

  4. Mapped orthogonal functions method applied to acoustic waves-based devices

    NASA Astrophysics Data System (ADS)

    Lefebvre, J. E.; Yu, J. G.; Ratolojanahary, F. E.; Elmaimouni, L.; Xu, W. J.; Gryba, T.

    2016-06-01

    This work presents the modelling of acoustic wave-based devices of various geometries through a mapped orthogonal functions method. A specificity of the method, namely the automatic incorporation of boundary conditions into equations of motion through position-dependent physical constants, is presented in detail. Formulations are given for two classes of problems: (i) problems with guided mode propagation and (ii) problems with stationary waves. The method's interest is demonstrated by several examples, a seven-layered plate, a 2D rectangular resonator and a 3D cylindrical resonator, showing how it is easy to obtain either dispersion curves and field profiles for devices with guided mode propagation or electrical response for devices with stationary waves. Extensions and possible further developments are also given.

  5. S-Boxes Based on Affine Mapping and Orbit of Power Function

    NASA Astrophysics Data System (ADS)

    Khan, Mubashar; Azam, Naveed Ahmed

    2015-06-01

    The demand of data security against computational attacks such as algebraic, differential, linear and interpolation attacks has been increased as a result of rapid advancement in the field of computation. It is, therefore, necessary to develop such cryptosystems which can resist current cryptanalysis and more computational attacks in future. In this paper, we present a multiple S-boxes scheme based on affine mapping and orbit of the power function used in Advanced Encryption Standard (AES). The proposed technique results in 256 different S-boxes named as orbital S-boxes. Rigorous tests and comparisons are performed to analyse the cryptographic strength of each of the orbital S-boxes. Furthermore, gray scale images are encrypted by using multiple orbital S-boxes. Results and simulations show that the encryption strength of the orbital S-boxes against computational attacks is better than that of the existing S-boxes.

  6. A family of chaotic pure analog coding schemes based on baker's map function

    NASA Astrophysics Data System (ADS)

    Liu, Yang; Li, Jing; Lu, Xuanxuan; Yuen, Chau; Wu, Jun

    2015-12-01

    This paper considers a family of pure analog coding schemes constructed from dynamic systems which are governed by chaotic functions—baker's map function and its variants. Various decoding methods, including maximum likelihood (ML), minimum mean square error (MMSE), and mixed ML-MMSE decoding algorithms, have been developed for these novel encoding schemes. The proposed mirrored baker's and single-input baker's analog codes perform a balanced protection against the fold error (large distortion) and weak distortion and outperform the classical chaotic analog coding and analog joint source-channel coding schemes in literature. Compared to the conventional digital communication system, where quantization and digital error correction codes are used, the proposed analog coding system has graceful performance evolution, low decoding latency, and no quantization noise. Numerical results show that under the same bandwidth expansion, the proposed analog system outperforms the digital ones over a wide signal-to-noise (SNR) range.

  7. 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

  8. Fitting of NWM Ray-traced Slant Factors to Closed-form Tropospheric Mapping Functions

    NASA Astrophysics Data System (ADS)

    Urquhart, L.; Nievinski, F. G.; Santos, M. C.

    2009-05-01

    Ray-tracing in numerical weather models (NWM) is a promising solution for describing the elevation angle- and azimuth-dependence of tropospheric delay, especially at very low elevation angles, in an attempt to de- correlate vertical position and zenith tropospheric delay during GPS estimation. On the other hand, mapping functions expressed in closed form remain imperative, demanded by the need for (i) fast processing and (ii) convenient distribution to end-users, who employ a variety of third-party GPS processing packages. We investigate the fitting of ray-tracing results to closed-form expressions. We neglect the variation of the tropospheric delay with latitude, longitude, and height, offering a mapping function valid for a specific station site (similarly as done for VMF1-Site [Boehm et al., 1996]). We focus on the variation of the delay with time, elevation angle, and azimuth. For the time-dependence, we choose to work with slant factors instead of slant delays, because the former are more stable in time than the latter; that is a consequence of the normalization by zenith delays which removes the bulk of the variation with time. For the elevation angle-dependence we compare the continued form fraction of Yan and Ping [1995] with that of Marini [1972] (normalized to yield unity at zenith, as given by Herring [1992]). The latter is more commonly used, but the former is expected to provide a better fit at elevation angles below five degrees. Since the ray-tracing results do not necessarily assume azimuthal symmetry, we have to account for the azimuth-dependence. For that we compare the single-direction model of Davis et al. [1993] with the inclusion of secondary directions [Seko et al., 2004] and arbitrary spherical harmonics [Böhm and Schuh, 2001]). We also assess whether physically-oblivious models (i.e., not derived from analytical idealized atmospheric models), such spline or polynomials, as suggested by Rocken et al. [2001], are adequate.

  9. 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

  10. 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

  11. 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

  12. A Novel Data-Driven Approach to Preoperative Mapping of Functional Cortex Using Resting-State Functional Magnetic Resonance Imaging

    PubMed Central

    Mitchell, Timothy J.; Hacker, Carl D.; Breshears, Jonathan D.; Szrama, Nick P.; Sharma, Mohit; Bundy, David T.; Pahwa, Mrinal; Corbetta, Maurizio; Snyder, Abraham Z.; Shimony, Joshua S.

    2013-01-01

    BACKGROUND: Recent findings associated with resting-state cortical networks have provided insight into the brain's organizational structure. In addition to their neuroscientific implications, the networks identified by resting-state functional magnetic resonance imaging (rs-fMRI) may prove useful for clinical brain mapping. OBJECTIVE: To demonstrate that a data-driven approach to analyze resting-state networks (RSNs) is useful in identifying regions classically understood to be eloquent cortex as well as other functional networks. METHODS: This study included 6 patients undergoing surgical treatment for intractable epilepsy and 7 patients undergoing tumor resection. rs-fMRI data were obtained before surgery and 7 canonical RSNs were identified by an artificial neural network algorithm. Of these 7, the motor and language networks were then compared with electrocortical stimulation (ECS) as the gold standard in the epilepsy patients. The sensitivity and specificity for identifying these eloquent sites were calculated at varying thresholds, which yielded receiver-operating characteristic (ROC) curves and their associated area under the curve (AUC). RSNs were plotted in the tumor patients to observe RSN distortions in altered anatomy. RESULTS: The algorithm robustly identified all networks in all patients, including those with distorted anatomy. When all ECS-positive sites were considered for motor and language, rs-fMRI had AUCs of 0.80 and 0.64, respectively. When the ECS-positive sites were analyzed pairwise, rs-fMRI had AUCs of 0.89 and 0.76 for motor and language, respectively. CONCLUSION: A data-driven approach to rs-fMRI may be a new and efficient method for preoperative localization of numerous functional brain regions. ABBREVIATIONS: AUC, area under the curve BA, Brodmann area BOLD, blood oxygen level dependent ECS, electrocortical stimulation fMRI, functional magnetic resonance imaging ICA, independent component analysis MLP, multilayer perceptron MP

  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. 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.

