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Sample records for functional diffusion maps

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  2. Challenges for the functional diffusion map in pediatric brain tumors

    PubMed Central

    Grech-Sollars, Matthew; Saunders, Dawn E.; Phipps, Kim P.; Kaur, Ramneek; Paine, Simon M.L.; Jacques, Thomas S.; Clayden, Jonathan D.; Clark, Chris A.

    2014-01-01

    Background The functional diffusion map (fDM) has been suggested as a tool for early detection of tumor treatment efficacy. We aim to study 3 factors that could act as potential confounders in the fDM: areas of necrosis, tumor grade, and change in tumor size. Methods Thirty-four pediatric patients with brain tumors were enrolled in a retrospective study, approved by the local ethics committee, to examine the fDM. Tumors were selected to encompass a range of types and grades. A qualitative analysis was carried out to compare how fDM findings may be affected by each of the 3 confounders by comparing fDM findings to clinical image reports. Results Results show that the fDM in areas of necrosis do not discriminate between treatment response and tumor progression. Furthermore, tumor grade alters the behavior of the fDM: a decrease in apparent diffusion coefficient (ADC) is a sign of tumor progression in high-grade tumors and treatment response in low-grade tumors. Our results also suggest using only tumor area overlap between the 2 time points analyzed for the fDM in tumors of varying size. Conclusions Interpretation of fDM results needs to take into account the underlying biology of both tumor and healthy tissue. Careful interpretation of the results is required with due consideration to areas of necrosis, tumor grade, and change in tumor size. PMID:24305721

  3. Challenges for the functional diffusion map in pediatric brain tumors.

    PubMed

    Grech-Sollars, Matthew; Saunders, Dawn E; Phipps, Kim P; Kaur, Ramneek; Paine, Simon M L; Jacques, Thomas S; Clayden, Jonathan D; Clark, Chris A

    2014-03-01

    The functional diffusion map (fDM) has been suggested as a tool for early detection of tumor treatment efficacy. We aim to study 3 factors that could act as potential confounders in the fDM: areas of necrosis, tumor grade, and change in tumor size. Thirty-four pediatric patients with brain tumors were enrolled in a retrospective study, approved by the local ethics committee, to examine the fDM. Tumors were selected to encompass a range of types and grades. A qualitative analysis was carried out to compare how fDM findings may be affected by each of the 3 confounders by comparing fDM findings to clinical image reports. Results show that the fDM in areas of necrosis do not discriminate between treatment response and tumor progression. Furthermore, tumor grade alters the behavior of the fDM: a decrease in apparent diffusion coefficient (ADC) is a sign of tumor progression in high-grade tumors and treatment response in low-grade tumors. Our results also suggest using only tumor area overlap between the 2 time points analyzed for the fDM in tumors of varying size. Interpretation of fDM results needs to take into account the underlying biology of both tumor and healthy tissue. Careful interpretation of the results is required with due consideration to areas of necrosis, tumor grade, and change in tumor size.

  4. The Functional Diffusion Map: An Imaging Biomarker for the Early Prediction of Cancer Treatment Outcome1

    PubMed Central

    Moffat, Bradford A; Chenevert, Thomas L; Meyer, Charles R; Mckeever, Paul E; Hall, Daniel E; Hoff, Benjamin A; Johnson, Timothy D; Rehemtulla, Alnawaz; Ross, Brian D

    2006-01-01

    Abstract Functional diffusion map (fDM) has been recently reported as an early and quantitative biomarker of clinical brain tumor treatment outcome. This MRI approach spatially maps and quantifies treatment-induced changes in tumor water diffusion values resulting from alterations in cell density/cell membrane function and microenvironment. This current study was designed to evaluate the capability of fDM for preclinical evaluation of dose escalation studies and to determine if these changes were correlated with outcome measures (cell kill and overall survival). Serial T2-weighted and diffusion MRI were carried out on rodents with orthotopically implanted 9L brain tumors receiving three doses of 1,3-bis(2-chloroethyl)-1-nitrosourea (6.65, 13.3, and 26.6 mg/kg, i.p.). All images were coregistered to baseline T2-weighted images for fDM analysis. Analysis of tumor fDM data on day 4 posttreatment detected dosedependent changes in tumor diffusion values, which were also found to be spatially dependent. Histologic analysis of treated tumors confirmed spatial changes in cellularity as observed by fDM. Early changes in tumor diffusion values were found to be highly correlative with drug dose and independent biologic outcome measures (cell kill and survival). Therefore, the fDM imaging biomarker for early prediction of treatment efficacy can be used in the drug development process. PMID:16756718

  5. Factorized Diffusion Map Approximation

    PubMed Central

    Amizadeh, Saeed; Valizadegan, Hamed; Hauskrecht, Milos

    2013-01-01

    Diffusion maps are among the most powerful Machine Learning tools to analyze and work with complex high-dimensional datasets. Unfortunately, the estimation of these maps from a finite sample is known to suffer from the curse of dimensionality. Motivated by other machine learning models for which the existence of structure in the underlying distribution of data can reduce the complexity of estimation, we study and show how the factorization of the underlying distribution into independent subspaces can help us to estimate diffusion maps more accurately. Building upon this result, we propose and develop an algorithm that can automatically factorize a high dimensional data space in order to minimize the error of estimation of its diffusion map, even in the case when the underlying distribution is not decomposable. Experiments on both the synthetic and real-world datasets demonstrate improved estimation performance of our method over the standard diffusion-map framework. PMID:25309676

  6. Graded functional diffusion map-defined characteristics of apparent diffusion coefficients predict overall survival in recurrent glioblastoma treated with bevacizumab.

    PubMed

    Ellingson, Benjamin M; Cloughesy, Timothy F; Lai, Albert; Mischel, Paul S; Nghiemphu, Phioanh L; Lalezari, Shadi; Schmainda, Kathleen M; Pope, Whitney B

    2011-10-01

    Diffusion imaging has shown promise as a predictive and prognostic biomarker in glioma. We assessed the ability of graded functional diffusion maps (fDMs) and apparent diffusion coefficient (ADC) characteristics to predict overall survival (OS) in recurrent glioblastoma multiforme (GBM) patients treated with bevacizumab. Seventy-seven patients with recurrent GBMs were retrospectively examined. MRI scans were obtained before and approximately 6 weeks after treatment with bevacizumab. Graded fDMs were created by registering datasets to each patient's pretreatment scan and then performing voxel-wise subtraction between post- and pretreatment ADC maps. Voxels were categorized according to the degree of change in ADC within pretreatment fluid-attenuated inversion recovery (FLAIR) and contrast-enhancing regions of interest (ROIs). We found that the volume of tissue showing decreased ADC within both FLAIR and contrast-enhancing regions stratified OS (log-rank, P < .05). fDMs applied to contrast-enhancing ROIs more accurately predicted OS compared with fDMs applied to FLAIR ROIs. Graded fDMs (showing voxels with decreased ADC between 0.25 and 0.4 µm(2)/ms) were more predictive of OS than traditional (single threshold) fDMs, and the predictive ability of graded fDMs could be enhanced even further by adding the ADC characteristics from the fDM-classified voxels to the analysis (log-rank, P < .001). These results demonstrate that spatially resolved diffusion-based tumor metrics are a powerful imaging biomarker of survival in patients with recurrent GBM treated with bevacizumab.

  7. 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.

  8. Orientability and Diffusion Maps

    PubMed Central

    Singer, Amit; Wu, Hau-tieng

    2010-01-01

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

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

    PubMed Central

    Ceschin, Rafael; Panigrahy, Ashok; Gopalakrishnan, Vanathi

    2015-01-01

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

  10. Significant temporal evolution of diffusion anisotropy for evaluating early response to radiosurgery in patients with vestibular schwannoma: findings from functional diffusion maps.

    PubMed

    Lin, Y-C; Wang, C-C; Wai, Y Y; Wan, Y-L; Ng, S-H; Chen, Y-L; Liu, H-L; Wang, J-J

    2010-02-01

    Outcome evaluation in clinical oncology is conventionally based on long-term volumetric changes in the tumor size. The purpose of this study was to prospectively investigate the usefulness of fDMs in incorporating anisotropic diffusion in the evaluation of early response after radiosurgery in patients with vestibular schwannoma. The MD, FA, and IVDC were calculated by using simple averaging methods and fDMs. Six patients with vestibular schwannoma treated with stereotactic radiosurgery underwent longitudinal DTI studies on a 3T MR imaging scanner (maximum follow-up, 6 months). Posttreatment DTI data were spatially coregistered with pretreatment scans. Tumors did not change significantly in size until 6 months after treatment. Diffusion indices changed significantly during the study period. There was a transient decrease in averaged MD followed by a significant increase. IVDC showed an opposite behavior compared with MD. FA decreased continuously throughout the study period. Functional diffusion maps showed a heterogeneous response of tumors to treatment, thereby providing complementary information to simple averaged values. DTI allows early detection of therapeutic-induced changes in patients with vestibular schwannoma. Functional diffusion maps incorporating anisotropic diffusion may aid in assessing the heterogeneity of the therapeutic response in this patient group.

  11. Evaluation of low-grade glioma structural changes after chemotherapy using DTI-based histogram analysis and functional diffusion maps.

    PubMed

    Castellano, Antonella; Donativi, Marina; Rudà, Roberta; De Nunzio, Giorgio; Riva, Marco; Iadanza, Antonella; Bertero, Luca; Rucco, Matteo; Bello, Lorenzo; Soffietti, Riccardo; Falini, Andrea

    2016-05-01

    To explore the role of diffusion tensor imaging (DTI)-based histogram analysis and functional diffusion maps (fDMs) in evaluating structural changes of low-grade gliomas (LGGs) receiving temozolomide (TMZ) chemotherapy. Twenty-one LGG patients underwent 3T-MR examinations before and after three and six cycles of dose-dense TMZ, including 3D-fluid-attenuated inversion recovery (FLAIR) sequences and DTI (b = 1000 s/mm(2), 32 directions). Mean diffusivity (MD), fractional anisotropy (FA), and tensor-decomposition DTI maps (p and q) were obtained. Histogram and fDM analyses were performed on co-registered baseline and post-chemotherapy maps. DTI changes were compared with modifications of tumour area and volume [according to Response Assessment in Neuro-Oncology (RANO) criteria], and seizure response. After three cycles of TMZ, 20/21 patients were stable according to RANO criteria, but DTI changes were observed in all patients (Wilcoxon test, P ≤ 0.03). After six cycles, DTI changes were more pronounced (P ≤ 0.005). Seventy-five percent of patients had early seizure response with significant improvement of DTI values, maintaining stability on FLAIR. Early changes of the 25th percentiles of p and MD predicted final volume change (R(2) = 0.614 and 0.561, P < 0.0005, respectively). TMZ-related changes were located mainly at tumour borders on p and MD fDMs. DTI-based histogram and fDM analyses are useful techniques to evaluate the early effects of TMZ chemotherapy in LGG patients. • DTI helps to assess the efficacy of chemotherapy in low-grade gliomas. • Histogram analysis of DTI metrics quantifies structural changes in tumour tissue. • Functional diffusion maps (fDMs) spatially localize the changes of DTI metrics. • Changes in DTI histograms and fDMs precede changes in conventional MRI. • Early changes in DTI histograms and fDMs correlate with seizure response.

  12. Diffusion MRI quality control and functional diffusion map results in ACRIN 6677/RTOG 0625: A multicenter, randomized, phase II trial of bevacizumab and chemotherapy in recurrent glioblastoma

    PubMed Central

    ELLINGSON, BENJAMIN M.; KIM, EUNHEE; WOODWORTH, DAVIS C.; MARQUES, HELGA; BOXERMAN, JERROLD L.; SAFRIEL, YAIR; McKINSTRY, ROBERT C.; BOKSTEIN, FELIX; JAIN, RAJAN; CHI, T. LINDA; SORENSEN, A. GREGORY; GILBERT, MARK R.; BARBORIAK, DANIEL P.

    2015-01-01

    Functional diffusion mapping (fDM) is a cancer imaging technique that quantifies voxelwise changes in apparent diffusion coefficient (ADC). Previous studies have shown value of fDMs in bevacizumab therapy for recurrent glioblastoma multiforme (GBM). The aim of the present study was to implement explicit criteria for diffusion MRI quality control and independently evaluate fDM performance in a multicenter clinical trial (RTOG 0625/ACRIN 6677). A total of 123 patients were enrolled in the current multicenter trial and signed institutional review board-approved informed consent at their respective institutions. MRI was acquired prior to and 8 weeks following therapy. A 5-point QC scoring system was used to evaluate DWI quality. fDM performance was evaluated according to the correlation of these metrics with PFS and OS at the first follow-up time-point. Results showed ADC variability of 7.3% in NAWM and 10.5% in CSF. A total of 68% of patients had usable DWI data and 47% of patients had high quality DWI data when also excluding patients that progressed before the first follow-up. fDM performance was improved by using only the highest quality DWI. High pre-treatment contrast enhancing tumor volume was associated with shorter PFS and OS. A high volume fraction of increasing ADC after therapy was associated with shorter PFS, while a high volume fraction of decreasing ADC was associated with shorter OS. In summary, DWI in multicenter trials are currently of limited value due to image quality. Improvements in consistency of image quality in multicenter trials are necessary for further advancement of DWI biomarkers. PMID:25672376

  13. Diffeomorphic metric mapping of high angular resolution diffusion imaging based on Riemannian structure of orientation distribution functions.

    PubMed

    Du, Jia; Goh, Alvina; Qiu, Anqi

    2012-05-01

    In this paper, we propose a novel large deformation diffeomorphic registration algorithm to align high angular resolution diffusion images (HARDI) characterized by orientation distribution functions (ODFs). Our proposed algorithm seeks an optimal diffeomorphism of large deformation between two ODF fields in a spatial volume domain and at the same time, locally reorients an ODF in a manner such that it remains consistent with the surrounding anatomical structure. To this end, we first review the Riemannian manifold of ODFs. We then define the reorientation of an ODF when an affine transformation is applied and subsequently, define the diffeomorphic group action to be applied on the ODF based on this reorientation. We incorporate the Riemannian metric of ODFs for quantifying the similarity of two HARDI images into a variational problem defined under the large deformation diffeomorphic metric mapping framework. We finally derive the gradient of the cost function in both Riemannian spaces of diffeomorphisms and the ODFs, and present its numerical implementation. Both synthetic and real brain HARDI data are used to illustrate the performance of our registration algorithm.

  14. Vector Diffusion Maps and the Connection Laplacian

    PubMed Central

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

    2013-01-01

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

  15. Functional mapping of flow and back-diffusion rate of N-isopropyl-p-iodoamphetamine in human brain.

    PubMed

    Yonekura, Y; Nishizawa, S; Mukai, T; Iwasaki, Y; Fukuyama, H; Ishikawa, M; Tamaki, N; Konishil, J

    1993-05-01

    Iodine-123-labeled N-isopropyl-p-iodoamphetamine (IMP) has been reported to be an excellent tracer for mapping cerebral blood flow with single-photon emission computed tomography (SPECT). Clinical interpretation of these SPECT images, however, requires further understanding of the kinetics of IMP in the human brain. In order to evaluate the kinetic behavior of IMP in normal and diseased areas, we measured flow and back-diffusion rates with serial dynamic SPECT scans following an intravenous bolus injection of IMP using a multi-detector SPECT scanner. Arterial input function was determined by octanol extracted radioactivity of serial arterial blood samples. Average values for influx rate (K1) and back-diffusion rate (k2) were 0.43 ml/g/min and 0.014 min-1 in the normal cerebral cortex, 0.43 and 0.013 in the basal ganglia, 0.28 and 0.012 in the white matter and 0.48 and 0.016 in the cerebellar hemisphere. The partition coefficient (K1/k2 ratio) was 32.4 ml/g in the cerebral cortex, 35.3 in the basal ganglia, 24.7 in the white matter and 30.4 in the cerebellum. The K1-to-k2 ratio in the infarcted and ischemic regions as well as in the tumor was smaller than that of the normal cortex. Accurate measurement of local cerebral blood flow (LCBF) based on the microsphere model was possible only on the early SPECT images, but a relative pattern of LCBF can be assessed with SPECT images obtained within 1 hr after injection except for tumors.

  16. Fractal properties of anomalous diffusion in intermittent maps

    NASA Astrophysics Data System (ADS)

    Korabel, Nickolay; Klages, Rainer; Chechkin, Aleksei V.; Sokolov, Igor M.; Gonchar, Vsevolod Yu.

    2007-03-01

    An intermittent nonlinear map generating subdiffusion is investigated. Computer simulations show that the generalized diffusion coefficient of this map has a fractal, discontinuous dependence on control parameters. An amended continuous time random-walk theory well approximates the coarse behavior of this quantity in terms of a continuous function. This theory also reproduces a full suppression of the strength of diffusion, which occurs at the dynamical transition from normal to anomalous diffusion. Similarly, the probability density function of this map exhibits a nontrivial fine structure while its coarse functional form is governed by a time fractional diffusion equation. A more detailed understanding of the irregular structure of the generalized diffusion coefficient is provided by an anomalous Taylor-Green-Kubo formula establishing a relation to de Rham-type fractal functions.

  17. Functional diffusion maps (fDMs) evaluated before and after radiochemotherapy predict progression-free and overall survival in newly diagnosed glioblastoma.

    PubMed

    Ellingson, Benjamin M; Cloughesy, Timothy F; Zaw, Taryar; Lai, Albert; Nghiemphu, Phioanh L; Harris, Robert; Lalezari, Shadi; Wagle, Naveed; Naeini, Kourosh M; Carrillo, Jose; Liau, Linda M; Pope, Whitney B

    2012-03-01

    Functional diffusion mapping (fDM) has shown promise as a sensitive imaging biomarker for predicting survival in initial studies consisting of a small number of patients, mixed tumor grades, and before routine use of anti-angiogenic therapy. The current study tested whether fDM performed before and after radiochemotherapy could predict progression-free and overall survival in 143 patients with newly diagnosed glioblastoma from 2007 through 2010, many treated with anti-angiogenic therapy after recurrence. Diffusion and conventional MRI scans were obtained before and 4 weeks after completion of radiotherapy and concurrent temozolomide treatment. FDM was created by coregistering pre- and posttreatment apparent diffusion coefficient (ADC) maps and then performing voxel-wise subtraction. FDMs were categorized according to the degree of change in ADC in pre- and posttreatment fluid-attenuated inversion recovery (FLAIR) and contrast-enhancing regions. The volume fraction of fDM-classified increasing ADC(+), decreasing ADC(-), and change in ADC(+/-) were tested to determine whether they were predictive of survival. Both Bonferroni-corrected univariate log-rank analysis and Cox proportional hazards modeling demonstrated that patients with decreasing ADC in a large volume fraction of pretreatment FLAIR or contrast-enhancing regions were statistically more likely to progress earlier and expire sooner than in patients with a lower volume fraction. The current study supports the hypothesis that fDM is a sensitive imaging biomarker for predicting survival in glioblastoma.

  18. 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.

  19. Earthquake-explosion discrimination using diffusion maps

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  20. Functional diffusion map as an early imaging biomarker for high-grade glioma: correlation with conventional radiologic response and overall survival.

    PubMed

    Hamstra, Daniel A; Galbán, Craig J; Meyer, Charles R; Johnson, Timothy D; Sundgren, Pia C; Tsien, Christina; Lawrence, Theodore S; Junck, Larry; Ross, David J; Rehemtulla, Alnawaz; Ross, Brian D; Chenevert, Thomas L

    2008-07-10

    Assessment of radiologic response (RR) for brain tumors utilizes the Macdonald criteria 8 to 10 weeks from the start of treatment. Diffusion magnetic resonance imaging (MRI) using a functional diffusion map (fDM) may provide an earlier measure to predict patient survival. Sixty patients with high-grade glioma were enrolled onto a study of intratreatment MRI at 1, 3, and 10 weeks. Receiver operating characteristic curve analysis was used to evaluate imaging parameters as a function of patient survival at 1 year. Both log-rank and Cox proportional hazards models were utilized to assess overall survival. Greater increases in diffusion in response to therapy over time were observed in those patients alive at 1 year compared with those who died as a result of disease. The volume of tumor with increased diffusion by fDM at 3 weeks was the strongest predictor of patient survival at 1 year, with larger fDM predicting longer median survival (52.6 v 10.9 months; log-rank, P < .003; hazard ratio [HR] = 2.7; 95% CI, 1.5 to 5.9). Radiologic response at 10 weeks had similar prognostic value (median survival, 31.6 v 10.9 months; log-rank P < .0007; HR = 2.9; 95% CI, 1.7 to 7.2). Radiologic response and fDM differed in 25% of cases. A composite index of response including fDM and RR provided a robust predictor of patient survival and may identify patients in whom RR does not correlate with clinical outcome. Compared with conventional neuroimaging, fDM provided an earlier assessment of equal predictive value, and the combination of fDM and RR provided a more accurate prediction of patient survival than either metric alone.

  1. 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.

  2. Mapping the human brain at rest with diffuse optical tomography

    PubMed Central

    White, Brian R.; Snyder, Abraham Z.; Cohen, Alexander L.; Petersen, Steven E.; Raichle, Marcus E.; Schlaggar, Bradley L.; Culver, Joseph P.

    2014-01-01

    Diffuse optical tomography (DOT) is a portable functional neuroimaging technique that is able to simultaneously measure both oxy- and deoxyhemoglobin responses to brain activity. Herein, we demonstrate a technique for mapping functional connections in the brain by measuring the spatial distribution of temporal correlations in resting brain activity. Simultaneous DOT imaging over the motor and visual cortices yielded robust correlation maps reproducing the expected functional neural architecture. These functional connectivity methods will have utility in certain populations, such as those who are unconscious or very young, who have difficulty performing the behaviors required in traditional task-based functional neuroimaging paradigms. PMID:19964102

  3. A Mapping method for mixing with diffusion

    NASA Astrophysics Data System (ADS)

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

    2012-11-01

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

  4. Diffusion-Weighted MRI as a Biomarker of Tumor Radiation Treatment Response Heterogeneity: A Comparative Study of Whole-Volume Histogram Analysis versus Voxel-Based Functional Diffusion Map Analysis1

    PubMed Central

    Lemasson, Benjamin; Galbán, Craig J; Boes, Jennifer L; Li, Yinghua; Zhu, Yuan; Heist, Kevin A; Johnson, Timothy D; Chenevert, Thomas L; Galbán, Stefanie; Rehemtulla, Alnawaz; Ross, Brian D

    2013-01-01

    RATIONALE: Treatment of glioblastoma (GBM) remains challenging due in part to its histologic intratumoral heterogeneity that contributes to its overall poor treatment response. Our goal was to evaluate a voxel-based biomarker, the functional diffusion map (fDM), as an imaging biomarker to detect heterogeneity of tumor response in a radiation dose escalation protocol using a genetically engineered murine GBM model. EXPERIMENTAL DESIGN: Twenty-four genetically engineered murine GBM models [Ink4a-Arf-/-/Ptenloxp/loxp/Ntv-a RCAS/PDGF(+)/Cre(+)] were randomized in four treatment groups (n = 6 per group) consisting of daily doses of 0, 1, 2, and 4 Gy delivered for 5 days. Contrast-enhanced T1-weighted and diffusion-weighted magnetic resonance imaging (MRI) scans were acquired for tumor delineation and quantification of apparent diffusion coefficient (ADC) maps, respectively. MRI experiments were performed daily for a week and every 2 days thereafter. For each animal, the area under the curve (AUC) of the percentage change of the ADC (AUCADC) and that of the increase in fDM values (AUCfDM+) were determined within the first 5 days following therapy initiation. RESULTS: Animal survival increased with increasing radiation dose. Treatment induced a dose-dependent increase in tumor ADC values. The strongest correlation between survival and ADC measurements was observed using the AUCfDM+ metric (R2 = 0.88). CONCLUSION: This study showed that the efficacy of a voxel-based imaging biomarker (fDM) was able to detect spatially varying changes in tumors, which were determined to be a more sensitive predictor of overall response versus whole-volume tumor measurements (AUCADC). Finally, fDM provided for visualization of treatment-associated spatial heterogeneity within the tumor. PMID:24151536

  5. Thermal Diffusivity Mapping of Solids by Scanning Photoacoustic Piezoelectric Technique

    NASA Astrophysics Data System (ADS)

    Zhao, Binxing; Gao, Chunming; Yan, Laijun; Wang, Yafei

    2016-12-01

    Quantitative thermal diffusivity mapping of solid samples was achieved using the scanning photoacoustic piezoelectric (PAPE) technique. Based on the frequency-domain PAPE theoretical model, the methodology of the scanning PAPE thermal diffusivity mapping is introduced. An experimental setup capable of spatial and frequency scanning was established. Thermal diffusivity mapping of homogeneous and inhomogeneous samples was carried out. The obtained thermal diffusivity images are consistent with the optical images in image contrast and consistent with the reference values in thermal diffusivity. Results show that the scanning PAPE technique is able to determine the thermal diffusivity distribution of solids, hence providing an effective method for thermal diffusivity mapping.

  6. Clinical applications and characteristics of apparent diffusion coefficient maps for the brain of two dogs.

    PubMed

    Kim, Boeun; Yi, Kangjae; Jung, Sunyoung; Ji, Seoyeon; Choi, Mincheol; Yoon, Junghee

    2014-01-01

    Diffusion-weighted imaging (DWI) and apparent diffusion coefficient (ADC) mapping are functional magnetic resonance imaging techniques for detecting water diffusion. DWI and the ADC map were performed for intracranial lesions in two dogs. In necrotizing leukoencephalitis, cavitated lesions contained a hypointense center with a hyperintense periphery on DWI, and hyperintense signals on the ADC maps. In metastatic sarcoma, masses including a necrotic region were hypointense with DWI, and hyperintense on the ADC map with hyperintense perilesional edema on DWI and ADC map. Since DWI and ADC data reflect the altered water diffusion, they can provide additional information at the molecular level.

  7. Clinical applications and characteristics of apparent diffusion coefficient maps for the brain of two dogs

    PubMed Central

    Kim, Boeun; Yi, Kangjae; Jung, Sunyoung; Ji, Seoyeon; Choi, Mincheol

    2014-01-01

    Diffusion-weighted imaging (DWI) and apparent diffusion coefficient (ADC) mapping are functional magnetic resonance imaging techniques for detecting water diffusion. DWI and the ADC map were performed for intracranial lesions in two dogs. In necrotizing leukoencephalitis, cavitated lesions contained a hypointense center with a hyperintense periphery on DWI, and hyperintense signals on the ADC maps. In metastatic sarcoma, masses including a necrotic region were hypointense with DWI, and hyperintense on the ADC map with hyperintense perilesional edema on DWI and ADC map. Since DWI and ADC data reflect the altered water diffusion, they can provide additional information at the molecular level. PMID:24675836

  8. Identification of early and distinct glioblastoma response patterns treated by boron neutron capture therapy not predicted by standard radiographic assessment using functional diffusion map.

    PubMed

    Hiramatsu, Ryo; Kawabata, Shinji; Furuse, Motomasa; Miyatake, Shin-Ichi; Kuroiwa, Toshihiko

    2013-08-01

    Radiologic response of brain tumors is traditionally assessed according to the Macdonald criteria 10 weeks from the start of therapy. Because glioblastoma (GB) responds in days rather than weeks after boron neutron capture therapy (BNCT) that is a form of tumor-selective particle radiation, it is inconvenient to use the Macdonald criteria to assess the therapeutic efficacy of BNCT by gadolinium-magnetic resonance imaging (Gd-MRI). Our study assessed the utility of functional diffusion map (fDM) for evaluating response patterns in GB treated by BNCT. The fDM is an image assessment using time-dependent changes of apparent diffusion coefficient (ADC) in tumors on a voxel-by-voxel approach. Other than time-dependent changes of ADC, fDM can automatically assess minimum/maximum ADC, Response Evaluation Criteria In Solid Tumors (RECIST), and the volume of enhanced lesions on Gd-MRI over time. We assessed 17 GB patients treated by BNCT using fDM. Additionally, in order to verify our results, we performed a histopathological examination using F98 rat glioma models. Only the volume of tumor with decreased ADC by fDM at 2 days after BNCT was a good predictor for GB patients treated by BNCT (P value = 0.022 by log-rank test and 0.033 by wilcoxon test). In a histopathological examination, brain sections of F98 rat glioma models treated by BNCT showed cell swelling of both the nuclei and the cytoplasm compared with untreated rat glioma models. The fDM could identify response patterns in BNCT-treated GB earlier than a standard radiographic assessment. Early detection of treatment failure can allow a change or supplementation before tumor progression and might lead to an improvement of GB patients' prognosis.

  9. Identification of early and distinct glioblastoma response patterns treated by boron neutron capture therapy not predicted by standard radiographic assessment using functional diffusion map

    PubMed Central

    2013-01-01

    Background Radiologic response of brain tumors is traditionally assessed according to the Macdonald criteria 10 weeks from the start of therapy. Because glioblastoma (GB) responds in days rather than weeks after boron neutron capture therapy (BNCT) that is a form of tumor-selective particle radiation, it is inconvenient to use the Macdonald criteria to assess the therapeutic efficacy of BNCT by gadolinium-magnetic resonance imaging (Gd-MRI). Our study assessed the utility of functional diffusion map (fDM) for evaluating response patterns in GB treated by BNCT. Methods The fDM is an image assessment using time-dependent changes of apparent diffusion coefficient (ADC) in tumors on a voxel-by-voxel approach. Other than time-dependent changes of ADC, fDM can automatically assess minimum/maximum ADC, Response Evaluation Criteria In Solid Tumors (RECIST), and the volume of enhanced lesions on Gd-MRI over time. We assessed 17 GB patients treated by BNCT using fDM. Additionally, in order to verify our results, we performed a histopathological examination using F98 rat glioma models. Results Only the volume of tumor with decreased ADC by fDM at 2 days after BNCT was a good predictor for GB patients treated by BNCT (P value = 0.022 by log-rank test and 0.033 by wilcoxon test). In a histopathological examination, brain sections of F98 rat glioma models treated by BNCT showed cell swelling of both the nuclei and the cytoplasm compared with untreated rat glioma models. Conclusions The fDM could identify response patterns in BNCT-treated GB earlier than a standard radiographic assessment. Early detection of treatment failure can allow a change or supplementation before tumor progression and might lead to an improvement of GB patients’ prognosis. PMID:23915330

  10. Mapping cognitive function.

    PubMed

    Stufflebeam, Steven M; Rosen, Bruce R

    2007-11-01

    Cognitive functions are fundamental to being human. Although tremendous progress has been made in the science of cognition using neuroimaging, the clinical applications of neuroimaging are just beginning to be realized. This article focuses on selected technologies, analysis techniques, and applications that have, or will soon have, direct clinical impact. The authors discuss how cognition can be imaged using MR imaging, functional MR imaging, positron emission tomography, magnetoencephalography and electroencephalography, and MR imaging diffusion tensor imaging. A unifying theme of this article is the concept that a more complete understanding of cognition only comes through integration of multimodal structural and functional imaging technologies.

  11. Mapping functional connectivity

    Treesearch

    Peter Vogt; Joseph R. Ferrari; Todd R. Lookingbill; Robert H. Gardner; Kurt H. Riitters; Katarzyna Ostapowicz

    2009-01-01

    An objective and reliable assessment of wildlife movement is important in theoretical and applied ecology. The identification and mapping of landscape elements that may enhance functional connectivity is usually a subjective process based on visual interpretations of species movement patterns. New methods based on mathematical morphology provide a generic, flexible,...

  12. Apparent exchange rate mapping with diffusion MRI.

    PubMed

    Lasič, Samo; Nilsson, Markus; Lätt, Jimmy; Ståhlberg, Freddy; Topgaard, Daniel

    2011-08-01

    Water exchange through the cell membranes is an important feature of cells and tissues. The rate of exchange is determined by factors such as membrane lipid composition and organization, as well as the type and activity of aquaporins. A method for noninvasively estimating the rate of water exchange would be useful for characterizing pathological conditions, e.g., tumors, multiple sclerosis, and ischemic stroke, expected to be associated with a change of the membrane barrier properties. This study describes the filter exchange imaging method for determining the rate of water exchange between sites having different apparent diffusion coefficients. The method is based on the filter-exchange pulsed gradient spin-echo NMR spectroscopy experiment, which is here modified to be compatible with the constraints of clinical MR scanners. The data is analyzed using a model-free approach yielding maps of the apparent exchange rate, here being introduced in analogy with the concept of the apparent diffusion coefficient. Proof-of-principle experiments are performed on microimaging and whole-body clinical scanners using yeast suspension phantoms. The limitations and appropriate experimental conditions are examined. The results demonstrate that filter exchange imaging is a fast and reliable method for characterizing exchange, and that it has the potential to become a powerful diagnostic tool.

  13. 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

  14. 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.

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

    PubMed

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

    2016-07-26

    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.

  16. 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.

  17. 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.

  18. Mapping Diffusion in a Living Cell via the Phasor Approach

    PubMed Central

    Ranjit, Suman; Lanzano, Luca; Gratton, Enrico

    2014-01-01

    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

  19. Eigenmode analysis of advective-diffusive transport in micromixers by the diffusive mapping method

    NASA Astrophysics Data System (ADS)

    Anderson, Patrick; Speetjens, Michel; Gorodetskyi, Oleksandr; Giona, Max; Mixing Collaboration

    2013-11-01

    Advective-diffusive transport in microflows is studied by means of the diffusive map- ping method, a recent extension of the mapping method by Gorodetskyi et al. (Phys. Fluids 24, 2012) that includes molecular diffusion. This greatly expands the application area of the mapping technique and makes the powerful concepts of eigenmode decompo- sition and spectral analysis of scalar transport accessible to an important class of flows: inline micromixers with diffusion. The staggered herringbone micro-mixer is adopted as a prototypical three-dimensional micro mixer. Simulations with the diffusive mapping method are in close agreement with experimental observations in literature and expose a strong impact of diffusion on the transport. Diffusion enables crossing of Lagrangian trans- port barriers and thus smoothens concentration gradients and accelerates homogenization. Spectral analysis of the mapping matrix reveals this already occurs on a modal level in that individual eigenmodes progressively smoothen and spread out across transport bar- riers with stronger diffusion. Concurrently, the corresponding eigenvalues diminish and thus fundamentally alter the mixing process by invariably causing homogenization, irre- spective of the Lagrangian flow structure. This happens faster and exhibits an earlier emergence of the dominant eigenmode the stronger the diffusion. Lagrangian structures may still affect the spectral properties in that flows comprising both islands and chaotic seas typically result in a richer set of eigenmodes compared to cases with global chaos.

  20. Diffusion-based population statistics using tract probability maps.

    PubMed

    Wassermann, Demian; Kanterakis, Efstathios; Gur, Ruben C; Deriche, Rachid; Verma, Ragini

    2010-01-01

    We present a novel technique for the tract-based statistical analysis of diffusion imaging data. In our technique, we represent each white matter (WM) tract as a tract probability map (TPM): a function mapping a point to its probability of belonging to the tract. We start by automatically clustering the tracts identified in the brain via tractography into TPMs using a novel Gaussian process framework. Then, each tract is modeled by the skeleton of its TPM, a medial representation with a tubular or sheet-like geometry. The appropriate geometry for each tract is implicitly inferred from the data instead of being selected a priori, as is done by current tract-specific approaches. The TPM representation makes it possible to average diffusion imaging based features along directions locally perpendicular to the skeleton of each WM tract, increasing the sensitivity and specificity of statistical analyses on the WM. Our framework therefore facilitates the automated analysis of WM tract bundles, and enables the quantification and visualization of tract-based statistical differences between groups. We have demonstrated the applicability of our framework by studying WM differences between 34 schizophrenia patients and 24 healthy controls.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

    Shetty, Anil N; Chiang, Sharon; Maletic-Savatic, Mirjana; Kasprian, Gregor; Vannucci, Marina; Lee, Wesley

    2014-01-01

    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.

  3. Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps.

    PubMed

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

    2015-12-08

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

  4. Hash function based on chaotic map lattices

    NASA Astrophysics Data System (ADS)

    Wang, Shihong; Hu, Gang

    2007-06-01

    A new hash function system, based on coupled chaotic map dynamics, is suggested. By combining floating point computation of chaos and some simple algebraic operations, the system reaches very high bit confusion and diffusion rates, and this enables the system to have desired statistical properties and strong collision resistance. The chaos-based hash function has its advantages for high security and fast performance, and it serves as one of the most highly competitive candidates for practical applications of hash function for software realization and secure information communications in computer networks.

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

    PubMed

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

    2015-01-14

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

  6. Diffusion Maps Clustering for Magnetic Resonance Q-Ball Imaging Segmentation

    PubMed Central

    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

  7. Mapping Cognitive Function

    PubMed Central

    Stufflebeam, Steven M.; Rosen, Bruce

    2009-01-01

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

  8. 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.

  9. 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.

  10. Incomplete initial nutation diffusion imaging: An ultrafast, single-scan approach for diffusion mapping.

    PubMed

    Ianuş, Andrada; Shemesh, Noam

    2017-09-03

    Diffusion MRI is confounded by the need to acquire at least two images separated by a repetition time, thereby thwarting the detection of rapid dynamic microstructural changes. The issue is exacerbated when diffusivity variations are accompanied by rapid changes in T2 . The purpose of the present study is to accelerate diffusion MRI acquisitions such that both reference and diffusion-weighted images necessary for quantitative diffusivity mapping are acquired in a single-shot experiment. A general methodology termed incomplete initial nutation diffusion imaging (INDI), capturing two diffusion contrasts in a single shot, is presented. This methodology creates a longitudinal magnetization reservoir that facilitates the successive acquisition of two images separated by only a few milliseconds. The theory behind INDI is presented, followed by proof-of-concept studies in water phantom, ex vivo, and in vivo experiments at 16.4 and 9.4 T. Mean diffusivities extracted from INDI were comparable with diffusion tensor imaging and the two-shot isotropic diffusion encoding in the water phantom. In ex vivo mouse brain tissues, as well as in the in vivo mouse brain, mean diffusivities extracted from conventional isotropic diffusion encoding and INDI were in excellent agreement. Simulations for signal-to-noise considerations identified the regimes in which INDI is most beneficial. The INDI method accelerates diffusion MRI acquisition to single-shot mode, which can be of great importance for mapping dynamic microstructural properties in vivo without T2 bias. Magn Reson Med, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

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

    PubMed

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

    2011-04-14

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

  12. 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

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

    PubMed

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

    2016-02-01

    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.

  14. Enhancing scattering images for orientation recovery with diffusion map

    SciTech Connect

    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

  15. Microscopic thermal diffusivity mapping using an infrared camera

    SciTech Connect

    Wang, H.; Dinwiddie, R.B.

    1997-12-31

    Standard flash thermal diffusivity measurements utilize a single-point infrared detector to measure the average temperature rise of the sample surface after a heat pulse. The averaging of infrared radiation over the sample surface could smear out the microscopic thermal diffusivity variations in some specimens, especially in fiber-reinforced composite materials. A high-speed, high-sensitivity infrared camera was employed in this study of composite materials. With a special microscope attachment, the spatial resolution of the camera can reach 5.4 {micro}m. The images can then be processed to generate microscopic thermal diffusivity maps of the material. SRM 1462 stainless steel was tested to evaluate the accuracy of the system. Thermal diffusivity micrographs of carbon-carbon composites and SCS-6/borosilicate glass were generated. Thermal diffusivity values of the carbon fiber bundles parallel to the heat flow were found to be higher than the matrix material. A thermal coupling effect between SCS-6 fiber and matrix was observed. The thermal coupling and measured thermal diffusivity value of the fiber were also dependent upon the thickness of the specimen.

  16. 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.

  17. Integrating diffusion maps with umbrella sampling: application to alanine dipeptide.

    PubMed

    Ferguson, Andrew L; Panagiotopoulos, Athanassios Z; Debenedetti, Pablo G; Kevrekidis, Ioannis G

    2011-04-07

    Nonlinear dimensionality reduction techniques can be applied to molecular simulation trajectories to systematically extract a small number of variables with which to parametrize the important dynamical motions of the system. For molecular systems exhibiting free energy barriers exceeding a few k(B)T, inadequate sampling of the barrier regions between stable or metastable basins can lead to a poor global characterization of the free energy landscape. We present an adaptation of a nonlinear dimensionality reduction technique known as the diffusion map that extends its applicability to biased umbrella sampling simulation trajectories in which restraining potentials are employed to drive the system into high free energy regions and improve sampling of phase space. We then propose a bootstrapped approach to iteratively discover good low-dimensional parametrizations by interleaving successive rounds of umbrella sampling and diffusion mapping, and we illustrate the technique through a study of alanine dipeptide in explicit solvent.

  18. Development of a method for mapping monthly average hourly diffuse erythemal ultraviolet radiation

    NASA Astrophysics Data System (ADS)

    Choosri, P.; Janjai, S.; Nunez, M.; Buntoung, S.; Chanalert, W.

    2017-08-01

    In this study, a model for calculating monthly average hourly diffuse erythemal solar ultraviolet (EUV) radiation under all sky conditions in Thailand was developed. The model is a function of air mass, aerosol optical depth and satellite-derived cloud index, as these parameters are sensitive to diffuse EUV radiation. Diffuse EUV irradiance were measured using UV-biometers equipped with shade ball during April 2011-March 2014 at four stations in Thailand. Data from these stations were used to formulate the model. The model was validated using an independent dataset (April 2014-March 2016) at the same sites. The modeled diffuse EUV irradiance showed good agreement with that from the ground-based measurements, with root mean square difference (RMSD) of 12.7% and mean bias difference (MBD) of -2.8%. The use of satellite data provided a simple and practical method to calculate monthly average hourly diffuse EUV irradiance over Thailand. Spatial monthly distributions are shown as maps.

  19. Diffusion-convection function of cosmic rays

    NASA Technical Reports Server (NTRS)

    Zhang, G.; Yang, G.

    1985-01-01

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

  20. Boltzmann's H-function and diffusion processes.

    PubMed

    Hubbard, Joseph B; Lund, Steven P; Halter, Michael

    2013-10-24

    There exists a generalization of Boltzmann's H-function that allows for nonuniformly populated stationary states, which may exist far from thermodynamic equilibrium. Here we describe a method for obtaining a generalized or collective diffusion coefficient D directly from this H-function, the only constraints being that the relaxation process is Markov (short memory), continuous in the reaction coordinate, and local in the sense of a flux/force relationship. As an application of this H-function method, we simulate the self-consistent extraction of D via Langevin/Fokker-Planck (L/FP) dynamics on various potential energy landscapes. We observe that the initial epoch of relaxation, which is far removed from the stationary state, provides the most reliable estimates of D. The construction of an H-function that guarantees conformity with the second law of thermodynamics has been generalized to allow for diffusion coefficients that may depend on both the reaction coordinate and time, and the extension to an arbitrary number of reaction coordinates is straightforward. For this multidimensional case, the diffusion tensor must be positive definite in the sense that its eigenvalues must be real and positive. To illustrate the behavior of the proposed collective diffusion coefficient, we simulate the H-function for a variety of Langevin systems. In particular, the impacts on H and D of landscape shape, sample size, selection of an initial distribution, finite dynamic observation range, stochastic correlations, and short/long-term memory effects are examined.

  1. [The Map of Auditory Function].

    PubMed

    Fujimoto, So; Komura, Yutaka

    2017-04-01

    Brodmann areas 41 and 42 are located in the superior temporal gyrus and regarded as auditory cortices. The fundamental function in audition is frequency analysis; however, the findings on tonotopy maps of the human auditory cortex were not unified until recently when they were compared to the findings on inputs and outputs of the monkey auditory cortex. The auditory cortex shows plasticity after conditioned learning and surgery of cochlear implant. It is also involved in speech perception, music appreciation, and auditory hallucination in schizophrenia through interactions with other brain areas, such as the thalamus, frontal cortex, and limbic systems.

  2. 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.

  3. 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.

  4. Moment expansion for mapping of the confined diffusion

    NASA Astrophysics Data System (ADS)

    Kalinay, Pavol

    2013-03-01

    The mapping of diffusion in a 2D channel with varying cross section A(x) onto the longitudinal coordinate x is revisited. We present an algorithm based on construction of a specific hierarchy of equations for the transverse moments of the 2D density. Elimination of all the moments but the zeroth one, the 1D density p(x,t), results in the mapped equation. Our calculation validates the earlier mapping procedure [P. Kalinay and J. K. Percus, Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.74.041203 74, 041203 (2006); P. Kalinay and J. K. Percus, Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.78.021103 78, 021103 (2008)], presuming existence of the backward mapping operator, and it naturally arrives at the extended Fick-Jacobs equation [D. Reguera and J. M. Rubì, Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.64.061106 64, 061106 (2001)] in the stationary flow, without any phenomenological conjectures.

  5. Interhemispheric connectivity revealed by diffusion tensor imaging fiber tracking derived from navigated transcranial magnetic stimulation maps as a sign of language function at risk in patients with brain tumors.

    PubMed

    Sollmann, Nico; Negwer, Chiara; Tussis, Lorena; Hauck, Theresa; Ille, Sebastian; Maurer, Stefanie; Giglhuber, Katrin; Bauer, Jan S; Ringel, Florian; Meyer, Bernhard; Krieg, Sandro M

    2017-01-01

    OBJECTIVE Resection of brain tumors in language-eloquent areas entails the risk of postoperative aphasia. It has been demonstrated via navigated transcranial magnetic stimulation (nTMS) that language function can partially shift to the unaffected hemisphere due to tumor-induced plasticity. Therefore, this study was designed to evaluate whether interhemispheric connectivity (IC) detected by nTMS-based diffusion tensor imaging-fiber tracking (DTI-FT) can be used to predict surgery-related aphasia in patients with brain tumors. METHODS Thirty-eight patients with left-sided perisylvian brain lesions underwent cortical language mapping of both hemispheres by nTMS prior to awake surgery. Then, nTMS-based DTI-FT was conducted with a fractional anisotropy (FA) of 0.01 and 0.2 to visualize nTMS-based IC. Receiver operating characteristics were calculated for the prediction of a postoperative (irrespective of the preoperative state) and a new surgery-related aphasia by the presence of detectable IC. RESULTS Language mapping by nTMS was possible in all patients. Seventeen patients (44.7%) suffered from surgery-related worsening of language performance (transient aphasia according to 3-month follow-up in 16 subjects [42.1%]; new permanent aphasia according to 3-month follow-up in 1 patient [2.6%]). Regarding the correlation of aphasia to nTMS-based IC, statistically significant differences were revealed for both evaluated FA values. However, better results were observed for tractography with an FA of 0.2, which led to a specificity of 93% (postoperative aphasia) and 90% (surgery-related aphasia). For postoperative aphasia, the corresponding OR was 0.1282 (95% CI 0.0143-1.1520), and for surgery-related aphasia the OR was 0.1184 (95% CI 0.0208-0.6754). CONCLUSIONS According to these results, IC detected by preoperative nTMS-based DTI-FT might be regarded as a risk factor for surgery-related aphasia, with a specificity of up to 93%. However, because the majority of enrolled

  6. 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.

  7. LETTER TO THE EDITOR: Fractal diffusion coefficient from dynamical zeta functions

    NASA Astrophysics Data System (ADS)

    Cristadoro, Giampaolo

    2006-03-01

    Dynamical zeta functions provide a powerful method to analyse low-dimensional dynamical systems when the underlying symbolic dynamics is under control. On the other hand, even simple one-dimensional maps can show an intricate structure of the grammar rules that may lead to a non-smooth dependence of global observables on parameters changes. A paradigmatic example is the fractal diffusion coefficient arising in a simple piecewise linear one-dimensional map of the real line. Using the Baladi-Ruelle generalization of the Milnor-Thurnston kneading determinant, we provide the exact dynamical zeta function for such a map and compute the diffusion coefficient from its smallest zero.

  8. Diffusion abnormality maps in demyelinating disease: correlations with clinical scores.

    PubMed

    Onu, Mihaela; Roceanu, Adina; Sboto-Frankenstein, Uta; Bendic, Robert; Tarta, Eugen; Preoteasa, Florentin; Bajenaru, Ovidiu

    2012-03-01

    Magnetic resonance imaging (MRI) has been explored as a noninvasive tool to assess pathology in multiple sclerosis (MS) patients. However, the correlation between classical MRI measures and physical disability is modest in MS. The diffusion tensor imaging (DTI) MRI technique holds particular promise in this regard. The present study shows brain regions where FA and individual diffusivities abnormalities are present and check their correlations with physical disability clinical scores. Eight patients and 12 matched healthy controls were recruited. The Multiple Sclerosis Functional Composite was administered. For MR-DTI acquisitions, a Genesis Signa 1.5 T MR system, an EP/SE scanning sequence, 25 gradient directions were used. Tract Based Spatial Statistics (TBSS) group comparisons showed reduced FA and increased individual diffusivities in several brain regions in patients. Significant correlations were found between FA and: EDSS, 9-HPT(NON)DOM and 25 FW score; between λ2 and: P100 (r&l), 9-HPT(NON)DOM and 25 FW; between λ3 and: 9-HPT(NON)DOM and 25 FW score. Fractional anisotropy and individual radial diffusivities proved to be important markers of motor disabilities in MS patients when the disease duration mean and the disability scores values range are relatively high. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    DOE PAGES

    Adam, R.; Ade, P. A. R.; Aghanim, N.; ...

    2016-09-20

    We report that Planck has mapped the microwave sky in temperature over nine frequency bands between 30 and 857 GHz and in polarization over seven frequency bands between 30 and 353 GHz in polarization. In this paper we consider the problem of diffuse astrophysical component separation, and process these maps within a Bayesian framework to derive an internally consistent set of full-sky astrophysical component maps. Component separation dedicated to cosmic microwave background (CMB) reconstruction is described in a companion paper. For the temperature analysis, we combine the Planck observations with the 9-yr Wilkinson Microwave Anisotropy Probe (WMAP) sky maps andmore » the Haslam et al. 408 MHz map, to derive a joint model of CMB, synchrotron, free-free, spinning dust, CO, line emission in the 94 and 100 GHz channels, and thermal dust emission. Full-sky maps are provided for each component, with an angular resolution varying between 7.5 and 1deg. Global parameters (monopoles, dipoles, relative calibration, and bandpass errors) are fitted jointly with the sky model, and best-fit values are tabulated. For polarization, the model includes CMB, synchrotron, and thermal dust emission. These models provide excellent fits to the observed data, with rms temperature residuals smaller than 4μK over 93% of the sky for all Planck frequencies up to 353 GHz, and fractional errors smaller than 1% in the remaining 7% of the sky. The main limitations of the temperature model at the lower frequencies are internal degeneracies among the spinning dust, free-free, and synchrotron components; additional observations from external low-frequency experiments will be essential to break these degeneracies. The main limitations of the temperature model at the higher frequencies are uncertainties in the 545 and 857 GHz calibration and zero-points. For polarization, the main outstanding issues are instrumental systematics in the 100–353 GHz bands on large angular scales in the form of

  11. Determination of reaction coordinates via locally scaled diffusion map

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

    We present a multiscale method for the determination of collective reaction coordinates for macromolecular dynamics based on two recently developed mathematical techniques: diffusion map and the determination of local intrinsic dimensionality of large datasets. Our method accounts for the local variation of molecular configuration space, and the resulting global coordinates are correlated with the time scales of the molecular motion. To illustrate the approach, we present results for two model systems: all-atom alanine dipeptide and coarse-grained src homology 3 protein domain. We provide clear physical interpretation for the emerging coordinates and use them to calculate transition rates. The technique is general enough to be applied to any system for which a Boltzmann-sampled set of molecular configurations is available.

  12. Mapping High-Frequency Waves in the Reconnection Diffusion Region

    NASA Astrophysics Data System (ADS)

    Viberg, H.; Khotyaintsev, Y. V.; Vaivads, A.; Andre, M.

    2012-12-01

    We study the occurrence of high frequency waves, between the electron cyclotron and plasma frequency, in a reconnection diffusion region in the Earth's magnetotail at a distance of about 19 RE from the Earth. Most of the wave activity is concentrated in the separatrix regions, with no significant activity observed in the inflow and outflow regions. Different types of waves are observed at the outer part of the separatrix region depending on the plasma characteristics in the inflow region. For the cold ~100 eV lobe plasma in the inflow we observe Langmuir waves which are generated by the bump-on-tail instability of a several keV electron beam propagating in the cold background plasma. For the hotter ~1 keV inflow plasma, which is similar to the plasmasheet population, electron cyclotron waves are observed in this region, most probably generated by low energy (several tens of eV) electron beams. Deeper into the separatrix region (closer to the current sheet), we observe mostly electrostatic solitary waves (ESWs) in association with two counter-streaming electron beams: low energy beam towards the X-line, and high energy beam away from the X-line. Observations of HF waves provide important information about electron dynamics in the diffusion region, and allow for precise mapping of kinetic boundaries.

  13. Special surgical considerations for functional brain mapping.

    PubMed

    Kekhia, Hussein; Rigolo, Laura; Norton, Isaiah; Golby, Alexandra J

    2011-04-01

    The development of functional mapping techniques gives neurosurgeons many options for preoperative planning. Integrating functional and anatomic data can inform patient selection and surgical planning and makes functional mapping more accessible than when only invasive studies were available. However, the applications of functional mapping to neurosurgical patients are still evolving. Functional imaging remains complex and requires an understanding of the underlying physiologic and imaging characteristics. Neurosurgeons must be accustomed to interpreting highly processed data. Successful implementation of functional image-guided procedures requires efficient interactions between neurosurgeon, neurologist, radiologist, neuropsychologist, and others, but promises to enhance the care of patients.

  14. Thermal Diffusivity Mapping of Graphene Based Polymer Nanocomposites.

    PubMed

    Gresil, Matthieu; Wang, Zixin; Poutrel, Quentin-Arthur; Soutis, Constantinos

    2017-07-17

    Nanoparticle dispersion is widely recognised as a challenge in polymer nanocomposites fabrication. The dispersion quality can affect the physical and thermomechanical properties of the material system. Qualitative transmission electronic microscopy, often cumbersome, remains as the 'gold standard' for dispersion characterisation. However, quantifying dispersion at macroscopic level remains a difficult task. This paper presents a quantitative dispersion characterisation method using non-contact infrared thermography mapping that measures the thermal diffusivity (α) of the graphene nanocomposite and relates α to a dispersion index. The main advantage of the proposed method is its ability to evaluate dispersion over a large area at reduced effort and cost, in addition to measuring the thermal properties of the system. The actual resolution of this thermal mapping reaches 200 µm per pixel giving an accurate picture of graphene nanoplatelets (GNP) dispersion. The post-dispersion treatment shows an improvement in directional thermal conductivity of the composite of up to 400% increase at 5 wt% of GNP. The Maxwell-Garnet effective medium approximation is proposed to estimate thermal conductivity that compare favourably to measured data. The development of a broadly applicable dispersion quantification method will provide a better understanding of reinforcement mechanisms and effect on performance of large scale composite structures.

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

    PubMed

    Van De Water, Willem; Bohr, Tomas

    1993-10-01

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

  16. 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.

  17. Fermi Bubble Edges: Spectrum and Diffusion Function

    NASA Astrophysics Data System (ADS)

    Keshet, Uri; Gurwich, Ilya

    2017-05-01

    Current measurements of the γ-ray Fermi bubbles (FB) are based on model-dependent tracers, carry substantial systematic uncertainties, and contain some discrepancies between each other. We show that gradient filters pick out the FB edges, which are found to smoothly connect to the bipolar X-ray structure emanating from the Galactic center, thus supporting the interpretation of the FBs as a Galactic-scale phenomenon. The sharp edges facilitate a direct, model-free measurement of the peripheral FB spectrum. The result is strikingly similar to the full FB-integrated spectrum, softened by a power law of index η ≃ (0.2-0.3). This is naturally explained, in both hadronic and leptonic models, if cosmic rays are injected at the edge, and diffuse away preferentially at higher energies E. The inferred, averaged diffusion function in the (more plausible) leptonic model, D{(E)≃ {10}29.5(E/10{GeV})}0.48+/- 0.02 {{cm}}2 {{{s}}}-1, is consistent with estimates for Kraichnan-like turbulence. Our results, in particular the minute spatial variations in η, indicate that the FB edge is a strong, Mach ≳5, forward shock.

  18. Discrete mappings with an explicit discrete Lyapunov function related to integrable mappings

    NASA Astrophysics Data System (ADS)

    Inoue, Hironori; Takahashi, Daisuke; Matsukidaira, Junta

    2006-05-01

    We propose discrete mappings of second order that have a discrete analogue of Lyapunov function. The mappings are extensions of the integrable Quispel-Roberts-Thompson (QRT) mapping, and a discrete Lyapunov function of the mappings is identical to an explicit conserved quantity of the QRT mapping. Moreover we can obtain a differential and an ultradiscrete limit of the mappings preserving the existence of Lyapunov function. We also give applications of a mapping with an adjusted parameter, a probabilistic mapping and coupled mappings.

  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. Asymptotic Green's functions for time-fractional diffusion equation and their application for anomalous diffusion problem

    NASA Astrophysics Data System (ADS)

    Zhokh, Alexey A.; Trypolskyi, Andrey I.; Strizhak, Peter E.

    2017-06-01

    Asymptotic Green's functions for short and long times for time-fractional diffusion equation, derived by simple and heuristic method, are provided in case if fractional derivative is presented in Caputo sense. The applicability of the asymptotic Green's functions for solving the anomalous diffusion problem on a semi-infinite rod is demonstrated. The initial value problem for longtime solution of the time-fractional diffusion equation by Green's function approach is resolved.

  1. Evaluation of Field Map and Nonlinear Registration Methods for Correction of Susceptibility Artifacts in Diffusion MRI

    PubMed Central

    Wang, Sijia; Peterson, Daniel J.; Gatenby, J. C.; Li, Wenbin; Grabowski, Thomas J.; Madhyastha, Tara M.

    2017-01-01

    Correction of echo planar imaging (EPI)-induced distortions (called “unwarping”) improves anatomical fidelity for diffusion magnetic resonance imaging (MRI) and functional imaging investigations. Commonly used unwarping methods require the acquisition of supplementary images during the scanning session. Alternatively, distortions can be corrected by nonlinear registration to a non-EPI acquired structural image. In this study, we compared reliability using two methods of unwarping: (1) nonlinear registration to a structural image using symmetric normalization (SyN) implemented in Advanced Normalization Tools (ANTs); and (2) unwarping using an acquired field map. We performed this comparison in two different test-retest data sets acquired at differing sites (N = 39 and N = 32). In both data sets, nonlinear registration provided higher test-retest reliability of the output fractional anisotropy (FA) maps than field map-based unwarping, even when accounting for the effect of interpolation on the smoothness of the images. In general, field map-based unwarping was preferable if and only if the field maps were acquired optimally. PMID:28270762

  2. Mapping Prefrontal Cortex Functions in Human Infancy

    ERIC Educational Resources Information Center

    Grossmann, Tobias

    2013-01-01

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

  3. 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…

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

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

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

  5. Functional maps within a single neuron

    PubMed Central

    Johnston, Daniel

    2012-01-01

    The presence and plasticity of dendritic ion channels are well established. However, the literature is divided on what specific roles these dendritic ion channels play in neuronal information processing, and there is no consensus on why neuronal dendrites should express diverse ion channels with different expression profiles. In this review, we present a case for viewing dendritic information processing through the lens of the sensory map literature, where functional gradients within neurons are considered as maps on the neuronal topograph. Under such a framework, drawing analogies from the sensory map literature, we postulate that the formation of intraneuronal functional maps is driven by the twin objectives of efficiently encoding inputs that impinge along different dendritic locations and of retaining homeostasis in the face of changes that are required in the coding process. In arriving at this postulate, we relate intraneuronal map physiology to the vast literature on sensory maps and argue that such a metaphorical association provides a fresh conceptual framework for analyzing and understanding single-neuron information encoding. We also describe instances where the metaphor presents specific directions for research on intraneuronal maps, derived from analogous pursuits in the sensory map literature. We suggest that this perspective offers a thesis for why neurons should express and alter ion channels in their dendrites and provides a framework under which active dendrites could be related to neural coding, learning theory, and homeostasis. PMID:22933729

  6. Investigating the tradeoffs between spatial resolution and diffusion sampling for brain mapping with diffusion tractography: time well spent?

    PubMed

    Calabrese, Evan; Badea, Alexandra; Coe, Christopher L; Lubach, Gabriele R; Styner, Martin A; Johnson, G Allan

    2014-11-01

    Interest in mapping white matter pathways in the brain has peaked with the recognition that altered brain connectivity may contribute to a variety of neurologic and psychiatric diseases. Diffusion tractography has emerged as a popular method for postmortem brain mapping initiatives, including the ex-vivo component of the human connectome project, yet it remains unclear to what extent computer-generated tracks fully reflect the actual underlying anatomy. Of particular concern is the fact that diffusion tractography results vary widely depending on the choice of acquisition protocol. The two major acquisition variables that consume scan time, spatial resolution, and diffusion sampling, can each have profound effects on the resulting tractography. In this analysis, we determined the effects of the temporal tradeoff between spatial resolution and diffusion sampling on tractography in the ex-vivo rhesus macaque brain, a close primate model for the human brain. We used the wealth of autoradiography-based connectivity data available for the rhesus macaque brain to assess the anatomic accuracy of six time-matched diffusion acquisition protocols with varying balance between spatial and diffusion sampling. We show that tractography results vary greatly, even when the subject and the total acquisition time are held constant. Further, we found that focusing on either spatial resolution or diffusion sampling at the expense of the other is counterproductive. A balanced consideration of both sampling domains produces the most anatomically accurate and consistent results.

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

    PubMed Central

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

    2003-01-01

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

  8. 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.

  9. 7T multi-shell hybrid diffusion imaging (HYDI) for mapping brain connectivity in mice

    NASA Astrophysics Data System (ADS)

    Daianu, Madelaine; Jahanshad, Neda; Villalon-Reina, Julio E.; Prasad, Gautam; Jacobs, Russell E.; Barnes, Samuel; Zlokovic, Berislav V.; Montagne, Axel; Thompson, Paul M.

    2015-03-01

    Diffusion weighted imaging (DWI) is widely used to study microstructural characteristics of the brain. High angular resolution diffusion imaging (HARDI) samples diffusivity at a large number of spherical angles, to better resolve neural fibers that mix or cross. Here, we implemented a framework for advanced mathematical analysis of mouse 5-shell HARDI (b=1000, 3000, 4000, 8000, 12000 s/mm2), also known as hybrid diffusion imaging (HYDI). Using q-ball imaging (QBI) at ultra-high field strength (7 Tesla), we computed diffusion and fiber orientation distribution functions (dODF, fODF) to better detect crossing fibers. We also computed a quantitative anisotropy (QA) index, and deterministic tractography, from the peak orientation of the fODFs. We found that the signal to noise ratio (SNR) of the QA was significantly higher in single and multi-shell reconstructed data at the lower b-values (b=1000, 3000, 4000 s/mm2) than at higher b-values (b=8000, 12000 s/mm2); the b=1000 s/mm2 shell increased the SNR of the QA in all multi-shell reconstructions, but when used alone or in <5-shell reconstruction, it led to higher angular error for the major fibers, compared to 5-shell HYDI. Multi-shell data reconstructed major fibers with less error than single-shell data, and was most successful at reducing the angular error when the lowest shell was excluded (b=1000 s/mm2). Overall, high-resolution connectivity mapping with 7T HYDI offers great potential for understanding unresolved changes in mouse models of brain disease.

  10. 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

  11. Function representation with circle inversion map systems

    NASA Astrophysics Data System (ADS)

    Boreland, Bryson; Kunze, Herb

    2017-01-01

    The fractals literature develops the now well-known concept of local iterated function systems (using affine maps) with grey-level maps (LIFSM) as an approach to function representation in terms of the associated fixed point of the so-called fractal transform. While originally explored as a method to achieve signal (and 2-D image) compression, more recent work has explored various aspects of signal and image processing using this machinery. In this paper, we develop a similar framework for function representation using circle inversion map systems. Given a circle C with centre õ and radius r, inversion with respect to C transforms the point p˜ to the point p˜', such that p˜ and p˜' lie on the same radial half-line from õ and d(õ, p˜)d(õ, p˜') = r2, where d is Euclidean distance. We demonstrate the results with an example.

  12. Neurite Orientation Dispersion and Density Imaging Color Maps to Characterize Brain Diffusion in Neurologic Disorders.

    PubMed

    Caverzasi, Eduardo; Papinutto, Nico; Castellano, Antonella; Zhu, Alyssa H; Scifo, Paola; Riva, Marco; Bello, Lorenzo; Falini, Andrea; Bharatha, Aditya; Henry, Roland G

    2016-09-01

    Neurite orientation dispersion and density imaging (NODDI) has recently been developed to overcome diffusion technique limitations in modeling biological systems. This manuscript reports a preliminary investigation into the use of a single color-coded map to represent NODDI-derived information. An optimized diffusion-weighted imaging protocol was acquired in several clinical neurological contexts including demyelinating disease, neoplastic process, stroke, and toxic/metabolic disease. The NODDI model was fitted to the diffusion datasets. NODDI is based on a three-compartment diffusion model and provides maps that quantify the contributions to the total diffusion signal in each voxel. The NODDI compartment maps were combined into a single 4-dimensional volume visualized as RGB image (red for anisotropic Gaussian diffusion, green for non-Gaussian anisotropic diffusion, and blue for isotropic Gaussian diffusion), in which the relative contributions of the different microstructural compartments can be easily appreciated. The NODDI color maps better describe the heterogeneity of neoplastic as well inflammatory lesions by identifying different tissue components within areas apparently homogeneous on conventional imaging. Moreover, NODDI color maps seem to be useful for identifying vasogenic edema differently from tumor-infiltrated edema. In multiple sclerosis, the NODDI color maps enable a visual assessment of the underlying microstructural changes, possibly highlighting an increased inflammatory component, within lesions and potentially in normal-appearing white matter. The NODDI color maps could make this technique valuable in a clinical setting, providing comprehensive and accessible information in normal and pathological brain tissues in different neurological pathologies. Copyright © 2016 by the American Society of Neuroimaging.

  13. 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.

  14. Mapping of Diffusion and Nanohardness Properties of Fcc Co-Al-V Alloys Using Ternary Diffusion Couples

    NASA Astrophysics Data System (ADS)

    Wang, Chuanyun; Xu, Guanglong; Cui, Yuwen

    2017-07-01

    Ternary diffusion behavior in Co-Al-V ternary alloys was investigated at 1373 K and 1473 K (1100 °C and 1200 °C) by the solid-state diffusion-couple technique. The extraction and interpolation of diffusion data allows the diffusion properties of Fcc Co-Al-V alloys to be mapped in the composition arrays of Al and V. A full picture of the diffusion properties was then constructed by interpolating all accessible interdiffusivities and impurity diffusivities of Co-Al binary and Co-Al-V ternary with a Redlich-Kister polynomial, in a graphic manner depicting a rapid increase of Al diffusion with increasing Al and a weak decrease with the V addition alone. Further incorporation of a nanoindentation technique enables the nanohardness property of the Co-Al-V fcc alloys to be screened in the Al and V arrays. The hardenability in the Co-Al-V alloy system has been evidenced; specifically, the alloy arrays containing higher contents of V, being solution-and-quenching processed, exhibit more effective strengthening than those with the addition of Al. The discovery of Co-Al-V alloys with comparable nanohardness but differing alloy compositions could facilitate the strengthening design of next generation Co-based alloys.

  15. Mapping of Diffusion and Nanohardness Properties of Fcc Co-Al-V Alloys Using Ternary Diffusion Couples

    NASA Astrophysics Data System (ADS)

    Wang, Chuanyun; Xu, Guanglong; Cui, Yuwen

    2017-09-01

    Ternary diffusion behavior in Co-Al-V ternary alloys was investigated at 1373 K and 1473 K (1100 °C and 1200 °C) by the solid-state diffusion-couple technique. The extraction and interpolation of diffusion data allows the diffusion properties of Fcc Co-Al-V alloys to be mapped in the composition arrays of Al and V. A full picture of the diffusion properties was then constructed by interpolating all accessible interdiffusivities and impurity diffusivities of Co-Al binary and Co-Al-V ternary with a Redlich-Kister polynomial, in a graphic manner depicting a rapid increase of Al diffusion with increasing Al and a weak decrease with the V addition alone. Further incorporation of a nanoindentation technique enables the nanohardness property of the Co-Al-V fcc alloys to be screened in the Al and V arrays. The hardenability in the Co-Al-V alloy system has been evidenced; specifically, the alloy arrays containing higher contents of V, being solution-and-quenching processed, exhibit more effective strengthening than those with the addition of Al. The discovery of Co-Al-V alloys with comparable nanohardness but differing alloy compositions could facilitate the strengthening design of next generation Co-based alloys.

  16. The importance of diffuse f functions for transition metals

    NASA Technical Reports Server (NTRS)

    Langhoff, S. R.; Bauschlicher, C. W., Jr.

    1986-01-01

    The importance of a diffuse f function for determining the dissociation energy (De) of Cu2 and the 3F-3D energy separation in Ni atom is investigated. It is found that the diffuse f contributes at most 0.05 eV to the De of Cu2 when added to a basis containing tight f functions and a flexibly contracted d basis. The diffuse f function is found to decrease the 3F-3D separation in Ni, but by substantially less than the tight f functions.

  17. The importance of diffuse f functions for transition metals

    NASA Technical Reports Server (NTRS)

    Langhoff, S. R.; Bauschlicher, C. W., Jr.

    1986-01-01

    The importance of a diffuse f function for determining the dissociation energy (De) of Cu2 and the 3F-3D energy separation in Ni atom is investigated. It is found that the diffuse f contributes at most 0.05 eV to the De of Cu2 when added to a basis containing tight f functions and a flexibly contracted d basis. The diffuse f function is found to decrease the 3F-3D separation in Ni, but by substantially less than the tight f functions.

  18. 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.

  19. PSF mapping-based correction of eddy-current-induced distortions in diffusion-weighted echo-planar imaging.

    PubMed

    In, Myung-Ho; Posnansky, Oleg; Speck, Oliver

    2016-05-01

    To accurately correct diffusion-encoding direction-dependent eddy-current-induced geometric distortions in diffusion-weighted echo-planar imaging (DW-EPI) and to minimize the calibration time at 7 Tesla (T). A point spread function (PSF) mapping based eddy-current calibration method is newly presented to determine eddy-current-induced geometric distortions even including nonlinear eddy-current effects within the readout acquisition window. To evaluate the temporal stability of eddy-current maps, calibration was performed four times within 3 months. Furthermore, spatial variations of measured eddy-current maps versus their linear superposition were investigated to enable correction in DW-EPIs with arbitrary diffusion directions without direct calibration. For comparison, an image-based eddy-current correction method was additionally applied. Finally, this method was combined with a PSF-based susceptibility-induced distortion correction approach proposed previously to correct both susceptibility and eddy-current-induced distortions in DW-EPIs. Very fast eddy-current calibration in a three-dimensional volume is possible with the proposed method. The measured eddy-current maps are very stable over time and very similar maps can be obtained by linear superposition of principal-axes eddy-current maps. High resolution in vivo brain results demonstrate that the proposed method allows more efficient eddy-current correction than the image-based method. The combination of both PSF-based approaches allows distortion-free images, which permit reliable analysis in diffusion tensor imaging applications at 7T. © 2015 Wiley Periodicals, Inc.

  20. 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.

  1. Diffusion-based method for producing density-equalizing maps

    PubMed Central

    Gastner, Michael T.; Newman, M. E. J.

    2004-01-01

    Map makers have for many years searched for a way to construct cartograms, maps in which the sizes of geographic regions such as countries or provinces appear in proportion to their population or some other analogous property. Such maps are invaluable for the representation of census results, election returns, disease incidence, and many other kinds of human data. Unfortunately, to scale regions and still have them fit together, one is normally forced to distort the regions' shapes, potentially resulting in maps that are difficult to read. Many methods for making cartograms have been proposed, some of them are extremely complex, but all suffer either from this lack of readability or from other pathologies, like overlapping regions or strong dependence on the choice of coordinate axes. Here, we present a technique based on ideas borrowed from elementary physics that suffers none of these drawbacks. Our method is conceptually simple and produces useful, elegant, and easily readable maps. We illustrate the method with applications to the results of the 2000 U.S. presidential election, lung cancer cases in the State of New York, and the geographical distribution of stories appearing in the news. PMID:15136719

  2. 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

  3. Functional mapping of ontogeny in flowering plants.

    PubMed

    Zhao, Xiyang; Tong, Chunfa; Pang, Xiaoming; Wang, Zhong; Guo, Yunqian; Du, Fang; Wu, Rongling

    2012-05-01

    All organisms face the problem of how to perform a sequence of developmental changes and transitions during ontogeny. We revise functional mapping, a statistical model originally derived to map genes that determine developmental dynamics, to take into account the entire process of ontogenetic growth from embryo to adult and from the vegetative to reproductive phase. The revised model provides a framework that reconciles the genetic architecture of development at different stages and elucidates a comprehensive picture of the genetic control mechanisms of growth that change gradually from a simple to a more complex level. We use an annual flowering plant, as an example, to demonstrate our model by which to map genes and their interactions involved in embryo and postembryonic growth. The model provides a useful tool to study the genetic control of ontogenetic growth in flowering plants and any other organisms through proper modifications based on their biological characteristics.

  4. Exploring the human genome with functional maps

    PubMed Central

    Huttenhower, Curtis; Haley, Erin M.; Hibbs, Matthew A.; Dumeaux, Vanessa; Barrett, Daniel R.; Coller, Hilary A.; Troyanskaya, Olga G.

    2009-01-01

    Human genomic data of many types are readily available, but the complexity and scale of human molecular biology make it difficult to integrate this body of data, understand it from a systems level, and apply it to the study of specific pathways or genetic disorders. An investigator could best explore a particular protein, pathway, or disease if given a functional map summarizing the data and interactions most relevant to his or her area of interest. Using a regularized Bayesian integration system, we provide maps of functional activity and interaction networks in over 200 areas of human cellular biology, each including information from ∼30,000 genome-scale experiments pertaining to ∼25,000 human genes. Key to these analyses is the ability to efficiently summarize this large data collection from a variety of biologically informative perspectives: prediction of protein function and functional modules, cross-talk among biological processes, and association of novel genes and pathways with known genetic disorders. In addition to providing maps of each of these areas, we also identify biological processes active in each data set. Experimental investigation of five specific genes, AP3B1, ATP6AP1, BLOC1S1, LAMP2, and RAB11A, has confirmed novel roles for these proteins in the proper initiation of macroautophagy in amino acid-starved human fibroblasts. Our functional maps can be explored using HEFalMp (Human Experimental/Functional Mapper), a web interface allowing interactive visualization and investigation of this large body of information. PMID:19246570

  5. Sparse solution of fiber orientation distribution function by diffusion decomposition.

    PubMed

    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 L 2 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    DOE PAGES

    Adam, R.; Ade, P. A. R.; Aghanim, N.; ...

    2016-09-20

    In this paper, we present foreground-reduced cosmic microwave background (CMB) maps derived from the full Planck data set in both temperature and polarization. Compared to the corresponding Planck 2013 temperature sky maps, the total data volume is larger by a factor of 3.2 for frequencies between 30 and 70 GHz, and by 1.9 for frequencies between 100 and 857 GHz. In addition, systematic errors in the forms of temperature-to-polarization leakage, analogue-to-digital conversion uncertainties, and very long time constant errors have been dramatically reduced, to the extent that the cosmological polarization signal may now be robustly recovered on angular scales ℓ ≳ 40. On the very largest scales, instrumental systematic residuals are still non-negligible compared to the expected cosmological signal, and modes with ℓ< 20 are accordingly suppressed in the current polarization maps by high-pass filtering. As in 2013, four different CMB component separation algorithms are applied to these observations, providing a measure of stability with respect to algorithmic and modelling choices. Additionally, the resulting polarization maps have rms instrumental noise ranging between 0.21 and 0.27μK averaged over 55' pixels, and between 4.5 and 6.1μK averaged over 3more » $$'\\atop{.}$$4 pixels. The cosmological parameters derived from the analysis of temperature power spectra are in agreement at the 1σ level with the Planck 2015 likelihood. Unresolved mismatches between the noise properties of the data and simulations prevent a satisfactory description of the higher-order statistical properties of the polarization maps. Thus, the primary applications of these polarization maps are those that do not require massive simulations for accurate estimation of uncertainties, for instance estimation of cross-spectra and cross-correlations, or stacking analyses. However, the amplitude of primordial non-Gaussianity is consistent with zero within 2σ for all local, equilateral, and

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

    NASA Astrophysics Data System (ADS)

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

    2006-03-01

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

  10. Diffusion anisotropy color-coded map of cerebral white matter: quantitative comparison between orthogonal anisotropic diffusion-weighted imaging and diffusion tensor imaging.