  15. Mapping memory function in the medial temporal lobe with the immediate-early gene Arc.

    PubMed

    Sauvage, Magdalena M; Nakamura, Nozomu H; Beer, Zachery

    2013-10-01

    For the past two decades an increasing number of studies have underlined the crucial role of the immediate - early gene Arc in plasticity processes thought to sustain memory function. Because of the high spatial and temporal resolution of this technique, the detection of Arc products appears to have become a new standard for the mapping of cognitive processes. To date, most Arc studies have focused on identifying the contribution of the hippocampal subfields CA1 and CA3 to spatial processes. In contrast, few have investigated their role in non-spatial memory, or the role of other medial temporal lobe (MTL) areas in spatial and non-spatial memory. This short review describes recent studies focusing on these issues. After a brief overview of Arc's functions, we report a set of studies that put to the test some well-accepted theories in recognition memory. First, we describe data indicating that the parahippocampal areas may not be strictly segregated into spatial and non-spatial streams, as originally described. Second, we report findings revealing a functional segregation along the dorsoventral axis in CA1, but not in CA3. Finally, we bring evidence for a segregation of CA3 along the proximodistal axis and discuss the involvement of a proximal CA3-distal CA1 network during non-spatial memory. In summary, 'Arc imaging' appears to be a powerful tool to identify neural substrates of cognitive processes, not only in the hippocampus but also in the remaining of the MTL. Moreover, because of its fundamental role in synaptic processes, it offers a rare and exciting opportunity to further bridge plasticity processes and memory function. PMID:23648768

  16. ERK1 and ERK2 Map Kinases: Specific Roles or Functional Redundancy?

    PubMed Central

    Buscà, Roser; Pouysségur, Jacques; Lenormand, Philippe

    2016-01-01

    The MAP kinase signaling cascade Ras/Raf/MEK/ERK has been involved in a large variety of cellular and physiological processes that are crucial for life. Many pathological situations have been associated to this pathway. More than one isoform has been described at each level of the cascade. In this review we devoted our attention to ERK1 and ERK2, which are the effector kinases of the pathway. Whether ERK1 and ERK2 specify functional differences or are in contrast functionally redundant, constitutes an ongoing debate despite the huge amount of studies performed to date. In this review we compiled data on ERK1 vs. ERK2 gene structures, protein sequences, expression levels, structural and molecular mechanisms of activation and substrate recognition. We have also attempted to perform a rigorous analysis of studies regarding the individual roles of ERK1 and ERK2 by the means of morpholinos, siRNA, and shRNA silencing as well as gene disruption or gene replacement in mice. Finally, we comment on a recent study of gene and protein evolution of ERK isoforms as a distinct approach to address the same question. Our review permits the evaluation of the relevance of published studies in the field especially when measurements of global ERK activation are taken into account. Our analysis favors the hypothesis of ERK1 and ERK2 exhibiting functional redundancy and points to the concept of the global ERK quantity, and not isoform specificity, as being the essential determinant to achieve ERK function. PMID:27376062

  17. LRR Conservation Mapping to Predict Functional Sites within Protein Leucine-Rich Repeat Domains

    PubMed Central

    Helft, Laura; Reddy, Vignyan; Chen, Xiyang; Koller, Teresa; Federici, Luca; Fernández-Recio, Juan; Gupta, Rishabh; Bent, Andrew

    2011-01-01

    Computational prediction of protein functional sites can be a critical first step for analysis of large or complex proteins. Contemporary methods often require several homologous sequences and/or a known protein structure, but these resources are not available for many proteins. Leucine-rich repeats (LRRs) are ligand interaction domains found in numerous proteins across all taxonomic kingdoms, including immune system receptors in plants and animals. We devised Repeat Conservation Mapping (RCM), a computational method that predicts functional sites of LRR domains. RCM utilizes two or more homologous sequences and a generic representation of the LRR structure to identify conserved or diversified patches of amino acids on the predicted surface of the LRR. RCM was validated using solved LRR+ligand structures from multiple taxa, identifying ligand interaction sites. RCM was then used for de novo dissection of two plant microbe-associated molecular pattern (MAMP) receptors, EF-TU RECEPTOR (EFR) and FLAGELLIN-SENSING 2 (FLS2). In vivo testing of Arabidopsis thaliana EFR and FLS2 receptors mutagenized at sites identified by RCM demonstrated previously unknown functional sites. The RCM predictions for EFR, FLS2 and a third plant LRR protein, PGIP, compared favorably to predictions from ODA (optimal docking area), Consurf, and PAML (positive selection) analyses, but RCM also made valid functional site predictions not available from these other bioinformatic approaches. RCM analyses can be conducted with any LRR-containing proteins at www.plantpath.wisc.edu/RCM, and the approach should be modifiable for use with other types of repeat protein domains. PMID:21789174

  18. Mode coupling theory analysis of electrolyte solutions: Time dependent diffusion, intermediate scattering function, and ion solvation dynamics

    NASA Astrophysics Data System (ADS)

    Roy, Susmita; Yashonath, Subramanian; Bagchi, Biman

    2015-03-01

    A self-consistent mode coupling theory (MCT) with microscopic inputs of equilibrium pair correlation functions is developed to analyze electrolyte dynamics. We apply the theory to calculate concentration dependence of (i) time dependent ion diffusion, (ii) intermediate scattering function of the constituent ions, and (iii) ion solvation dynamics in electrolyte solution. Brownian dynamics with implicit water molecules and molecular dynamics method with explicit water are used to check the theoretical predictions. The time dependence of ionic self-diffusion coefficient and the corresponding intermediate scattering function evaluated from our MCT approach show quantitative agreement with early experimental and present Brownian dynamic simulation results. With increasing concentration, the dispersion of electrolyte friction is found to occur at increasingly higher frequency, due to the faster relaxation of the ion atmosphere. The wave number dependence of intermediate scattering function, F(k, t), exhibits markedly different relaxation dynamics at different length scales. At small wave numbers, we find the emergence of a step-like relaxation, indicating the presence of both fast and slow time scales in the system. Such behavior allows an intriguing analogy with temperature dependent relaxation dynamics of supercooled liquids. We find that solvation dynamics of a tagged ion exhibits a power law decay at long times—the decay can also be fitted to a stretched exponential form. The emergence of the power law in solvation dynamics has been tested by carrying out long Brownian dynamics simulations with varying ionic concentrations. The solvation time correlation and ion-ion intermediate scattering function indeed exhibit highly interesting, non-trivial dynamical behavior at intermediate to longer times that require further experimental and theoretical studies.