    PubMed

    Uwano, Ikuko; Sasaki, Makoto; Kudo, Kohsuke; Fujiwara, Shunrou; Yamaguchi, Mao; Saito, Ayumi; Ogasawara, Kuniaki; Ogawa, Akira

    2013-04-01

    Diffusion anisotropy color-coded maps of cerebral white matter can be generated from orthogonal anisotropic diffusion-weighted imaging (DWI) using the three-dimensional anisotropy contrast (3DAC) technique, but its precision has not been fully validated. Hence, we attempted to determine whether 3DAC is comparable to a diffusion tensor imaging (DTI) color map. We examined 15 healthy individuals and generated color-coded maps using 3DAC as well as using primary eigenvector (e1) and fractional anisotropy (FA) from identical DTI datasets. The difference in the direction of the 3DAC vector from e1 (θ) in cerebral white matter was evaluated. Correlations between θ and FA or obliqueness of e1 were also examined. In cerebral white matter, θ had significantly negative and positive correlations with FA values and e1 obliqueness, respectively. Among white matter tracts, the pyramidal tract, cingulum, and corpus callosum, which had significantly high FA and/or low obliqueness, exhibited similar coloration and significantly smaller θ (4.4° ± 1.6°, 9.3° ± 2.8°, and 11.2° ± 1.1°, respectively) than the entire white matter (13.9° ± 1.1°). The 3DAC could visualize directional information of white matter tracts as precisely DTI-based color maps did, particularly when FA was large and/or e1 directions were orthogonal. Copyright © 2012 by the American Society of Neuroimaging.

  11. Anatomic mapping of molecular subtypes in diffuse glioma.

    PubMed

    Tang, Qisheng; Lian, Yuxi; Yu, Jinhua; Wang, Yuanyuan; Shi, Zhifeng; Chen, Liang

    2017-09-15

    Tumor location served as an important prognostic factor in glioma patients was considered to postulate molecular features according to cell origin theory. However, anatomic distribution of unique molecular subtypes was not widely investigated. The relationship between molecular phenotype and histological subgroup were also vague based on tumor location. Our group focuses on the study of glioma anatomic location of distinctive molecular subgroups and histology subtypes, and explores the possibility of their consistency based on clinical background. We retrospectively reviewed 143 cases with both molecular information (IDH1/TERT/1p19q) and MRI images diagnosed as cerebral diffuse gliomas. The anatomic distribution was analyzed between distinctive molecular subgroups and its relationship with histological subtypes. The influence of tumor location, molecular stratification and histology diagnosis on survival outcome was investigated as well. Anatomic locations of cerebral diffuse glioma indicate varied clinical outcome. Based on that, it can be stratified into five principal molecular subgroups according to IDH1/TERT/1p19q status. Triple-positive (IDH1 and TERT mutation with 1p19q codeletion) glioma tended to be oligodendroglioma present with much better clinical outcome compared to TERT mutation only group who is glioblastoma inclined (median overall survival 39 months VS 18 months). Five molecular subgroups were demonstrated with distinctive locational distribution. This kind of anatomic feature is consistent with its corresponding histological subtypes. Each molecular subgroup in glioma has unique anatomic location which indicates distinctive clinical outcome. Molecular diagnosis can be served as perfect complementary tool for the precise diagnosis. Integration of histomolecular diagnosis will be much more helpful in routine clinical practice in the future.

  12. 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.

  13. Resting-state functional connectivity in the human brain revealed with diffuse optical tomography

    PubMed Central

    White, Brian R.; Snyder, Abraham Z.; Cohen, Alexander L.; Petersen, Steven E.; Raich-le, Marcus E.; Schlaggar, Bradley L.; Culver, Joseph P.

    2009-01-01

    Mapping resting-state networks allows insight into the brain's functional architecture and physiology and has rapidly become important in contemporary neuroscience research. Diffuse optical tomography (DOT) is an emerging functional neuroimaging technique with the advantages, relative to functional magnetic resonance imaging (fMRI), of portability and the ability to simultaneously measure both oxy- and deoxy-hemoglobin. Previous optical studies have evaluated the temporal features of spontaneous resting brain signals. Herein, we develop techniques for spatially mapping functional connectivity with DOT (fc-DOT). Simultaneous imaging over the motor and visual cortices yielded robust correlation maps reproducing the expected functional neural architecture. The localization of the maps was confirmed with task-response studies and with subject-matched fc-MRI. These fc-DOT methods provide a task-less approach to mapping brain function in populations that were previously difficult to research. Our advances may permit new studies of early childhood development and of unconscious patients. In addition, the comprehensive hemoglobin contrasts of fc-DOT enable innovative studies of the biophysical origin of the functional connectivity signal. PMID:19344773

  14. 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…

  15. 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…

  16. 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.

  17. Graded functional diffusion map–defined characteristics of apparent diffusion coefficients predict overall survival in recurrent glioblastoma treated with bevacizumab

    PubMed Central

    Ellingson, Benjamin M.; Cloughesy, Timothy F.; Lai, Albert; Mischel, Paul S.; Nghiemphu, Phioanh L.; Lalezari, Shadi; Schmainda, Kathleen M.; Pope, Whitney B.

    2011-01-01

    Diffusion imaging has shown promise as a predictive and prognostic biomarker in glioma. We assessed the ability of graded functional diffusion maps (fDMs) and apparent diffusion coefficient (ADC) characteristics to predict overall survival (OS) in recurrent glioblastoma multiforme (GBM) patients treated with bevacizumab. Seventy-seven patients with recurrent GBMs were retrospectively examined. MRI scans were obtained before and approximately 6 weeks after treatment with bevacizumab. Graded fDMs were created by registering datasets to each patient's pretreatment scan and then performing voxel-wise subtraction between post- and pretreatment ADC maps. Voxels were categorized according to the degree of change in ADC within pretreatment fluid-attenuated inversion recovery (FLAIR) and contrast-enhancing regions of interest (ROIs). We found that the volume of tissue showing decreased ADC within both FLAIR and contrast-enhancing regions stratified OS (log-rank, P < .05). fDMs applied to contrast-enhancing ROIs more accurately predicted OS compared with fDMs applied to FLAIR ROIs. Graded fDMs (showing voxels with decreased ADC between 0.25 and 0.4 µm2/ms) were more predictive of OS than traditional (single threshold) fDMs, and the predictive ability of graded fDMs could be enhanced even further by adding the ADC characteristics from the fDM-classified voxels to the analysis (log-rank, P < .001). These results demonstrate that spatially resolved diffusion-based tumor metrics are a powerful imaging biomarker of survival in patients with recurrent GBM treated with bevacizumab. PMID:21856685

  18. Modeling of GPS tropospheric delay wet Neill mapping function (NMF)

    NASA Astrophysics Data System (ADS)

    Sakidin, Hamzah; Ahmad, Asmala; Bugis, Ismadi

    2014-10-01

    The modeling of the GPS tropospheric delay mapping function should be revised by modifying or simplify its mathematical model. Some current mapping functions models are separated into hydrostatic and the wet part. The current tropospheric delay models use mapping functions in the form of continued fractions. This model is quite complex and need to be simplified. By using regression method, the wet mapping function models has been selected to be simplified. There are eleven operations for wet mapping function component of Neill Mapping Function (NMF), to be carried out before getting the mapping function scale factor. So, there is a need to simplify the mapping function models to allow faster calculation and also better understanding of the models.

  19. 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.

  20. 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…

  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. 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

  3. 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.

  4. Transport, diffusion, and energy studies in the Arnold-Beltrami-Childress map

    NASA Astrophysics Data System (ADS)

    Das, Swetamber; Gupte, Neelima

    2017-09-01

    We study the transport and diffusion properties of passive inertial particles described by a six-dimensional dissipative bailout embedding map. The base map chosen for the study is the three-dimensional incompressible Arnold-Beltrami-Childress (ABC) map chosen as a representation of volume preserving flows. There are two distinct cases: the two-action and the one-action cases, depending on whether two or one of the parameters (A ,B ,C ) exceed 1. The embedded map dynamics is governed by two parameters (α ,γ ), which quantify the mass density ratio and dissipation, respectively. There are important differences between the aerosol (α <1 ) and the bubble (α >1 ) regimes. We have studied the diffusive behavior of the system and constructed the phase diagram in the parameter space by computing the diffusion exponents η . Three classes have been broadly classified—subdiffusive transport (η <1 ), normal diffusion (η ≈1 ), and superdiffusion (η >1 ) with η ≈2 referred to as the ballistic regime. Correlating the diffusive phase diagram with the phase diagram for dynamical regimes seen earlier, we find that the hyperchaotic bubble regime is largely correlated with normal and superdiffusive behavior. In contrast, in the aerosol regime, ballistic superdiffusion is seen in regions that largely show periodic dynamical behaviors, whereas subdiffusive behavior is seen in both periodic and chaotic regimes. The probability distributions of the diffusion exponents show power-law scaling for both aerosol and bubbles in the superdiffusive regimes. We further study the Poincáre recurrence times statistics of the system. Here, we find that recurrence time distributions show power law regimes due to the existence of partial barriers to transport in the phase space. Moreover, the plot of average particle kinetic energies versus the mass density ratio for the two-action case exhibits a devil's staircase-like structure for higher dissipation values. We explain these results

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

    PubMed Central

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

    2015-01-01

    The functional neuroanatomy of speech processing has been investigated using positron emission tomography (PET) and functional magnetic resonance imaging (fMRI) for more than 20 years. 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 processes. Using sentences with two levels of linguistic complexity, along with a control condition consisting of unintelligible noise-vocoded speech, we recovered a hierarchical organization of the 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

  6. Mapping Functional Connectivity in Patients with Brain Lesions

    PubMed Central

    Guggisberg, Adrian G.; Honma, Susanne M.; Findlay, Anne M.; Dalal, Sarang S.; Kirsch, Heidi E.; Berger, Mitchel S.; Nagarajan, Srikantan S.

    2013-01-01

    OBJECTIVE Although electrophysiological measures of functional connectivity between brain areas are widely used, the spatial distribution of functional interactions as well as the disturbance introduced by focal brain lesions remains poorly understood. Based on the rationale that damaged brain tissue can be expected to be disconnected from the physiological interactions among healthy areas, this study aimed to map the functionality of brain areas according to their connectivity with other areas. METHODS Magnetoencephalographic (MEG) recordings of spontaneous cortical activity during resting state were obtained from 15 consecutive patients with focal brain lesions and from 14 healthy controls. Neural activity at each volume element (voxel) in the brain was estimated using an adaptive spatial filtering technique. For each brain voxel, the mean imaginary coherence of all its connections with other brain voxels was then caluculated as an index of functional connectivity, and the results compared across brain regions and between subjects. RESULTS The magnitude of the mean imaginary coherence of all voxels and subjects was greatest in the alpha frequency range corresponding to the human cortical idling rhythm. In healthy subjects, functionally critical brain areas such as the somatosensory and language cortices had the highest alpha coherence. When compared to healthy controls, all lesion patients had diffuse or scattered brain areas with decreased coherence. Patients with lesion-induced neurological deficits displayed decreased connectivity estimates in the corresponding brain area compared to intact contralateral regions. In tumor patients without preoperative neurological deficits, brain areas showing decreased coherence could be surgically resected without the occurrence of post-surgical deficits. CONCLUSION Resting state coherence measured with MEG is capable of mapping the functional connectivity of the brain, and can therefore offer valuable information for use in

  7. Functional materials discovery using energy-structure-function maps.

    PubMed

    Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz; Holden, Daniel; Little, Marc A; Chong, Samantha Y; Slater, Benjamin J; McMahon, David P; Bonillo, Baltasar; Stackhouse, Chloe J; Stephenson, Andrew; Kane, Christopher M; Clowes, Rob; Hasell, Tom; Cooper, Andrew I; Day, Graeme M

    2017-03-30

    Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

  8. Functional materials discovery using energy-structure-function maps

    NASA Astrophysics Data System (ADS)

    Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz; Holden, Daniel; Little, Marc A.; Chong, Samantha Y.; Slater, Benjamin J.; McMahon, David P.; Bonillo, Baltasar; Stackhouse, Chloe J.; Stephenson, Andrew; Kane, Christopher M.; Clowes, Rob; Hasell, Tom; Cooper, Andrew I.; Day, Graeme M.

    2017-03-01

    Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

  9. Precision Functional Mapping of Individual Human Brains.

    PubMed

    Gordon, Evan M; Laumann, Timothy O; Gilmore, Adrian W; Newbold, Dillan J; Greene, Deanna J; Berg, Jeffrey J; Ortega, Mario; Hoyt-Drazen, Catherine; Gratton, Caterina; Sun, Haoxin; Hampton, Jacqueline M; Coalson, Rebecca S; Nguyen, Annie L; McDermott, Kathleen B; Shimony, Joshua S; Snyder, Abraham Z; Schlaggar, Bradley L; Petersen, Steven E; Nelson, Steven M; Dosenbach, Nico U F

    2017-08-16

    Human functional MRI (fMRI) research primarily focuses on analyzing data averaged across groups, which limits the detail, specificity, and clinical utility of fMRI resting-state functional connectivity (RSFC) and task-activation maps. To push our understanding of functional brain organization to the level of individual humans, we assembled a novel MRI dataset containing 5 hr of RSFC data, 6 hr of task fMRI, multiple structural MRIs, and neuropsychological tests from each of ten adults. Using these data, we generated ten high-fidelity, individual-specific functional connectomes. This individual-connectome approach revealed several new types of spatial and organizational variability in brain networks, including unique network features and topologies that corresponded with structural and task-derived brain features. We are releasing this highly sampled, individual-focused dataset as a resource for neuroscientists, and we propose precision individual connectomics as a model for future work examining the organization of healthy and diseased individual human brains. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    PubMed

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

    2016-04-01

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

  11. Infarct volume on apparent diffusion coefficient maps correlates with length of stay and outcome after middle cerebral artery stroke.

    PubMed

    Engelter, Stefan T; Provenzale, James M; Petrella, Jeffrey R; DeLong, David M; Alberts, Mark J

    2003-01-01

    Diffusion-weighted MRI (DWI) can depict acute ischemia based on decreased apparent diffusion coefficient (ADC) values. ADC maps, unlike DWI (which have contributions from T2 properties), solely reflect diffusion properties. Recent studies indicate that severity of neurological deficit corresponds with degree of ADC alteration. To determine whether infarct volume on ADC maps correlates with length of hospitalization and clinical outcome in patients with acute ischemic middle cerebral artery (MCA) stroke. Forty-five consecutive patients with acute (3 SDs below the average ADC value of a contralateral control region. Infarct volume was correlated with length of hospitalization and 6-month outcome assessed with Glasgow Outcome Scale (GOS), Modified Rankin Score (mRS), Barthel Index (BI) and a dichotomized outcome status with favorable outcome defined as GOS 1, mRS or=95. Infarct volume on ADC maps ranged from 0.2 to 187 cm(3) and was significantly correlated with length of hospitalization (p < 0.001, r = 0.67). Furthermore, ADC infarct volume was significantly correlated with GOS (r = 0.73), mRS (r = 0.68), BI (r = 0.67) and outcome status (r = 0.65) (each p < 0.001). Multiple logistic regression revealed a statistically significant correlation between ADC infarct volume and outcome status (p < 0.05), but none for Canadian Neurological Scale score, age and gender (p >0.05 each). Infarct volume measured by using a quantitative definition for infarcted tissue on ADC maps correlated significantly with length of hospitalization (as a possible surrogate marker for short-term outcome) and functional outcome after 6 months. ADC infarct volume may provide prognostic information for patients with acute ischemic MCA stroke. Copyright 2003 S. Karger AG, Basel

  12. 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.

  13. Mapping the functional yeast ABC transporter interactome

    PubMed Central

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

    2013-01-01

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

  14. Improved Diffuse Foreground Subtraction with the ILC Method: CMB Map and Angular Power Spectrum Using Planck and WMAP Observations

    NASA Astrophysics Data System (ADS)

    Sudevan, Vipin; Aluri, Pavan K.; Yadav, Sarvesh Kumar; Saha, Rajib; Souradeep, Tarun

    2017-06-01

    We report an improved technique for diffuse foreground minimization from Cosmic Microwave Background (CMB) maps using a new multiphase iterative harmonic space internal-linear-combination (HILC) approach. Our method nullifies a foreground leakage that was present in the old and usual iterative HILC method. In phase 1 of the multiphase technique, we obtain an initial cleaned map using the single iteration HILC approach over the desired portion of the sky. In phase 2, we obtain a final CMB map using the iterative HILC approach; however, now, to nullify the leakage, during each iteration, some of the regions of the sky that are not being cleaned in the current iteration are replaced by the corresponding cleaned portions of the phase 1 map. We bring all input frequency maps to a common and maximum possible beam and pixel resolution at the beginning of the analysis, which significantly reduces data redundancy, memory usage, and computational cost, and avoids, during the HILC weight calculation, the deconvolution of partial sky harmonic coefficients by the azimuthally symmetric beam and pixel window functions, which in a strict mathematical sense, are not well defined. Using WMAP 9 year and Planck 2015 frequency maps, we obtain foreground-cleaned CMB maps and a CMB angular power spectrum for the multipole range 2≤slant {\\ell }≤slant 2500. Our power spectrum matches the published Planck results with some differences at different multipole ranges. We validate our method by performing Monte Carlo simulations. Finally, we show that the weights for HILC foreground minimization have the intrinsic characteristic that they also tend to produce a statistically isotropic CMB map.

  15. Apparent diffusion coefficient maps in the assessment of surgical patients with lumbar spine degeneration

    PubMed Central

    Kalinin, Andrey A.; Patel, Arpan A.; Miller, Eric J.; Bohl, Michael A.; Stepanov, Ivan A.; Bardonova, Liudmila A.; Kerimbaev, Talgat; Asantsev, Anton O.; Giers, Morgan B.; Preul, Mark C.; Byvaltsev, Vadim A.

    2017-01-01

    Purpose To assess the utility of apparent diffusion coefficient (ADC) maps for the assessment of patients with advanced degenerative lumbar spine disease and describe characteristic features of ADC maps in various degenerative lumbar spinal conditions. Methods T1-weighted, T2-weighted and diffusion weighted (DWI) MR images of 100 consecutive patients admitted to the spinal surgery service were assessed. ADC maps were generated from DWI images using Osyrix software. The ADC values and characteristic ADC maps were assessed in the regions of interest over the different pathological entities of the lumbar spine. Results The study included 452 lumbar vertebral segments available for analysis of ADCs. Characteristic ADC map features were identified for protrusion, extrusion and sequester types of lumbar disk herniations, spondylolisthesis, reactive Modic endplate changes, Pfirrmann grades of IVD degeneration, and compromised spinal nerves. Compromised nerve roots had significantly higher mean ADC values than adjacent (p < 0.001), contralateral (p < 0.001) or adjacent contralateral (p < 0.001) nerve roots. Compared to the normal bone marrow, Modic I changes showed higher ADC values (p = 0.01) and Modic 2 changes showed lower ADC values (p = 0.02) respectively. ADC values correlated with the Pfirrmann grading, however differed from herniated and non-herniated disks of the matched Pfirrmann 3 and 4 grades. Conclusion Quantitative and qualitative evaluation of ADC mapping may provide additional useful information regarding the fluid dynamics of the degenerated spine and may complement standard MRI imaging protocol for the comprehensive assessment of surgical patients with lumbar spine pathology. ADC maps were advantageous in differentiating reactive bone marrow changes, and more precise assessment of the disk degeneration state. ADC mapping of compressed nerve roots showed promise but requires further investigation on a larger cohort of patients. PMID:28846710

  16. Apparent diffusion coefficient maps in the assessment of surgical patients with lumbar spine degeneration.

    PubMed

    Belykh, Evgenii; Kalinin, Andrey A; Patel, Arpan A; Miller, Eric J; Bohl, Michael A; Stepanov, Ivan A; Bardonova, Liudmila A; Kerimbaev, Talgat; Asantsev, Anton O; Giers, Morgan B; Preul, Mark C; Byvaltsev, Vadim A

    2017-01-01

    To assess the utility of apparent diffusion coefficient (ADC) maps for the assessment of patients with advanced degenerative lumbar spine disease and describe characteristic features of ADC maps in various degenerative lumbar spinal conditions. T1-weighted, T2-weighted and diffusion weighted (DWI) MR images of 100 consecutive patients admitted to the spinal surgery service were assessed. ADC maps were generated from DWI images using Osyrix software. The ADC values and characteristic ADC maps were assessed in the regions of interest over the different pathological entities of the lumbar spine. The study included 452 lumbar vertebral segments available for analysis of ADCs. Characteristic ADC map features were identified for protrusion, extrusion and sequester types of lumbar disk herniations, spondylolisthesis, reactive Modic endplate changes, Pfirrmann grades of IVD degeneration, and compromised spinal nerves. Compromised nerve roots had significantly higher mean ADC values than adjacent (p < 0.001), contralateral (p < 0.001) or adjacent contralateral (p < 0.001) nerve roots. Compared to the normal bone marrow, Modic I changes showed higher ADC values (p = 0.01) and Modic 2 changes showed lower ADC values (p = 0.02) respectively. ADC values correlated with the Pfirrmann grading, however differed from herniated and non-herniated disks of the matched Pfirrmann 3 and 4 grades. Quantitative and qualitative evaluation of ADC mapping may provide additional useful information regarding the fluid dynamics of the degenerated spine and may complement standard MRI imaging protocol for the comprehensive assessment of surgical patients with lumbar spine pathology. ADC maps were advantageous in differentiating reactive bone marrow changes, and more precise assessment of the disk degeneration state. ADC mapping of compressed nerve roots showed promise but requires further investigation on a larger cohort of patients.

  17. 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.

  18. A Stable Finite-Difference Scheme for Population Growth and Diffusion on a Map

    PubMed Central

    Callegari, S.; Lake, G. R.; Tkachenko, N.; Weissmann, J. D.; Zollikofer, Ch. P. E.

    2017-01-01

    We describe a general Godunov-type splitting for numerical simulations of the Fisher–Kolmogorov–Petrovski–Piskunov growth and diffusion equation on a world map with Neumann boundary conditions. The procedure is semi-implicit, hence quite stable. Our principal application for this solver is modeling human population dispersal over geographical maps with changing paleovegetation and paleoclimate in the late Pleistocene. As a proxy for carrying capacity we use Net Primary Productivity (NPP) to predict times for human arrival in the Americas. PMID:28085882

  19. 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

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

    PubMed

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

    2013-12-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

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

    PubMed

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

    2014-12-01

    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. >20ms, the sensitivity to small axons (diameter<2μm) 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 (1-5ms). 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 of ~1.27-5.54μm). The estimated values were in good agreement with histology, including the small axon diameters (<2.5μm). This study establishes a framework for the quantification of nerve morphology using the OGSE method with high sensitivity to small axons.

  3. 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

  4. 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.

  5. 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.

  6. A new substitution-diffusion based image cipher using chaotic standard and logistic maps

    NASA Astrophysics Data System (ADS)

    Patidar, Vinod; Pareek, N. K.; Sud, K. K.

    2009-07-01

    In this paper, we propose a new loss-less symmetric image cipher based on the widely used substitution-diffusion architecture which utilizes chaotic standard and logistic maps. It is specifically designed for the coloured images, which are 3D arrays of data streams. The initial condition, system parameter of the chaotic standard map and number of iterations together constitute the secret key of the algorithm. The first round of substitution/confusion is achieved with the help of intermediate XORing keys calculated from the secret key. Then two rounds of diffusion namely the horizontal and vertical diffusions are completed by mixing the properties of horizontally and vertically adjacent pixels, respectively. In the fourth round, a robust substitution/confusion is accomplished by generating an intermediate chaotic key stream (CKS) image in a novel manner with the help of chaotic standard and logistic maps. The security and performance of the proposed image encryption technique has been analyzed thoroughly using various statistical analysis, key sensitivity analysis, differential analysis, key space analysis, speed analysis, etc. Results of the various types of analysis are encouraging and suggest that the proposed image encryption technique is able to manage the trade offs between the security and speed and hence suitable for the real-time secure image and video communication applications.

  7. Improved atmospheric mapping functions for VLBI and GPS

    NASA Astrophysics Data System (ADS)

    Niell, A. E.

    2000-10-01

    New mapping functions based on in situ meteorological parameters have been developed for calculating the radio path length through the atmosphere at elevations down to 3°. The hydrostatic component of the mapping function is related to the geopotential height of the 200 mb isobaric pressure level above the site and provides a factor of two improvement in accuracy and precision over previous hydrostatic mapping functions at mid-latitudes. The wet component of the mapping function is calculated from the vertical profile of wet refractivity at the site but will provide an improvement of only about twenty-five percent. However, since the effect of known errors in the hydrostatic mapping function dominates that from the wet component, except near the equator, implementation of these mapping functions should reduce the contribution of the atmosphere to errors in estimates by VLBI and GPS of both the vertical component of site position and the radio propagation delay due to water vapor in the atmosphere.

  8. Electron distribution function formation in regions of diffuse aurora

    NASA Astrophysics Data System (ADS)

    Khazanov, G. V.; Tripathi, A. K.; Sibeck, D.; Himwich, E.; Glocer, A.; Singhal, R. P.

    2015-11-01

    The precipitation of high-energy magnetospheric electrons (E ˜ 600 eV-10 KeV) in the diffuse aurora contributes significant energy flux into the Earth's ionosphere. To fully understand the formation of this flux at the upper ionospheric boundary, ˜700-800 km, it is important to consider the coupled ionosphere-magnetosphere system. In the diffuse aurora, precipitating electrons initially injected from the plasma sheet via wave-particle interaction processes degrade in the atmosphere toward lower energies and produce secondary electrons via impact ionization of the neutral atmosphere. These precipitating electrons can be additionally reflected upward from the two conjugate ionospheres, leading to a series of multiple reflections through the magnetosphere. These reflections greatly influence the initially precipitating flux at the upper ionospheric boundary (700-800 km) and the resultant population of secondary electrons and electrons cascading toward lower energies. In this paper, we present the solution of the Boltzman-Landau kinetic equation that uniformly describes the entire electron distribution function in the diffuse aurora, including the affiliated production of secondary electrons (E < 600 eV) and its energy interplay in the magnetosphere and two conjugated ionospheres. This solution takes into account, for the first time, the formation of the electron distribution function in the diffuse auroral region, beginning with the primary injection of plasma sheet electrons via both electrostatic electron cyclotron harmonic waves and whistler mode chorus waves to the loss cone, and including their subsequent multiple atmospheric reflections in the two magnetically conjugated ionospheres. It is demonstrated that magnetosphere-ionosphere coupling is key in forming the electron distribution function in the diffuse auroral region.

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

    DOE PAGES

    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.

  10. 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.

  11. Functional Mapping with Simultaneous MEG and EEG.

    PubMed

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

    2010-06-14

    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.

  12. 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

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

    PubMed

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

    2016-11-09

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

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

    PubMed

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

    2006-02-01

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

  15. 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.

  16. Semiparametric Bayesian local functional models for diffusion tensor tract statistics☆

    PubMed Central

    Hua, Zhaowei; Dunson, David B.; Gilmore, John H.; Styner, Martin A.; Zhu, Hongtu

    2012-01-01

    We propose a semiparametric Bayesian local functional model (BFM) for the analysis of multiple diffusion properties (e.g., fractional anisotropy) along white matter fiber bundles with a set of covariates of interest, such as age and gender. BFM accounts for heterogeneity in the shape of the fiber bundle diffusion properties among subjects, while allowing the impact of the covariates to vary across subjects. A nonparametric Bayesian LPP2 prior facilitates global and local borrowings of information among subjects, while an infinite factor model flexibly represents low-dimensional structure. Local hypothesis testing and credible bands are developed to identify fiber segments, along which multiple diffusion properties are significantly associated with covariates of interest, while controlling for multiple comparisons. Moreover, BFM naturally group subjects into more homogeneous clusters. Posterior computation proceeds via an efficient Markov chain Monte Carlo algorithm. A simulation study is performed to evaluate the finite sample performance of BFM. We apply BFM to investigate the development of white matter diffusivities along the splenium of the corpus callosum tract and the right internal capsule tract in a clinical study of neurodevelopment in new born infants. PMID:22732565

  17. Leading Non-Gaussian Corrections for Diffusion Orientation Distribution Function

    PubMed Central

    Jensen, Jens H.; Helpern, Joseph A.; Tabesh, Ali

    2014-01-01

    An analytical representation of the leading non-Gaussian corrections for a class of diffusion orientation distribution functions (dODFs) is presented. This formula is constructed out of the diffusion and diffusional kurtosis tensors, both of which may be estimated with diffusional kurtosis imaging (DKI). By incorporating model-independent non-Gaussian diffusion effects, it improves upon the Gaussian approximation used in diffusion tensor imaging (DTI). This analytical representation therefore provides a natural foundation for DKI-based white matter fiber tractography, which has potential advantages over conventional DTI-based fiber tractography in generating more accurate predictions for the orientations of fiber bundles and in being able to directly resolve intra-voxel fiber crossings. The formula is illustrated with numerical simulations for a two-compartment model of fiber crossings and for human brain data. These results indicate that the inclusion of the leading non-Gaussian corrections can significantly affect fiber tractography in white matter regions, such as the centrum semiovale, where fiber crossings are common. PMID:24738143

  18. 3FunMap: full-sib family functional mapping of dynamic traits.

    PubMed

    Tong, Chunfa; Wang, Zhong; Zhang, Bo; Shi, Jisen; Wu, Rongling

    2011-07-15

    Functional mapping that embeds the developmental mechanisms of complex traits shows great power to study the dynamic pattern of genetic effects triggered by individual quantitative trait loci (QTLs). A full-sib family, produced by crossing two heterozygous parents, is characteristic of uncertainties about cross-type at a locus and linkage phase between different loci. Integrating functional mapping into a full-sib family requires a model selection procedure capable of addressing these uncertainties. 3FunMap, written in VC++ 6.0, provides a flexible and extensible platform to perform full-sib functional mapping of dynamic traits. Functions in the package encompass linkage phase determination, marker map construction and the pattern identification of QTL segregation, dynamic tests of QTL effects, permutation tests and numerical simulation. We demonstrate the features of 3FunMap through real data analysis and computer simulation. http://statgen.psu.edu/software.

  19. Large deformation diffeomorphic metric mapping of orientation distribution functions.

    PubMed

    Du, Jia; Goh, Alvina; Qiu, Anqi

    2011-01-01

    We propose a novel large deformation diffeomorphic registration algorithm to align high angular resolution diffusion images (HARDI) characterized by Orientation Distribution Functions (ODF). Our proposed algorithm seeks an optimal diffeomorphism of large deformation between two ODF fields in a spatial volume domain and at the same time, locally reorients an ODF in a manner such that it remains consistent with the surrounding anatomical structure. We first extend ODFs traditionally defined in a unit sphere to a generalized ODF defined in R3. This makes it easy for an affine transformation as well as a diffeomorphic group action to be applied on the ODF. We then construct a Riemannian space of the generalized ODFs and incorporate its Riemannian metric for the similarity of ODFs into a variational problem defined under the large deformation diffeomorphic metric mapping (LDDMM) framework. We finally derive the gradient of the cost function in both Riemannian spaces of diffeomorphisms and the generalized ODFs, and present its numerical implementation. Both synthetic and real brain HARDI data are used to illustrate the performance of our registration algorithm.

  20. Stochastic Functional Data Analysis: A Diffusion Model-based Approach

    PubMed Central

    Zhu, Bin; Song, Peter X.-K.; Taylor, Jeremy M.G.

    2011-01-01

    Summary This paper presents a new modeling strategy in functional data analysis. We consider the problem of estimating an unknown smooth function given functional data with noise. The unknown function is treated as the realization of a stochastic process, which is incorporated into a diffusion model. The method of smoothing spline estimation is connected to a special case of this approach. The resulting models offer great flexibility to capture the dynamic features of functional data, and allow straightforward and meaningful interpretation. The likelihood of the models is derived with Euler approximation and data augmentation. A unified Bayesian inference method is carried out via a Markov Chain Monte Carlo algorithm including a simulation smoother. The proposed models and methods are illustrated on some prostate specific antigen data, where we also show how the models can be used for forecasting. PMID:21418053

  1. 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.

  2. A diffusible factor involved in MAP-kinase ERK2-regulated development of Dictyostelium.

    PubMed

    Maeda, M; Kuwayama, H

    2000-06-01

    Mitogen-activated protein (MAP)-kinase extracellular signal regulated kinase (ERK2) is essential for regulation of the intracellular cyclic adenosine monophosphate (cAMP) level in Dictyostelium. The mutant lacking ERK2, erk2-null, is arrested at the pre-aggregation stage, but develops into a fruiting body in a mixed population of wild-type and mutant cells. This fact implies that wild-type cells provide a certain factor that is missing in erk2-null. It was clarified that both wild-type strains KAx3 and Ax2 secreted a diffusible factor that enables erk2-null to develop. The fruiting body formed from erk2-null cells was smaller than that formed by the wild-type cells and consisted of a small sorus supported by a slender stalk with a single row of vacuolated stalk cells. The resulting spores were able to germinate and multiply on a bacterial lawn, but they were unable to develop unless the factor was provided. After 8 h of starvation, wild-type cells started to secrete the factor, which had a molecular mass of less than 3 kDa and was heat stable. The effect of this factor could not be mimicked by either cAMP or folate. Adenylyl cyclase A and cell surface cAMP receptors cAR1 and cAR3 were all indispensable components for the factor to function. Considering the molecular mass and the mode of action, this factor could be a novel one. Possible targets of this factor are discussed in terms of cAMP-dependent protein kinase activation.

  3. Multislice diffusion mapping for 3-D evolution of cerebral ischemia in a rat stroke model.

    PubMed

    Reith, W; Hasegawa, Y; Latour, L L; Dardzinski, B J; Sotak, C H; Fisher, M

    1995-01-01

    Diffusion-weighted magnetic resonance imaging (DWI) can quantitatively demonstrate cerebral ischemia within minutes after the onset of ischemia. The use of a DWI echo-planar multislice technique in this study and the mapping of the apparent diffusion coefficient (ADC) of water, a reliable indicator of ischemic regions, allow for the detection of the three-dimensional (3-D) evolution of ischemia in a rat stroke model. We evaluated 13 time points from 5 to 180 minutes after occlusion of the middle cerebral artery (MCA) and monitored the 3-D spread of ischemia. Within 5 minutes after the onset of ischemia, regions with reduced ADC values occurred. The core of the lesion, with the lowest absolute ADC values, first appeared in the lateral caudoputamen and frontoparietal cortex, then spread to adjacent areas. The volume of ischemic tissue was 224 +/- 48.5 mm3 (mean +/- SEM) after 180 minutes, ranging from 92 to 320 mm3, and this correlated well with the corrected infarct volume at postmortem (194 +/- 23.1 mm3, r = 0.72, p < 0.05). This experiment demonstrated that 3-D multislice diffusion mapping can detect ischemic regions noninvasively 5 minutes after MCA occlusion and follow the development of ischemia. The distribution of changes in absolute ADC values within the ischemic region can be followed over time, giving important information about the evolution of focal ischemia.

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

    NASA Astrophysics Data System (ADS)

    Tekkaya, Ceren

    2003-01-01

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

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

    PubMed

    Zhang, Changzhe; Bu, Yuxiang

    2016-09-14

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

  6. A functional methylome map of ulcerative colitis

    PubMed Central

    Häsler, Robert; Feng, Zhe; Bäckdahl, Liselotte; Spehlmann, Martina E.; Franke, Andre; Teschendorff, Andrew; Rakyan, Vardhman K.; Down, Thomas A.; Wilson, Gareth A.; Feber, Andrew; Beck, Stephan; Schreiber, Stefan; Rosenstiel, Philip

    2012-01-01

    The etiology of inflammatory bowel diseases is only partially explained by the current genetic risk map. It is hypothesized that environmental factors modulate the epigenetic landscape and thus contribute to disease susceptibility, manifestation, and progression. To test this, we analyzed DNA methylation (DNAm), a fundamental mechanism of epigenetic long-term modulation of gene expression. We report a three-layer epigenome-wide association study (EWAS) using intestinal biopsies from 10 monozygotic twin pairs (n = 20 individuals) discordant for manifestation of ulcerative colitis (UC). Genome-wide expression scans were generated using Affymetrix UG 133 Plus 2.0 arrays (layer 1). Genome-wide DNAm scans were carried out using Illumina 27k Infinium Bead Arrays to identify methylation variable positions (MVPs, layer 2), and MeDIP-chip on Nimblegen custom 385k Tiling Arrays to identify differentially methylated regions (DMRs, layer 3). Identified MVPs and DMRs were validated in two independent patient populations by quantitative real-time PCR and bisulfite-pyrosequencing (n = 185). The EWAS identified 61 disease-associated loci harboring differential DNAm in cis of a differentially expressed transcript. All constitute novel candidate risk loci for UC not previously identified by GWAS. Among them are several that have been functionally implicated in inflammatory processes, e.g., complement factor CFI, the serine protease inhibitor SPINK4, and the adhesion molecule THY1 (also known as CD90). Our study design excludes nondisease inflammation as a cause of the identified changes in DNAm. This study represents the first replicated EWAS of UC integrated with transcriptional signatures in the affected tissue and demonstrates the power of EWAS to uncover unexplained disease risk and molecular events of disease manifestation. PMID:22826509

  7. A functional methylome map of ulcerative colitis.

    PubMed

    Häsler, Robert; Feng, Zhe; Bäckdahl, Liselotte; Spehlmann, Martina E; Franke, Andre; Teschendorff, Andrew; Rakyan, Vardhman K; Down, Thomas A; Wilson, Gareth A; Feber, Andrew; Beck, Stephan; Schreiber, Stefan; Rosenstiel, Philip

    2012-11-01

    The etiology of inflammatory bowel diseases is only partially explained by the current genetic risk map. It is hypothesized that environmental factors modulate the epigenetic landscape and thus contribute to disease susceptibility, manifestation, and progression. To test this, we analyzed DNA methylation (DNAm), a fundamental mechanism of epigenetic long-term modulation of gene expression. We report a three-layer epigenome-wide association study (EWAS) using intestinal biopsies from 10 monozygotic twin pairs (n = 20 individuals) discordant for manifestation of ulcerative colitis (UC). Genome-wide expression scans were generated using Affymetrix UG 133 Plus 2.0 arrays (layer 1). Genome-wide DNAm scans were carried out using Illumina 27k Infinium Bead Arrays to identify methylation variable positions (MVPs, layer 2), and MeDIP-chip on Nimblegen custom 385k Tiling Arrays to identify differentially methylated regions (DMRs, layer 3). Identified MVPs and DMRs were validated in two independent patient populations by quantitative real-time PCR and bisulfite-pyrosequencing (n = 185). The EWAS identified 61 disease-associated loci harboring differential DNAm in cis of a differentially expressed transcript. All constitute novel candidate risk loci for UC not previously identified by GWAS. Among them are several that have been functionally implicated in inflammatory processes, e.g., complement factor CFI, the serine protease inhibitor SPINK4, and the adhesion molecule THY1 (also known as CD90). Our study design excludes nondisease inflammation as a cause of the identified changes in DNAm. This study represents the first replicated EWAS of UC integrated with transcriptional signatures in the affected tissue and demonstrates the power of EWAS to uncover unexplained disease risk and molecular events of disease manifestation.