  19. Creating probabilistic maps of the face network in the adolescent brain: a multicentre functional MRI study.

    PubMed

    Tahmasebi, Amir M; Artiges, Eric; Banaschewski, Tobias; Barker, Gareth J; Bruehl, Ruediger; Büchel, Christian; Conrod, Patricia J; Flor, Herta; Garavan, Hugh; Gallinat, Jürgen; Heinz, Andreas; Ittermann, Bernd; Loth, Eva; Mareckova, Klara; Martinot, Jean-Luc; Poline, Jean-Baptiste; Rietschel, Marcella; Smolka, Michael N; Ströhle, Andreas; Schumann, Gunter; Paus, Tomáš

    2012-04-01

    Large-scale magnetic resonance (MR) studies of the human brain offer unique opportunities for identifying genetic and environmental factors shaping the human brain. Here, we describe a dataset collected in the context of a multi-centre study of the adolescent brain, namely the IMAGEN Study. We focus on one of the functional paradigms included in the project to probe the brain network underlying processing of ambiguous and angry faces. Using functional MR (fMRI) data collected in 1,110 adolescents, we constructed probabilistic maps of the neural network engaged consistently while viewing the ambiguous or angry faces; 21 brain regions responding to faces with high probability were identified. We were also able to address several methodological issues, including the minimal sample size yielding a stable location of a test region, namely the fusiform face area (FFA), as well as the effect of acquisition site (eight sites) and scanner (four manufacturers) on the location and magnitude of the fMRI response to faces in the FFA. Finally, we provided a comparison between male and female adolescents in terms of the effect sizes of sex differences in brain response to the ambiguous and angry faces in the 21 regions of interest. Overall, we found a stronger neural response to the ambiguous faces in several cortical regions, including the fusiform face area, in female (vs. male) adolescents, and a slightly stronger response to the angry faces in the amygdala of male (vs. female) adolescents. PMID:21416563

  20. SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function.

    PubMed

    Tomer, Raju; Lovett-Barron, Matthew; Kauvar, Isaac; Andalman, Aaron; Burns, Vanessa M; Sankaran, Sethuraman; Grosenick, Logan; Broxton, Michael; Yang, Samuel; Deisseroth, Karl

    2015-12-17

    The goal of understanding living nervous systems has driven interest in high-speed and large field-of-view volumetric imaging at cellular resolution. Light sheet microscopy approaches have emerged for cellular-resolution functional brain imaging in small organisms such as larval zebrafish, but remain fundamentally limited in speed. Here, we have developed SPED light sheet microscopy, which combines large volumetric field-of-view via an extended depth of field with the optical sectioning of light sheet microscopy, thereby eliminating the need to physically scan detection objectives for volumetric imaging. SPED enables scanning of thousands of volumes-per-second, limited only by camera acquisition rate, through the harnessing of optical mechanisms that normally result in unwanted spherical aberrations. We demonstrate capabilities of SPED microscopy by performing fast sub-cellular resolution imaging of CLARITY mouse brains and cellular-resolution volumetric Ca(2+) imaging of entire zebrafish nervous systems. Together, SPED light sheet methods enable high-speed cellular-resolution volumetric mapping of biological system structure and function. PMID:26687363

  1. Word Mapping and Executive Functioning in Young Monolingual and Bilingual Children

    PubMed Central

    Bialystok, Ellen; Barac, Raluca; Blaye, Agnes; Poulin-Dubois, Diane

    2010-01-01

    The effect of bilingualism on the cognitive skills of young children was investigated by comparing performance of 162 children who belonged to one of two age groups (approximately 3- and 4½-year-olds) and one of three language groups on a series of tasks examining executive control and word mapping. The children were monolingual English speakers, monolingual French speakers, or bilinguals who spoke English and one of a large number of other languages. Monolinguals obtained higher scores than bilinguals on a receptive vocabulary test and were more likely to demonstrate the mutual exclusivity constraint, especially at the younger ages. However, bilinguals obtained higher scores than both groups of monolinguals on three tests of executive functioning: Luria’s tapping task measuring response inhibition, the Opposite Worlds task requiring children to assign incongruent labels to a sequence of animal pictures, and reverse categorization in which children needed to reclassify a set of objects into incongruent categories after an initial classification. There were no differences between the groups in the ANT flanker task requiring executive control to ignore a misleading cue. This evidence for a bilingual advantage in aspects of executive functioning at an earlier age than previously reported is discussed in terms of the possibility that bilingual language production may not be the only source of these developmental effects. PMID:21197133

  2. 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

  3. 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.

  4. CSF1R mutations in hereditary diffuse leukoencephalopathy with spheroids are loss of function

    PubMed Central

    Pridans, Clare; Sauter, Kristin A.; Baer, Kristin; Kissel, Holger; Hume, David A.

    2013-01-01

    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. PMID:24145216

  5. 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.

  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. Bioinformatics Knowledge Map for Analysis of Beta-Catenin Function in Cancer

    PubMed Central

    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

  8. 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

  9. Dirichlet-to-Neumann maps, abstract Weyl-Titchmarsh M-functions, and a generalized index of unbounded meromorphic operator-valued functions

    NASA Astrophysics Data System (ADS)

    Behrndt, Jussi; Gesztesy, Fritz; Holden, Helge; Nichols, Roger

    2016-09-01

    We introduce a generalized index for certain meromorphic, unbounded, operator-valued functions. The class of functions is chosen such that energy parameter dependent Dirichlet-to-Neumann maps associated to uniformly elliptic partial differential operators, particularly, non-self-adjoint Schrödinger operators, on bounded Lipschitz domains, and abstract operator-valued Weyl-Titchmarsh M-functions and Donoghue-type M-functions corresponding to closed extensions of symmetric operators belong to it. The principal purpose of this paper is to prove index formulas that relate the difference of the algebraic multiplicities of the discrete eigenvalues of Robin realizations of non-self-adjoint Schrödinger operators, and more abstract pairs of closed operators in Hilbert spaces with the generalized index of the corresponding energy dependent Dirichlet-to-Neumann maps and abstract Weyl-Titchmarsh M-functions, respectively.

  10. Multi-modal pharmacokinetic modelling for DCE-MRI: using diffusion weighted imaging to constrain the local arterial input function

    NASA Astrophysics Data System (ADS)

    Hamy, Valentin; Modat, Marc; Shipley, Rebecca; Dikaios, Nikos; Cleary, Jon; Punwani, Shonit; Ourselin, Sebastien; Atkinson, David; Melbourne, Andrew

    2014-03-01

    The routine acquisition of multi-modal magnetic resonance imaging data in oncology yields the possibility of combined model fitting of traditionally separate models of tissue structure and function. In this work we hypothesise that diffusion weighted imaging data may help constrain the fitting of pharmacokinetic models to dynamic contrast enhanced (DCE) MRI data. Parameters related to tissue perfusion in the intra-voxel incoherent motion (IVIM) modelling of diffusion weighted MRI provide local information on how tissue is likely to perfuse that can be utilised to guide DCE modelling via local modification of the arterial input function (AIF). In this study we investigate, based on multi-parametric head and neck MRI of 8 subjects (4 with head and neck tumours), the benefit of incorporating parameters derived from the IVIM model within the DCE modelling procedure. Although we find the benefit of this procedure to be marginal on the data used in this work, it is conceivable that a technique of this type will be of greater use in a different application.