  8. A generalized diffusion frame for parsimonious representation of functions on data defined manifolds.

    PubMed

    Mhaskar, H N

    2011-05-01

    One of the now standard techniques in semi-supervised learning is to think of a high dimensional data as a subset of a low dimensional manifold embedded in a high dimensional ambient space, and to use projections of the data on eigenspaces of a diffusion map. This paper is motivated by a recent work of Coifman and Maggioni on diffusion wavelets to accomplish such projections approximately using iterates of the heat kernel. In greater generality, we consider a quasi-metric measure space X (in place of the manifold), and a very general operator T defined on the class of integrable functions on X (in place of the diffusion map). We develop a representation of functions on X in terms of linear combinations of iterates of T. Our construction obviates the need to compute the eigenvalues and eigenfunctions of the operator. In addition, the local smoothness of a function f is characterized by the local norm behavior of the terms in our representation of f. This property is similar to that of the classical wavelet representations. Although the operator T utilizes the values of the target function on the entire space, this ability results in automatic "feature detection", leading to a parsimonious representation of the target function. In the case when X is a smooth compact manifold (without boundary), our theory allows T to be any operator that commutes with the heat operator, subject to certain conditions on its eigenvalues. In particular, T can be chosen to be the heat operator itself, or a Green's operator corresponding to a suitable pseudo-differential operator. Copyright © 2011 Elsevier Ltd. All rights reserved.

  9. 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.

  10. Mapping carrier diffusion in single silicon core-shell nanowires with ultrafast optical microscopy.

    PubMed

    Seo, M A; Yoo, J; Dayeh, S A; Picraux, S T; Taylor, A J; Prasankumar, R P

    2012-12-12

    Recent success in the fabrication of axial and radial core-shell heterostructures, composed of one or more layers with different properties, on semiconductor nanowires (NWs) has enabled greater control of NW-based device operation for various applications. (1-3) However, further progress toward significant performance enhancements in a given application is hindered by the limited knowledge of carrier dynamics in these structures. In particular, the strong influence of interfaces between different layers in NWs on transport makes it especially important to understand carrier dynamics in these quasi-one-dimensional systems. Here, we use ultrafast optical microscopy (4) to directly examine carrier relaxation and diffusion in single silicon core-only and Si/SiO(2) core-shell NWs with high temporal and spatial resolution in a noncontact manner. This enables us to reveal strong coherent phonon oscillations and experimentally map electron and hole diffusion currents in individual semiconductor NWs for the first time.

  11. 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

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

    PubMed

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

    2015-12-01

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

  13. 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.

  14. Response Variance in Functional Maps: Neural Darwinism Revisited

    PubMed Central

    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

  15. Functional Mapping of Dynamic Traits with Robust t-Distribution

    PubMed Central

    Wu, Cen; Li, Gengxin; Zhu, Jun; Cui, Yuehua

    2011-01-01

    Functional mapping has been a powerful tool in mapping quantitative trait loci (QTL) underlying dynamic traits of agricultural or biomedical interest. In functional mapping, multivariate normality is often assumed for the underlying data distribution, partially due to the ease of parameter estimation. The normality assumption however could be easily violated in real applications due to various reasons such as heavy tails or extreme observations. Departure from normality has negative effect on testing power and inference for QTL identification. In this work, we relax the normality assumption and propose a robust multivariate -distribution mapping framework for QTL identification in functional mapping. Simulation studies show increased mapping power and precision with the distribution than that of a normal distribution. The utility of the method is demonstrated through a real data analysis. PMID:21966378

  16. 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

  17. 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.

  18. 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.

  19. Decoupling function and anatomy in atlases of functional connectivity patterns: language mapping in tumor patients.

    PubMed

    Langs, Georg; Sweet, Andrew; Lashkari, Danial; Tie, Yanmei; Rigolo, Laura; Golby, Alexandra J; Golland, Polina

    2014-12-01

    In this paper we construct an atlas that summarizes functional connectivity characteristics of a cognitive process from a population of individuals. The atlas encodes functional connectivity structure in a low-dimensional embedding space that is derived from a diffusion process on a graph that represents correlations of fMRI time courses. The functional atlas is decoupled from the anatomical space, and thus can represent functional networks with variable spatial distribution in a population. In practice the atlas is represented by a common prior distribution for the embedded fMRI signals of all subjects. We derive an algorithm for fitting this generative model to the observed data in a population. Our results in a language fMRI study demonstrate that the method identifies coherent and functionally equivalent regions across subjects. The method also successfully maps functional networks from a healthy population used as a training set to individuals whose language networks are affected by tumors. Copyright © 2014. Published by Elsevier Inc.

  20. Thrombotic Thrombocytopenic Purpura with Reversible Neurological Features: Brain Diffusion MRI with ADC Map, Spect and EEG Findings. A Case Report.

    PubMed

    Yerdelen, D; Göksel, B K; Yıldırım, T; Karataş, M; Karaca, S; Reyhan, M; Ozdoğu, H

    2006-11-30

    Although nervous system involvement is common in thrombotic thrombocytopenic purpura (TTP), abnormalities on computerized tomography, magnetic resonance imaging and electroencephalography are not encountered so frequently and if present, these abnormalities are often reversible. We describe a 39-year-old woman with recurring transient focal neurological findings found to have laboratory findings consistent with TTP. In cerebral diffusion weighted images (DWI), diffuse cortical hyperintensity was noted in right frontal lobe, but the ADC (apparent diffusion coefficient) map was normal. Electroencephalography demonstrated lateralized slowing and repeated DWI showed diffuse cortical hyperintensity in the right hemisphere. SPECT showed luxury perfusion in the right hemisphere areas. The patient's condition resolved with plasmapheresis. Our patient illustrates that diffuse hemispheric involvement can be seen in DWI and EEG, and SPECT may show luxury perfusion after resolution of neurological findings in TTP cases. To our knowledge, this is the first TTP case in which the ADC map was normal.

  1. Diagnostic Ability of Retinal Nerve Fiber Layer Thickness Deviation Map for Localized and Diffuse Retinal Nerve Fiber Layer Defects

    PubMed Central

    Shin, Joong Won; Seong, Mincheol; Lee, Jung Wook; Hong, Eun Hee

    2017-01-01

    Purpose. To evaluate the diagnostic ability of the retinal nerve fiber layer (RNFL) deviation map for glaucoma with localized or diffuse RNFL defects. Methods. Eyes of 139 glaucoma patients and 165 healthy subjects were enrolled. All participants were imaged with Cirrus HD-OCT (Carl Zeiss Meditec, Dublin, CA, USA). A RNFL defect was defined as at least 10 contiguous red (<1% level) superpixels in RNFL deviation map. The area, location, and angular width of RNFL defects were automatically measured. We compared sensitivities, specificities, and area under the receiver operating characteristic curves (AUCs) of RNFL deviation map and circumpapillary RNFL thickness for localized and diffuse RNFL defects. Subgroup analysis was performed according to the severity of glaucoma. Results. For localized defects, the area of RNFL defects (AUC, 0.991; sensitivity, 97%; specificity, 90%) in deviation map showed a higher diagnostic performance (p = 0.002) than the best circumpapillary RNFL parameter (inferior RNFL thickness; AUC, 0.914; sensitivity, 79%; specificity, 92%). For diffuse defects, there was no significant difference between the RNFL deviation map and circumpapillary RNFL parameters. In mild glaucoma with localized defect, RNFL deviation map showed a better diagnostic performance than circumpapillary RNFL measurement. Conclusions. RNFL deviation map is a useful tool for evaluating glaucoma regardless of localized or diffuse defect type and has advantages over circumpapillary RNFL measurement for detecting localized RNFL defects. PMID:28168048

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

    PubMed

    Andrzejczak, Chris; Karwowski, Waldemar; Mikusinski, Piotr

    2012-01-01

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

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

    PubMed

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

    2013-10-24

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

  4. The Association between Diffuse Myocardial Fibrosis on Cardiac Magnetic Resonance T1 Mapping and Myocardial Dysfunction in Diabetic Rabbits

    PubMed Central

    Zeng, Mu; Qiao, Yingyan; Wen, Zhaoying; Liu, Jun; Xiao, Enhua; Tan, Changlian; Xie, Yibin; An, Jing; Zhang, Zishu; Fan, Zhanming; Li, Debiao

    2017-01-01

    The objective of this study was to assess the relationship between imaging surrogates for diffuse fibrosis and myocardial dysfunction. Thirty-six New Zealand white rabbits were classified into two groups: a control group (n = 18) and an alloxan-induced diabetes mellitus (DM) group (n = 18). For all rabbits, conventional ultrasonography, two-dimensional speckle tracking, and cardiac magnetic resonance (CMR) T1 mapping were performed; all of the rabbits were then sacrificed for Masson’s staining. The extracellular volume (ECV) was calculated from pre- and post-contrast T1 values and compared with myocardial function measured by echocardiography using Pearson’s correlation. In the DM group, ECV increased as the duration of diabetes increased, consistent with the changes in myocardial fibrosis verified by pathology. Moreover, ECV was strongly correlated with the early diastolic strain rate (r = −0.782, p < 0.001) and moderately correlated with the radial systolic peak strain (r = 0.478, p = 0.045). Thus, ECV is an effective surrogate for myocardial diffuse fibrosis on CMR imaging, and higher ECV values are associated with an increased impairment of myocardial diastolic function. PMID:28338005

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

    PubMed

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

    2012-11-01

    Spatial transformation for diffusion spectrum imaging (DSI) is an important step for group analyses of DSI datasets. In this study, we developed a transformation method for DSI datasets under the framework of large deformation diffeomorphic metric mapping (LDDMM), which is termed LDDMM-DSI. The proposed method made use of the fact that a DSI dataset is 6D, and generalized the original 2D/3D LDDMM algorithm to the 6D case with some modifications made for the DSI datasets. In this manner, the conventional reorientation problem that arises from transforming diffusion-weighted datasets was avoided by making the DSI datasets capable of being freely deformed in the q-space. The algorithm treated the data-matching task as a variational problem under the LDDMM framework and sought optimal velocity fields from which the generated transformations were diffeomorphic and the transformation curve was a geodesic. The mathematical materials and numerical implementation are detailed in the paper, and experiments were performed to analyze the proposed method on real brain DSI datasets. The results showed that the method was capable of registering different DSI datasets in both global structural shapes and local diffusion profiles. In conclusion, the proposed method can facilitate group analyses of DSI datasets and the generation of a DSI template. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. Diffeomorphic metric mapping of hybrid diffusion imaging based on BFOR signal basis.

    PubMed

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

    2013-01-01

    In this paper, we 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), denoted as LDDMM-HYDI. 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 thus reduces memory requirement. In addition, since the BFOR signal basis is orthonormal, the L2 norm that quantifies the differences in 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. Using real HYDI datasets, 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.

  7. 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.

  8. 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

  9. 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.

  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. Investigation of the Dynamical Structure and Diffusion in a System of Hamiltonian Type: 4-Dimensional Symplectic Map

    NASA Astrophysics Data System (ADS)

    Todorovic, N.

    2009-09-01

    The Nekhoroshev theorem (Nekhoroshev 1977) is one of the most important theorems in modern Hamiltonian dynamics. This theorem applies to quasi integrable Hamiltonian systems of type H(I,\\varphi)=h(I)+\\varepsilon f (I, \\varphi), where h(I) is the integrable approximation, f(I, \\varphi) the perturbing function, \\varepsilon is a small perturbing parameter, Iin R^n are the actions and \\varphi in T^n the angles of the system. With some additional geometrical and analytical properties, the theorem provides the stability of actions in exponentially long times. In recent years it has been shown that with some modifications the Nekhoroshev theorem can be applied to the problems in Solar system dynamics (Morbidelli and Guzzo 1997, Guzzo et al 2002, Efthymiopoulos and Sándor 2105, Pavlović and Guzzo 2008). In this work, we are interested to observe numerically a Nekhoroshev like behavior on a model given with a 4-dimensional symplectic map. The model is not in the quasi-integrable form, i.e. independently from the perturbation it contains some additional hyperbolic structures (they appear in the model as primary resonances). Since the hyperbolic structures exist even for zero perturbation, the system will belong to the class of the so called a priori unstable systems. The main numerical tool used here was the Fast Lyapunov Indicator- FLI, introduced in (Froschlé et al. 1997, 2000). As an indicator of chaotic motion, FLI gives very precise and fast information about the chaoticity of an orbit. Also, among regular orbits, FLI is able to differentiate resonant from nonresonant motions. This property of FLI allows us to visualize the studied system and to obtain the Arnold web of the model (Froschlé et al. 2000). In such a way it was possible to observe the transition from a stable Nekhoroshev like structure (regular orbits dominate) to a globally chaotic system where resonances overlap, also known as Chirikov regime. Numerically, this transition happens when between 50

  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. 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.

  14. 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

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

    PubMed

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

    2016-02-01

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

  16. T1 mapping in dilated cardiomyopathy with cardiac magnetic resonance: quantification of diffuse myocardial fibrosis and comparison with endomyocardial biopsy.

    PubMed

    aus dem Siepen, Fabian; Buss, Sebastian J; Messroghli, Daniel; Andre, Florian; Lossnitzer, Dirk; Seitz, Sebastian; Keller, Marius; Schnabel, Philipp A; Giannitsis, Evangelos; Korosoglou, Grigorios; Katus, Hugo A; Steen, Henning

    2015-02-01

    The aim of this study was to determine the value of extracellular volume fraction (ECV) for the non-invasive assessment of diffuse myocardial fibrosis (MF) in different stages of systolic left ventricular (LV) dysfunction in dilated cardiomyopathy (DCM) in comparison with endomyocardial biopsy. Non-invasive ECV assessment using cardiovascular magnetic resonance (CMR) T1 mapping reflects diffuse MF in patients with severe DCM, but earlier stages of DCM with mild LV functional impairment have not been investigated yet. Forty-five subjects with mild functional impairment and LV dilation ['early DCM', ejection fraction (EF) 45-55%], 29 with LV dysfunction and volume dilatation ('DCM', EF <45%) and 56 healthy volunteers (controls) underwent standard CMR imaging, late gadolinium enhancement (LGE) and T1 mapping for the calculation of ECV. The collagen volume fraction (CVF) was quantified histologically from endomyocardial biopsies of 24 DCM patients out of the study cohort. The ECV between 'early DCM' (25 ± 4%), 'DCM' (27 ± 4%), and controls (23 ± 3; P < 0.05 for all) differed significantly. There was a weak inverse correlation between ECV and EF (r = -0.35; P < 0.01). A strong correlation between ECV and CVF could be detected (r = 0.85; P = 0.01). The cut-off value for ECV to differentiate between healthy myocardium and DCM was 26% (specificity 91.1%, sensitivity 62.1%, area under the curve 0.8, P < 0.0001). ECV is already elevated at early stages of functional impairment, whereby an overlap between early DCM and controls is present. But 31% of the early DCM patients had an ECV fraction above the mean ±2 SD ECV of controls. ECV measurement with CMR reflects myocardial collagen content in DCM. Therefore, CMR-based assessment of ECV may have the potential to serve as a non-invasive tool for the quantification of diffuse MF in order to monitor therapy response and aid risk stratification in different stages of DCM. Published on behalf of the European Society of

  17. ChalkBoard: Mapping Functions to Polygons

    NASA Astrophysics Data System (ADS)

    Matlage, Kevin; Gill, Andy

    ChalkBoard is a domain specific language for describing images. The ChalkBoard language is uncompromisingly functional and encourages the use of modern functional idioms. ChalkBoard uses off-the-shelf graphics cards to speed up rendering of functional descriptions. In this paper, we describe the design of the core ChalkBoard language, and the architecture of our static image generation accelerator.

  18. Fractional Brownian motions: memory, diffusion velocity, and correlation functions

    NASA Astrophysics Data System (ADS)

    Fuliński, A.

    2017-02-01

    Fractional Brownian motions (FBMs) have been observed recently in the measured trajectories of individual molecules or small particles in the cytoplasm of living cells and in other dense composite systems, among others. Various types of FBMs differ in a number of ways, including the strength, range and type of damping of the memory encoded in their definitions, but share several basic characteristics: distributions, non-ergodic properties, and scaling of the second moment, which makes it difficult to determine which type of Brownian motion (fractional or normal) the measured trajectory belongs to. Here, we show, by introducing FBMs with regulated range and strength of memory, that it is the structure of memory which determines their physical properties, including mean velocity of diffusion; therefore, the course and kinetics of several processes (including coagulation and some chemical reactions). We also show that autocorrelation functions possess characteristic features which enable identification of an observed FBM, and of the type of memory governing its trajectory. In memoriam Marian Smoluchowski, on the 100th anniversary of the publication of his seminal papers on Brownian motion and diffusion-limited kinetics.

  19. A Comparative evaluation of voxel-based spatial mapping in diffusion tensor imaging.

    PubMed

    Cabeen, Ryan P; Bastin, Mark E; Laidlaw, David H

    2017-02-01

    This paper presents a comparative evaluation of methods for automated voxel-based spatial mapping in diffusion tensor imaging studies. Such methods are an essential step in computational pipelines and provide anatomically comparable measurements across a population in atlas-based studies. To better understand their strengths and weaknesses, we tested a total of eight methods for voxel-based spatial mapping in two types of diffusion tensor templates. The methods were evaluated with respect to scan-rescan reliability and an application to normal aging. The methods included voxel-based analysis with and without smoothing, two types of region-based analysis, and combinations thereof with skeletonization. The templates included a study-specific template created with DTI-TK and the IIT template serving as a standard template. To control for other factors in the pipeline, the experiments used a common dataset, acquired at 1.5T with a single shell high angular resolution diffusion MR imaging protocol, and tensor-based spatial normalization with DTI-TK. Scan-rescan reliability was assessed using the coefficient of variation (CV) and intraclass correlation (ICC) in eight subjects with three scans each. Sensitivity to normal aging was assessed in a population of 80 subjects aged 25-65 years old, and methods were compared with respect to the anatomical agreement of significant findings and the R(2) of the associated models of fractional anisotropy. The results show that reliability depended greatly on the method used for spatial mapping. The largest differences in reliability were found when adding smoothing and comparing voxel-based and region-based analyses. Skeletonization and template type were found to have either a small or negligible effect on reliability. The aging results showed agreement among the methods in nine brain areas, with some methods showing more sensitivity than others. Skeletonization and smoothing were not major factors affecting sensitivity to aging

  20. Pre-surgical language mapping with functional magnetic resonance imaging.

    PubMed

    Bookheimer, Susan

    2007-06-01

    Patients with lesions in or near eloquent cortex typically undergo one of several invasive techniques to prevent loss of function following surgery. One of the most promising potential clinical applications of functional magnetic resonance imaging (fMRI) is to map these functions as part of the pre-surgical work-up to identify patients at-risk, guide the surgical entry, or tailor the surgical procedure to prevent deficits. While motor and sensory mapping are relatively straightforward, language mapping is far more complex. The language system is variable in location across individuals and in many cases may reorganize partially or completely to the contralateral hemisphere. In addition, multiple regions of the brain contribute to language functioning including essential regions that must not be removed in surgery, and contributory regions that may result in transient or insignificant impairments post-surgery. Despite these challenges, an increasing number of studies have supported the use of fMRI for pre-surgical language mapping in a variety of disorders. This article reviews the literature from three disorders for which patients benefit from preoperative language mapping: epilepsy, brain tumors, and arteriovenous malformations. Each disorder presents unique challenges to language mapping. Specific case studies are presented highlighting the both the potential benefits of preclinical fMRI for language mapping as well as the potential risks and pitfalls.

  1. 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.

  2. Cortical stimulation parameters for functional mapping.

    PubMed

    Corley, Jacquelyn A; Nazari, Pouya; Rossi, Vincent J; Kim, Nora C; Fogg, Louis F; Hoeppner, Thomas J; Stoub, Travis R; Byrne, Richard W

    2017-02-01

    There is significant variation in how patients respond to cortical electrical stimulation. It has been hypothesized that individual demographic and pathologic factors, such as age, sex, disease duration, and MRI findings, may explain this discrepancy. The purpose of our study is to identify specific patient characteristics and their effect on cortical stimulation, and discover the extent of variation in behavioral responses that exists among patients with epilepsy. We retrospectively analyzed data from 92 patients with medically intractable epilepsy who had extra-operative cortical electrical stimulation. Mapping records were evaluated and information gathered about demographic data, as well as the thresholds of stimulation for motor, sensory, speech, and other responses; typical seizure behavior; and the induction of afterdischarges. Ninety-two patient cortical stimulation mapping reports were analyzed. The average of the minimum thresholds for motor response was 4.15mA±2.67. The average of the minimum thresholds for sensory response was 3.50mA±2.15. The average of the minimum thresholds for speech response was 4.48mA±2.42. The average of the minimum thresholds for afterdischarge was 4.33mA±2.37. Most striking were the degree of variability and wide range of thresholds seen between patients and within the different regions of the same patient. Wide ranges of thresholds exist for the different responses between patients and within different regions of the same patient. With multivariate analysis in these series, no clinical or demographic factors predicted physiological response or afterdischarge threshold levels. Published by Elsevier Ltd.

  3. 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.

  4. 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

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

    PubMed

    González-Block, Miguel A; Rouvier, Mariel; Becerril, Victor; Sesia, Paola

    2011-03-15

    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. 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. 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. Concept mapping enabled the identification of critical functions constituting adaptive maternal health systems, including aspects of actor perspectives that are seldom included in normative and analytical frameworks

  6. 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.

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

    SciTech Connect

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

    2016-09-20

    We report that Planck has mapped the microwave sky in temperature over nine frequency bands between 30 and 857 GHz and in polarization over seven frequency bands between 30 and 353 GHz in polarization. In this paper we consider the problem of diffuse astrophysical component separation, and process these maps within a Bayesian framework to derive an internally consistent set of full-sky astrophysical component maps. Component separation dedicated to cosmic microwave background (CMB) reconstruction is described in a companion paper. For the temperature analysis, we combine the Planck observations with the 9-yr Wilkinson Microwave Anisotropy Probe (WMAP) sky maps and the Haslam et al. 408 MHz map, to derive a joint model of CMB, synchrotron, free-free, spinning dust, CO, line emission in the 94 and 100 GHz channels, and thermal dust emission. Full-sky maps are provided for each component, with an angular resolution varying between 7.5 and 1deg. Global parameters (monopoles, dipoles, relative calibration, and bandpass errors) are fitted jointly with the sky model, and best-fit values are tabulated. For polarization, the model includes CMB, synchrotron, and thermal dust emission. These models provide excellent fits to the observed data, with rms temperature residuals smaller than 4μK over 93% of the sky for all Planck frequencies up to 353 GHz, and fractional errors smaller than 1% in the remaining 7% of the sky. The main limitations of the temperature model at the lower frequencies are internal degeneracies among the spinning dust, free-free, and synchrotron components; additional observations from external low-frequency experiments will be essential to break these degeneracies. The main limitations of the temperature model at the higher frequencies are uncertainties in the 545 and 857 GHz calibration and zero-points. For polarization, the main outstanding issues are instrumental systematics in the 100–353 GHz bands on large angular scales in the form of temperature

  8. Understanding the geometry of transport: Diffusion maps for Lagrangian trajectory data unravel coherent sets

    NASA Astrophysics Data System (ADS)

    Banisch, Ralf; Koltai, Péter

    2017-03-01

    Dynamical systems often exhibit the emergence of long-lived coherent sets, which are regions in state space that keep their geometric integrity to a high extent and thus play an important role in transport. In this article, we provide a method for extracting coherent sets from possibly sparse Lagrangian trajectory data. Our method can be seen as an extension of diffusion maps to trajectory space, and it allows us to construct "dynamical coordinates," which reveal the intrinsic low-dimensional organization of the data with respect to transport. The only a priori knowledge about the dynamics that we require is a locally valid notion of distance, which renders our method highly suitable for automated data analysis. We show convergence of our method to the analytic transfer operator framework of coherence in the infinite data limit and illustrate its potential on several two- and three-dimensional examples as well as real world data.

  9. Mapping remodeling of thalamocortical projections in the living reeler mouse brain by diffusion tractography

    PubMed Central

    Harsan, Laura-Adela; Dávid, Csaba; Reisert, Marco; Schnell, Susanne; Hennig, Jürgen; von Elverfeldt, Dominik; Staiger, Jochen F.

    2013-01-01

    A major challenge in neuroscience is to accurately decipher in vivo the entire brain circuitry (connectome) at a microscopic level. Currently, the only methodology providing a global noninvasive window into structural brain connectivity is diffusion tractography. The extent to which the reconstructed pathways reflect realistic neuronal networks depends, however, on data acquisition and postprocessing factors. Through a unique combination of approaches, we designed and evaluated herein a framework for reliable fiber tracking and mapping of the living mouse brain connectome. One important wiring scheme, connecting gray matter regions and passing fiber-crossing areas, was closely examined: the lemniscal thalamocortical (TC) pathway. We quantitatively validated the TC projections inferred from in vivo tractography with correlative histological axonal tracing in the same wild-type and reeler mutant mice. We demonstrated noninvasively that changes in patterning of the cortical sheet, such as highly disorganized cortical lamination in reeler, led to spectacular compensatory remodeling of the TC pathway. PMID:23610438

  10. Assessment of allograft function using diffusion-weighted magnetic resonance imaging in kidney transplant patients.

    PubMed

    Kaul, Anupma; Sharma, Raj Kumar; Gupta, Rakesh Kumar; Lal, Hira; Yadav, Abhishek; Bhadhuria, Dharmendra; Prasad, Narayan; Gupta, Amit

    2014-11-01

    Developing a non-invasive method such as diffusion-weighted magnetic resonance imaging (DWMRI) could be used as a feasible and reproducible modality in the differential diagnosis of allograft dysfunction. We assessed the functional status of the renal allograft by DWMRI and its applicability in assessment of graft dysfunction on all end-stage renal transplant patients who attained normal renal function on the 7th day post-transplantation. Follow-up imaging of the recipient allograft was performed at the end of 90 and 180 days and in case of graft dysfunction. Kidney biopsies were performed to correlate with the corresponding MRI. The apparent diffusion coefficient (ADC) maps of the cortex and medulla were obtained by studying the DWMRI. The ADC values were significantly lower in the medulla compared with the cortex in normal donor kidneys and normally functioning transplanted kidneys, while they decreased significantly when rejection occurred. The reduction in ADC values occurred both in the cortex and in the medulla, and correlated with the degree of rejection on the kidney biopsies. The ADC values increased significantly during the recovery from rejection. We conclude that DWMRI can be beneficial in the diagnosis and follow-up of transplant patients during acute rejection.

  11. Task-specific functional brain geometry from model maps.

    PubMed

    Langs, Georg; Samaras, Dimitris; Paragios, Nikos; Honorio, Jean; Alia-Klein, Nelly; Tomasi, Dardo; Volkow, Nora D; Goldstein, Rita Z

    2008-01-01

    In this paper we propose model maps to derive and represent the intrinsic functional geometry of a brain from functional magnetic resonance imaging (fMRI) data for a specific task. Model maps represent the coherence of behavior of individual fMRI-measurements for a set of observations, or a time sequence. The maps establish a relation between individual positions in the brain by encoding the blood oxygen level dependent (BOLD) signal over a time period in a Markov chain. They represent this relation by mapping spatial positions to a new metric space, the model map. In this map the Euclidean distance between two points relates to the joint modeling behavior of their signals and thus the co-dependencies of the corresponding signals. The map reflects the functional as opposed to the anatomical geometry of the brain. It provides a quantitative tool to explore and study global and local patterns of resource allocation in the brain. To demonstrate the merit of this representation, we report quantitative experimental results on 29 fMRI time sequences, each with sub-sequences corresponding to 4 different conditions for two groups of individuals. We demonstrate that drug abusers exhibit lower differentiation in brain interactivity between baseline and reward related tasks, which could not be quantified until now.

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

    NASA Astrophysics Data System (ADS)

    Vroblesky, D. A.

    2001-05-01

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

  13. 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.

  14. Foliation Mapping at Depth Using Receiver Functions

    NASA Astrophysics Data System (ADS)

    Mahan, K. H.; Schulte-Pelkum, V.

    2013-12-01

    Seismic azimuthal and radial anisotropy are often treated separately for convenience and computational simplicity. When tilted symmetry axis anisotropy is present, nonlinear coupling effects lead to strong Love-to-Rayleigh scattering in surface waves and high-amplitude azimuthally dependent conversions in P-to-SV and P-to-SH converted body waves. The majority of receiver function studies that use waveform modeling thus infer steeply tilted symmetry axes of anisotropy - not because those are more common than horizontal symmetry axes in the lithosphere, but because of their much higher signal amplitudes compared to the horizontal symmetry axis case. Receiver function waveform modeling is subject to many tradeoffs; the signal amplitude depends on the tilt angle, strength of anisotropy, isotropic velocity contrast, and details of the elastic tensor symmetry (such as slow or fast symmetry axis, shape factor, etc.). We present an alternative approach that reduces the information in the waveforms to two parameters, namely the strike and depth of anisotropic and dipping structures. The method is based on finding polarity reversals in converted phases and makes use of a systematic relationship in back-azimuth between radial and tangential component receiver functions. It is insensitive to the tradeoffs mentioned above. We show that the technique reduces complex azimuthally dependent receiver functions to simple parameters that can be interpreted in a geological context. We present examples from Taiwan, the Himalaya, and the western US.

  15. 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.

  16. A fast algorithm for functional mapping of complex traits.

    PubMed Central

    Zhao, Wei; Wu, Rongling; Ma, Chang-Xing; Casella, George

    2004-01-01

    By integrating the underlying developmental mechanisms for the phenotypic formation of traits into a mapping framework, functional mapping has emerged as an important statistical approach for mapping complex traits. In this note, we explore the feasibility of using the simplex algorithm as an alternative to solve the mixture-based likelihood for functional mapping of complex traits. The results from the simplex algorithm are consistent with those from the traditional EM algorithm, but the simplex algorithm has considerably reduced computational times. Moreover, because of its nonderivative nature and easy implementation with current software, the simplex algorithm enjoys an advantage over the EM algorithm in the dynamic modeling and analysis of complex traits. PMID:15342547

  17. Intraoperative Functional Mapping and Monitoring during Glioma Surgery

    PubMed Central

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

    2015-01-01

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

  18. 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…

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

    ERIC Educational Resources Information Center

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

    2007-01-01

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

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

    PubMed

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

    2014-10-01

    We first propose a large deformation diffeomorphic metric mapping algorithm to align multiple b-value diffusion weighted imaging (mDWI) data, specifically acquired via hybrid diffusion imaging (HYDI). We denote this algorithm as LDDMM-HYDI. We then propose a Bayesian probabilistic model for estimating the white matter atlas from HYDIs. We adopt the work given in Hosseinbor et al. (2013) and represent the q-space diffusion signal with the Bessel Fourier orientation reconstruction (BFOR) signal basis. The BFOR framework provides the representation of mDWI in the q-space and the analytic form of the emsemble average propagator (EAP) reconstruction, as well as reduces memory requirement. In addition, since the BFOR signal basis is orthonormal, the L(2) norm that quantifies the differences in the q-space signals of any two mDWI datasets can be easily computed as the sum of the squared differences in the BFOR expansion coefficients. In this work, we show that the reorientation of the q-space signal due to spatial transformation can be easily defined on the BFOR signal basis. We incorporate the BFOR signal basis into the LDDMM framework and derive the gradient descent algorithm for LDDMM-HYDI with explicit orientation optimization. Additionally, we extend the previous Bayesian atlas estimation framework for scalar-valued images to HYDIs and derive the expectation-maximization algorithm for solving the HYDI atlas estimation problem. Using real HYDI datasets, we show that the Bayesian model generates the white matter atlas with anatomical details. Moreover, we show that it is important to consider the variation of mDWI reorientation due to a small change in diffeomorphic transformation in the LDDMM-HYDI optimization and to incorporate the full information of HYDI for aligning mDWI. Finally, we show that the LDDMM-HYDI outperforms the LDDMM algorithm with diffusion tensors generated from each shell of HYDI. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights

  1. 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

  2. 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

  3. Comparing diffuse optical tomography and functional magnetic resonance imaging signals during a cognitive task: pilot study.

    PubMed

    Hernández-Martin, Estefania; Marcano, Francisco; Casanova, Oscar; Modroño, Cristian; Plata-Bello, Julio; González-Mora, Jose Luis

    2017-01-01

    Diffuse optical tomography (DOT) measures concentration changes in both oxy- and deoxyhemoglobin providing three-dimensional images of local brain activations. A pilot study, which compares both DOT and functional magnetic resonance imaging (fMRI) volumes through t-maps given by canonical statistical parametric mapping (SPM) processing for both data modalities, is presented. The DOT series were processed using a method that is based on a Bayesian filter application on raw DOT data to remove physiological changes and minimum description length application index to select a number of singular values, which reduce the data dimensionality during image reconstruction and adaptation of DOT volume series to normalized standard space. Therefore, statistical analysis is performed with canonical SPM software in the same way as fMRI analysis is done, accepting DOT volumes as if they were fMRI volumes. The results show the reproducibility and ruggedness of the method to process DOT series on group analysis using cognitive paradigms on the prefrontal cortex. Difficulties such as the fact that scalp-brain distances vary between subjects or cerebral activations are difficult to reproduce due to strategies used by the subjects to solve arithmetic problems are considered. T-images given by fMRI and DOT volume series analyzed in SPM show that at the functional level, both DOT and fMRI measures detect the same areas, although DOT provides complementary information to fMRI signals about cerebral activity.

  4. Probing Cosmology with Minkowski Functionals of Weak Lensing Maps

    NASA Astrophysics Data System (ADS)

    Kratochvil, Jan Michael; Lim, E. A.; Wang, S.; Haiman, Z.; May, M.; Huffenberger, K.

    2011-01-01

    Minkowski functionals (MFs) are alternative probes of non-Gaussianity of random fields and probe the morphology and topology. We apply them to constrain cosmological parameters from weak gravitational lensing maps. We use MFs with Monte Carlo-optimized threshold bins to distinguish between different cosmological models from simulated convergence maps. We find that MFs discern better than the power spectrum from the same maps, thus providing evidence that they probe nonlinear structure formation and measure information beyond the power spectrum. The lensing maps were created with our new huge Inspector Gadget lensing simulation pipeline on the IBM Blue Gene at Brookhaven National Laboratory, allowing us to create an extensive simulation suite of ninety 5123-particle N-body simulations and sample many cosmological models and initial conditions.

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

    PubMed

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

    2016-01-01

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

  6. 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

  7. Molecules in motion: influences of diffusion on metabolic structure and function in skeletal muscle

    PubMed Central

    Kinsey, Stephen T.; Locke, Bruce R.; Dillaman, Richard M.

    2011-01-01

    Metabolic processes are often represented as a group of metabolites that interact through enzymatic reactions, thus forming a network of linked biochemical pathways. Implicit in this view is that diffusion of metabolites to and from enzymes is very fast compared with reaction rates, and metabolic fluxes are therefore almost exclusively dictated by catalytic properties. However, diffusion may exert greater control over the rates of reactions through: (1) an increase in reaction rates; (2) an increase in diffusion distances; or (3) a decrease in the relevant diffusion coefficients. It is therefore not surprising that skeletal muscle fibers have long been the focus of reaction–diffusion analyses because they have high and variable rates of ATP turnover, long diffusion distances, and hindered metabolite diffusion due to an abundance of intracellular barriers. Examination of the diversity of skeletal muscle fiber designs found in animals provides insights into the role that diffusion plays in governing both rates of metabolic fluxes and cellular organization. Experimental measurements of metabolic fluxes, diffusion distances and diffusion coefficients, coupled with reaction–diffusion mathematical models in a range of muscle types has started to reveal some general principles guiding muscle structure and metabolic function. Foremost among these is that metabolic processes in muscles do, in fact, appear to be largely reaction controlled and are not greatly limited by diffusion. However, the influence of diffusion is apparent in patterns of fiber growth and metabolic organization that appear to result from selective pressure to maintain reaction control of metabolism in muscle. PMID:21177946

  8. Pancreatic neuroendocrine tumors: correlation between histogram analysis of apparent diffusion coefficient maps and tumor grade.

    PubMed

    Pereira, Jose Antonio Sousa; Rosado, Elsa; Bali, Maria; Metens, Thierry; Chao, Shih-Li

    2015-10-01

    To explore the role of histogram analysis of apparent diffusion coefficient (ADC) MRI maps based on entire tumor volume data in determining pancreatic neuroendocrine tumor (PNT) grade. Retrospective evaluation of 22 patients with PNTs included low-grade (G1; n = 15), intermediate-grade (G2; n = 4), and high-grade (G3; n = 3) tumors. Regions of interest containing the lesion were drawn on every section of the ADC map containing the tumor and summated to obtain histograms for entire tumor volume. Calculated histographic parameters included mean ADC (mADC), 5th percentile ADC, 10th percentile ADC, 25th percentile ADC, 50th percentile ADC, 75th percentile ADC (ADC75), 90th percentile ADC (ADC90) and 95th percentile ADC (ADC95), skewness and kurtosis. Histogram parameters were correlated with tumor grade by repeated measures analysis of variance with Tukey-Kramer post hoc comparisons. The mADC, ADC75, ADC90, and ADC95 were significantly higher in G1 tumors (1283 ± 267; 1404 ± 300; 1495 ± 318; 1562 ± 347 × 10(-6) mm(2)/s) compared to G2 (892 ± 390; 952 ± 381; 1036 ± 384; 1072 ± 374 × 10(-6) mm(2)/s) and to G3 tumors (733 ± 225; 864 ± 284; 1008 ± 288; 1152 ± 192 × 10(-6) mm(2)/s) (p value <0.05). Skewness and kurtosis were significantly different between G1 (0.041 ± 0.466; 2.802 ± 0.679) and G3 (1.01 ± 1.140; 5.963 ± 4.008) tumors (p value <0.05). Tumor volume (mL) was significantly higher on G3 (55 ± 15.7) compared to G1 (1.9 ± 2.7) and G2 (4.5 ± 3.6) tumors (p value <0.05). In this small sample size, we did not detect statistically significant parameters between G2 (n = 4) and G3 (n = 3) tumors. Histographic analysis of ADC maps on the basis of the entire tumor volume can be useful in differentiating histologic grades of PNTs.