  11. Functional Connectivity Density Mapping of Depressive Symptoms and Loneliness in Non-Demented Elderly Male

    PubMed Central

    Lan, Chen-Chia; Tsai, Shih-Jen; Huang, Chu-Chung; Wang, Ying-Hsiu; Chen, Tong-Ru; Yeh, Heng-Liang; Liu, Mu-En; Lin, Ching-Po; Yang, Albert C.

    2016-01-01

    Background: Depression and loneliness are prevalent and highly correlated phenomena among the elderly and influence both physical and mental health. Brain functional connectivity changes associated with depressive symptoms and loneliness are not fully understood. Methods: A cross-sectional functional MRI study was conducted among 85 non-demented male elders. Geriatric depression scale-short form (GDS) and loneliness scale were used to evaluate the severity of depressive symptoms and loneliness, respectively. Whole brain voxel-wise resting-state functional connectivity density (FCD) mapping was performed to delineate short-range FCD (SFCD) and long-range FCD (LFCD). Regional correlations between depressive symptoms or loneliness and SFCD or LFCD were examined using general linear model (GLM), with age incorporated as a covariate and depressive symptoms and loneliness as predictors. Results: Positive correlations between depressive symptoms and LFCD were observed in left rectal gyrus, left superior frontal gyrus, right supraorbital gyrus, and left inferior temporal gyrus. Positive correlations between depressive symptoms and SFCD were observed in left middle frontal gyrus, left superior frontal gyrus, bilateral superior medial frontal gyrus, left inferior temporal gyrus, and left middle occipital region. Positive correlations between SFCD and loneliness were centered over bilateral lingual gyrus. Conclusion: Depressive symptoms are associated with FCD changes over frontal and temporal regions, which may involve the cognitive control, affective regulation, and default mode networks. Loneliness is associated with FCD changes in bilateral lingual gyri that are known to be important in social cognition. Depressive symptoms and loneliness may be associated with different brain regions in non-demented elderly male. PMID:26793101

  12. Deriving soil function maps to assess related ecosystem services using imaging spectroscopy in the Lyss agricultural area, Switzerland

    NASA Astrophysics Data System (ADS)

    Diek, Sanne; de Jong, Rogier; Braun, Daniela; Böhler, Jonas; Schaepman, Michael

    2014-05-01

    Soils play an important role in the benefits offered by ecosystems services. In densely populated Switzerland soils are a scarce resource, with high pressure on services ranging from urban expansion to over-utilization. Key change drivers include erosion, soil degradation, land management change and (chemical) pollution, which should be taken into consideration. Therefore there is an emerging need for an integrated, sustainable and efficient system assessing the management of soil and land as a resource. The use of remote sensing can offer spatio-temporal and quantitative information of extended areas. In particular imaging spectroscopy has shown to perfectly complement existing sampling schemes as secondary information for digital soil mapping. Although only the upper-most layer of soil interacts with light when using reflectance spectroscopy, it still can offer valuable information that can be utilized by farmers and decision makers. Fully processed airborne imaging spectrometer data from APEX as well as land cover classification for the agricultural area in Lyss were available. Based on several spectral analysis methods we derived multiple soil properties, including soil organic matter, soil texture, and mineralogy; complemented by vegetation parameters, including leaf area index, chlorophyll content, pigment distribution, and water content. The surface variables were retrieved using a combination of index-based and physically-based retrievals. Soil properties in partly to fully vegetated areas were interpolated using regression kriging based methods. This allowed the continuous assessment of potential soil functions as well as non-contiguous maps of abundances of combined soil and vegetation parameters. Based on a simple regression model we could make a rough estimate of ecosystem services. This provided the opportunity to look at the differences between the interpolated soil function maps and the non-contiguous (but combined) vegetation and soil function maps

  13. Cingulum correlates of cognitive functions in patients with mild cognitive impairment and early Alzheimer's disease: a diffusion spectrum imaging study.

    PubMed

    Lin, Yi-Cheng; Shih, Yao-Chia; Tseng, Wen-Yih I; Chu, Yu-Hsiu; Wu, Meng-Tien; Chen, Ta-Fu; Tang, Pei-Fang; Chiu, Ming-Jang

    2014-05-01

    Diffusion spectrum imaging (DSI) of MRI can detect neural fiber tract changes. We investigated integrity of cingulum bundle (CB) in patients with mild cognitive impairment (MCI) and early Alzheimer's disease (EAD) using DSI tractography and explored its relationship with cognitive functions. We recruited 8 patients with MCI, 9 with EAD and 15 healthy controls (HC). All subjects received a battery of neuropsychological tests to access their executive, memory and language functions. We used a 3.0-tesla MRI scanner to obtain T1- and T2-weighted images for anatomy and used a pulsed gradient twice-refocused spin-echo diffusion echo-planar imaging sequence to acquire DSI. Patients with EAD performed significantly poorer than the HC on most tests in executive and memory functions. Significantly smaller general fractional anisotropy (GFA) values were found in the posterior and inferior segments of left CB and of the anterior segment of right CB of the EAD compared with those of the HC. Spearman's correlation on the patient groups showed that GFA values of the posterior segment of the left CB were significantly negatively associated with the time used to complete Color Trails Test Part II and positively correlated with performance of the logical memory and visual reproduction. GFA values of inferior segment of bilateral CB were positively associated with the performance of visual recognition. DSI tractography demonstrates significant preferential degeneration of the CB on the left side in patients with EAD. The location-specific degeneration is associated with corresponding declines in both executive and memory functions. PMID:24414091

  14. Functional constraints method for constructing exact solutions to delay reaction-diffusion equations and more complex nonlinear equations

    NASA Astrophysics Data System (ADS)

    Polyanin, Andrei D.; Zhurov, Alexei I.

    2014-03-01

    We propose a new method for constructing exact solutions to nonlinear delay reaction-diffusion equations of the form ut=kuxx+F(u,w), where u=u(x,t),w=u(x,t-τ), and τ is the delay time. The method is based on searching for solutions in the form u=∑n=1Nξn(x)ηn(t), where the functions ξn(x) and ηn(t) are determined from additional functional constraints (which are difference or functional equations) and the original delay partial differential equation. All of the equations considered contain one or two arbitrary functions of a single argument. We describe a considerable number of new exact generalized separable solutions and a few more complex solutions representing a nonlinear superposition of generalized separable and traveling wave solutions. All solutions involve free parameters (in some cases, infinitely many parameters) and so can be suitable for solving certain problems and testing approximate analytical and numerical methods for nonlinear delay PDEs. The results are extended to a wide class of nonlinear partial differential-difference equations involving arbitrary linear differential operators of any order with respect to the independent variables x and t (in particular, this class includes the nonlinear delay Klein-Gordon equation) as well as to some partial functional differential equations with time-varying delay.

  15. Mapping the microvascular and the associated absolute values of oxy-hemoglobin concentration through turbid media via local off-set diffuse optical imaging

    NASA Astrophysics Data System (ADS)

    Chen, Chen; Klämpfl, Florian; Stelzle, Florian; Schmidt, Michael

    2014-11-01

    An imging resolution of micron-scale has not yet been discovered by diffuse optical imaging (DOI), while a superficial response was eliminated. In this work, we report on a new approach of DOI with a local off-set alignment to subvert the common boundary conditions of the modified Beer-Lambert Law (MBLL). It can resolve a superficial target in micron scale under a turbid media. To validate both major breakthroughs, this system was used to recover a subsurface microvascular mimicking structure under an skin equivalent phantom. This microvascular was included with oxy-hemoglobin solution in variant concentrations to distiguish the absolute values of CtRHb and CtHbO2 . Experimental results confirmed the feasibility of recovering the target vascular of 50 µm in diameter, and graded the values of the concentrations of oxy-hemoglobin from 10 g/L to 50 g/L absolutely. Ultimately, this approach could evolve into a non-invasive imaging system to map the microvascular pattern and the associated oximetry under a human skin in-vivo.

  16. In Vivo Assessment of Neurodegeneration in Niemann-Pick Type C Mice by Quantitative T2 Mapping and Diffusion Tensor Imaging

    PubMed Central

    Totenhagen, John W.; Lope-Piedrafita, Silvia; Borbon, Ivan A.; Yoshimaru, Eriko S.; Erickson, Robert P.; Trouard, Theodore P.

    2013-01-01

    Purpose To quantitatively and non-invasively assess neurological disease progression in a mouse model of Niemann-Pick type C (NPC) disease by measuring white matter status with MRI techniques of T2 mapping and Diffusion Tensor Imaging (DTI). Materials and Methods Quantitative T2 and DTI experiments were performed in-vivo in NPC disease model and control mice at three time points to quantify differences and changes in white matter with measurements of T2 relaxation and DTI parameters. Histological staining for myelin content was also performed at two time points to compare with the MRI findings. Results The results of the T2 and DTI measurements show significant differences in white matter areas of the brain in the NPC disease model compared to control mice at several time points, and were seen to change over time in both groups. Conclusions The findings of this study suggest that quantitative MRI measurements may be suitable in-vivo biomarkers of disease status for future studies of NPC disease models. The changes in white matter measurements between time points in both control and NPC disease groups suggest that white matter structures continue to change and develop over time in the NPC model and can be tracked with MRI techniques. PMID:22045516

  17. Nanoscale mapping of lithium-ion diffusion in a cathode within an all-solid-state lithium-ion battery by advanced scanning probe microscopy techniques.

    PubMed

    Zhu, Jing; Lu, Li; Zeng, Kaiyang

    2013-02-26

    High-resolution real-space mapping of Li-ion diffusion in the LiNi(1/3)Co(1/3)Mn(1/3)O₂ cathode within an all-solid-state thin film Li-ion battery has been conducted using advanced scanning probe microscopy techniques, namely, band excitation electrochemical strain microscopy (BE-ESM) and conductive atomic force microscopy. In addition, local variations of the electrochemical response in the LiNi(1/3)Co(1/3)Mn(1/3)O₂ thin film cathode at different cycling stages have been investigated. This work demonstrates the unique feature and applications of the BE-ESM technique on battery research. The results allow us to establish a direct relationship of the changes in ionic mobility as well as the electrochemical activity at the nanoscale with the numbers of charge/discharge cycles. Furthermore, various factors influencing the BE-ESM measurements, including sample mechanical properties (e.g., elastic and dissipative properties) as well as surface electrical properties, have also been studied to investigate the coupling effects on the electrochemical strain. The study on the relationships between the Li-ion redistribution and microstructure of the electrode materials within thin film Li-ion battery will provide further understanding of the electrochemical degradation mechanisms of Li-ion rechargeable batteries at the nanoscale. PMID:23336441

  18. Mapping the mouse brain with rs-fMRI: An optimized pipeline for functional network identification.

    PubMed

    Zerbi, Valerio; Grandjean, Joanes; Rudin, Markus; Wenderoth, Nicole

    2015-12-01

    The use of resting state fMRI (rs-fMRI) in translational research is a powerful tool to assess brain connectivity and investigate neuropathology in mouse models. However, despite encouraging initial results, the characterization of consistent and robust resting state networks in mice remains a methodological challenge. One key reason is that the quality of the measured MR signal is degraded by the presence of structural noise from non-neural sources. Notably, in the current pipeline of the Human Connectome Project, a novel approach has been introduced to clean rs-fMRI data, which involves automatic artifact component classification and data cleaning (FIX). FIX does not require any external recordings of physiology or the segmentation of CSF and white matter. In this study, we evaluated the performance of FIX for analyzing mouse rs-fMRI data. Our results showed that FIX can be easily applied to mouse datasets and detects true signals with 100% accuracy and true noise components with very high accuracy (>98%), thus reducing both within- and between-subject variability of rs-fMRI connectivity measurements. Using this improved pre-processing pipeline, maps of 23 resting state circuits in mice were identified including two networks that displayed default mode network-like topography. Hierarchical clustering grouped these neural networks into meaningful larger functional circuits. These mouse resting state networks, which are publicly available, might serve as a reference for future work using mouse models of neurological disorders. PMID:26296501

  19. Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe

    PubMed Central

    Heinken, Almut; Khan, M. Tanweer; Paglia, Giuseppe; Rodionov, Dmitry A.; Harmsen, Hermie J. M.

    2014-01-01

    The human gut microbiota plays a central role in human well-being and disease. In this study, we present an integrated, iterative approach of computational modeling, in vitro experiments, metabolomics, and genomic analysis to accelerate the identification of metabolic capabilities for poorly characterized (anaerobic) microorganisms. We demonstrate this approach for the beneficial human gut microbe Faecalibacterium prausnitzii strain A2-165. We generated an automated draft reconstruction, which we curated against the limited biochemical data. This reconstruction modeling was used to develop in silico and in vitro a chemically defined medium (CDM), which was validated experimentally. Subsequent metabolomic analysis of the spent medium for growth on CDM was performed. We refined our metabolic reconstruction according to in vitro observed metabolite consumption and secretion and propose improvements to the current genome annotation of F. prausnitzii A2-165. We then used the reconstruction to systematically characterize its metabolic properties. Novel carbon source utilization capabilities and inabilities were predicted based on metabolic modeling and validated experimentally. This study resulted in a functional metabolic map of F. prausnitzii, which is available for further applications. The presented workflow can be readily extended to other poorly characterized and uncharacterized organisms to yield novel biochemical insights about the target organism. PMID:25002542

  20. Cellular resolution maps of X-chromosome inactivation: implications for neural development, function, and disease

    PubMed Central

    Wu, Hao; Luo, Junjie; Yu, Huimin; Rattner, Amir; Mo, Alisa; Wang, Yanshu; Smallwood, Philip M.; Erlanger, Bracha; Wheelan, Sarah J.; Nathans, Jeremy