  9. 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. Copyright © 2014, American Association for the Advancement of Science.

  10. 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.

  11. Functional pathway mapping analysis for hypoxia-inducible factors

    PubMed Central

    2011-01-01

    Background Hypoxia-inducible factors (HIFs) are transcription factors that play a crucial role in response to hypoxic stress in living organisms. The HIF pathway is activated by changes in cellular oxygen levels and has significant impacts on the regulation of gene expression patterns in cancer cells. Identifying functional conservation across species and discovering conserved regulatory motifs can facilitate the selection of reference species for empirical tests. This paper describes a cross-species functional pathway mapping strategy based on evidence of homologous relationships that employs matrix-based searching techniques for identifying transcription factor-binding sites on all retrieved HIF target genes. Results HIF-related orthologous and paralogous genes were mapped onto the conserved pathways to indicate functional conservation across species. Quantitatively measured HIF pathways are depicted in order to illustrate the extent of functional conservation. The results show that in spite of the evolutionary process of speciation, distantly related species may exhibit functional conservation owing to conservative pathways. The novel terms OrthRate and ParaRate are proposed to quantitatively indicate the flexibility of a homologous pathway and reveal the alternative regulation of functional genes. Conclusion The developed functional pathway mapping strategy provides a bioinformatics approach for constructing biological pathways by highlighting the homologous relationships between various model species. The mapped HIF pathways were quantitatively illustrated and evaluated by statistically analyzing their conserved transcription factor-binding elements. Keywords hypoxia-inducible factor (HIF), hypoxia-response element (HRE), transcription factor (TF), transcription factor binding site (TFBS), KEGG (Kyoto Encyclopedia of Genes and Genomes), cross-species comparison, orthology, paralogy, functional pathway PMID:21689478

  12. Functional pathway mapping analysis for hypoxia-inducible factors.

    PubMed

    Chuang, Chia-Sheng; Pai, Tun-Wen; Hu, Chin-Hua; Tzou, Wen-Shyong; Dah-Tsyr Chang, Margaret; Chang, Hao-Teng; Chen, Chih-Chia

    2011-06-20

    Hypoxia-inducible factors (HIFs) are transcription factors that play a crucial role in response to hypoxic stress in living organisms. The HIF pathway is activated by changes in cellular oxygen levels and has significant impacts on the regulation of gene expression patterns in cancer cells. Identifying functional conservation across species and discovering conserved regulatory motifs can facilitate the selection of reference species for empirical tests. This paper describes a cross-species functional pathway mapping strategy based on evidence of homologous relationships that employs matrix-based searching techniques for identifying transcription factor-binding sites on all retrieved HIF target genes. HIF-related orthologous and paralogous genes were mapped onto the conserved pathways to indicate functional conservation across species. Quantitatively measured HIF pathways are depicted in order to illustrate the extent of functional conservation. The results show that in spite of the evolutionary process of speciation, distantly related species may exhibit functional conservation owing to conservative pathways. The novel terms OrthRate and ParaRate are proposed to quantitatively indicate the flexibility of a homologous pathway and reveal the alternative regulation of functional genes. The developed functional pathway mapping strategy provides a bioinformatics approach for constructing biological pathways by highlighting the homologous relationships between various model species. The mapped HIF pathways were quantitatively illustrated and evaluated by statistically analyzing their conserved transcription factor-binding elements. hypoxia-inducible factor (HIF), hypoxia-response element (HRE), transcription factor (TF), transcription factor binding site (TFBS), KEGG (Kyoto Encyclopedia of Genes and Genomes), cross-species comparison, orthology, paralogy, functional pathway.

  13. 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.

  14. Functional preoperative and intraoperative mapping and monitoring: increasing safety and efficacy in glioma surgery.

    PubMed

    Ottenhausen, Malte; Krieg, Sandro M; Meyer, Bernhard; Ringel, Florian

    2015-01-01

    Greater extent of resection (EOR) of low-grade gliomas is associated with improved survival. Proximity to eloquent cortical regions often limits resectability and elevates the risk of surgery-related deficits. Therefore, functional localization of eloquent cortex or subcortical fiber tracts can enhance the EOR and functional outcome. Imaging techniques such as functional MRI and diffusion tensor imaging fiber tracking, and neurophysiological methods like navigated transcranial magnetic stimulation and magnetoencephalography, make it possible to identify eloquent areas prior to resective surgery and to tailor indication and surgical approach but also to assess the surgical risk. Intraoperative monitoring with direct cortical stimulation and subcortical stimulation enables surgeons to preserve essential functional tissue during surgery. Through tailored pre- and intraoperative mapping and monitoring the EOR can be maximized, with reduced rates of surgery-related deficits.

  15. 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

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

    PubMed

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

    2015-02-01

    During human brain development from fetal stage to adulthood, the white matter (WM) tracts undergo dramatic changes. Diffusion tensor imaging (DTI), a widely used magnetic resonance imaging (MRI) modality, offers insight into the dynamic changes of WM fibers as these fibers can be noninvasively traced and three-dimensionally (3D) reconstructed with DTI tractography. The DTI and conventional T1 weighted MRI images also provide sufficient cortical anatomical details for mapping the cortical regions of interests (ROIs). In this paper, we described basic concepts and methods of DTI techniques that can be used to trace major WM tracts noninvasively from fetal brain of 14 postconceptional weeks (pcw) to adult brain. We applied these techniques to acquire DTI data and trace, reconstruct and visualize major WM tracts during development. After categorizing major WM fiber bundles into five unique functional tract groups, namely limbic, brain stem, projection, commissural and association tracts, we revealed formation and maturation of these 3D reconstructed WM tracts of the developing human brain. The structural and connectional imaging data offered by DTI provides the anatomical backbone of transcriptional atlas of the developing human brain. Copyright © 2014 Elsevier Inc. All rights reserved.

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

    PubMed Central

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

    2014-01-01

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

  18. Comparison of CT perfusion summary maps to early diffusion-weighted images in suspected acute middle cerebral artery stroke.

    PubMed

    Benson, John; Payabvash, Seyedmehdi; Salazar, Pascal; Jagadeesan, Bharathi; Palmer, Christopher S; Truwit, Charles L; McKinney, Alexander M

    2015-04-01

    To assess the accuracy and reliability of one vendor's (Vital Images, Toshiba Medical, Minnetonka, MN) automated CT perfusion (CTP) summary maps in identification and volume estimation of infarcted tissue in patients with acute middle cerebral artery (MCA) distribution infarcts. From 1085 CTP examinations over 5.5 years, 43 diffusion-weighted imaging (DWI)-positive patients were included who underwent both CTP and DWI <12 h after symptom onset, with another 43 age-matched patients as controls (DWI-negative). Automated delay-corrected postprocessing software (DC-SVD) generated both infarct "core only" and "core+penumbra" CTP summary maps. Three reviewers independently tabulated Alberta Stroke Program Early CT scores (ASPECTS) of both CTP summary maps and coregistered DWI. Of 86 included patients, 36 had DWI infarct volumes ≤70 ml, 7 had volumes >70 ml, and 43 were negative; the automated CTP "core only" map correctly classified each as >70 ml or ≤70 ml, while the "core+penumbra" map misclassified 4 as >70 ml. There were strong correlations between DWI volume with both summary map-based volumes: "core only" (r=0.93), and "core+penumbra" (r=0.77) (both p<0.0001). Agreement between ASPECTS scores of infarct core on DWI with summary maps was 0.65-0.74 for "core only" map, and 0.61-0.65 for "core+penumbra" (both p<0.0001). Using DWI-based ASPECTS scores as the standard, the accuracy of the CTP-based maps were 79.1-86.0% for the "core only" map, and 83.7-88.4% for "core+penumbra." Automated CTP summary maps appear to be relatively accurate in both the detection of acute MCA distribution infarcts, and the discrimination of volumes using a 70 ml threshold. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  19. 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.

  20. Coarse-graining the dynamics of a driven interface in the presence of mobile impurities: effective description via diffusion maps.

    PubMed

    Sonday, Benjamin E; Haataja, Mikko; Kevrekidis, Ioannis G

    2009-09-01

    Developing effective descriptions of the microscopic dynamics of many physical phenomena can both dramatically enhance their computational exploration and lead to a more fundamental understanding of the underlying physics. Previously, an effective description of a driven interface in the presence of mobile impurities, based on an Ising variant model and a single empirical coarse variable, was partially successful [M. Haataja, Phys. Rev. Lett. 92, 160603 (2004)]; yet it underlined the necessity of selecting additional coarse variables in certain parameter regimes. In this paper we use a data mining approach to help identify the coarse variables required. We discuss the implementation of this diffusion map approach, the selection of a similarity measure between system snapshots required in the approach, and the correspondence between empirically selected and automatically detected coarse variables. We conclude by illustrating the use of the diffusion map variables in assisting the atomistic simulations and we discuss the translation of information between fine and coarse descriptions using lifting and restriction operators.

  1. Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics.

    PubMed

    Preto, Jordane; Clementi, Cecilia

    2014-09-28

    The reaction pathways characterizing macromolecular systems of biological interest are associated with high free energy barriers. Resorting to the standard all-atom molecular dynamics (MD) to explore such critical regions may be inappropriate as the time needed to observe the relevant transitions can be remarkably long. In this paper, we present a new method called Extended Diffusion-Map-directed Molecular Dynamics (extended DM-d-MD) used to enhance the sampling of MD trajectories in such a way as to rapidly cover all important regions of the free energy landscape including deep metastable states and critical transition paths. Moreover, extended DM-d-MD was combined with a reweighting scheme enabling to save on-the-fly information about the Boltzmann distribution. Our algorithm was successfully applied to two systems, alanine dipeptide and alanine-12. Due to the enhanced sampling, the Boltzmann distribution is recovered much faster than in plain MD simulations. For alanine dipeptide, we report a speedup of one order of magnitude with respect to plain MD simulations. For alanine-12, our algorithm allows us to highlight all important unfolded basins in several days of computation when one single misfolded event is barely observable within the same amount of computational time by plain MD simulations. Our method is reaction coordinate free, shows little dependence on the a priori knowledge of the system, and can be implemented in such a way that the biased steps are not computationally expensive with respect to MD simulations thus making our approach well adapted for larger complex systems from which little information is known.

  2. 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.

  3. MAP-2 immunolabeling can distinguish diffuse from dense-core amyloid plaques in brains with Alzheimer's disease.

    PubMed

    D'Andrea, M R; Nagele, R G

    2002-03-01

    Alzheimer's disease (AD) neuropathology is characterized by the presence of diffuse and dense-core (neuritic) amyloid plaques in specific areas of the brain. The origin of these plaques and the relationship between them is poorly understood. Current methods to identify clearly these types of plaques in the AD brains are largely dependent upon morphological characteristics. Dense-core amyloid plaques in the entorhinal cortex and hippocampus of AD brains might arise from the lysis of neurons overburdened by excessive intracellular deposition of amyloid beta1-42 (Abeta42) peptide. The local release of active lysosomal enzymes, which persist within these plaques, might degrade most of the released intracellular proteins, leaving behind only those that are resistant to proteolytic digestion, such as ubiquitin, tau, neurofilament proteins and amyloid. To test the possibility that proteins that are sensitive to proteolysis may be degraded selectively in plaques, we used immunohistochemistry to examine the distribution of microtubule-associated protein-2 (MAP-2), a protein localized primarily in neuronal dendrites and known to be sensitive to proteolysis. Uniform MAP-2 immunolabeling was detected throughout the somatodendritic compartment of neurons in age-matched control cortical brain tissues as well as throughout areas of Abeta42-positive diffuse plaques in AD brains. In contrast, analysis of serial sections revealed that MAP-2 was absent from Abeta42-positive dense-core plaques in AD brains. Our results indicate that this differential MAP-2 immunolabeling pattern among plaques may be employed as a reliable and sensitive method to distinguish dense-core plaques from diffuse plaques within AD brain tissue. Furthermore, this biochemical distinction indicates that dense-core and diffuse plaques are formed by different mechanisms.

  4. Functional connectivity networks for preoperative brain mapping in neurosurgery.

    PubMed

    Hart, Michael G; Price, Stephen J; Suckling, John

    2016-08-26

    OBJECTIVE Resection of focal brain lesions involves maximizing the resection while preserving brain function. Mapping brain function has entered a new era focusing on distributed connectivity networks at "rest," that is, in the absence of a specific task or stimulus, requiring minimal participant engagement. Central to this frame shift has been the development of methods for the rapid assessment of whole-brain connectivity with functional MRI (fMRI) involving blood oxygenation level-dependent imaging. The authors appraised the feasibility of fMRI-based mapping of a repertoire of functional connectivity networks in neurosurgical patients with focal lesions and the potential benefits of resting-state connectivity mapping for surgical planning. METHODS Resting-state fMRI sequences with a 3-T scanner and multiecho echo-planar imaging coupled to independent component analysis were acquired preoperatively from 5 study participants who had a right temporoparietooccipital glioblastoma. Seed-based functional connectivity analysis was performed with InstaCorr. Network identification focused on 7 major functional connectivity networks described in the literature and a putative language network centered on Broca's area. RESULTS All 8 functional connectivity networks were identified in each participant. Tumor-related topological changes to the default mode network were observed in all participants. In addition, each participant had at least 1 other abnormal network, and each network was abnormal in at least 1 participant. Individual patterns of network irregularities were identified with a qualitative approach and included local displacement due to mass effect, loss of a functional network component, and recruitment of new regions. CONCLUSIONS Resting-state fMRI can reliably and rapidly detect common functional connectivity networks in patients with glioblastoma and also has sufficient sensitivity for identifying patterns of network alterations. Mapping of functional

  5. Mapping the core mass function to the initial mass function

    NASA Astrophysics Data System (ADS)

    Guszejnov, Dávid; Hopkins, Philip F.

    2015-07-01

    It has been shown that fragmentation within self-gravitating, turbulent molecular clouds (`turbulent fragmentation') can naturally explain the observed properties of protostellar cores, including the core mass function (CMF). Here, we extend recently developed analytic models for turbulent fragmentation to follow the time-dependent hierarchical fragmentation of self-gravitating cores, until they reach effectively infinite density (and form stars). We show that turbulent fragmentation robustly predicts two key features of the initial mass function (IMF). First, a high-mass power-law scaling very close to the Salpeter slope, which is a generic consequence of the scale-free nature of turbulence and self-gravity. We predict the IMF slope (-2.3) is slightly steeper than the CMF slope (-2.1), owing to the slower collapse and easier fragmentation of large cores. Secondly, a turnover mass, which is set by a combination of the CMF turnover mass (a couple solar masses, determined by the `sonic scale' of galactic turbulence, and so weakly dependent on galaxy properties), and the equation of state (EOS). A `soft' EOS with polytropic index γ < 1.0 predicts that the IMF slope becomes `shallow' below the sonic scale, but fails to produce the full turnover observed. An EOS, which becomes `stiff' at sufficiently low surface densities Σgas ˜ 5000 M⊙ pc-2, and/or models, where each collapsing core is able to heat and effectively stiffen the EOS of a modest mass (˜0.02 M⊙) of surrounding gas, are able to reproduce the observed turnover. Such features are likely a consequence of more detailed chemistry and radiative feedback.

  6. Applications of blood-oxygen-level-dependent functional magnetic resonance imaging and diffusion tensor imaging in epilepsy.

    PubMed

    Chaudhary, Umair J; Duncan, John S

    2014-11-01

    The lifetime prevalence of epilepsy ranges from 2.7 to 12.4 per 1000 in Western countries. Around 30% of patients with epilepsy remain refractory to antiepileptic drugs and continue to have seizures. Noninvasive imaging techniques such as functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) have helped to better understand mechanisms of seizure generation and propagation, and to localize epileptic, eloquent, and cognitive networks. In this review, the clinical applications of fMRI and DTI are discussed, for mapping cognitive and epileptic networks and organization of white matter tracts in individuals with epilepsy.

  7. Realistic Electric Field Mapping of Anisotropic Muscle During Electrical Stimulation Using a Combination of Water Diffusion Tensor and Electrical Conductivity.

    PubMed

    Choi, Bup Kyung; Oh, Tong In; Sajib, Saurav Zk; Kim, Jin Woong; Kim, Hyung Joong; Kwon, Oh In; Woo, Eung Je

    2017-04-01

    To realistically map the electric fields of biological tissues using a diffusion tensor magnetic resonance electrical impedance tomography (DT-MREIT) method to estimate tissue response during electrical stimulation. Imaging experiments were performed using chunks of bovine muscle. Two silver wire electrodes were positioned inside the muscle tissue for electrical stimulation. Electric pulses were applied with a 100-V amplitude and 100-μs width using a voltage stimulator. During electrical stimulation, we collected DT-MREIT data from a 3T magnetic resonance imaging scanner. We adopted the projected current density method to calculate the electric field. Based on the relation between the water diffusion tensor and the conductivity tensor, we computed the position-dependent scale factor using the measured magnetic flux density data. Then, a final conductivity tensor map was reconstructed using the multiplication of the water diffusion tensor and the scale factor. The current density images from DT-MREIT data represent the internal current flows that exist not only in the electrodes but also in surrounding regions. The reconstructed electric filed map from our anisotropic conductivity tensor with the projected current density shows coverage that is more than 2 times as wide, and higher signals in both the electrodes and surrounding tissues, than the previous isotropic method owing to the consideration of tissue anisotropy. An electric field map obtained by an anisotropic reconstruction method showed different patterns from the results of the previous isotropic reconstruction method. Since accurate electric field mapping is important to correctly estimate the coverage of the electrical treatment, future studies should include more rigorous validations of the new method through in vivo and in situ experiments.

  8. Realistic Electric Field Mapping of Anisotropic Muscle During Electrical Stimulation Using a Combination of Water Diffusion Tensor and Electrical Conductivity

    PubMed Central

    2017-01-01

    Purpose To realistically map the electric fields of biological tissues using a diffusion tensor magnetic resonance electrical impedance tomography (DT-MREIT) method to estimate tissue response during electrical stimulation. Methods Imaging experiments were performed using chunks of bovine muscle. Two silver wire electrodes were positioned inside the muscle tissue for electrical stimulation. Electric pulses were applied with a 100-V amplitude and 100-μs width using a voltage stimulator. During electrical stimulation, we collected DT-MREIT data from a 3T magnetic resonance imaging scanner. We adopted the projected current density method to calculate the electric field. Based on the relation between the water diffusion tensor and the conductivity tensor, we computed the position-dependent scale factor using the measured magnetic flux density data. Then, a final conductivity tensor map was reconstructed using the multiplication of the water diffusion tensor and the scale factor. Results The current density images from DT-MREIT data represent the internal current flows that exist not only in the electrodes but also in surrounding regions. The reconstructed electric filed map from our anisotropic conductivity tensor with the projected current density shows coverage that is more than 2 times as wide, and higher signals in both the electrodes and surrounding tissues, than the previous isotropic method owing to the consideration of tissue anisotropy. Conclusions An electric field map obtained by an anisotropic reconstruction method showed different patterns from the results of the previous isotropic reconstruction method. Since accurate electric field mapping is important to correctly estimate the coverage of the electrical treatment, future studies should include more rigorous validations of the new method through in vivo and in situ experiments. PMID:28446015

  9. Decay of random correlation functions for unimodal maps

    NASA Astrophysics Data System (ADS)

    Baladi, Viviane; Benedicks, Michael; Maume-Deschamps, Véronique

    2000-10-01

    Since the pioneering results of Jakobson and subsequent work by Benedicks-Carleson and others, it is known that quadratic maps tfa( χ) = a - χ2 admit a unique absolutely continuous invariant measure for a positive measure set of parameters a. For topologically mixing tfa, Young and Keller-Nowicki independently proved exponential decay of correlation functions for this a.c.i.m. and smooth observables. We consider random compositions of small perturbations tf + ωt, with tf = tfa or another unimodal map satisfying certain nonuniform hyperbolicity axioms, and ωt chosen independently and identically in [-ɛ, ɛ]. Baladi-Viana showed exponential mixing of the associated Markov chain, i.e., averaging over all random itineraries. We obtain stretched exponential bounds for the random correlation functions of Lipschitz observables for the sample measure μωof almost every itinerary.

  10. Solutions of fractional reaction-diffusion equations in terms of the H-function

    NASA Astrophysics Data System (ADS)

    Haubold, H. J.; Mathai, A. M.; Saxena, R. K.

    2007-12-01

    This paper deals with the investigation of the solution of an unified fractional reaction-diffusion equation associated with the Caputo derivative as the time-derivative and Riesz-Feller fractional derivative as the space-derivative. The solution is derived by the application of the Laplace and Fourier transforms in closed form in terms of the H-function. The results derived are of general nature and include the results investigated earlier by many authors, notably by Mainardi et al. (2001, 2005) for the fundamental solution of the space-time fractional diffusion equation, and Saxena et al. (2006a, b) for fractional reaction-diffusion equations. The advantage of using Riesz-Feller derivative lies in the fact that the solution of the fractional reaction-diffusion equation containing this derivative includes the fundamental solution for space-time fractional diffusion, which itself is a generalization of neutral fractional diffusion, space-fractional diffusion, and time-fractional diffusion. These specialized types of diffusion can be interpreted as spatial probability density functions evolving in time and are expressible in terms of the H-functions in compact form.

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

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

    PubMed

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

    2015-02-25

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

  13. 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.

  14. Pulmonary functional magnetic resonance imaging: asthma temporal-spatial maps.

    PubMed

    Svenningsen, Sarah; Guo, Fumin; Kirby, Miranda; Choy, Stephen; Wheatley, Andrew; McCormack, David G; Parraga, Grace

    2014-11-01

    Hyperpolarized (3)He magnetic resonance imaging (MRI) previously revealed the temporal and spatial heterogeneity of ventilation defects in asthmatics, but these findings have not been used in treatment studies or to guide personalized therapy. Our objective was to exploit the temporal and spatial information inherent to (3)He MRI and develop image processing methods to generate pulmonary ventilation temporal-spatial maps that could be used to measure, optimize, and guide asthma therapy. In this proof-of-concept study, seven asthmatics provided written informed consent to an approved protocol and underwent spirometry and (3)He MRI on three occasions, each 5 ± 2 days apart. A registration and segmentation pipeline was developed to generate three-dimensional, temporal-spatial, pulmonary function maps. Briefly, (3)He ventilation images were segmented to generate ventilation masks that were coregistered and voxels classified according to their temporal behavior. This enabled the regional mapping of temporally persistent and intermittent ventilation defects that were normalized to the (1)H MRI thoracic cavity volume to generate persistent ventilation defect percent (VDPP) and intermittent ventilation defect percent (VDPI). (3)He temporal-spatial pulmonary function maps identified temporally persistent and intermittent ventilation defects. VDP(I) was significantly greater in the posterior (P = .04) and inferior (P = .04) lung as compared to the anterior and superior lung. Persistent and intermittent ventilation defect percent were strongly correlated with forced expiratory volume in one second/forced vital capacity (VDP(P): r = -0.87, P = .01; VDP(I): r = -0.96, P = .0008). Temporal-spatial pulmonary maps generated from (3)He MRI can be used to quantify temporally persistent and intermittent ventilation defects as asthma intermediate end points and targets for therapy. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

  15. 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.

  16. 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

  17. 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.

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

    PubMed Central

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

    2014-01-01

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

  19. On the emergence of the Green's function in the correlations of a diffuse field

    NASA Astrophysics Data System (ADS)

    Lobkis, Oleg I.; Weaver, Richard L.

    2001-12-01

    A diffuse acoustic field is shown to have correlations equal to the Green's function of the body. Simple plausibility arguments for this assertion are followed by a more detailed proof. A careful version of the statement is found to include caveats in regard to how diffuse the field truly is, the spectrum of the diffuse field, and the phase of the receivers. Ultrasonic laboratory tests confirm the assertion. The main features of the direct signal between two transducers are indeed recovered by cross correlating their responses to a diffuse field generated by a third transducer. The quality of the recovery improves with increased averaging and the use of multiple sources. Applications are discussed.

  20. Insights from probability distribution functions of intensity maps

    NASA Astrophysics Data System (ADS)

    Breysse, Patrick C.; Kovetz, Ely D.; Behroozi, Peter S.; Dai, Liang; Kamionkowski, Marc

    2017-05-01

    In the next few years, intensity-mapping surveys that target lines such as CO, Lyα and C ii stand to provide powerful probes of high-redshift astrophysics. However, these line emissions are highly non-Gaussian, and so the typical power-spectrum methods used to study these maps will leave out a significant amount of information. We propose a new statistic, the probability distribution of voxel intensities, which can access this extra information. Using a model of a CO intensity map at z ˜ 3 as an example, we demonstrate that this voxel intensity distribution (VID) provides substantial constraining power beyond what is obtainable from the power spectrum alone. We find that a future survey is similar to the planned CO Mapping Array Pathfinder (COMAP). Full experiment could constrain the CO luminosity function to the order of ˜10 per cent. We also explore the effects of contamination from continuum emission, interloper lines and gravitational lensing on our constraints and find that the VID statistic retains significant constraining power even in pessimistic scenarios.

  1. 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

  2. Functional implications of orientation maps in primary visual cortex

    NASA Astrophysics Data System (ADS)

    Koch, Erin; Jin, Jianzhong; Alonso, Jose M.; Zaidi, Qasim

    2016-11-01

    Stimulus orientation in the primary visual cortex of primates and carnivores is mapped as iso-orientation domains radiating from pinwheel centres, where orientation preferences of neighbouring cells change circularly. Whether this orientation map has a function is currently debated, because many mammals, such as rodents, do not have such maps. Here we show that two fundamental properties of visual cortical responses, contrast saturation and cross-orientation suppression, are stronger within cat iso-orientation domains than at pinwheel centres. These differences develop when excitation (not normalization) from neighbouring oriented neurons is applied to different cortical orientation domains and then balanced by inhibition from un-oriented neurons. The functions of the pinwheel mosaic emerge from these local intra-cortical computations: Narrower tuning, greater cross-orientation suppression and higher contrast gain of iso-orientation cells facilitate extraction of object contours from images, whereas broader tuning, greater linearity and less suppression of pinwheel cells generate selectivity for surface patterns and textures.

  3. Functional implications of orientation maps in primary visual cortex

    PubMed Central

    Koch, Erin; Jin, Jianzhong; Alonso, Jose M.; Zaidi, Qasim

    2016-01-01

    Stimulus orientation in the primary visual cortex of primates and carnivores is mapped as iso-orientation domains radiating from pinwheel centres, where orientation preferences of neighbouring cells change circularly. Whether this orientation map has a function is currently debated, because many mammals, such as rodents, do not have such maps. Here we show that two fundamental properties of visual cortical responses, contrast saturation and cross-orientation suppression, are stronger within cat iso-orientation domains than at pinwheel centres. These differences develop when excitation (not normalization) from neighbouring oriented neurons is applied to different cortical orientation domains and then balanced by inhibition from un-oriented neurons. The functions of the pinwheel mosaic emerge from these local intra-cortical computations: Narrower tuning, greater cross-orientation suppression and higher contrast gain of iso-orientation cells facilitate extraction of object contours from images, whereas broader tuning, greater linearity and less suppression of pinwheel cells generate selectivity for surface patterns and textures. PMID:27876796

  4. Reducing surgical levels by paraspinal mapping and diffusion tensor imaging techniques in lumbar spinal stenosis.

    PubMed

    Chen, Hua-Biao; Wan, Qi; Xu, Qi-Feng; Chen, Yi; Bai, Bo

    2016-04-25

    Correlating symptoms and physical examination findings with surgical levels based on common imaging results is not reliable. In patients who have no concordance between radiological and clinical symptoms, the surgical levels determined by conventional magnetic resonance imaging (MRI) and neurogenic examination (NE) may lead to a more extensive surgery and significant complications. We aimed to confirm that whether the use of diffusion tensor imaging (DTI) and paraspinal mapping (PM) techniques can further prevent the occurrence of false positives with conventional MRI, distinguish which are clinically relevant from levels of cauda equina and/or nerve root lesions based on MRI, and determine and reduce the decompression levels of lumbar spinal stenosis than MRI + NE, while ensuring or improving surgical outcomes. We compared the data between patients who underwent MRI + (PM or DTI) and patients who underwent conventional MRI + NE to determine levels of decompression for the treatment of lumbar spinal stenosis. Outcome measures were assessed at 2 weeks, 3 months, 6 months, and 12 months postoperatively. One hundred fourteen patients (59 in the control group, 54 in the experimental group) underwent decompression. The levels of decompression determined by MRI + (PM or DTI) in the experimental group were significantly less than that determined by MRI + NE in the control group (p = 0.000). The surgical time, blood loss, and surgical transfusion were significantly less in the experimental group (p = 0.001, p = 0.011, p = 0.001, respectively). There were no differences in improvement of the visual analog scale back and leg pain (VAS-BP, VAS-LP) scores and Oswestry Disability Index (ODI) scores at 2 weeks, 3 months, 6 months, and 12 months after operation between the experimental and control groups. MRI + (PM or DTI) showed clear benefits in determining decompression levels of lumbar spinal stenosis than MRI + NE. In patients with lumbar spinal

  5. Prediction of Infarct Lesion Volumes by Processing Magnetic Resonance Apparent Diffusion Coefficient Maps in Patients with Acute Ischemic Stroke.

    PubMed

    Qian, Qi; Huang, Hai-Tao; Xu, Li; Jin, Ping; Lin, Min

    2016-12-01

    We aimed to investigate the diagnostic value of apparent diffusion coefficient (ADC) maps in magnetic resonance imaging (MRI) in the volume of acute cerebral infarction (ACI). A total of 207 ACI patients were selected in our study. The cerebral infarction (CI) volume in the initial diffusion-weighted imaging examination, minimum ADC value, relative apparent diffusion coefficient (rADC) value, and mean ADC value were measured. The correlations between age, smoking, drinking, hypertension, diabetes, coronary heart disease, clinical stage, the lowest ADC value, the mean ADC value, and the mean rADC value with CI volume were analyzed by logistic regression analysis. A receiver operating characteristic (ROC) curve was used to analyze the diagnostic value of the ADC value in the ACI volume. There was a significant difference in the distribution of the CI volume in ACI patients (P <.05). A significant difference was found in the signal intensity and percentage distribution of ADC map in patients of different CI groups with different CI volumes (P <.05). The signal of the ADC map was positively correlated with the CI volume. The mean ADC and rADC values had significant differences between different CI volumes (all P <.05). Logistic regression analysis revealed that the mean ADC value was significantly correlated with the CI volume (P <.05). Analysis of the ROC curve showed that the quantitative value of ADC has a diagnostic value for the ACI volume. This study has shown that the signal intensity change on the ADC map in MRI and quantitative analysis of the ADC value can be used as a reference for predicting the ACI volume. Copyright © 2016 National Stroke Association. Published by Elsevier Inc. All rights reserved.

  6. Network Plasticity and Intraoperative Mapping for Personalized Multimodal Management of Diffuse Low-Grade Gliomas.

    PubMed

    Ghinda, Cristina Diana; Duffau, Hugues

    2017-01-01

    Gliomas are the most frequent primary brain tumors and include a variety of different histological tumor types and malignancy grades. Recent achievements in terms of molecular and imaging fields have created an unprecedented opportunity to perform a comprehensive interdisciplinary assessment of the glioma pathophysiology, with direct implications in terms of the medical and surgical treatment strategies available for patients. The current paradigm shift considers glioma management in a comprehensive perspective that takes into account the intricate connectivity of the cerebral networks. This allowed significant improvement in the outcome of patients with lesions previously considered inoperable. The current review summarizes the current theoretical framework integrating the adult human brain plasticity and functional reorganization within a dynamic individualized treatment strategy for patients affected by diffuse low-grade gliomas. The concept of neuro-oncology as a brain network surgery has major implications in terms of the clinical management and ensuing outcomes, as indexed by the increased survival and quality of life of patients managed using such an approach.

  7. Network Plasticity and Intraoperative Mapping for Personalized Multimodal Management of Diffuse Low-Grade Gliomas

    PubMed Central

    Ghinda, Cristina Diana; Duffau, Hugues

    2017-01-01

    Gliomas are the most frequent primary brain tumors and include a variety of different histological tumor types and malignancy grades. Recent achievements in terms of molecular and imaging fields have created an unprecedented opportunity to perform a comprehensive interdisciplinary assessment of the glioma pathophysiology, with direct implications in terms of the medical and surgical treatment strategies available for patients. The current paradigm shift considers glioma management in a comprehensive perspective that takes into account the intricate connectivity of the cerebral networks. This allowed significant improvement in the outcome of patients with lesions previously considered inoperable. The current review summarizes the current theoretical framework integrating the adult human brain plasticity and functional reorganization within a dynamic individualized treatment strategy for patients affected by diffuse low-grade gliomas. The concept of neuro-oncology as a brain network surgery has major implications in terms of the clinical management and ensuing outcomes, as indexed by the increased survival and quality of life of patients managed using such an approach. PMID:28197403

  8. Comparison of 3D Orientation Distribution Functions Measured with Confocal Microscopy and Diffusion MRI

    PubMed Central

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

    2016-01-01

    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 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

  9. Density functional calculation of activation energies for lattice and grain boundary diffusion in alumina

    NASA Astrophysics Data System (ADS)

    Lei, Yinkai; Gong, Yu; Duan, Zhiyao; Wang, Guofeng

    2013-06-01

    To acquire knowledge on the lattice and grain boundary diffusion processes in alumina, we have determined the activation energies of elementary O and Al diffusive jumps in the bulk crystal, Σ3(0001) grain boundaries, and Σ3(101¯0) grain boundaries of α-Al2O3 using the first-principles density functional theory method. Specifically, we calculated the activation energies for four elementary jumps of both O and Al lattice diffusion in alumina. It was predicted that the activation energy of O lattice diffusion varied from 3.58 to 5.03 eV, while the activation energy of Al lattice diffusion ranged from 1.80 to 3.17 eV. As compared with experimental measurements, the theoretical predictions of the activation energy for lattice diffusion were lower and thus implied that there might be other high-energy diffusive jumps in the experimental alumina samples. Moreover, our results suggested that the Al lattice diffusion was faster than the O lattice diffusion in alumina, in agreement with experiment observations. Furthermore, it was found from our calculations for α-Al2O3 that the activation energies of O and Al grain boundary diffusion in the high-energy Σ3(0001) grain boundaries were significantly lower than those of the lattice diffusion. In contrast, the activation energies of O and Al grain boundary diffusion in the low-energy Σ3(101¯0) grain boundaries could be even higher than those of the lattice diffusion.

  10. Mapping Sedimentary Basins Across Canada Using Receiver Function Analysis

    NASA Astrophysics Data System (ADS)

    Cassidy, J. F.; Kao, H.; Kim, H.; Dehler, S.; Dosso, S.; Halliday, J.

    2008-12-01

    Receiver function studies are being applied within several sedimentary basins across Canada to map basin geometry and sediment thickness. Teleseismic receiver functions are ideal, in many ways, for this type of study. They provide site-specific information, constraints on the shear wave velocity, interface geometry, and they can be used to identify structures from the near-surface to mantle depths. Although the frequency content of teleseismic waveforms limits the resolution, high-frequency receiver functions can resolve layers as thin as 1-2 km. In the Western Canada Sedimentary Basin (near Edmonton, Alberta), receiver functions were used to image the 2.5-km-thick sedimentary package at this site and a low-velocity zone in the upper crust. Currently, a deployment of 10 broadband seismic stations in Atlantic Canada is targeting the Paleozoic and Carboniferous sedimentary basins in the Gulf of St. Lawrence. Significant variations in the arrival time of the continental Moho phase along a north-south transect indicate crustal thickness variations, with the earliest Moho arrivals being in the central part of the basin, indicating a thinner crust here. The direct arrivals in the receiver functions at stations in the southern part of the gulf are broad, indicating notable thicknesses of near-surface sediments. These observations are consistent with what is known about the regional geology and the centrally-located Maritimes Basin. These initial observations, and other geophysical data for the region, will feed into interpretations of crustal structure developed through numerical modelling.In the Nechako Basin of central BC, receiver functions from seven broadband seismograph stations are being used to map sediments in this basin that are overlain by volcanic basalts. These receiver function show clear evidence for shallow dipping low-velocity layers. Constrains on the basin geometry and sediment thickness will be used to improve assessments of oil and gas potential in

  11. A Radial Basis Function (RBF)-Finite Difference (FD) Method for Diffusion and Reaction-Diffusion Equations on Surfaces.

    PubMed

    Shankar, Varun; Wright, Grady B; Kirby, Robert M; Fogelson, Aaron L

    2016-06-01

    In this paper, we present a method based on Radial Basis Function (RBF)-generated Finite Differences (FD) for numerically solving diffusion and reaction-diffusion equations (PDEs) on closed surfaces embedded in ℝ (d) . Our method uses a method-of-lines formulation, in which surface derivatives that appear in the PDEs are approximated locally using RBF interpolation. The method requires only scattered nodes representing the surface and normal vectors at those scattered nodes. All computations use only extrinsic coordinates, thereby avoiding coordinate distortions and singularities. We also present an optimization procedure that allows for the stabilization of the discrete differential operators generated by our RBF-FD method by selecting shape parameters for each stencil that correspond to a global target condition number. We show the convergence of our method on two surfaces for different stencil sizes, and present applications to nonlinear PDEs simulated both on implicit/parametric surfaces and more general surfaces represented by point clouds.

  12. A Radial Basis Function (RBF)-Finite Difference (FD) Method for Diffusion and Reaction-Diffusion Equations on Surfaces

    PubMed Central

    Shankar, Varun; Wright, Grady B.; Kirby, Robert M.; Fogelson, Aaron L.