    2014-01-01

    Female eutherian mammals use X-chromosome inactivation (XCI) to epigenetically regulate gene expression from ~4% of genes. To quantitatively map the topography of XCI for defined cell types at single cell resolution, we have generated female mice that carry X-linked, Cre-activated, and nuclear-localized fluorescent reporters – GFP on one X-chromosome and tdTomato on the other. Using these reporters in combination with different Cre drivers we have defined the topographies of XCI mosaicism for multiple CNS cell types and of retinal vascular dysfunction in a model of Norrie Disease. Depending on cell type, fluctuations in the XCI mosaic are observed over a wide range of spatial scales, from neighboring cells to left vs. right sides of the body. These data imply a major role for XCI in generating female-specific, genetically directed, stochastic diversity in eutherian mammals on spatial scales that would be predicted to affect CNS function within and between individuals. PMID:24411735

  1. Cellular resolution maps of X chromosome inactivation: implications for neural development, function, and disease.

    PubMed

    Wu, Hao; Luo, Junjie; Yu, Huimin; Rattner, Amir; Mo, Alisa; Wang, Yanshu; Smallwood, Philip M; Erlanger, Bracha; Wheelan, Sarah J; Nathans, Jeremy

    2014-01-01

    Female eutherian mammals use X chromosome inactivation (XCI) to epigenetically regulate gene expression from ∼4% of the genome. To quantitatively map the topography of XCI for defined cell types at single cell resolution, we have generated female mice that carry X-linked, Cre-activated, and nuclear-localized fluorescent reporters--GFP on one X chromosome and tdTomato on the other. Using these reporters in combination with different Cre drivers, we have defined the topographies of XCI mosaicism for multiple CNS cell types and of retinal vascular dysfunction in a model of Norrie disease. Depending on cell type, fluctuations in the XCI mosaic are observed over a wide range of spatial scales, from neighboring cells to left versus right sides of the body. These data imply a major role for XCI in generating female-specific, genetically directed, stochastic diversity in eutherian mammals on spatial scales that would be predicted to affect CNS function within and between individuals. PMID:24411735

  2. Mapping quantal touch using 7 Tesla functional magnetic resonance imaging and single-unit intraneural microstimulation

    PubMed Central

    Sanchez Panchuelo, Rosa Maria; Ackerley, Rochelle; Glover, Paul M; Bowtell, Richard W; Wessberg, Johan

    2016-01-01

    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. DOI: http://dx.doi.org/10.7554/eLife.12812.001 PMID:27154626

  3. Referential Mapping: A Technique for Attaching Functional Significance to the Innovative Utterances of an African Grey Parrot (Psittascus Erithacus).

    ERIC Educational Resources Information Center

    Pepperberg, Irene M.

    1990-01-01

    Spontaneous combinations and phonological variations of the vocalizations of an African Grey parrot were treated as if they were intentional requests or comments. The success of these "referential mapping" procedures in attaching functional significance to the parrot's vocalizations may have implications for intervention programs for humans with…

  4. Functional Mapping of Protein-Protein Interactions in an Enzyme Complex by Directed Evolution

    PubMed Central

    Roderer, Kathrin; Neuenschwander, Martin; Codoni, Giosiana; Sasso, Severin; Gamper, Marianne; Kast, Peter

    2014-01-01

    The shikimate pathway enzyme chorismate mutase converts chorismate into prephenate, a precursor of Tyr and Phe. The intracellular chorismate mutase (MtCM) of Mycobacterium tuberculosis is poorly active on its own, but becomes >100-fold more efficient upon formation of a complex with the first enzyme of the shikimate pathway, 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase (MtDS). The crystal structure of the enzyme complex revealed involvement of C-terminal MtCM residues with the MtDS interface. Here we employed evolutionary strategies to probe the tolerance to substitution of the C-terminal MtCM residues from positions 84–90. Variants with randomized positions were subjected to stringent selection in vivo requiring productive interactions with MtDS for survival. Sequence patterns identified in active library members coincide with residue conservation in natural chorismate mutases of the AroQδ subclass to which MtCM belongs. An Arg-Gly dyad at positions 85 and 86, invariant in AroQδ sequences, was intolerant to mutation, whereas Leu88 and Gly89 exhibited a preference for small and hydrophobic residues in functional MtCM-MtDS complexes. In the absence of MtDS, selection under relaxed conditions identifies positions 84–86 as MtCM integrity determinants, suggesting that the more C-terminal residues function in the activation by MtDS. Several MtCM variants, purified using a novel plasmid-based T7 RNA polymerase gene expression system, showed that a diminished ability to physically interact with MtDS correlates with reduced activatability and feedback regulatory control by Tyr and Phe. Mapping critical protein-protein interaction sites by evolutionary strategies may pinpoint promising targets for drugs that interfere with the activity of protein complexes. PMID:25551646

  5. Mapping the functional properties of soft biological tissues under shear loading

    NASA Astrophysics Data System (ADS)

    Buckley, Mark Raymond

    The structure and composition of articular cartilage and other load-bearing biological tissues are highly complex and heterogeneous. As a result, their functional mechanical properties exhibit clear spatial variations. Unlocking the structure-function relationship in these materials is critical for devising strategies to restore tissue impaired by injury or disease and can provide a template for successful implant design. Here, we describe a tissue deformation imaging stage (TDIS) allowing for simultaneous force measurement and visualization of microscale deformation in soft biological tissues under controlled shear strain. In combination with a fast confocal microscope, the TDIS is used to test the microscale response of articular cartilage to shear loading. To obtain the location-specific shear modulus of this tissue, we employ a high-resolution technique that involves tracking the deformation of a line photobleached into a fluorescently stained sample loaded in the TDIS. We find that the quasi-static and dynamic shear moduli are lowest roughly 100 mum below the articular surface. Here, articular cartilage is highly nonlinear, stiffening under increased shear strain and becoming more compliant under increased compressive strain. Using a simple thought model, we relate these results to structural features of the collagen network in articular cartilage. Furthermore, we demonstrate that the region of maximum compliance is also the primary site of shear energy dissipation in articular cartilage. Our findings suggest that damage to or surgical removal of the surface of this tissue will increase the joint's susceptibility to shear-induced damage. Finally, similar experiments are performed on intervertebral disc and growth plate, demonstrating the versatility of our in-situ strain mapping techniques.