    2014-01-01

    In this paper, we present a method based on Radial Basis Function (RBF)-generated Finite Differences (FD) for numerically solving diffusion and reaction-diffusion equations (PDEs) on closed surfaces embedded in ℝd. Our method uses a method-of-lines formulation, in which surface derivatives that appear in the PDEs are approximated locally using RBF interpolation. The method requires only scattered nodes representing the surface and normal vectors at those scattered nodes. All computations use only extrinsic coordinates, thereby avoiding coordinate distortions and singularities. We also present an optimization procedure that allows for the stabilization of the discrete differential operators generated by our RBF-FD method by selecting shape parameters for each stencil that correspond to a global target condition number. We show the convergence of our method on two surfaces for different stencil sizes, and present applications to nonlinear PDEs simulated both on implicit/parametric surfaces and more general surfaces represented by point clouds. PMID:25983388

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

    PubMed

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

    2003-01-01

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

  14. Correction of B0-Susceptibility Induced Distortion in Diffusion-weighted Images Using Large-Deformation Diffeomorphic Metric Mapping

    PubMed Central

    Huang, Hao; Ceritoglu, Can; Li, Xin; Qiu, Anqi; Miller, Michael I.; van Zijl, Peter C.M.; Mori, Susumu

    2008-01-01

    Geometric distortion caused by B0-inhomogeneity is one of the most important problems for diffusion weighted images (DWI) using single shot, echo planar imaging (SS-EPI). In this study, large-Deformation, Diffeomorphic Metric Mapping (LDDMM) algorithm has been tested for the correction of geometric distortion in diffusion tensor images (DTI). Based on data from nine normal subjects, the amount of distortion caused by B0-susceptibility in the 3T magnet was characterized. The distortion quality was validated by manually placing landmarks in the target and DTI images before and after distortion correction. The distortion was found to be up to 15 millimeters in the population-averaged map and could be more than 20 millimeters in individual images. Both qualitative demonstration and quantitative statistical results suggest that the highly elastic geometric distortion caused by spatial inhomogeneity of the B0 field in DTI using SS-EPI can be effectively corrected by LDDMM. This postprocessing method is especially useful for correcting existent DTI data without phase maps. PMID:18499384

  15. Histogram analysis of apparent diffusion coefficient map of diffusion-weighted MRI in endometrial cancer: a preliminary correlation study with histological grade.

    PubMed

    Woo, Sungmin; Cho, Jeong Yeon; Kim, Sang Youn; Kim, Seung Hyup

    2014-12-01

    Until now, several investigators have explored the value of diffusion-weighted magnetic resonance imaging (DWI) for the preoperative tumor grading of endometrial cancer. However, the diagnostic value of DWI with quantitative analysis of apparent diffusion coefficient (ADC) has been controversial. To explore the role of histogram analysis of ADC maps based on entire tumor volume in determining the grade of endometrial cancer. This study was IRB-approved with waiver of informed consent. Thirty-three patients with endometrial cancer underwent DWI (b = 0, 600, 1000 s/mm(2)), and corresponding ADC maps were acquired. Regions of interest (ROIs) were drawn on all slices of the ADC map in which the tumor was visualized including areas of necrosis to derive volume-based histographic ADC data. Histogram parameters (5th-95th percentiles, mean, standard deviation, skewness, kurtosis) were correlated with histological grade using one-way ANOVA with Tukey-Kramer test for post hoc comparisons, and were compared between high (grade 3) and low (grades 1/2) grade using Student t-test. ROC curve analysis was performed to determine the optimum threshold value for each parameter, and their corresponding sensitivity and specificity. The standard deviation, quartile, 75th, 90th, and 95th percentiles of ADC showed significant differences between grades (P ≤ 0.03 for all) and between high and low grades (P ≤ 0.024 for all). There were no significant correlations between tumor grade and other parameters. ROC curve analysis yielded sensitivities and specificities of 75% and 96%, 62.5% and 92%, 100% and 52%, 100% and 72%, and 100% and 88%, using standard deviation, quartile, 75th, 90th, and 95th percentiles for determining high grade with corresponding areas under the curve (AUCs) of 0.787, 0.792, 0.765, 0.880, and 0.925, respectively. Histogram analysis of ADC maps based on entire tumor volume can be useful for predicting the histological grade of endometrial cancer. The 90th and 95th

  16. Connectome-based lesion-symptom mapping (CLSM): A novel approach to map neurological function.

    PubMed

    Gleichgerrcht, Ezequiel; Fridriksson, Julius; Rorden, Chris; Bonilha, Leonardo

    2017-01-01

    Lesion-symptom mapping is a key tool in understanding the relationship between structure and function in neuroscience as it can provide objective evidence about which regions are crucial for a given process. Initial limitations with this approach were largely overcome by voxel-based lesion-symptom mapping (VLSM), a method introduced in the early 2000s, which allows for a whole-brain approach to study the association between damaged areas and behavioral impairment by applying an independent statistical test at every voxel. By doing so, this technique eliminated the need to predefine regions of interest or classify patients into groups based on arbitrary cutoff scores. VLSM has nonetheless its own limitations; chiefly, a bias towards recognizing cortical necrosis/gliosis but with poor sensitivity for detecting injury along long white matter tracts, thus ignoring cortical disconnection, which can per se lead to behavioral impairment. Here, we propose a complementary method that, instead, establishes a statistical relationship between the strength of connections between all brain regions of the brain (as defined by a standard brain atlas) and the array of behavioral performance seen in patients with brain injury: connectome-based lesion-symptom mapping (CLSM). Whole-brain CLSM therefore has the potential to identify key connections for behavior independently of a priori assumptions with applicability across a broad spectrum of neurological and psychiatric diseases. We propose that this approach can further our understanding of brain-structure relationships and is worth exploring in clinical and theoretical contexts.

  17. Mapping the global topography of the cost function in STELLOPT

    NASA Astrophysics Data System (ADS)

    Lucia, M.; Mynick, H. E.; Pomphrey, N.

    2011-10-01

    Stellarator designs have long been optimized for reduced neoclassical transport, but optimization for reduced turbulent transport is a relatively nascent research thrust. Recent work has addressed this ``turbulent optimization'' by using the GENE/GIST nonlinear gyrokinetic code and the STELLOPT stellarator optimization code. That work demonstrated that STELLOPT can produce stellarator designs that reduce the turbulent transport without adversely affecting other design metrics. STELLOPT utilizes a Levenberg-Marquardt (LM) algorithm to find a local minimum of a cost function in a shape space z of coefficients that define the plasma boundary. However, a visualization of the topography of the cost function in z space might reveal a lower global minimum and provide insight into why the LM algorithm missed it. The current work uses STELLOPT to provide this capability, replacing its LM algorithm with one that produces maps of the wider topography of the cost function. Analysis of these maps will be used to gain insight into the properties of the studied design configurations and to identify possible improvements to STELLOPT's optimization algorithm. Supported by U.S. DOE contract DE-AC02-09CH11466 and by U.S. DOD NDSEG fellowship.

  18. Nested Association Mapping for Identification of Functional Markers

    PubMed Central

    Guo, Baohong; Sleper, David A.; Beavis, William D.

    2010-01-01

    Identification of functional markers (FMs) provides information about the genetic architecture underlying complex traits. An approach that combines the strengths of linkage and association mapping, referred to as nested association mapping (NAM), has been proposed to identify FMs in many plant species. The ability to identify and resolve FMs for complex traits depends upon a number of factors including frequency of FM alleles, magnitudes of their genetic effects, disequilibrium among functional and nonfunctional markers, statistical analysis methods, and mating design. The statistical characteristics of power, accuracy, and precision to identify FMs with a NAM population were investigated using three simulation studies. The simulated data sets utilized publicly available genetic sequences and simulated FMs were identified using least-squares variable selection methods. Results indicate that FMs with simple additive genetic effects that contribute at least 5% to the phenotypic variability in at least five segregating families of a NAM population consisting of recombinant inbred progeny derived from 28 matings with a single reference inbred will have adequate power to accurately and precisely identify FMs. This resolution and power are possible even for genetic architectures consisting of disequilibrium among multiple functional and nonfunctional markers in the same genomic region, although the resolution of FMs will deteriorate rapidly if more than two FMs are tightly linked within the same amplicon. Finally, nested mating designs involving several reference parents will have a greater likelihood of resolving FMs than single reference designs. PMID:20551444

  19. The contribution of electrophysiology to functional connectivity mapping

    PubMed Central

    Schölvinck, Marieke L; Leopold, David A; Brookes, Matthew J; Khader, Patrick H

    2014-01-01

    A powerful way to probe brain function is to assess the relationship between simultaneous changes in activity across different parts of the brain. In recent years, the temporal activity correlation between brain areas has frequently been taken as a measure of their functional connections. Evaluating ‘functional connectivity’ in this way is particularly popular in the fMRI community, but has also drawn interest among electrophysiologists. Like hemodynamic fluctuations observed with fMRI, electrophysiological signals display significant temporal fluctuations, even in the absence of a stimulus. These neural fluctuations exhibit correlational structure over a wide range of spatial and temporal scales. Initial evidence suggests that certain aspects of this correlational structure bear a high correspondence to so-called functional networks defined using fMRI. The growing family of methods to study activity covariation, combined with the diverse neural mechanisms that contribute to the spontaneous fluctuations, have somewhat blurred the operational concept of functional connectivity. What is clear is that spontaneous activity is a conspicuous, energy-consuming feature of the brain. Given its prominence and its practical applications for the functional connectivity mapping of brain networks, it is of increasing importance that we understand its neural origins as well as its contribution to normal brain function. PMID:23587686

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

    NASA Astrophysics Data System (ADS)

    Regele, Jonathan

    2015-11-01

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

  1. 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)

  2. Mapping areas at risk of diffuse phosphorus losses to water: a pilot study of Lake Haderslev Dam, Denmark.

    PubMed

    Andersen, Hans Estrup; Heckrath, Goswin; Thodsen, Hans

    2008-01-01

    Haderslev Dam is a 272 ha lake in southern Denmark with a high recreational value. For decades the lake has been severely eutrophicated due to excessive phosphorus loading. Major point sources were cut off in the early 1990s and an upstream wetland was recreated. However, the ecological quality remains unsatisfactory. In this study we estimate the importance of agriculture on diffuse phosphorus (P) input to the lake by modelling combined with independent estimates for contributions from scattered dwellings not connected to a sewer and from background losses. We apply a newly developed Danish P index to the lake catchment for mapping of risk areas for diffuse phosphorus losses. For risk areas we suggest mitigation measures and estimate the effect of the mitigation measures on the total P loading of the lake as well as the associated costs.

  3. Mapping breast cancer blood flow index, composition, and metabolism in a human subject using combined diffuse optical spectroscopic imaging and diffuse correlation spectroscopy

    NASA Astrophysics Data System (ADS)

    Yazdi, Hossein S.; O'Sullivan, Thomas D.; Leproux, Anais; Hill, Brian; Durkin, Amanda; Telep, Seraphim; Lam, Jesse; Yazdi, Siavash S.; Police, Alice M.; Carroll, Robert M.; Combs, Freddie J.; Strömberg, Tomas; Yodh, Arjun G.; Tromberg, Bruce J.

    2017-04-01

    Diffuse optical spectroscopic imaging (DOSI) and diffuse correlation spectroscopy (DCS) are model-based near-infrared (NIR) methods that measure tissue optical properties (broadband absorption, μa, and reduced scattering, μs‧) and blood flow (blood flow index, BFI), respectively. DOSI-derived μa values are used to determine composition by calculating the tissue concentration of oxy- and deoxyhemoglobin (HbO2, HbR), water, and lipid. We developed and evaluated a combined, coregistered DOSI/DCS handheld probe for mapping and imaging these parameters. We show that uncertainties of 0.3 mm-1 (37%) in μs‧ and 0.003 mm-1 (33%) in μa lead to ˜53% and 9% errors in BFI, respectively. DOSI/DCS imaging of a solid tissue-simulating flow phantom and a breast cancer patient reveals well-defined spatial distributions of BFI and composition that clearly delineates both the flow channel and the tumor. BFI reconstructed with DOSI-corrected μa and μs‧ values had a tumor/normal contrast of 2.7, 50% higher than the contrast using commonly assumed fixed optical properties. In conclusion, spatially coregistered imaging of DOSI and DCS enhances intrinsic tumor contrast and information content. This is particularly important for imaging diseased tissues where there are significant spatial variations in μa and μs‧ as well as potential uncoupling between flow and metabolism.

  4. 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

  5. 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.

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

    PubMed

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

    2006-05-01

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

  7. A New Mapping Function Based on GNSS-RO observations

    NASA Astrophysics Data System (ADS)

    Benedetto, Catia; Rosciano, Elisa; Vespe, Francesco; Vizziello, Giuseppe

    2015-04-01

    The coordinates of a static Global Navigation Satellite System (GNSS) station placed on the ground are estimated together with the delay suffered by the incoming satellite signals through the atmosphere. The tropospheric delay (TD) is shaped as the product of the zenith delay (ZTD) times a mapping function (MF) depending on the sine of elevation angles. In processing chain, ZTD is just estimated together with the coordinates; while the MF is modelled apart, in an independent way, by using atmospheric profiles retrieved with balloon observations ( RAOB) as done for the Niell MF (1996) or provided by climate or Numerical Weather Prediction (NWP) models as in the Vienna MFs. The several space missions devoted to GNSS-RO (e.g. COSMIC-FORMOSAT, METOP, CHAMP, GRACE end others) are providing a huge amount of data which makes worthwhile to be attempted the reconstruction of a new mapping function based on such kind of data. Thus we have built the "Matera" MF ( MTMF) based just on GNSS-RO observations. The new MTMF will be applied to a network of EUREF GNSS stations in the Mediterranean area. Formal errors and repeatability of ZTD and coordinates estimated with the MTMF will be compared with those achieved applying other MF. In validation activities we plan to use the Bernese software.

  8. Mapping morphological shape as a high-dimensional functional curve.

    PubMed

    Fu, Guifang; Huang, Mian; Bo, Wenhao; Hao, Han; Wu, Rongling

    2017-01-06

    Detecting how genes regulate biological shape has become a multidisciplinary research interest because of its wide application in many disciplines. Despite its fundamental importance, the challenges of accurately extracting information from an image, statistically modeling the high-dimensional shape and meticulously locating shape quantitative trait loci (QTL) affect the progress of this research. In this article, we propose a novel integrated framework that incorporates shape analysis, statistical curve modeling and genetic mapping to detect significant QTLs regulating variation of biological shape traits. After quantifying morphological shape via a radius centroid contour approach, each shape, as a phenotype, was characterized as a high-dimensional curve, varying as angle θ runs clockwise with the first point starting from angle zero. We then modeled the dynamic trajectories of three mean curves and variation patterns as functions of θ Our framework led to the detection of a few significant QTLs regulating the variation of leaf shape collected from a natural population of poplar, Populus szechuanica var tibetica This population, distributed at altitudes 2000-4500 m above sea level, is an evolutionarily important plant species. This is the first work in the quantitative genetic shape mapping area that emphasizes a sense of 'function' instead of decomposing the shape into a few discrete principal components, as the majority of shape studies do. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  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. © 2016 by the Society for the Study of Reproduction, Inc.

  10. High Resolution Mapping of Protein Sequence–Function Relationships

    PubMed Central

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

    2010-01-01

    We present a large-scale approach to investigate the functional consequences of sequence variation in a protein. The approach entails the display of hundreds of thousands of protein variants, moderate selection for activity, and high throughput DNA sequencing to quantify the performance of each variant. Using this strategy, we tracked the performance of >600,000 variants of a human WW domain after three and six rounds of selection by phage display for binding to its peptide ligand. Binding properties of these variants defined a high-resolution map of mutational preference across the WW domain; each position possessed unique features that could not be captured by a few representative mutations. Our approach could be applied to many in vitro or in vivo protein assays, providing a general means for understanding how protein function relates to sequence. PMID:20711194

  11. 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.

  12. Diffusion MRI-based cortical complexity alterations associated with executive function in multiple sclerosis.

    PubMed

    Muhlert, Nils; Sethi, Varun; Schneider, Torben; Daga, Pankaj; Cipolotti, Lisa; Haroon, Hamied A; Parker, Geoff J M; Ourselin, Sebastian; Wheeler-Kingshott, Claudia A M; Miller, David H; Ron, Maria A; Chard, Declan T

    2013-07-01

    To report a novel magnetic resonance imaging measure (diffusion orientational complexity [DOC]) in a study of people with multiple sclerosis (MS) and healthy controls and to determine patterns of abnormality, correlations with conventional diffusion measures, and associations with cognitive function. We performed high angular resolution diffusion imaging (HARDI) and measured DOC, mean diffusivity (MD), and fractional anisotropy (FA) in 51 MS patients and 28 healthy controls. All subjects had a 2-mm isotropic HARDI scan on a 3 T scanner using a 32-channel head receiver coil. DOC, MD, and FA were measured in three regions of interest (ROIs) in frontal cortex linked to executive function, two ROIs in occipital cortex thought unlikely to affect cognition, and in the whole cortex. Frontal cortex DOC was significantly decreased in MS patients. DOC correlated mostly with FA but not MD in controls and with MD but not FA in people with MS. In regression models that included all three diffusion-based measures, frontal cortex DOC and frontal cortex FA independently predicted executive function scores. DOC is a new useful measure of functionally relevant cortical pathology in MS, providing information that complements conventional diffusion measures. Copyright © 2013 Wiley Periodicals, Inc.

  13. Conductivity tensor mapping of the human brain using diffusion tensor MRI

    PubMed Central

    Tuch, David S.; Wedeen, Van J.; Dale, Anders M.; George, John S.; Belliveau, John W.

    2001-01-01

    Knowledge of the electrical conductivity properties of excitable tissues is essential for relating the electromagnetic fields generated by the tissue to the underlying electrophysiological currents. Efforts to characterize these endogenous currents from measurements of the associated electromagnetic fields would significantly benefit from the ability to measure the electrical conductivity properties of the tissue noninvasively. Here, using an effective medium approach, we show how the electrical conductivity tensor of tissue can be quantitatively inferred from the water self-diffusion tensor as measured by diffusion tensor magnetic resonance imaging. The effective medium model indicates a strong linear relationship between the conductivity and diffusion tensor eigenvalues (respectively, σ and d) in agreement with theoretical bounds and experimental measurements presented here (σ/d ≈ 0.844 ± 0.0545 S⋅s/mm3, r2 = 0.945). The extension to other biological transport phenomena is also discussed. PMID:11573005

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

    PubMed Central

    2016-01-01

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

  15. Presurgical functional MR imaging of language and motor functions: validation with intraoperative electrocortical mapping.

    PubMed

    Bizzi, Alberto; Blasi, Valeria; Falini, Andrea; Ferroli, Paolo; Cadioli, Marcello; Danesi, Ugo; Aquino, Domenico; Marras, Carlo; Caldiroli, Dario; Broggi, Giovanni

    2008-08-01

    To prospectively determine the sensitivity and specificity of functional magnetic resonance (MR) imaging for mapping language and motor functions in patients with a focal mass adjacent to eloquent cortex, by using intraoperative electrocortical mapping (ECM) as the reference standard. The ethics committee approved the study, and patients gave written informed consent. Thirty-four consecutive patients (16 women, 18 men; mean age, 43.2 years) were included who met the following three criteria: They had a focal mass in or adjacent to eloquent cortex of the language or motor system, they had the ability to perform the functional MR imaging task, and they had to undergo surgery with intraoperative ECM. Functional MR imaging with verb generation (n = 17) or finger tapping of the contralateral hand (n = 17) was performed at 1.5 T with a block design and an echo-planar gradient-echo T2*-weighted sequence. Cortex essential for language or hand motor functions was mapped with ECM. A site-by-site comparison between functional MR imaging and ECM was performed with the aid of a neuronavigational device. Sensitivity and specificity were calculated according to task performed, histopathologic findings, and tumor grade. Exact 95% confidence intervals were calculated for each sensitivity and specificity value. For 34 consecutive patients, there were 28 with gliomas, two with metastases, one with meningioma, and three with cavernous angiomas. A total of 251 cortical sites were tested with ECM; overall functional MR imaging sensitivity and specificity were 83% and 82%, respectively. Sensitivity (65%) was lower and specificity (93%) was higher in World Health Organization grade IV gliomas compared with grade II (sensitivity, 93%; specificity, 79%) and III (sensitivity, 93%; specificity, 76%) gliomas. At 3 months after surgery, language proficiency was unchanged in 15 patients; functionality of the contralateral arm was unchanged in 14 patients and improved in one patient. Functional

  16. 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.

  17. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  19. 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

  20. 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

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

    PubMed

    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.

  2. 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

  3. 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.

  4. 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.

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

    PubMed

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

    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.

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

    DOE PAGES

    Chen, Fengxiang; Zhang, Yong; Gfroerer, T. H.; ...

    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

  7. 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.

  8. Mapping the Transmission Functions of Single-Molecule Junctions

    SciTech Connect

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

    2016-06-08

    Charge transport characteristics of single-molecule junctions are often governed by a transmission function that dictates the probability of electrons or holes tunneling across the junction. Here, we present a new and simple technique for measuring the transmission function of molecular junctions in the coherent tunneling limit, over an energy range of 2 eV around the Fermi energy. We create molecular junctions in an ionic environment with electrodes having different areas exposed, 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 ab initio. 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.

  9. Mapping the Transmission Functions of Single-Molecule Junctions

    DOE PAGES

    Capozzi, Brian; Low, Jonathan Z.; Xia, Jianlong; ...

    2016-06-08

    Charge transport characteristics of single-molecule junctions are often governed by a transmission function that dictates the probability of electrons or holes tunneling across the junction. Here, we present a new and simple technique for measuring the transmission function of molecular junctions in the coherent tunneling limit, over an energy range of 2 eV around the Fermi energy. We create molecular junctions in an ionic environment with electrodes having different areas exposed, 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 junctionmore » 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 ab initio. 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.« less

  10. Three-directional acceleration phase mapping of myocardial function.

    PubMed

    Staehle, Felix; Jung, Bernd A; Bauer, Simon; Leupold, Jochen; Bock, Jelena; Lorenz, Ramona; Föll, Daniela; Markl, Michael

    2011-05-01

    An optimized acceleration encoded phase contrast method termed "acceleration phase mapping" for the assessment of regional myocardial function is presented. Based on an efficient gradient waveform design using two-sided encoding for in vivo three-directional acceleration mapping, echo and repetition times TE = 12-14 ms and TR = 15-17 ms for low accelerations sensitivity aenc = 5-8 m/s(2) were achieved. In addition to phantom validation, the technique was applied in a study with 10 healthy volunteers at 1.5T and 3T to evaluate its feasibility to assess regional myocardial acceleration at 1.5T and 3T. Results of the acceleration measurements were compared with the temporal derivative of myocardial velocities from three-directional velocity encoded standard phase contrast MRI in the same volunteers. The feasibility to assess myocardial acceleration along the radial, circumferential, and longitudinal direction of the left ventricle was demonstrated. Despite improved signal-to-noise-ratio at 3T (34% increase compared with 1.5T), image quality with respect to susceptibility artifacts was better 1.5T compared with 3T. Analysis of global and regional left ventricular acceleration showed characteristic patterns of systolic and diastolic acceleration and deceleration. Comparisons of directly measured and derived myocardial acceleration dynamics over the cardiac cycle revealed good correlation (r = 0.45-0.68, P < 0.01) between both methods. Copyright © 2010 Wiley-Liss, Inc.

  11. Clinical application of apparent diffusion coefficient mapping in voxel-based morphometry in the diagnosis of Alzheimer's disease.

    PubMed

    Takahashi, H; Ishii, K; Kashiwagi, N; Watanabe, Y; Tanaka, H; Murakami, T; Tomiyama, N

    2017-02-01

    To evaluate the performance of apparent diffusion coefficient (ADC) mapping compared with voxel-based morphometry and to demonstrate the clinical usefulness of ADC mapping in the diagnosis of Alzheimer's disease (AD). The study population comprised 31 patients with AD (group A) and 24 patients without dementia (group B) who underwent three-dimensional (3D) T1-weighted imaging (WI) and two-dimensional (2D) echo-planar diffusion-weighted imaging (DWI) at 3 T. The volume and ADC of the regional grey matter (GM) in the bilateral hippocampi, precunei, and the anterior and posterior cingulate gyri were calculated using a voxel-based method for automatic segmentation of brain structures. The significance of intergroup differences in each volume and ADC of all regional GM was tested using analysis of variance (ANOVA) with Bonferroni correction. Intergroup regional GM differences in each volume and ADC were evaluated using statistical parametric mapping (SPM). In group A, the volumes of the precunei (mean value: group A/B=18.93/21.48 cm(3)) and the anterior cingulate gyri (mean value: group A/B=6.1/7.81 cm(3)) were significantly less than in group B (p<0.05). The ADC in group A was significantly larger than that in group B in the bilateral hippocampi (mean value: group A/B=right 1020.79×10(-6)/877.23×10(-6) mm(2)/s; left 1072.89×10(-6)/900.2×10(-6) mm(2)/s) and posterior cingulate gyri (mean value: group A/B=1006.77×10(-6)/876.88×10(-6) mm(2)/s; p<0.05). SPM showed that the areas of increased ADC were more extensive than the areas of decreased volume in the bilateral hippocampi, precunei, and posterior cingulate gyri in group A, compared with those in group B (p<0.001). Evaluation of ADC mapping can quantify changes in brain water diffusivity and may improve the performance of automatic morphometric diagnosis of AD. Copyright © 2016 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

  12. Mapping Molecular Diffusion in the Plasma Membrane by Multiple-Target Tracing (MTT)

    PubMed Central

    Rouger, Vincent; Bertaux, Nicolas; Trombik, Tomasz; Mailfert, Sébastien; Billaudeau, Cyrille; Marguet, Didier; Sergé, Arnauld

    2012-01-01

    Our goal is to obtain a comprehensive description of molecular processes occurring at cellular membranes in different biological functions. We aim at characterizing the complex organization and dynamics of the plasma membrane at single-molecule level, by developing analytic tools dedicated to Single-Particle Tracking (SPT) at high density: Multiple-Target Tracing (MTT)1. Single-molecule videomicroscopy, offering millisecond and nanometric resolution1-11, allows a detailed representation of membrane organization12-14 by accurately mapping descriptors such as cell receptors localization, mobility, confinement or interactions. We revisited SPT, both experimentally and algorithmically. Experimental aspects included optimizing setup and cell labeling, with a particular emphasis on reaching the highest possible labeling density, in order to provide a dynamic snapshot of molecular dynamics as it occurs within the membrane. Algorithmic issues concerned each step used for rebuilding trajectories: peaks detection, estimation and reconnection, addressed by specific tools from image analysis15,16. Implementing deflation after detection allows rescuing peaks initially hidden by neighboring, stronger peaks. Of note, improving detection directly impacts reconnection, by reducing gaps within trajectories. Performances have been evaluated using Monte-Carlo simulations for various labeling density and noise values, which typically represent the two major limitations for parallel measurements at high spatiotemporal resolution. The nanometric accuracy17 obtained for single molecules, using either successive on/off photoswitching or non-linear optics, can deliver exhaustive observations. This is the basis of nanoscopy methods17 such as STORM18, PALM19,20, RESOLFT21 or STED22,23, which may often require imaging fixed samples. The central task is the detection and estimation of diffraction-limited peaks emanating from single-molecules. Hence, providing adequate assumptions such as

  13. The effects of diffusion blur on Snellen and grating acuity and foveal function in amblyopia.

    PubMed

    Han, S H; Kim, S K; Lee, J B; Lee, M S

    1998-08-01

    In order to verify that the effects of diffusion blur on Snellen and grating acuity in amblyopic eyes resemble those obtained from the peripheral or central retina in normal controls, we conducted the following experiment using a liquid crystal window (Edmund Scientific Co.) to produce diffusion blur on Snellen and grating acuity. Spatial frequencies used for a Snellen chart and Teller acuity card were 3.2, 6.5, 13.0, 26.0 cyc/cm at a working distance of 55 cm. The values of diffusive blur on central and peripheral visual acuity obtained from 20 normal healthy control eyes were compared with those values of central visual acuity in 26 amblyopic eyes. The diffusion blur had a strong negative effect on both Snellen and grating acuity in amblyopic eyes, but it had more potent effects on grating acuity (p < 0.05). The diffusion blur values obtained from the central amblyopic retina were more compatible with those of the central retina than with those of the peripheral retina in the control group (p > 0.05). Snellen acuity obtained from diffusion blur overestimated grating acuity in the normal central acuity group and amblyopic central acuity group. The result of this investigation demonstrated that the liquid crystal diffusion blur had a strong negative effect on both Snellen and grating acuity and suggested that the visual function of an amblyopic retina resembled that of a normal central retina.

  14. 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.

  15. Probing dissociative molecular dications by mapping vibrational wave functions

    SciTech Connect

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

    2011-04-15

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

  16. Anatomic connectivity assessed using pathway radial diffusivity is related to functional connectivity in monosynaptic pathways.

    PubMed

    Lowe, Mark J; Koenig, Katherine A; Beall, Erik B; Sakaie, Ken A; Stone, Lael; Bermel, Robert; Phillips, Michael D

    2014-09-01

    This work presents a pathway-dependent anatomic and functional connectivity analysis in 19 patients with relapse-remitting multiple sclerosis (MS) and 16 age-, education-, and gender-matched controls. An MS population is used in this study as a model for anatomic connectivity, permitting us to observe relationships between anatomic and functional connectivity more easily. A combined resting-state functional magnetic resonance imaging (fMRI) and whole-brain, high angular resolution diffusion imaging analysis is performed in three independent, monosynaptic pathways. The pathways chosen were transcallosal pathway connecting the bilateral primary sensorimotor regions, right and left posterior portion of the Papez circuit, connecting the posterior cingulate cortex and hippocampus. The Papez circuit is known to be involved in memory function, one of the most frequently impacted cognitive domains in patients with MS. We show that anatomic connectivity, as measured with diffusion-weighted imaging, and functional connectivity, as measured with resting-state fMRI, are significantly reduced in patients as compared with controls for at least some of the pathways considered. In addition when all pathway measures are combined, anatomic and functional connectivity are significantly correlated in patients with MS as well as healthy controls. We suggest that anatomic and functional connectivity are related for monosynaptic pathways and that radial diffusivity, as a diffusion-tensor-based measure of white matter integrity, is a robust measure of anatomic connectivity in the general population.

  17. Relationship between two different functions derived from diffusion-based decompression theory.

    PubMed

    Ashida, H; Ikeda, T; Tikuisis, P; Nishi, R Y

    2005-01-01

    Hempleman's diffusion-based decompression theory yields two different functions; one is expressed by a simple root function and the other by a complex series function. Although both functions predict the same rate of gas uptake for relatively short exposure times, no clear mathematical explanation has been published that describes the relationship between the two functions. We clarified that (1) the root function is the solution of the one-dimensional diffusion equation for a semi-infinite slab, (2) the series function is an applicable solution for a finite slab thickness, (3) the parameter values of the root function can be used to determine the parameter values of the series function, and (4) the predictions of gas kinetics from both functions agree until an adequate amount of diffusing inert gas reaches the boundary at the opposite end of the finite slab. The last point allows the use of the simpler root function for predicting short no-stop decompression limits. Experience dictates that the inert gas accumulation for a 22 min at 100 feet of seawater (fsw) dive is considered safe for no-stop decompression. Although the constraint, Depth square root of Bottom Time = 100 square root of 22, has been applied as an index to determine either the safe depth or bottom time (given the other) for no-stop decompression, it should not be applied more broadly to dives requiring decompression stops.

  18. Site and Orbit Repeatabilities using Adaptive Mapping Functions

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  19. Maps of current density using density-functional methods.

    PubMed

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

    2008-08-21

    The performance of several density-functional theory (DFT) methods for the calculation of current densities induced by a uniform magnetic field is examined. Calculations are performed using the BLYP and KT3 generalized-gradient approximations, together with the B3LYP hybrid functional. For the latter, both conventional and optimized effective potential (OEP) approaches are used. Results are also determined from coupled-cluster singles-and-doubles (CCSD) electron densities by a DFT constrained search procedure using the approach of Wu and Yang (WY). The current densities are calculated within the CTOCD-DZ2 distributed origin approach. Comparisons are made with results from Hartree-Fock (HF) theory. Several small molecules for which correlation is known to be especially important in the calculation of magnetic response properties are considered-namely, O(3), CO, PN, and H(2)CO. As examples of aromatic and antiaromatic systems, benzene and planarized cyclooctatetraene molecules are considered, with specific attention paid to the ring current phenomenon and its Kohn-Sham orbital origin. Finally, the o-benzyne molecule is considered as a computationally challenging case. The HF and DFT induced current maps show qualitative differences, while among the DFT methods the maps show a similar qualitative structure. To assess quantitative differences in the calculated current densities with different methods, the maximal moduli of the induced current densities are compared and integration of the current densities to yield shielding constants is performed. In general, the maximal modulus is reduced in moving from HF to B3LYP and BLYP, and further reduced in moving to KT3, OEP(B3LYP), and WY(CCSD). The latter three methods offer the most accurate shielding constants in comparison with both experimental and ab initio data and hence the more reliable route to DFT calculation of induced current density in molecules.

  20. Maps of current density using density-functional methods

    NASA Astrophysics Data System (ADS)

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

    2008-08-01

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

  1. Automatic and controlled stimulus processing in conflict tasks: Superimposed diffusion processes and delta functions.

    PubMed

    Ulrich, Rolf; Schröter, Hannes; Leuthold, Hartmut; Birngruber, Teresa

    2015-05-01

    An elaborated diffusion process model (a Diffusion Model for Conflict Tasks, DMC) is introduced that combines conceptual features of standard diffusion models with the notion of controlled and automatic processes. DMC can account for a variety of distributional properties of reaction time (RT) in conflict tasks (e.g., Eriksen flanker, Simon, Stroop). Specifically, DMC is compatible with all observed shapes of delta functions, including negative-going delta functions that are particularly challenging for the class of standard diffusion models. Basically, DMC assumes that the activations of controlled and automatic processes superimpose to trigger a response. Monte Carlo simulations demonstrate that the unfolding of automatic activation in time largely determines the shape of delta functions. Furthermore, the predictions of DMC are consistent with other phenomena observed in conflict tasks such as error rate patterns. In addition, DMC was successfully fitted to experimental data of the standard Eriksen flanker and the Simon task. Thus, the present paper reconciles the prominent and successful class of diffusion models with the empirical finding of negative-going delta functions.

  2. Is the use of diffuse functions essential for the properly description of noncovalent interactions involving anions?

    PubMed

    Bauzá, Antonio; Quiñonero, David; Deyà, Pere M; Frontera, Antonio

    2013-03-28

    It is commonly assumed that theoretical DFT or ab initio calculations involving anions require the utilization of diffuse functions in order to obtain reliable results. In large systems, the use of diffuse functions in the calculations increases the computational cost and, more importantly, sometimes provokes self-consistent-field (SCF) convergence problems, especially in open shell systems. Nowadays, the popular and often used bases for studying noncovalent interactions are the correlation-consistent polarized basis sets of Dunning and co-workers, denoted as cc-pVXZ (X = D, T, etc.), and the Turbomole def2 basis set family (def2-SVP and def2-TZVP). In this paper we study the effect of the utilization of diffuse functions on the energetic and geometric features of several noncovalent complexes, including hydrogen, halogen, and pnicogen bonding, lithium bonds, anion-π interactions, and van der Waals interactions.

  3. Mapping social target detection with functional magnetic resonance imaging.

    PubMed

    Dichter, Gabriel S; Felder, Jennifer N; Bodfish, James W; Sikich, Linmarie; Belger, Aysenil

    2009-03-01

    The neural correlates of cognitive control and social processing functions, as well as the characteristic patterns of anomalous brain activation patterns in psychiatric conditions associated with impairment in these functions, have been well characterized. However, these domains have primarily been examined in isolation. The present study used event-related functional magnetic resonance imaging to map brain areas recruited during a target-detection task designed to evaluate responses to both non-social (i.e. shape) and social (i.e. face) target stimuli. Both shape and face targets activated a similar brain network, including the postcentral gyrus, the anterior and posterior cingulate gyri and the right midfrontal gyrus, whereas face targets additionally activated the thalamus, fusiform and temporooccipital cortex, lingual gyrus and paracingulate gyrus. Comparison of activations to social and non-social target events revealed that a small portion of the dorsal anterior cingulate gyrus (Brodmann's area 32) and the supracalcarine cortex were preferentially activated to face targets. These findings indicate that non-social and social stimuli embedded within a cognitive control task activate overlapping and distinct brain regions. Clinical cognitive neuroscience research of disorders characterized by cognitive dysfunction and impaired social processing would benefit from the use of tasks that evaluate the combined effects of deficits in these two domains.

  4. 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

  5. Analytic model for the runaway distribution function in the presence of spatial diffusion

    SciTech Connect

    Catto, P.J. Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 ); Myra, J.R. ); Wootton, A.J. )

    1994-03-01

    A steady-state kinetic model for runaway electrons in the presence of radial diffusion in a stochastic magnetic field is adopted and solved for a constant magnetic diffusivity. The model is constructed to recover the correct runaway production rate in the absence of spatial diffusion. The parallel energetic electron distribution function [ital f] is found by matching the solutions from three regions in parallel velocity space and is employed to form moments of [ital f]. Upper and lower bounds on the spatial diffusion are obtained by using these moments and the model exhibits the strong sensitivity to collisionality needed to explain the difference between similar plasmas with little or no hard x-ray signal and those with significant hard x-ray signals.

  6. Determination of Moisture Diffusivity as a Function of Both Moisture and Temperature

    NASA Astrophysics Data System (ADS)

    Pavlík, Z.; Černý, R.

    2012-09-01

    The effect of moisture and temperature on liquid water transport in porous media was studied. Specimens of autoclaved aerated concrete were subjected to one-sided water penetration in isothermal conditions at temperatures of 20 °C, 40 °C, 60 °C, and 80 °C. After specified time intervals, moisture profiles were determined gravimetrically. The moisture diffusivity was calculated for a particular temperature as a function of moisture content, using an inverse analysis. The results demonstrate the dependence of the moisture diffusivity on the moisture content and the temperature of the samples. The moisture diffusivity for high moisture content can be as much as one order of magnitude greater than for the lowest moisture content studied. The moisture diffusivity was found to increase by as much as a factor of two when the temperature is increased from 20 °C to 80 °C.

  7. Remote sensing of prefrontal cortex function with diffusive light

    NASA Astrophysics Data System (ADS)

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

    2004-12-01

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

  8. Evaluation of Symmetric Neutral-Atmosphere Mapping Functions Using Ray-Tracing Through Radiosonde Observations

    NASA Astrophysics Data System (ADS)

    Souri, A. H.; Sharifi, M. A.

    2013-12-01

    The aim of this paper is to compare the validity of six recent symmetric mapping functions. The mapping function models the elevation angle dependence of the tropospheric delay. Niell Mapping Function (NMF), Vienna Mapping Function (VMF1), University of New Brunswick- VMF1 (UNB-VMF1) mapping functions, Global Mapping Function (GMF) and Global Pressure and Temperature (GPT2)/GMF are evaluated by using ray tracing through 25 radiosonde stations covering different climatic regions in one year. The ray-traced measurements are regarded as "ground truth". The ray-tracing approach is performed for diverse elevation angle starting at 5° to 15°. The results for both hydrostatic and non-hydrostatic components of mapping functions support the efficiency of online-mapping functions. The latitudinal dependence of standard deviation for 5° is also demonstrated. Although all the tested mapping functions can provide satisfactory results when used for elevation angles above 15°, for high precision geodetic measurements, it is highly recommended that the online-mapping functions (UNBs and VMF1) be used.The results suggest that UNB models, like VMF have strengths and weaknesses and do not stand out as being consistently better or worse than the VMF1. The GPT2/GMF provided better accuracy than GMF and NMF. Since all of them do not require site specific data; therefore GPT2/GMF can be useful as regards its ease of use.

  9. Oxygen vacancy diffusion in bulk SrTiO3 from density functional theory calculations

    SciTech Connect

    Zhang, Lipeng; Liu, Bin; Zhuang, Houlong; Kent, Paul R. C.; Cooper, Valentino R.; Ganesh, Panchapakesan; Xu, Haixuan

    2016-04-01

    Point defects and point defect diffusion contribute significantly to the properties of perovskite materials. However, even for the prototypical case of oxygen vacancies in SrTiO3 (STO), predictions vary widely. Here we present a comprehensive and systematic study of the diffusion barriers for this material. We use density functional theory (DFT) and assess the role of different cell sizes, density functionals, and charge states. Our results show that vacancy-induced octahedral rotations, which are limited by the boundary conditions of the supercell, can significantly affect the computed oxygen vacancy diffusion energy barrier. The diffusion energy barrier of a charged oxygen vacancy is lower than that of a neutral one. Unexpectedly, we find that with increasing supercell size, the effects of the oxygen vacancy charge state, the type of DFT exchange and correlation functional on the energy barrier diminish, and the different DFT predictions asymptote to a value in the range of 0.39-0.49 eV. This work provides important insight and guidance that should be considered for investigations of point defect diffusion in other perovskite materials and in oxide superlattices.

  10. Oxygen vacancy diffusion in bulk SrTiO3 from density functional theory calculations

    DOE PAGES

    Zhang, Lipeng; Liu, Bin; Zhuang, Houlong; ...

    2016-04-01

    Point defects and point defect diffusion contribute significantly to the properties of perovskite materials. However, even for the prototypical case of oxygen vacancies in SrTiO3 (STO), predictions vary widely. Here we present a comprehensive and systematic study of the diffusion barriers for this material. We use density functional theory (DFT) and assess the role of different cell sizes, density functionals, and charge states. Our results show that vacancy-induced octahedral rotations, which are limited by the boundary conditions of the supercell, can significantly affect the computed oxygen vacancy diffusion energy barrier. The diffusion energy barrier of a charged oxygen vacancy ismore » lower than that of a neutral one. Unexpectedly, we find that with increasing supercell size, the effects of the oxygen vacancy charge state, the type of DFT exchange and correlation functional on the energy barrier diminish, and the different DFT predictions asymptote to a value in the range of 0.39-0.49 eV. This work provides important insight and guidance that should be considered for investigations of point defect diffusion in other perovskite materials and in oxide superlattices.« less

  11. 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

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

    SciTech Connect

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

    2016-09-20

    In this paper, we present foreground-reduced cosmic microwave background (CMB) maps derived from the full Planck data set in both temperature and polarization. Compared to the corresponding Planck 2013 temperature sky maps, the total data volume is larger by a factor of 3.2 for frequencies between 30 and 70 GHz, and by 1.9 for frequencies between 100 and 857 GHz. In addition, systematic errors in the forms of temperature-to-polarization leakage, analogue-to-digital conversion uncertainties, and very long time constant errors have been dramatically reduced, to the extent that the cosmological polarization signal may now be robustly recovered on angular scales ℓ ≳ 40. On the very largest scales, instrumental systematic residuals are still non-negligible compared to the expected cosmological signal, and modes with ℓ< 20 are accordingly suppressed in the current polarization maps by high-pass filtering. As in 2013, four different CMB component separation algorithms are applied to these observations, providing a measure of stability with respect to algorithmic and modelling choices. Additionally, the resulting polarization maps have rms instrumental noise ranging between 0.21 and 0.27μK averaged over 55' pixels, and between 4.5 and 6.1μK averaged over 3$'\\atop{.}$4 pixels. The cosmological parameters derived from the analysis of temperature power spectra are in agreement at the 1σ level with the Planck 2015 likelihood. Unresolved mismatches between the noise properties of the data and simulations prevent a satisfactory description of the higher-order statistical properties of the polarization maps. Thus, the primary applications of these polarization maps are those that do not require massive simulations for accurate estimation of uncertainties, for instance estimation of cross-spectra and cross-correlations, or stacking analyses. However, the amplitude of primordial non-Gaussianity is consistent with zero within 2σ for all local, equilateral, and orthogonal

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Pogosyan, Dmitri; Codis, Sandrine; Pichon, Christophe

    2016-10-01

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

  15. Automated Talairach atlas labels for functional brain mapping.

    PubMed

    Lancaster, J L; Woldorff, M G; Parsons, L M; Liotti, M; Freitas, C S; Rainey, L; Kochunov, P V; Nickerson, D; Mikiten, S A; Fox, P T

    2000-07-01

    An automated coordinate-based system to retrieve brain labels from the 1988 Talairach Atlas, called the Talairach Daemon (TD), was previously introduced [Lancaster et al., 1997]. In the present study, the TD system and its 3-D database of labels for the 1988 Talairach atlas were tested for labeling of functional activation foci. TD system labels were compared with author-designated labels of activation coordinates from over 250 published functional brain-mapping studies and with manual atlas-derived labels from an expert group using a subset of these activation coordinates. Automated labeling by the TD system compared well with authors' labels, with a 70% or greater label match averaged over all locations. Author-label matching improved to greater than 90% within a search range of +/-5 mm for most sites. An adaptive grey matter (GM) range-search utility was evaluated using individual activations from the M1 mouth region (30 subjects, 52 sites). It provided an 87% label match to Brodmann area labels (BA 4 & BA 6) within a search range of +/-5 mm. Using the adaptive GM range search, the TD system's overall match with authors' labels (90%) was better than that of the expert group (80%). When used in concert with authors' deeper knowledge of an experiment, the TD system provides consistent and comprehensive labels for brain activation foci. Additional suggested applications of the TD system include interactive labeling, anatomical grouping of activation foci, lesion-deficit analysis, and neuroanatomy education.

  16. 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

  17. A mapping of the electron localization function for earth materials

    NASA Astrophysics Data System (ADS)

    Gibbs, G. V.; Cox, D. F.; Ross, N. L.; Crawford, T. D.; Burt, J. B.; Rosso, K. 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

  18. A tumour control probability model for radiotherapy of prostate cancer using magnetic resonance imaging-based apparent diffusion coefficient maps.

    PubMed

    Casares-Magaz, Oscar; van der Heide, Uulke A; Rørvik, Jarle; Steenbergen, Peter; Muren, Ludvig Paul

    2016-04-01

    Standard tumour control probability (TCP) models assume uniform tumour cell density across the tumour. The aim of this study was to develop an individualised TCP model by including index-tumour regions extracted form multi-parametric magnetic resonance imaging (MRI) and apparent diffusion coefficient (ADC) maps-based cell density distributions. ADC maps in a series of 20 prostate cancer patients were applied to estimate the initial number of cells within each voxel, using three different approaches for the relation between ADC values and cell density: a linear, a binary and a sigmoid relation. All TCP models were based on linear-quadratic cell survival curves assuming α/β=1.93Gy (consistent with a recent meta-analysis) and α set to obtain a 70% of TCP when 77Gy was delivered to the entire prostate in 35 fractions (α=0.18Gy(-1)). Overall, TCP curves based on ADC maps showed larger differences between individuals than those assuming uniform cell densities. The range of the dose required to reach 50% TCP across the patient cohort was 20.1Gy, 18.7Gy and 13.2Gy using an MRI-based voxel density (linear, binary and sigmoid approach, respectively), compared to 4.1Gy using a constant density. Inclusion of tumour-index information together with ADC maps-based cell density increases inter-patient tumour response differentiation for use in prostate cancer RT, resulting in TCP curves with a larger range in D50% across the cohort compared with those based on uniform cell densities. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  19. Diffusion kernel-based logistic regression models for protein function prediction.

    PubMed

    Lee, Hyunju; Tu, Zhidong; Deng, Minghua; Sun, Fengzhu; Chen, Ting

    2006-01-01

    Assigning functions to unknown proteins is one of the most important problems in proteomics. Several approaches have used protein-protein interaction data to predict protein functions. We previously developed a Markov random field (MRF) based method to infer a protein's functions using protein-protein interaction data and the functional annotations of its protein interaction partners. In the original model, only direct interactions were considered and each function was considered separately. In this study, we develop a new model which extends direct interactions to all neighboring proteins, and one function to multiple functions. The goal is to understand a protein's function based on information on all the neighboring proteins in the interaction network. We first developed a novel kernel logistic regression (KLR) method based on diffusion kernels for protein interaction networks. The diffusion kernels provide means to incorporate all neighbors of proteins in the network. Second, we identified a set of functions that are highly correlated with the function of interest, referred to as the correlated functions, using the chi-square test. Third, the correlated functions were incorporated into our new KLR model. Fourth, we extended our model by incorporating multiple biological data sources such as protein domains, protein complexes, and gene expressions by converting them into networks. We showed that the KLR approach of incorporating all protein neighbors significantly improved the accuracy of protein function predictions over the MRF model. The incorporation of multiple data sets also improved prediction accuracy. The prediction accuracy is comparable to another protein function classifier based on the support vector machine (SVM), using a diffusion kernel. The advantages of the KLR model include its simplicity as well as its ability to explore the contribution of neighbors to the functions of proteins of interest.

  20. Linear mapping functions for high-dimensional indexing in image databases

    NASA Astrophysics Data System (ADS)

    Sumanasekara, Santha; Ramakrishna, Medahalli V.

    2000-10-01

    The problem of indexing high-dimensional data has received renewed interest because of its necessity in emerging multimedia databases. The limitations of traditional tree-based indexing and the dimensionality curse is well known. We have proposed a hierarchical indexing structure based on linear mapping functions, which is not tree-based, and not necessarily balanced. At each level of the hierarchy, a linear mapping function is used to distribute the data among buckets. The feasibility and the performance of the indexing structure is dependent on finding appropriate mapping functions for any given data set. In this paper we present the approach taken in arriving at a few classes of mapping functions. We have given a heuristic algorithm to determine the choice of the most appropriate mapping function for a given data set. The results of experiments with real life data are presented and they indicate that the proposed indexing structure with linear mapping functions is indeed practical.

  1. The link between diffusion MRI and tumor heterogeneity: Mapping cell eccentricity and density by diffusional variance decomposition (DIVIDE).

    PubMed

    Szczepankiewicz, Filip; van Westen, Danielle; Englund, Elisabet; Westin, Carl-Fredrik; Ståhlberg, Freddy; Lätt, Jimmy; Sundgren, Pia C; Nilsson, Markus

    2016-11-15

    only to cell density variance. The variance in meningiomas was caused primarily by microscopic anisotropy (mean±s.d.) MKA=1.11±0.33 vs MKI=0.44±0.20 (p<10(-3)), whereas in the gliomas, it was mostly caused by isotropic heterogeneity MKI=0.57±0.30 vs MKA=0.26±0.11 (p<0.05). In conclusion, DIVIDE allows non-invasive mapping of parameters that reflect variable cell eccentricity and density. These results constitute convincing evidence that a link exists between specific aspects of tissue heterogeneity and parameters from dMRI. Decomposing effects of microscopic anisotropy and isotropic heterogeneity facilitates an improved interpretation of tumor heterogeneity as well as diffusion anisotropy on both the microscopic and macroscopic scale.

  2. Adaptive diffusion kernel learning from biological networks for protein function prediction

    PubMed Central

    Sun, Liang; Ji, Shuiwang; Ye, Jieping

    2008-01-01

    Background Machine-learning tools have gained considerable attention during the last few years for analyzing biological networks for protein function prediction. Kernel methods are suitable for learning from graph-based data such as biological networks, as they only require the abstraction of the similarities between objects into the kernel matrix. One key issue in kernel methods is the selection of a good kernel function. Diffusion kernels, the discretization of the familiar Gaussian kernel of Euclidean space, are commonly used for graph-based data. Results In this paper, we address the issue of learning an optimal diffusion kernel, in the form of a convex combination of a set of pre-specified kernels constructed from biological networks, for protein function prediction. Most prior work on this kernel learning task focus on variants of the loss function based on Support Vector Machines (SVM). Their extensions to other loss functions such as the one based on Kullback-Leibler (KL) divergence, which is more suitable for mining biological networks, lead to expensive optimization problems. By exploiting the special structure of the diffusion kernel, we show that this KL divergence based kernel learning problem can be formulated as a simple optimization problem, which can then be solved efficiently. It is further extended to the multi-task case where we predict multiple functions of a protein simultaneously. We evaluate the efficiency and effectiveness of the proposed algorithms using two benchmark data sets. Conclusion Results show that the performance of linearly combined diffusion kernel is better than every single candidate diffusion kernel. When the number of tasks is large, the algorithms based on multiple tasks are favored due to their competitive recognition performance and small computational costs. PMID:18366736

  3. 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.

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

    ERIC Educational Resources Information Center

    Jabury, Donald Eugene

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

  5. Light source distribution and scattering phase function influence light transport in diffuse multi-layered media

    NASA Astrophysics Data System (ADS)

    Vaudelle, Fabrice; L'Huillier, Jean-Pierre; Askoura, Mohamed Lamine

    2017-06-01

    Red and near-Infrared light is often used as a useful diagnostic and imaging probe for highly scattering media such as biological tissues, fruits and vegetables. Part of diffusively reflected light gives interesting information related to the tissue subsurface, whereas light recorded at further distances may probe deeper into the interrogated turbid tissues. However, modelling diffusive events occurring at short source-detector distances requires to consider both the distribution of the light sources and the scattering phase functions. In this report, a modified Monte Carlo model is used to compute light transport in curved and multi-layered tissue samples which are covered with a thin and highly diffusing tissue layer. Different light source distributions (ballistic, diffuse or Lambertian) are tested with specific scattering phase functions (modified or not modified Henyey-Greenstein, Gegenbauer and Mie) to compute the amount of backscattered and transmitted light in apple and human skin structures. Comparisons between simulation results and experiments carried out with a multispectral imaging setup confirm the soundness of the theoretical strategy and may explain the role of the skin on light transport in whole and half-cut apples. Other computational results show that a Lambertian source distribution combined with a Henyey-Greenstein phase function provides a higher photon density in the stratum corneum than in the upper dermis layer. Furthermore, it is also shown that the scattering phase function may affect the shape and the magnitude of the Bidirectional Reflectance Distribution (BRDF) exhibited at the skin surface.

  6. Increasing the power of functional maps of the medial temporal lobe by using large deformation diffeomorphic metric mapping.

    PubMed

    Miller, Michael I; Beg, M Faisal; Ceritoglu, Can; Stark, Craig

    2005-07-05

    The functional magnetic resonance imagery responses of declarative memory tasks in the medial temporal lobe (MTL) are examined by using large deformation diffeomorphic metric mapping (LDDMM) to remove anatomical variations across subjects. LDDMM is used to map the structures of the MTL in multiple subjects into extrinsic atlas coordinates; these same diffeomorphic mappings are used to transfer the corresponding functional data activation to the same extrinsic coordinates. The statistical power in the averaged LDDMM mapped signals is significantly increased over conventional Talairach-Tournoux averaging. Activation patterns are highly localized within the MTL. Whereas the present demonstration has been aimed at enhancing alignment within the MTL, this technique is general and can be applied throughout the brain.

  7. Phase-contrast velocity mapping for highly diffusive fluids: optimal bipolar gradient pulse parameters for hyperpolarized helium-3.

    PubMed

    Martin, Lionel; Maître, Xavier; de Rochefort, Ludovic; Sarracanie, Mathieu; Friese, Marlies; Hagot, Pascal; Durand, Emmanuel

    2014-10-01

    In MR-velocity phase-contrast measurements, increasing the encoding bipolar gradient, i.e., decreasing the field of speed, usually improves measurement precision. However, in gases, fast diffusion during the bipolar gradient pulses may dramatically decrease the signal-to-noise ratio, thus degrading measurement precision. These two effects are contradictory. This work aims at determining the optimal sequence parameters to improve the velocity measurement precision. This work presents the theoretical optimization of bipolar gradient parameters (duration and amplitude) to improve velocity measurement precision. An analytical approximation is given as well as a numerical optimization. It is shown that the solution depends on the diffusion coefficient and T2 *. Experimental validation using hyperpolarized (3) He diluted in various buffer gases ((4) He, N2 , and SF6 ) is presented at 1.5 Tesla (T) in a straight pipe. Excellent agreement was found with the theoretical results for prediction of optimal field of speed and good agreement was found for the precision in measured velocity, but for SF6 buffered gas. The theoretical predictions were validated, providing a way to optimize velocity mapping in gases. Copyright © 2013 Wiley Periodicals, Inc.

  8. Intersubject variability in the analysis of diffusion tensor images at the group level: fractional anisotropy mapping and fiber tracking techniques.

    PubMed

    Müller, Hans-Peter; Unrath, Alexander; Riecker, Axel; Pinkhardt, Elmar H; Ludolph, Albert C; Kassubek, Jan

    2009-04-01

    Diffusion tensor imaging (DTI) provides comprehensive information about quantitative diffusion and connectivity in the human brain. Transformation into stereotactic standard space is a prerequisite for group studies and requires thorough data processing to preserve directional inter-dependencies. The objective of the present study was to optimize technical approaches for this preservation of quantitative and directional information during spatial normalization in data analyses at the group level. Different averaging methods for mean diffusion-weighted images containing DTI information were compared, i.e., region of interest-based fractional anisotropy (FA) mapping, fiber tracking (FT) and corresponding tractwise FA statistics (TFAS). The novel technique of intersubject FT that takes into account directional information of single data sets during the FT process was compared to standard FT techniques. Application of the methods was shown in the comparison of normal subjects and subjects with defined white matter pathology (alterations of the corpus callosum). Fiber tracking was applied to averaged data sets and showed similar results compared with FT on single subject data. The application of TFAS to averaged data showed averaged FA values around 0.4 for normal controls. The values were in the range of the standard deviation for averaged FA values for TFAS applied to single subject data. These results were independent of the applied averaging technique. A significant reduction of the averaged FA values was found in comparison to TFAS applied to data from subjects with defined white matter pathology (FA around 0.2). The applicability of FT techniques in the analysis of different subjects at the group level was demonstrated. Group comparisons as well as FT on group averaged data were shown to be feasible. The objective of this work was to identify the most appropriate method for intersubject averaging and group comparison which incorporates intersubject variability of

  9. Noninvasive intracranial pressure assessment based on a data-mining approach using a nonlinear mapping function.

    PubMed

    Kim, Sunghan; Scalzo, Fabien; Bergsneider, Marvin; Vespa, Paul; Martin, Neil; Hu, Xiao

    2012-03-01

    The current gold standard to determine intracranial pressure (ICP) involves an invasive procedure for direct access to the intracranial compartment. The risks associated with this invasive procedure include intracerebral hemorrhage, infection, and discomfort. We previously proposed an innovative data-mining framework of noninvasive ICP (NICP) assessment. The performance of the proposed framework relies on designing a good mapping function. We attempt to achieve performance gain by adopting various linear and nonlinear mapping functions. Our results demonstrate that a nonlinear mapping function based on the kernel spectral regression technique significantly improves the performance of the proposed data-mining framework for NICP assessment in comparison to other linear mapping functions.

  10. Symmetric Neutral-Atmosphere Mapping Functions: A Review of the State-Of-The-Art

    NASA Astrophysics Data System (ADS)

    Sharifi, M. A.; Souri, A. H.

    2013-12-01

    The aim of this paper is to review of six recent symmetric mapping functions. The mapping function can be largely used for GPS meteorological measurements, InSAR atmospheric corrections and precise measurements of very long baseline interferometry (VLBI). These spacebased techniques use radio signal that propagate through the Earth's atmosphere. The electrically-neutral region, predominantly the troposphere, affects the speed and direction of travel of radio waves leading to existence of excess path. The mapping function models the elevation angle dependence of the delay. Within the past decade, significant improvements have been achieved in order to use of Numerical Weather Models (NWM) for geodetic positioning. Ray-tracing algorithms have been performed through refractivity shells retrieved from NWMs in order to relate zenith delays to slant delays. Therefore, there seems to be a real need for deep review of recent developments in the mapping function domain. This paper proposes a comprehensive review of the symmetric mapping functions state of the art, their spatio-temporal variations and used NWM and generic models. Niell Mapping Function (NMF), Vienna Mapping Function (VMF1), University of New Brunswick-VMF1 (UNB-VMF1) mapping functions, Global Mapping Function (GMF) and Global Pressure and Temperature (GPT2)/GMF are reviewed in this paper.

  11. 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.

  12. Task-evoked brain functional magnetic susceptibility mapping by independent component analysis (χICA).

    PubMed

    Chen, Zikuan; Calhoun, Vince D

    2016-03-01

    Conventionally, independent component analysis (ICA) is performed on an fMRI magnitude dataset to analyze brain functional mapping (AICA). By solving the inverse problem of fMRI, we can reconstruct the brain magnetic susceptibility (χ) functional states. Upon the reconstructed χ dataspace, we propose an ICA-based brain functional χ mapping method (χICA) to extract task-evoked brain functional map. A complex division algorithm is applied to a timeseries of fMRI phase images to extract temporal phase changes (relative to an OFF-state snapshot). A computed inverse MRI (CIMRI) model is used to reconstruct a 4D brain χ response dataset. χICA is implemented by applying a spatial InfoMax ICA algorithm to the reconstructed 4D χ dataspace. With finger-tapping experiments on a 7T system, the χICA-extracted χ-depicted functional map is similar to the SPM-inferred functional χ map by a spatial correlation of 0.67 ± 0.05. In comparison, the AICA-extracted magnitude-depicted map is correlated with the SPM magnitude map by 0.81 ± 0.05. The understanding of the inferiority of χICA to AICA for task-evoked functional map is an ongoing research topic. For task-evoked brain functional mapping, we compare the data-driven ICA method with the task-correlated SPM method. In particular, we compare χICA with AICA for extracting task-correlated timecourses and functional maps. χICA can extract a χ-depicted task-evoked brain functional map from a reconstructed χ dataspace without the knowledge about brain hemodynamic responses. The χICA-extracted brain functional χ map reveals a bidirectional BOLD response pattern that is unavailable (or different) from AICA. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Intraoperative use of diffusion tensor imaging-based tractography for resection of gliomas located near the pyramidal tract: comparison with subcortical stimulation mapping and contribution to surgical outcomes.

    PubMed

    Vassal, F; Schneider, F; Nuti, C

    2013-10-01

    For gliomas, the goal of surgery is maximal tumour removal with the preservation of neurological function. We evaluated the contribution of the combination of diffusion tensor imaging-based fibre tracking (DTI-FT) of the pyramidal tract (PT) integrated to the navigation and subcortical direct electrical stimulations (DESs) to surgical outcomes. Ten patients underwent surgery for gliomas located in close relationship with the subcortical course of the PT. Preoperative DTI was performed with a three-Tesla magnetic resonance scanner applying an echo-planar sequence with 20 diffusion directions. DTI-FT data were systematically loaded into the navigation for intraoperative guidance. When the resection closely approached the PT as illustrated on navigation images, subcortical DESs were used to confirm the proximity of the PT by observing motor responses. The location of all subcortically stimulated points with positive motor response was correlated with the illustrated PT. Motor deficits were evaluated pre- and postoperatively, and compared with the extent of tumour removal. DTI-FT of the PT was successfully performed in all patients. A total of fifteen positive subcortical DESs were obtained in 8 of 10 patients; in these cases, the mean distance from the stimulated point to the PT was 6.2 ± 3.6 mm. The mean tumoural volumetric resection was 90.8 ± 10.4%, with a gross total resection in four patients. At one month after surgery, only one patient had a slight impairment of motor function (decreased fine motor hand skills). DTI-FT is an accurate technique to map the PT in the vicinity of brain tumours. By combining anatomical (DTI-FT) and functional (subcortical DES) studies for intraoperative localization of the PT, the authors achieved a good volumetric resection of tumours located in eloquent motor areas, with low morbidity. Careful use of this protocol requires the knowledge of some pitfalls, mainly the occurrence of brain shift during removal of large tumours.

  14. Mapping Diffuse HI Content in MHONGOOSE Galaxies NGC 1744 and NGC 7424

    NASA Astrophysics Data System (ADS)

    Sardone, Amy; Pisano, Daniel J.; Pingel, Nickolas

    2017-01-01

    The universe contains an abundance of neutral atomic hydrogen, or HI. This HI holds the key to knowing how stars are born, how galaxies form and develop, and how dark matter halos accrete gas from the cosmic web. One of the most crucial questions regarding galaxy formation today is how galaxies accrete their gas and how accretion processes affect subsequent star formation. We are trying to answer these questions by mapping the HI content in a four square degree region around galaxies NGC 1744 and NGC 7424, galaxies to be observed as part of the MHONGOOSE survey. NGC 1744 has already been observed extensively with the VLA, so we will be able to quantify the differences in emission. To do this our GBT maps must be sensitive to column densities on the order of ~1018 cm-2. With such low column densities, we will be able to search for features of the cosmic web in the form of tidal interactions and cosmic web filaments with its relation to star-forming galaxies.

  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. 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.

  17. Characterisation of Damaged Tubular Composites by Acoustic Emission, Thermal Diffusivity Mapping and TSR-RGB Projection Technique

    NASA Astrophysics Data System (ADS)

    Chandarana, Neha; Lansiaux, Henri; Gresil, Matthieu

    2016-11-01

    An increase in the use of composite materials, owing to improved design and fabrication processes, has led to cost reductions in many industries. Resistance to corrosion, high specific strength, and stiffness are just a few of their many attractive properties. However, damage tolerance remains a major concern in the implementation of composites and uncertainty regarding component lifetimes can lead to over-design and under-use of such materials. A combination of non-destructive evaluation (NDE) and structural health monitoring (SHM) have shown promise in improving confidence by enabling data collection in-situ and in real time. In this work, infrared thermography (IRT) is employed for NDE of tubular composite specimens before and after impact. Four samples are impacted with energies of 5 J, 7.5 J, and 10 J by an un-instrumented falling weight set-up. Acoustic emissions (AE) are monitored using bonded piezoelectric sensors during one of the four impact tests. IRT data is used to generate diffusivity and thermal depth mappings of each sample using the thermographic signal reconstruction (TSR) red green blue (RGB) projection technique. Analysis of AE data alone for a 10 J impact suggest significant damage to the fibres and matrix; this is in good agreement with the generated thermal depth mappings for each sample, which indicate damage through multiple fibre layers. IRT and AE data are correlated and validated by optical micrographs taken along the cross section of damage.

  18. Characterisation of Damaged Tubular Composites by Acoustic Emission, Thermal Diffusivity Mapping and TSR-RGB Projection Technique

    NASA Astrophysics Data System (ADS)

    Chandarana, Neha; Lansiaux, Henri; Gresil, Matthieu

    2017-04-01

    An increase in the use of composite materials, owing to improved design and fabrication processes, has led to cost reductions in many industries. Resistance to corrosion, high specific strength, and stiffness are just a few of their many attractive properties. However, damage tolerance remains a major concern in the implementation of composites and uncertainty regarding component lifetimes can lead to over-design and under-use of such materials. A combination of non-destructive evaluation (NDE) and structural health monitoring (SHM) have shown promise in improving confidence by enabling data collection in-situ and in real time. In this work, infrared thermography (IRT) is employed for NDE of tubular composite specimens before and after impact. Four samples are impacted with energies of 5 J, 7.5 J, and 10 J by an un-instrumented falling weight set-up. Acoustic emissions (AE) are monitored using bonded piezoelectric sensors during one of the four impact tests. IRT data is used to generate diffusivity and thermal depth mappings of each sample using the thermographic signal reconstruction (TSR) red green blue (RGB) projection technique. Analysis of AE data alone for a 10 J impact suggest significant damage to the fibres and matrix; this is in good agreement with the generated thermal depth mappings for each sample, which indicate damage through multiple fibre layers. IRT and AE data are correlated and validated by optical micrographs taken along the cross section of damage.

  19. 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…

  20. 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…

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

    PubMed

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

    2015-09-01

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

  2. Stochastic chaos induced by diffusion processes with identical spectral density but different probability density functions.

    PubMed

    Lei, Youming; Zheng, Fan

    2016-12-01

    Stochastic chaos induced by diffusion processes, with identical spectral density but different probability density functions (PDFs), is investigated in selected lightly damped Hamiltonian systems. The threshold amplitude of diffusion processes for the onset of chaos is derived by using the stochastic Melnikov method together with a mean-square criterion. Two quasi-Hamiltonian systems, namely, a damped single pendulum and damped Duffing oscillator perturbed by stochastic excitations, are used as illustrative examples. Four different cases of stochastic processes are taking as the driving excitations. It is shown that in such two systems the spectral density of diffusion processes completely determines the threshold amplitude for chaos, regardless of the shape of their PDFs, Gaussian or otherwise. Furthermore, the mean top Lyapunov exponent is employed to verify analytical results. The results obtained by numerical simulations are in accordance with the analytical results. This demonstrates that the stochastic Melnikov method is effective in predicting the onset of chaos in the quasi-Hamiltonian systems.

  3. Modified polarimetric bidirectional reflectance distribution function with diffuse scattering: surface parameter estimation

    NASA Astrophysics Data System (ADS)

    Zhan, Hanyu; Voelz, David G.

    2016-12-01

    The polarimetric bidirectional reflectance distribution function (pBRDF) describes the relationships between incident and scattered Stokes parameters, but the familiar surface-only microfacet pBRDF cannot capture diffuse scattering contributions and depolarization phenomena. We propose a modified pBRDF model with a diffuse scattering component developed from the Kubelka-Munk and Le Hors et al. theories, and apply it in the development of a method to jointly estimate refractive index, slope variance, and diffuse scattering parameters from a series of Stokes parameter measurements of a surface. An application of the model and estimation approach to experimental data published by Priest and Meier shows improved correspondence with measurements of normalized Mueller matrix elements. By converting the Stokes/Mueller calculus formulation of the model to a degree of polarization (DOP) description, the estimation results of the parameters from measured DOP values are found to be consistent with a previous DOP model and results.

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

    PubMed

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

    2009-04-09

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

  5. Diffusion of interstitial oxygen in silicon and germanium: a hybrid functional study

    NASA Astrophysics Data System (ADS)

    Colleoni, Davide; Pasquarello, Alfredo

    2016-12-01

    The minimum-energy paths for the diffusion of an interstitial O atom in silicon and germanium are studied through the nudged-elastic-band method and hybrid functional calculations. The reconsideration of the diffusion of O in silicon primarily serves the purpose of validating the procedure for studying the O diffusion in germanium. Our calculations show that the minimum energy path goes through an asymmetric transition state in both silicon and germanium. The stability of these transition states is found to be enhanced by the generation of unpaired electrons in the highest occupied single-particle states. Calculated energy barriers are 2.54 and 2.14 eV for Si and Ge, in very good agreement with corresponding experimental values of 2.53 and 2.08 eV, respectively.

  6. Stochastic chaos induced by diffusion processes with identical spectral density but different probability density functions

    NASA Astrophysics Data System (ADS)

    Lei, Youming; Zheng, Fan

    2016-12-01

    Stochastic chaos induced by diffusion processes, with identical spectral density but different probability density functions (PDFs), is investigated in selected lightly damped Hamiltonian systems. The threshold amplitude of diffusion processes for the onset of chaos is derived by using the stochastic Melnikov method together with a mean-square criterion. Two quasi-Hamiltonian systems, namely, a damped single pendulum and damped Duffing oscillator perturbed by stochastic excitations, are used as illustrative examples. Four different cases of stochastic processes are taking as the driving excitations. It is shown that in such two systems the spectral density of diffusion processes completely determines the threshold amplitude for chaos, regardless of the shape of their PDFs, Gaussian or otherwise. Furthermore, the mean top Lyapunov exponent is employed to verify analytical results. The results obtained by numerical simulations are in accordance with the analytical results. This demonstrates that the stochastic Melnikov method is effective in predicting the onset of chaos in the quasi-Hamiltonian systems.

  7. Symplectic Propagation of the Map, Tangent Map and Tangent Map Derivative through Quadrupole and Combined-Function Dipole Magnets without Truncation

    NASA Astrophysics Data System (ADS)

    Bruhwiler, D. L.; Cary, J. R.; Shasharina, S.

    1998-04-01

    The MAPA accelerator modeling code symplectically advances the full nonlinear map, tangent map and tangent map derivative through all accelerator elements. The tangent map and its derivative are nonlinear generalizations of Browns first- and second-order matrices(K. Brown, SLAC-75, Rev. 4 (1982), pp. 107-118.), and they are valid even near the edges of the dynamic aperture, which may be beyond the radius of convergence for a truncated Taylor series. In order to avoid truncation of the map and its derivatives, the Hamiltonian is split into pieces for which the map can be obtained analytically. Yoshidas method(H. Yoshida, Phys. Lett. A 150 (1990), pp. 262-268.) is then used to obtain a symplectic approximation to the map, while the tangent map and its derivative are appropriately composed at each step to obtain them with equal accuracy. We discuss our splitting of the quadrupole and combined-function dipole Hamiltonians and show that typically few steps are required for a high-energy accelerator.

  8. Diffusion tensor imaging of frontal white matter and executive functioning in cocaine-exposed children.

    PubMed

    Warner, Tamara Duckworth; Behnke, Marylou; Eyler, Fonda Davis; Padgett, Kyle; Leonard, Christiana; Hou, Wei; Garvan, Cynthia Wilson; Schmalfuss, Ilona M; Blackband, Stephen J

    2006-11-01

    Although animal studies have demonstrated frontal white matter and behavioral changes resulting from prenatal cocaine exposure, no human studies have associated neuropsychological deficits in attention and inhibition with brain structure. We used diffusion tensor imaging to investigate frontal white matter integrity and executive functioning in cocaine-exposed children. Six direction diffusion tensor images were acquired using a Siemens 3T scanner with a spin-echo echo-planar imaging pulse sequence on right-handed cocaine-exposed (n = 28) and sociodemographically similar non-exposed children (n = 25; mean age: 10.6 years) drawn from a prospective, longitudinal study. Average diffusion and fractional anisotropy were measured in the left and right frontal callosal and frontal projection fibers. Executive functioning was assessed using two well-validated neuropsychological tests (Stroop color-word test and Trail Making Test). Cocaine-exposed children showed significantly higher average diffusion in the left frontal callosal and right frontal projection fibers. Cocaine-exposed children were also significantly slower on a visual-motor set-shifting task with a trend toward lower scores on a verbal inhibition task. Controlling for gender and intelligence, average diffusion in the left frontal callosal fibers was related to prenatal exposure to alcohol and marijuana and an interaction between cocaine and marijuana exposure. Performance on the visual-motor set-shifting task was related to prenatal cocaine exposure and an interaction between cocaine and tobacco exposure. Significant correlations were found between test performance and fractional anisotropy in areas of the frontal white matter. Prenatal cocaine exposure, alone and in combination with exposure to other drugs, is associated with slightly poorer executive functioning and subtle microstructural changes suggesting less mature development of frontal white matter pathways. The relative contribution of postnatal

  9. 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

  10. Efficient floating diffuse functions for accurate characterization of the surface-bound excess electrons in water cluster anions.

    PubMed

    Zhang, Changzhe; Bu, Yuxiang

    2017-01-25

    In this work, the effect of diffuse function types (atom-centered diffuse functions versus floating functions and s-type versus p-type diffuse functions) on the structures and properties of three representative water cluster anions featuring a surface-bound excess electron is studied and we find that an effective combination of such two kinds of diffuse functions can not only reduce the computational cost but also, most importantly, considerably improve the accuracy of results and even avoid incorrect predictions of spectra and the EE shape. Our results indicate that (a) simple augmentation of atom-centered diffuse functions is beneficial for the vertical detachment energy convergence, but it leads to very poor descriptions for the singly occupied molecular orbital (SOMO) and lowest unoccupied molecular orbital (LUMO) distributions of the water cluster anions featuring a surface-bound excess electron and thus a significant ultraviolet spectrum redshift; (b) the ghost-atom-based floating diffuse functions can not only contribute to accurate electronic calculations of the ground state but also avoid poor and even incorrect descriptions of the SOMO and the LUMO induced by excessive augmentation of atom-centered diffuse functions; (c) the floating functions can be realized by ghost atoms and their positions could be determined through an optimization routine along the dipole moment vector direction. In addition, both the s- and p-type floating functions are necessary to supplement in the basis set which are responsible for the ground (s-type character) and excited (p-type character) states of the surface-bound excess electron, respectively. The exponents of the diffuse functions should also be determined to make the diffuse functions cover the main region of the excess electron distribution. Note that excessive augmentation of such diffuse functions is redundant and even can lead to unreasonable LUMO characteristics.

  11. 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)

  12. 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

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

    NASA Astrophysics Data System (ADS)

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

    2010-07-01

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

  14. 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).

  15. 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. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  16. 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.

  17. Functional Mapping in Pediatric Epilepsy Surgical Candidates: Functional Magnetic Resonance Imaging Under Sedation With Chloral Hydrate.