  6. Thoracic non-rigid registration combining self-organizing maps and radial basis functions.

    PubMed

    Matsopoulos, George K; Mouravliansky, Nikolaos A; Asvestas, Pantelis A; Delibasis, Konstantinos K; Kouloulias, Vassilis

    2005-06-01

    An automatic three-dimensional non-rigid registration scheme is proposed in this paper and applied to thoracic computed tomography (CT) data of patients with stage III non-small cell lung cancer (NSCLC). According to the registration scheme, initially anatomical set of points such as the vertebral spine, the ribs, and shoulder blades are automatically segmented slice by slice from the two CT scans of the same patient in order to serve as interpolant points. Based on these extracted features, a rigid-body transformation is then applied to provide a pre-registration of the data. To establish correspondence between the feature points, the novel application of the self-organizing maps (SOMs) is adopted. In particular, the automatic correspondence of the interpolant points is based on the initialization of the Kohonen neural network model capable to identify 500 corresponding pairs of points approximately in the two CT sets. Then, radial basis functions (RBFs) using the shifted log function is subsequently employed for elastic warping of the image volume, using the correspondence between the interpolant points, as obtained in the previous phase. Quantitative and qualitative results are also presented to validate the performance of the proposed elastic registration scheme resulting in an alignment error of 6 mm, on average, over 15 CT paired datasets. Finally, changes of the tumor volume in respect to each reference dataset are estimated for all patients, which indicate inspiration and/or movement of the patient during acquisition of the data. Thus, the practical implementation of this scheme could provide estimations of lung tumor volumes during radiotherapy treatment planning. PMID:15854844

  7. Maps of zeros of the grand canonical partition function in a statistical model of high energy collisions

    NASA Astrophysics Data System (ADS)

    Brambilla, M.; Giovannini, A.; Ugoccioni, R.

    2006-06-01

    Theorems on zeros of the truncated generating function in the complex plane are reviewed. When examined in the framework of a statistical model of high energy collisions based on the negative binomial (Pascal) multiplicity distribution, these results lead to maps of zeros of the grand canonical partition function which allow us to interpret in a novel way different classes of events in pp collisions at LHC c.m. energies.

  8. Brain structural connectivity increases concurrent with functional improvement: Evidence from diffusion tensor MRI in children with cerebral palsy during therapy

    PubMed Central

    Englander, Zoë A.; Sun, Jessica; Laura Case; Mikati, Mohamad A.; Kurtzberg, Joanne; Song, Allen W.

    2015-01-01

    Cerebral Palsy (CP) refers to a heterogeneous group of permanent but non-progressive movement disorders caused by injury to the developing fetal or infant brain (Bax et al., 2005). Because of its serious long-term consequences, effective interventions that can help improve motor function, independence, and quality of life are critically needed. Our ongoing longitudinal clinical trial to treat children with CP is specifically designed to meet this challenge. To maximize the potential for functional improvement, all children in this trial received autologous cord blood transfusions (with order randomized with a placebo administration over 2 years) in conjunction with more standard physical and occupational therapies. As a part of this trial, magnetic resonance imaging (MRI) is used to improve our understanding of how these interventions affect brain development, and to develop biomarkers of treatment efficacy. In this report, diffusion tensor imaging (DTI) and subsequent brain connectome analyses were performed in a subset of children enrolled in the clinical trial (n = 17), who all exhibited positive but varying degrees of functional improvement over the first 2-year period of the study. Strong correlations between increases in white matter (WM) connectivity and functional improvement were demonstrated; however no significant relationships between either of these factors with the age of the child at time of enrollment were identified. Thus, our data indicate that increases in brain connectivity reflect improved functional abilities in children with CP. In future work, this potential biomarker can be used to help differentiate the underlying mechanisms of functional improvement, as well as to identify treatments that can best facilitate functional improvement upon un-blinding of the timing of autologous cord blood transfusions at the completion of this study. PMID:25610796

  9. Brain structural connectivity increases concurrent with functional improvement: evidence from diffusion tensor MRI in children with cerebral palsy during therapy.

    PubMed

    Englander, Zoë A; Sun, Jessica; Laura Case; Mikati, Mohamad A; Kurtzberg, Joanne; Song, Allen W

    2015-01-01

    Cerebral Palsy (CP) refers to a heterogeneous group of permanent but non-progressive movement disorders caused by injury to the developing fetal or infant brain (Bax et al., 2005). Because of its serious long-term consequences, effective interventions that can help improve motor function, independence, and quality of life are critically needed. Our ongoing longitudinal clinical trial to treat children with CP is specifically designed to meet this challenge. To maximize the potential for functional improvement, all children in this trial received autologous cord blood transfusions (with order randomized with a placebo administration over 2 years) in conjunction with more standard physical and occupational therapies. As a part of this trial, magnetic resonance imaging (MRI) is used to improve our understanding of how these interventions affect brain development, and to develop biomarkers of treatment efficacy. In this report, diffusion tensor imaging (DTI) and subsequent brain connectome analyses were performed in a subset of children enrolled in the clinical trial (n = 17), who all exhibited positive but varying degrees of functional improvement over the first 2-year period of the study. Strong correlations between increases in white matter (WM) connectivity and functional improvement were demonstrated; however no significant relationships between either of these factors with the age of the child at time of enrollment were identified. Thus, our data indicate that increases in brain connectivity reflect improved functional abilities in children with CP. In future work, this potential biomarker can be used to help differentiate the underlying mechanisms of functional improvement, as well as to identify treatments that can best facilitate functional improvement upon un-blinding of the timing of autologous cord blood transfusions at the completion of this study. PMID:25610796

  10. Computational Diffusion Magnetic Resonance Imaging Based on Time-Dependent Bloch NMR Flow Equation and Bessel Functions.

    PubMed

    Awojoyogbe, Bamidele O; Dada, Michael O; Onwu, Samuel O; Ige, Taofeeq A; Akinwande, Ninuola I

    2016-04-01

    Magnetic resonance imaging (MRI) uses a powerful magnetic field along with radio waves and a computer to produce highly detailed "slice-by-slice" pictures of virtually all internal structures of matter. The results enable physicians to examine parts of the body in minute detail and identify diseases in ways that are not possible with other techniques. For example, MRI is one of the few imaging tools that can see through bones, making it an excellent tool for examining the brain and other soft tissues. Pulsed-field gradient experiments provide a straightforward means of obtaining information on the translational motion of nuclear spins. However, the interpretation of the data is complicated by the effects of restricting geometries as in the case of most cancerous tissues and the mathematical concept required to account for this becomes very difficult. Most diffusion magnetic resonance techniques are based on the Stejskal-Tanner formulation usually derived from the Bloch-Torrey partial differential equation by including additional terms to accommodate the diffusion effect. Despite the early success of this technique, it has been shown that it has important limitations, the most of which occurs when there is orientation heterogeneity of the fibers in the voxel of interest (VOI). Overcoming this difficulty requires the specification of diffusion coefficients as function of spatial coordinate(s) and such a phenomenon is an indication of non-uniform compartmental conditions which can be analyzed accurately by solving the time-dependent Bloch NMR flow equation analytically. In this study, a mathematical formulation of magnetic resonance flow sequence in restricted geometry is developed based on a general second order partial differential equation derived directly from the fundamental Bloch NMR flow equations. The NMR signal is obtained completely in terms of NMR experimental parameters. The process is described based on Bessel functions and properties that can make it

  11. Structure–function analysis of the extracellular domain of the pneumococcal cell division site positioning protein MapZ

    PubMed Central

    Manuse, Sylvie; Jean, Nicolas L.; Guinot, Mégane; Lavergne, Jean-Pierre; Laguri, Cédric; Bougault, Catherine M.; VanNieuwenhze, Michael S.; Grangeasse, Christophe; Simorre, Jean-Pierre

    2016-01-01

    Accurate placement of the bacterial division site is a prerequisite for the generation of two viable and identical daughter cells. In Streptococcus pneumoniae, the positive regulatory mechanism involving the membrane protein MapZ positions precisely the conserved cell division protein FtsZ at the cell centre. Here we characterize the structure of the extracellular domain of MapZ and show that it displays a bi-modular structure composed of two subdomains separated by a flexible serine-rich linker. We further demonstrate in vivo that the N-terminal subdomain serves as a pedestal for the C-terminal subdomain, which determines the ability of MapZ to mark the division site. The C-terminal subdomain displays a patch of conserved amino acids and we show that this patch defines a structural motif crucial for MapZ function. Altogether, this structure–function analysis of MapZ provides the first molecular characterization of a positive regulatory process of bacterial cell division. PMID:27346279

  12. Structure-function analysis of the extracellular domain of the pneumococcal cell division site positioning protein MapZ.

    PubMed

    Manuse, Sylvie; Jean, Nicolas L; Guinot, Mégane; Lavergne, Jean-Pierre; Laguri, Cédric; Bougault, Catherine M; VanNieuwenhze, Michael S; Grangeasse, Christophe; Simorre, Jean-Pierre

    2016-01-01

    Accurate placement of the bacterial division site is a prerequisite for the generation of two viable and identical daughter cells. In Streptococcus pneumoniae, the positive regulatory mechanism involving the membrane protein MapZ positions precisely the conserved cell division protein FtsZ at the cell centre. Here we characterize the structure of the extracellular domain of MapZ and show that it displays a bi-modular structure composed of two subdomains separated by a flexible serine-rich linker. We further demonstrate in vivo that the N-terminal subdomain serves as a pedestal for the C-terminal subdomain, which determines the ability of MapZ to mark the division site. The C-terminal subdomain displays a patch of conserved amino acids and we show that this patch defines a structural motif crucial for MapZ function. Altogether, this structure-function analysis of MapZ provides the first molecular characterization of a positive regulatory process of bacterial cell division. PMID:27346279

  13. Structure-function analysis of the extracellular domain of the pneumococcal cell division site positioning protein MapZ

    NASA Astrophysics Data System (ADS)

    Manuse, Sylvie; Jean, Nicolas L.; Guinot, Mégane; Lavergne, Jean-Pierre; Laguri, Cédric; Bougault, Catherine M.; Vannieuwenhze, Michael S.; Grangeasse, Christophe; Simorre, Jean-Pierre

    2016-06-01

    Accurate placement of the bacterial division site is a prerequisite for the generation of two viable and identical daughter cells. In Streptococcus pneumoniae, the positive regulatory mechanism involving the membrane protein MapZ positions precisely the conserved cell division protein FtsZ at the cell centre. Here we characterize the structure of the extracellular domain of MapZ and show that it displays a bi-modular structure composed of two subdomains separated by a flexible serine-rich linker. We further demonstrate in vivo that the N-terminal subdomain serves as a pedestal for the C-terminal subdomain, which determines the ability of MapZ to mark the division site. The C-terminal subdomain displays a patch of conserved amino acids and we show that this patch defines a structural motif crucial for MapZ function. Altogether, this structure-function analysis of MapZ provides the first molecular characterization of a positive regulatory process of bacterial cell division.

  14. On the Green's function of the partially diffusion-controlled reversible ABCD reaction for radiation chemistry codes

    NASA Astrophysics Data System (ADS)

    Plante, Ianik; Devroye, Luc

    2015-09-01

    Several computer codes simulating chemical reactions in particles systems are based on the Green's functions of the diffusion equation (GFDE). Indeed, many types of chemical systems have been simulated using the exact GFDE, which has also become the gold standard for validating other theoretical models. In this work, a simulation algorithm is presented to sample the interparticle distance for partially diffusion-controlled reversible ABCD reaction. This algorithm is considered exact for 2-particles systems, is faster than conventional look-up tables and uses only a few kilobytes of memory. The simulation results obtained with this method are compared with those obtained with the independent reaction times (IRT) method. This work is part of our effort in developing models to understand the role of chemical reactions in the radiation effects on cells and tissues and may eventually be included in event-based models of space radiation risks. However, as many reactions are of this type in biological systems, this algorithm might play a pivotal role in future simulation programs not only in radiation chemistry, but also in the simulation of biochemical networks in time and space as well.

  15. On the Green's function of the partially diffusion-controlled reversible ABCD reaction for radiation chemistry codes

    SciTech Connect

    Plante, Ianik; Devroye, Luc

    2015-09-15

    Several computer codes simulating chemical reactions in particles systems are based on the Green's functions of the diffusion equation (GFDE). Indeed, many types of chemical systems have been simulated using the exact GFDE, which has also become the gold standard for validating other theoretical models. In this work, a simulation algorithm is presented to sample the interparticle distance for partially diffusion-controlled reversible ABCD reaction. This algorithm is considered exact for 2-particles systems, is faster than conventional look-up tables and uses only a few kilobytes of memory. The simulation results obtained with this method are compared with those obtained with the independent reaction times (IRT) method. This work is part of our effort in developing models to understand the role of chemical reactions in the radiation effects on cells and tissues and may eventually be included in event-based models of space radiation risks. However, as many reactions are of this type in biological systems, this algorithm might play a pivotal role in future simulation programs not only in radiation chemistry, but also in the simulation of biochemical networks in time and space as well.

  16. Density-functional calculations of prefactors and activation energies for H diffusion in BaZrO3

    NASA Astrophysics Data System (ADS)

    Sundell, Per G.; Björketun, Mårten E.; Wahnström, Göran

    2007-09-01

    Density-functional calculations are used to investigate hydrogen diffusion in the solid-state proton conductor BaZrO3 . Activation energies and prefactors for the rate of proton transfer and reorientation are evaluated for a defect-free region of this simple cubic perovskite-structured oxide. Both semiclassical over-barrier jumps and phonon-assisted tunneling transitions between sites are considered. It is found that the classical barriers for the elementary transfer and reorientation steps are both of the order of 0.2eV . The quantum-mechanical zero-point motion effects are found to be sizable, to effectively reduce the barrier heights, and to make the prefactors similar for the transfer and reorientation steps. The Flynn-Stoneham model [Phys. Rev. B 1, 3966 (1970)] of phonon-assisted tunneling yields an activation energy of around 0.2eV and a very small prefactor for proton transfer, whereas the corresponding adiabatic model gives a similar activation energy but a much larger prefactor. It is suggested that the effect of other defects such as dopants has to be included for a proper description of hydrogen diffusion in this material.

  17. Rapidly calculated density functional theory (DFT) relaxed Iso-potential Phi Si