    PubMed

    Ives-Deliperi, Victoria L; Butler, James T

    2015-12-01

    Functional magnetic resonance imaging is a useful tool to lateralize and localize language in presurgical patients, as well as to localize other functionally salient cortex. The procedure is typically reserved for older children and adults, since it necessitates cooperation and participation in tasks. We have explored the applicability of functional magnetic resonance imaging for language and motor mapping at our epilepsy surgical center in younger children under sedation with chloral hydrate. A series of 24 consecutive patients undergoing magnetic resonance imaging, between ages 16 months and 11 years, were scanned under sedation. Assisted finger-tapping and foot-tapping tasks were conducted for the purpose of motor mapping in nine patients, and a speech-based auditory task was conducted in 23 of the 24 patients for the purpose of lateralizing and localizing language. Significant blood oxygen level-dependent signal increases in hand and foot regions of the primary motor cortex were generated in all but one patient who underwent the motor mapping tasks. Signal increases in receptive language cortex were convincingly generated in 12 of the 23 (52%) patients who underwent the speech-based auditory task. These results suggest that functional magnetic resonance imaging can help to localize motor and/or somatosensory cortex and language cortex in young children under sedation with chloral hydrate. This procedure may be used to assist in presurgical planning. The findings also imply that a sedating agent may be used in pediatric neuroimaging as an alternative to general anesthesia. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Multimodal functional mapping of sensorimotor cortex prior to resection of an epileptogenic perirolandic lesion.

    PubMed

    Kirsch, Heidi E; Sepkuty, Jehuda P; Crone, Nathan E

    2004-06-01

    The effects of chronic epileptogenic lesions on functional anatomy are under debate. Our recent experience during mapping and resection of a lesion in sensorimotor cortex supports the idea that epileptogenic lesions may prompt development of alternate cortical motor representations. Multimodal mapping may uncover alternate areas of functionality that make surgery feasible even when conventional neuroanatomy suggests otherwise. Newer methods such as electrocorticographic spectral analysis may complement traditional electrical cortical stimulation mapping.

  19. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Multi-mode Li diffusion in natural zircons: Evidence for diffusion in the presence of step-function concentration boundaries

    NASA Astrophysics Data System (ADS)

    Tang, Ming; Rudnick, Roberta L.; McDonough, William F.; Bose, Maitrayee; Goreva, Yulia

    2017-09-01

    Micron- to submicron-scale observations of Li distribution and Li isotope composition profiles can be used to infer the mechanisms of Li diffusion in natural zircon. Extreme fractionation (20-30‰) within each single crystal studied here confirms that Li diffusion commonly occurs in zircon. Sharp Li concentration gradients frequently seen in zircons suggest that the effective diffusivity of Li is significantly slower than experimentally determined (Cherniak and Watson, 2010; Trail et al., 2016), otherwise the crystallization/metamorphic heating of these zircons would have to be unrealistically fast (years to tens of years). Charge coupling with REE and Y has been suggested as a mechanism that may considerably reduce Li diffusivity in zircon (Ushikubo et al., 2008; Bouvier et al., 2012). We show that Li diffused in the direction of decreasing Li/Y ratio and increasing Li concentration (uphill diffusion) in one of the zircons, demonstrating charge coupling with REE and Y. Quantitative modeling reveals that Li may diffuse in at least two modes in natural zircons: one being slow and possibly coupled with REE+Y, and the other one being fast and not coupled with REE+Y. The partitioning of Li between these two modes during its diffusion may depend on the pre-diffusion substitution mechanism of REE and Y in the zircon lattice. Based on our results, sharp Li concentration gradients are not indicative of limited diffusion, and can be preserved at temperatures >700 °C on geologic timescales. Finally, large δ7 Li variations observed in the Hadean Jack Hills zircons may record kinetic fractionation, rather than a record of ancient intense weathering in the granite source materials.

  1. Phenotyping mouse pulmonary function in vivo with the lung diffusing capacity.

    PubMed

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

    2015-01-06

    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.

  2. Mapping brain structure and function: cellular resolution, global perspective.

    PubMed

    Zupanc, Günther K H

    2017-04-01

    A comprehensive understanding of the brain requires analysis, although from a global perspective, with cellular, and even subcellular, resolution. An important step towards this goal involves the establishment of three-dimensional high-resolution brain maps, incorporating brain-wide information about the cells and their connections, as well as the chemical architecture. The progress made in such anatomical brain mapping in recent years has been paralleled by the development of physiological techniques that enable investigators to generate global neural activity maps, also with cellular resolution, while simultaneously recording the organism's behavioral activity. Combination of the high-resolution anatomical and physiological maps, followed by theoretical systems analysis of the deduced network, will offer unprecedented opportunities for a better understanding of how the brain, as a whole, processes sensory information and generates behavior.

  3. 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.

  4. COMPLEX DIFFUSION ON IMAGE GRAPHS

    PubMed Central

    Seo, Dohyung; Vemuri, Baba C

    2009-01-01

    Complex diffusion was introduced in image processing literature as a means to achieve simultaneous denoising and enhancement of scalar valued images. In this paper, we present a novel geometric framework for achieving complex diffusion on color images expressed as image graphs. In this framework, we develop a new variational formulation for achieving complex diffusion. This formulation involves a modified harmonic map functional and is quite distinct from the Polyakov action described in earlier work by Sochen et al. Our formulation provides a framework for simultaneous (feature preserving) denoising and enhancement. We present results of comparison between the complex diffusion, and Beltrami flow all in the image graph framework. PMID:20490365

  5. 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.

  6. Effect of baseline magnetic resonance imaging (MRI) apparent diffusion coefficient lesion volume on functional outcome in ischemic stroke.

    PubMed

    Ma, Li; Gao, Pei-yi; Hu, Qing-mao; Lin, Yan; Jing, Li-na; Xue, Jing; Chen, Zhi-jun; Wang, Yong-jun; Liu, Mei-li; Cai, Ye-feng

    2011-06-01

    We explored the relationship between predicted infarct core, predicted ischemic penumbras and predicted final infarct volumes obtained though apparent diffusion coefficient (ADC)-based method, as well as other clinical variables, and functional outcome. Patients with acute cerebral ischemic stroke were retrospectively recruited. The National Institutes of Health Stroke Scale score was evaluated at baseline and the modified Rankin Scale (mRS) at day 90. Favorable outcome was defined as an mRS score of 0 to 2, and unfavorable outcome as 3 to 6. Multimodal stroke magnetic resonance imaging was carried out at presentation. The volumes of diffusion-weighted imaging (DWI) and perfusion-weighted imaging (PWI) were measured using the regions of interest (ROI) method. The volumes of predicted infarct core, predicted ischemic penumbra and predicted final infarct were obtained by an automated image analysis system based on baseline ADC maps. The association between baseline magnetic resonance imaging volumes, baseline clinical variables, and functional outcome was statistically analyzed. The study included 30 males and 20 females (mean±SD age, 56±10 years). Baseline DWI, PWI and PWI-DWI mismatch volumes were not correlated with day-90 mRS (P>0.05). Predicted infarct core, predicted ischemic penumbra and predicted final infarct through ADC-based method were all correlated with day-90 mRS (P<0.05). A better outcome was associated with a smaller predicted volume. Low baseline National Institutes of Health Stroke Scale and recanalization also demonstrated a trend toward a favorable outcome. Receiver operating characteristic analysis showed that the area under the curve of predicted final infarct volume and recanalization were higher with statistical significance (P<0.001). Predicted volumes obtained from ADC-based methods, especially predicted final infarct volume, as well as baseline National Institutes of Health Stroke Scale and recanalization may have effect on functional

  7. 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.

  8. Diffuse ventricular fibrosis measured by T₁ mapping on cardiac MRI predicts success of catheter ablation for atrial fibrillation.

    PubMed

    McLellan, Alex J A; Ling, Liang-han; Azzopardi, Sonia; Ellims, Andris H; Iles, Leah M; Sellenger, Michael A; Morton, Joseph B; Kalman, Jonathan M; Taylor, Andrew J; Kistler, Peter M

    2014-10-01

    There is a complex interplay between the atria and ventricles in atrial fibrillation (AF). Cardiac magnetic resonance (CMR) imaging provides detailed tissue characterization, identifying focal ventricular fibrosis with late gadolinium enhancement (ventricular late gadolinium enhancement) and diffuse fibrosis with postcontrast-enhanced T1 mapping. The aim of the present study was to investigate the relationship between postcontrast ventricular T1 relaxation time on CMR and freedom from AF after pulmonary vein isolation. One hundred three patients undergoing catheter ablation for symptomatic AF (66% paroxysmal AF; age, 58±10 years; left atrial area, 27±7 cm(2)) underwent preprocedure CMR to determine postcontrast ventricular T1 time. Follow-up included clinical review and 7-day Holter monitors at 6 monthly intervals. All patients underwent successful pulmonary vein isolation. At a mean follow-up of 15±7 months, the single procedure success was 74%. Postcontrast ventricular T1 time was significantly shorter in patients with recurrent AF (366±73 ms) versus patients without AF recurrence (428±90 ms; P=0.002). Univariate predictors of AF recurrence included postcontrast ventricular T1 time, AF type (paroxysmal versus persistent), AF duration, and body mass index. After multivariate analysis, ventricular T1 time (P=0.03) and AF duration (P=0.03) were the only independent predictors. Freedom from AF was present in 84% of patients with a postcontrast ventricular T1 time >380 ms versus 56% in patients with a postcontrast ventricular T1 time <380 ms (P=0.002). A shorter postcontrast ventricular T1 relaxation time on CMR is associated with reduced freedom from AF after catheter ablation. Diffuse ventricular fibrosis as demonstrated by CMR may, in part, explain recurrent AF after AF ablation. © 2014 American Heart Association, Inc.

  9. A skewed PDF combustion model for jet diffusion flames. [Probability density function (PDF)

    SciTech Connect

    Abou-Ellail, M.M.M.; Salem, H. )

    1990-11-01

    A combustion model based on restricted chemical equilibrium is described. A transport equation for the skewness of the mixture fraction is derived. It contains two adjustable constants. The computed values of the mean mixture fraction (f) and its variance and skewness (g and s) for a jet diffusion methane flame are used to obtain the shape of a shewed pdf. The skewed pdf is split into a turbulent part (beta function) and a nonturbulent part (delta function) at f = 0. The contribution of each part is directly related to the values of f, g, and s. The inclusion of intermittency in the skewed pdf appreciably improves the numerical predictions obtained for a turbulent jet diffusion methane flame for which experimental data are available.

  10. Spatial and temporal hemodynamic study of human primary visual cortex using simultaneous functional MRI and diffuse optical tomography

    PubMed Central

    Zhang, Xiaofeng; Toronov, Vladislav Y.; Webb, Andrew G.

    2011-01-01

    The blood oxygenation level dependent (BOLD) functional MRI and near infrared optical tomography have been widely used to investigate the hemodynamic response to functional stimulation in the human brain. In this paper, we present a complete methodology of integrating the two imaging modalities to study the underlying physiological mechanism of hemodynamic response in the human primary visual cortex. The integration was made feasible thanks to the development of an MRI-compatible optical probe. The optical imaging was conducted using a frequency-domain near infrared spectrometer. The 3-dimentional optical image reconstruction was based on diffuse optical tomography (DOT) using the perturbative approach. The sensitivity function of the forward problem was obtained using Monte Carlo method. From our preliminary observation, the spatial activation pattern of deoxyhemoglobin is consistent with the BOLD signal map. The patterns of oxy- and deoxyhemoglobin are very similar. The temporal hemodynamic response shows an increased total hemoglobin concentration, which indicates an increment of cerebral blood volume (CBV) during physiological activation. PMID:17282286

  11. 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%.

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

    PubMed

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

    2012-12-20

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

  13. 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.

  14. 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.

  15. Individualized structure-function mapping for glaucoma: practical constraints on map resolution for clinical and research applications.

    PubMed

    Denniss, Jonathan; Turpin, Andrew; McKendrick, Allison M

    2014-03-28

    We have developed customized maps that relate visual field and optic nerve head (ONH) regions according to individual anatomy. In this study, we aimed to determine feasible map resolution for research use, and to make a principled recommendation of sector size for clinical applications. Measurement variability in fovea-ONH distance and angle was estimated from 10 repeat OCT scans of 10 healthy people. Errors in estimating axial length from refractive error were determined from published data. Structure-function maps were generated, and customized to varied clinically-plausible anatomical parameters. For each parameter set (n = 210), 200 maps were generated by sampling from measurement/estimation error distributions. Mapped 1° sectors at each visual field location from each parameter set were normalized to difference from their mean. Variation (90% ranges) in normalized mapped sectors represents the precision of individualized maps. Standard deviations of repeated measures of fovea-ONH distance and angle were 61 μm and 0.97° (coefficients of variation 1.3% and 12.0%, respectively). Neither measure varied systematically with mean (Spearmans's ρ = 0.26, P = 0.47 for distance, ρ = -0.31, P = 0.39 for angle). Variation (90% ranges) in normalized mapped sectors varied across the visual field and ranged from 3° to 18° when axial length was measured accurately, and from 6° to 32° when axial length was estimated from refractive error. The 90% ranges represent the minimum feasible ONH sector size at each visual field location. For clinical use an easily interpretable scheme of 30° sectors is suggested.

  16. Graphical function mapping as a new way to explore cause-and-effect chains

    USGS Publications Warehouse

    Evans, Mary Anne

    2016-01-01

    Graphical function mapping provides a simple method for improving communication within interdisciplinary research teams and between scientists and nonscientists. This article introduces graphical function mapping using two examples and discusses its usefulness. Function mapping projects the outcome of one function into another to show the combined effect. Using this mathematical property in a simpler, even cartoon-like, graphical way allows the rapid combination of multiple information sources (models, empirical data, expert judgment, and guesses) in an intuitive visual to promote further discussion, scenario development, and clear communication.

  17. 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.

  18. MODELING OF THE ZODIACAL EMISSION FOR THE AKARI/IRC MID-INFRARED ALL-SKY DIFFUSE MAPS

    SciTech Connect

    Kondo, Toru; Ishihara, Daisuke; Kaneda, Hidehiro; Nakamichi, Keichiro; Takaba, Sachi; Kobayashi, Hiroshi; Ootsubo, Takafumi; Pyo, Jeonghyun; Onaka, Takashi E-mail: ishihara@u.phys.nagoya-u.ac.jp

    2016-03-15

    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.

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

    PubMed Central

    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.

    2012-01-01

    Abstract. 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. PMID:22502579

  20. MR spectroscopy, functional MRI, and diffusion-tensor imaging in the aging brain: a conceptual review.

    PubMed

    Minati, L; Grisoli, M; Bruzzone, M G

    2007-03-01

    In vivo magnetic resonance spectroscopy (MRS), functional magnetic resonance imaging (fMRI), and diffusion-tensor imaging (DTI) have recently opened new possibilities for noninvasively assessing the metabolic, functional, and connectivity correlates of aging in research and clinical settings. The purpose of this article is to provide a conceptual review intended for a multidisciplinary audience, covering physical principles and main findings related to normal aging and senile cognitive impairment. This article is divided into 3 sections, dedicated to MRS, to fMRI, and to DTI. The spectroscopy section surveys physiological function of the observable metabolites, concentration changes in normal aging and their interpretation, and correlation with cognitive performance. The functional MRI section surveys the hemispheric asymmetry reduction model from compensation and de-differentiation viewpoints, memory encoding, retrieval and consolidation, inhibitory control, perception and action, resting-state networks, and functional deactivations. The DTI section surveys age-related changes, correlation with behavioral scores, and transition to cognitive impairment.

  1. 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

  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.

  3. Bidirectional reflectance distribution function of diffuse reflectance standards around the retro-reflection direction

    NASA Astrophysics Data System (ADS)

    Rabal, A. M.; Ferrero, A.; Campos, J.; Pons, A.; Hernanz, M. L.

    2014-06-01

    The increase in the bidirectional reflectance distribution function around the retro-reflection direction was characterized for four common diffuse standard reflectance materials: Spectralon, matte white Russian opal glass, matte white ceramic standard and pressed barium sulphate (BaSO4) powder. The characterized increase or surge is high enough to be considered in low-uncertainty reflectance factor measurements, where the values are usually extrapolated around that direction due to instrumental limitations. In order to make the corrections for this surge, the coherent backscattering of light model and a much simpler exponential function were fitted to the measurements.

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

    NASA Astrophysics Data System (ADS)

    Diaw, A.; Murillo, M. S.

    2016-09-01

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

  5. Intrinsic functional brain mapping in reconstructed 4D magnetic susceptibility (χ) data space.

    PubMed

    Chen, Zikuan; Calhoun, Vince

    2015-02-15

    By solving an inverse problem of T2*-weighted magnetic resonance imaging for a dynamic fMRI study, we reconstruct a 4D magnetic susceptibility source (χ) data space for intrinsic functional mapping. A 4D phase dataset is calculated from a 4D complex fMRI dataset. The background field and phase wrapping effect are removed by a Laplacian technique. A 3D χ source map is reconstructed from a 3D phase image by a computed inverse MRI (CIMRI) scheme. A 4D χ data space is reconstructed by repeating the 3D χ source reconstruction for each time point. A functional map is calculated by a temporal correlation between voxel signals in the 4D χ space and the timecourse of the task paradigm. With a finger-tapping experiment, we obtain two 3D functional mappings in the 4D magnitude data space and in the reconstructed 4D χ data space. We find that the χ-based functional mapping reveals co-occurrence of bidirectional responses in a 3D activation map that is different from the conventional magnitude-based mapping. The χ-based functional mapping can also be achieved by a 3D deconvolution of a phase activation map. Based on a subject experimental comparison, we show that the 4D χ tomography method could produce a similar χ activation map as obtained by the 3D deconvolution method. By removing the dipole effect and other fMRI technological contaminations, 4D χ tomography provides a 4D χ data space that allows a more direct and truthful functional mapping of a brain activity. Published by Elsevier B.V.

  6. Conservation and Rewiring of Functional Modules Revealed by an Epistasis Map in Fission Yeast

    PubMed Central

    Roguev, Assen; Bandyopadhyay, Sourav; Zofall, Martin; Zhang, Ke; Fischer, Tamas; Collins, Sean R.; Qu, Hongjing; Shales, Michael; Park, Han-Oh; Hayles, Jacqueline; Hoe, Kwang-Lae; Kim, Dong-Uk; Ideker, Trey; Grewal, Shiv I.; Weissman, Jonathan S.; Krogan, Nevan J.

    2009-01-01

    An epistasis map (E-MAP) was constructed in the fission yeast, Schizosaccharomyces pombe, by systematically measuring the phenotypes associated with pairs of mutations. This high-density, quantitative genetic interaction map focused on various aspects of chromosome function, including transcription regulation and DNA repair/replication. The E-MAP uncovered a previously unidentified component of the RNA interference (RNAi) machinery (rsh1) and linked the RNAi pathway to several other biological processes. Comparison of the S. pombe E-MAP to an analogous genetic map from the budding yeast revealed that, whereas negative interactions were conserved between genes involved in similar biological processes, positive interactions and overall genetic profiles between pairs of genes coding for physically associated proteins were even more conserved. Hence, conservation occurs at the level of the functional module (protein complex), but the genetic cross talk between modules can differ substantially. PMID:18818364

  7. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast.

    PubMed

    Roguev, Assen; Bandyopadhyay, Sourav; Zofall, Martin; Zhang, Ke; Fischer, Tamas; Collins, Sean R; Qu, Hongjing; Shales, Michael; Park, Han-Oh; Hayles, Jacqueline; Hoe, Kwang-Lae; Kim, Dong-Uk; Ideker, Trey; Grewal, Shiv I; Weissman, Jonathan S; Krogan, Nevan J

    2008-10-17

    An epistasis map (E-MAP) was constructed in the fission yeast, Schizosaccharomyces pombe, by systematically measuring the phenotypes associated with pairs of mutations. This high-density, quantitative genetic interaction map focused on various aspects of chromosome function, including transcription regulation and DNA repair/replication. The E-MAP uncovered a previously unidentified component of the RNA interference (RNAi) machinery (rsh1) and linked the RNAi pathway to several other biological processes. Comparison of the S. pombe E-MAP to an analogous genetic map from the budding yeast revealed that, whereas negative interactions were conserved between genes involved in similar biological processes, positive interactions and overall genetic profiles between pairs of genes coding for physically associated proteins were even more conserved. Hence, conservation occurs at the level of the functional module (protein complex), but the genetic cross talk between modules can differ substantially.

  8. Analysis of event-related fMRI data using diffusion maps.

    PubMed

    Shen, Xilin; Meyer, François G

    2005-01-01

    The blood oxygen level-dependent (BOLD) signal in response to brief periods of stimulus can be detected using event-related functional magnetic resonance imaging (ER-fMRI). In this paper, we propose a new approach for the analysis of ER-fMRI data. We regard the time series as vectors in a high dimensional space (the dimension is the number of time samples). We believe that all activated times series share a common structure and all belong to a low dimensional manifold. On the other hand, we expect the background time series (after detrending) to form a cloud around the origin. We construct an embedding that reveals the organization of the data into an activated manifold and a cluster of non-activated time series. We use a graph partitioning technique-the normalized cut to find the separation between the activated manifold and the background time series. We have conducted several experiments with synthetic and in-vivo data that demonstrate the performance of our approach.

  9. Semantic Web Technology for Mapping and Applying Clinical Functional Assessment Information

    DTIC Science & Technology

    2015-05-01

    Award Number: W81XWH-13-2-0010 TITLE: Semantic Web Technology for Mapping and Applying Clinical Functional Assessment Information PRINCIPAL...SUBTITLE Semantic Web Technology for Mapping and Applying Clinical 5a. CONTRACT NUMBER W81XWH-13-2-0010 Functional Assessment Information 5b. GRANT...International Classification of Functioning, Disability, and Health (ICF). We developed the mechanisms to generate programmatically data-acquisition Web forms

  10. On the mapping associated with the complex representation of functions and processes.

    NASA Technical Reports Server (NTRS)

    Harger, R. O.

    1972-01-01

    The mapping between function spaces that is implied by the representation of a real 'bandpass' function by a complex 'low-pass' function is explicitly accepted. The discussion is extended to the representation of stationary random processes where the mapping is between spaces of random processes. This approach clarifies the nature of the complex representation, especially in the case of random processes and, in addition, derives the properties of the complex representation.-

  11. Temporal Profile of Microtubule Associated Protein (MAP-2) - A Novel Indicator of Diffuse Brain Injury Severity and Early Mortality after Brain Trauma.

    PubMed

    Papa, Linda; Robicsek, Steven A; Brophy, Gretchen M; Wang, Kevin K W; Hannay, H Julia; Heaton, Shelley C; Schmalfuss, Ilona; Gabrielli, Andrea; Hayes, Ronald L; Robertson, Claudia S

    2017-09-12

    This study compared CSF levels of MAP-2 from adult patients with severe TBI to uninjured controls over ten days, and examined the relationship between MAP-2 concentrations and acute clinical and radiologic measures of injury severity along with mortality at 2-weeks and over 6-months. This prospective study, conducted at two Level 1 Trauma Centers, enrolled adults with severe TBI (GCS ≤8) requiring a ventriculostomy as well as controls. Ventricular CSF was sampled from each patient at 6, 12, 24, 48, 72, 96, 120, 144, 168, 192, 216 and 240 hours following TBI and analyzed via ELISA for MAP-2 (ng/ml). Injury severity was assessed by the GCS score, Marshall Classification on CT, Rotterdam score and mortality. There were 151 patients enrolled, 130 TBI and 21 control patients. MAP-2 was detectable within 6 hours of injury and was significantly elevated compared to controls (P<0.001) at each time-point. MAP-2 was highest within 72 hours of injury and decreased gradually over 10 days. The area under the ROC curve for deciphering TBI versus controls at the earliest time-point CSF was obtained was 0.96 (95%CI 0.93-0.99) and for the maximal 24-hours level was 0.98 (95%CI 0.97-1.00). The AUC for initial MAP-2 levels predicting 2-week mortality was 0.80 at 6 hours; 0.81 at 12 hours; 0.75 at 18 hours, 0.75 at 24 hours; and 0.80 at 48 hours. Those with Diffuse Injury III-IV had much higher initial (p=0.033) and maximal (p=0.003) MAP-2 levels than those with Diffuse Injury I-II. There was a graded increase in the overall levels and peaks of MAP-2 as the degree of diffuse injury increased within the first 120 hours post-injury. These data suggest that early levels of MAP-2 reflect severity of diffuse brain injury and predict 2-week mortality in TBI patients. These findings have implications for counseling families and guiding multidisciplinary care.

  12. Diffusion Geometry Unravels the Emergence of Functional Clusters in Collective Phenomena

    NASA Astrophysics Data System (ADS)

    De Domenico, Manlio

    2017-04-01

    Collective phenomena emerge from the interaction of natural or artificial units with a complex organization. The interplay between structural patterns and dynamics might induce functional clusters that, in general, are different from topological ones. In biological systems, like the human brain, the overall functionality is often favored by the interplay between connectivity and synchronization dynamics, with functional clusters that do not coincide with anatomical modules in most cases. In social, sociotechnical, and engineering systems, the quest for consensus favors the emergence of clusters. Despite the unquestionable evidence for mesoscale organization of many complex systems and the heterogeneity of their interconnectivity, a way to predict and identify the emergence of functional modules in collective phenomena continues to elude us. Here, we propose an approach based on random walk dynamics to define the diffusion distance between any pair of units in a networked system. Such a metric allows us to exploit the underlying diffusion geometry to provide a unifying framework for the intimate relationship between metastable synchronization, consensus, and random search dynamics in complex networks, pinpointing the functional mesoscale organization of synthetic and biological systems.

  13. 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

  14. 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.

  15. FADTTSter: accelerating hypothesis testing with functional analysis of diffusion tensor tract statistics

    NASA Astrophysics Data System (ADS)

    Noel, Jean; Prieto, Juan C.; Styner, Martin

    2017-03-01

    Functional Analysis of Diffusion Tensor Tract Statistics (FADTTS) is a toolbox for analysis of white matter (WM) fiber tracts. It allows associating diffusion properties along major WM bundles with a set of covariates of interest, such as age, diagnostic status and gender, and the structure of the variability of these WM tract properties. However, to use this toolbox, a user must have an intermediate knowledge in scripting languages (MATLAB). FADTTSter was created to overcome this issue and make the statistical analysis accessible to any non-technical researcher. FADTTSter is actively being used by researchers at the University of North Carolina. FADTTSter guides non-technical users through a series of steps including quality control of subjects and fibers in order to setup the necessary parameters to run FADTTS. Additionally, FADTTSter implements interactive charts for FADTTS' outputs. This interactive chart enhances the researcher experience and facilitates the analysis of the results. FADTTSter's motivation is to improve usability and provide a new analysis tool to the community that complements FADTTS. Ultimately, by enabling FADTTS to a broader audience, FADTTSter seeks to accelerate hypothesis testing in neuroimaging studies involving heterogeneous clinical data and diffusion tensor imaging. This work is submitted to the Biomedical Applications in Molecular, Structural, and Functional Imaging conference. The source code of this application is available in NITRC.

  16. On the averaging of cardiac diffusion tensor MRI data: the effect of distance function selection

    NASA Astrophysics Data System (ADS)

    Giannakidis, Archontis; Melkus, Gerd; Yang, Guang; Gullberg, Grant T.

    2016-11-01

    Diffusion tensor magnetic resonance imaging (DT-MRI) allows a unique insight into the microstructure of highly-directional tissues. The selection of the most proper distance function for the space of diffusion tensors is crucial in enhancing the clinical application of this imaging modality. Both linear and nonlinear metrics have been proposed in the literature over the years. The debate on the most appropriate DT-MRI distance function is still ongoing. In this paper, we presented a framework to compare the Euclidean, affine-invariant Riemannian and log-Euclidean metrics using actual high-resolution DT-MRI rat heart data. We employed temporal averaging at the diffusion tensor level of three consecutive and identically-acquired DT-MRI datasets from each of five rat hearts as a means to rectify the background noise-induced loss of myocyte directional regularity. This procedure is applied here for the first time in the context of tensor distance function selection. When compared with previous studies that used a different concrete application to juxtapose the various DT-MRI distance functions, this work is unique in that it combined the following: (i) metrics were judged by quantitative—rather than qualitative—criteria, (ii) the comparison tools were non-biased, (iii) a longitudinal comparison operation was used on a same-voxel basis. The statistical analyses of the comparison showed that the three DT-MRI distance functions tend to provide equivalent results. Hence, we came to the conclusion that the tensor manifold for cardiac DT-MRI studies is a curved space of almost zero curvature. The signal to noise ratio dependence of the operations was investigated through simulations. Finally, the ‘swelling effect’ occurrence following Euclidean averaging was found to be too unimportant to be worth consideration.

  17. Mapping the Orientation of White Matter Fiber Bundles: A Comparative Study of Diffusion Tensor Imaging, Diffusional Kurtosis Imaging, and Diffusion Spectrum Imaging.

    PubMed

    Glenn, G R; Kuo, L-W; Chao, Y-P; Lee, C-Y; Helpern, J A; Jensen, J H

    2016-07-01

    White matter fiber tractography relies on fiber bundle orientation estimates from diffusion MR imaging. However, clinically feasible techniques such as DTI and diffusional kurtosis imaging use assumptions, which may introduce error into in vivo orientation estimates. In this study, fiber bundle orientations from DTI and diffusional kurtosis imaging are compared with diffusion spectrum imaging as a criterion standard to assess the performance of each technique. For each subject, full DTI, diffusional kurtosis imaging, and diffusion spectrum imaging datasets were acquired during 2 independent sessions, and fiber bundle orientations were estimated by using the specific theoretic assumptions of each technique. Angular variability and angular error measures were assessed by comparing the orientation estimates. Tractography generated with each of the 3 reconstructions was also examined and contrasted. Orientation estimates from all 3 techniques had comparable angular reproducibility, but diffusional kurtosis imaging decreased angular error throughout the white matter compared with DTI. Diffusion spectrum imaging and diffusional kurtosis imaging enabled the detection of crossing-fiber bundles, which had pronounced effects on tractography relative to DTI. Diffusion spectrum imaging had the highest sensitivity for detecting crossing fibers; however, the diffusion spectrum imaging and diffusional kurtosis imaging tracts were qualitatively similar. Fiber bundle orientation estimates from diffusional kurtosis imaging have less systematic error than those from DTI, which can noticeably affect tractography. Moreover, tractography obtained with diffusional kurtosis imaging is qualitatively comparable with that of diffusion spectrum imaging. Because diffusional kurtosis imaging has a shorter typical scan time than diffusion spectrum imaging, diffusional kurtosis imaging is potentially more suitable for a variety of clinical and research applications. © 2016 by American Journal of

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

    PubMed

    Zaider, M; Minerbo, G N

    1988-11-01

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

  19. 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.

  20. Mapping Viral Functional Domains for Genetic Diversity in Plants

    PubMed Central

    Pita, Justin S.

    2013-01-01

    Cucumber mosaic virus (CMV) comprises numerous isolates with various levels of in-host diversity. Subgroup-distinctive features of the Fny and LS strains provided us with a platform to genetically map the viral control elements for genetic variation in planta. We found that both RNAs 1 and 2 controlled levels of genetic diversity, and further fine mapping revealed that the control elements of mutation frequency reside within the first 596 amino acids (aa) of RNA 1. The 2a/2b overlapping region of the 2a protein also contributed to control of viral genetic variation. Furthermore, the 3′ nontranslated region (NTR) of RNA 3 constituted a hot spot of polymorphism, where the majority of fixed mutations found in the population were clustered. The 2b gene of CMV, a viral suppressor of gene silencing, controls the abundance of the fixed mutants in the viral population via a host-dependent mechanism. PMID:23115283

  1. Predicting functional neuroanatomical maps from fusing brain networks with genetic information.

    PubMed

    Ganglberger, Florian; Kaczanowska, Joanna; Penninger, Josef M; Hess, Andreas; Bühler, Katja; Haubensak, Wulf

    2017-09-03

    Functional neuroanatomical maps provide a mesoscale reference framework for studies from molecular to systems neuroscience and psychiatry. The underlying structure-function relationships are typically derived from functional manipulations or imaging approaches. Although highly informative, these are experimentally costly. The increasing amount of publicly available brain and genetic data offers a rich source that could be mined to address this problem computationally. Here, we developed an algorithm that fuses gene expression and connectivity data with functional genetic meta data and exploits cumulative effects to derive neuroanatomical maps related to multi-genic functions. We validated the approach by using public available mouse and human data. The generated neuroanatomical maps recapture known functional anatomical annotations from literature and functional MRI data. When applied to multi-genic meta data from mouse quantitative trait loci (QTL) studies and human neuropsychiatric databases, this method predicted known functional maps underlying behavioral or psychiatric traits. Taken together, genetically weighted connectivity analysis (GWCA) allows for high throughput functional exploration of brain anatomy in silico. It maps functional genetic associations onto brain circuitry for refining functional neuroanatomy, or identifying trait-associated brain circuitry, from genetic data. Copyright © 2017. Published by Elsevier Inc.

  2. 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.

  3. MAPS

    Atmospheric Science Data Center

    2014-07-03

    ... Measurement of Air Pollution from Satellites (MAPS) data were collected during Space Shuttle flights in 1981, ... Facts Correlative Data  - CDIAC - Spring & Fall 1994 - Field and Aircraft Campaigns SCAR-B Block:  ...

  4. Manifold reconnection and diffusion in strong chaos

    NASA Astrophysics Data System (ADS)

    Prado, S. D.; Corso, G.

    2000-08-01

    We analyse diffusion across a reconnecting zone in a regime of strong chaos. Numerical estimates from the angular correlation functions averaged over a suitable set of phase-space initial conditions are compared to a local diffusion coefficient obtained using Fick’s law. It emerges that the diffusion coefficient is enhanced from small to larger values as successive reconnection-like processes or more usual bifurcations take place. This feature is illustrated using a quadratic nontwist map.

  5. Mapping the functional neuroanatomy of spatial neglect and human parietal lobe functions: progress and challenges.

    PubMed

    Vuilleumier, Patrik

    2013-08-01

    Spatial neglect is generally defined by various deficits in processing information from one (e.g., left) side of space contralateral to focal (e.g., right) hemisphere damage. Although classically associated with parietal lobe functions, there is now compelling evidence that neglect can follow lesions in many different cortical and subcortical sites, suggesting a dysfunction in distributed brain networks. In addition, neglect is likely to result from a combination of distinct deficits that co-occur due to concomitant damage affecting juxtaposed brain areas and their connections, but the exact nature of core deficits and their neural substrates still remains unclear. The present review describes recent progress in identifying functional components of the neglect syndrome and relating them to distinct subregions of parietal cortex. A comprehensive understanding of spatial neglect will require a more precise definition of cognitive processes implicated in different behavioral manifestations, as well as meticulous mapping of these processes onto specific brain circuits, while taking into account functional changes in activity that may arise in structurally intact areas subsequent to damage in distant portions of the relevant networks.

  6. LGL: creating a map of protein function with an algorithm for visualizing very large biological networks.

    PubMed

    Adai, Alex T; Date, Shailesh V; Wieland, Shannon; Marcotte, Edward M

    2004-06-25

    Networks are proving to be central to the study of gene function, protein-protein interaction, and biochemical pathway data. Visualization of networks is important for their study, but visualization tools are often inadequate for working with very large biological networks. Here, we present an algorithm, called large graph layout (LGL), which can be used to dynamically visualize large networks on the order of hundreds of thousands of vertices and millions of edges. LGL applies a force-directed iterative layout guided by a minimal spanning tree of the network in order to generate coordinates for the vertices in two or three dimensions, which are subsequently visualized and interactively navigated with companion programs. We demonstrate the use of LGL in visualizing an extensive protein map summarizing the results of approximately 21 billion sequence comparisons between 145579 proteins from 50 genomes. Proteins are positioned in the map according to sequence homology and gene fusions, with the map ultimately serving as a theoretical framework that integrates inferences about gene function derived from sequence homology, remote homology, gene fusions, and higher-order fusions. We confirm that protein neighbors in the resulting map are functionally related, and that distinct map regions correspond to distinct cellular systems, enabling a computational strategy for discovering proteins' functions on the basis of the proteins' map positions. Using the map produced by LGL, we infer general functions for 23 uncharacterized protein families.

  7. 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

  8. Functional mapping of quantitative trait loci underlying the character process: a theoretical framework.

    PubMed

    Ma, Chang-Xing; Casella, George; Wu, Rongling

    2002-08-01

    Unlike a character measured at a finite set of landmark points, function-valued traits are those that change as a function of some independent and continuous variable. These traits, also called infinite-dimensional characters, can be described as the character process and include a number of biologically, economically, or biomedically important features, such as growth trajectories, allometric scalings, and norms of reaction. Here we present a new statistical infrastructure for mapping quantitative trait loci (QTL) underlying the character process. This strategy, termed functional mapping, integrates mathematical relationships of different traits or variables within the genetic mapping framework. Logistic mapping proposed in this article can be viewed as an example of functional mapping. Logistic mapping is based on a universal biological law that for each and every living organism growth over time follows an exponential growth curve (e.g., logistic or S-shaped). A maximum-likelihood approach based on a logistic-mixture model, implemented with the EM algorithm, is developed to provide the estimates of QTL positions, QTL effects, and other model parameters responsible for growth trajectories. Logistic mapping displays a tremendous potential to increase the power of QTL detection, the precision of parameter estimation, and the resolution of QTL localization due to the small number of parameters to be estimated, the pleiotropic effect of a QTL on growth, and/or residual correlations of growth at different ages. More importantly, logistic mapping allows for testing numerous biologically important hypotheses concerning the genetic basis of quantitative variation, thus gaining an insight into the critical role of development in shaping plant and animal evolution and domestication. The power of logistic mapping is demonstrated by an example of a forest tree, in which one QTL affecting stem growth processes is detected on a linkage group using our method, whereas it cannot

  9. Functional mapping of quantitative trait loci underlying the character process: a theoretical framework.

    PubMed Central

    Ma, Chang-Xing; Casella, George; Wu, Rongling

    2002-01-01

    Unlike a character measured at a finite set of landmark points, function-valued traits are those that change as a function of some independent and continuous variable. These traits, also called infinite-dimensional characters, can be described as the character process and include a number of biologically, economically, or biomedically important features, such as growth trajectories, allometric scalings, and norms of reaction. Here we present a new statistical infrastructure for mapping quantitative trait loci (QTL) underlying the character process. This strategy, termed functional mapping, integrates mathematical relationships of different traits or variables within the genetic mapping framework. Logistic mapping proposed in this article can be viewed as an example of functional mapping. Logistic mapping is based on a universal biological law that for each and every living organism growth over time follows an exponential growth curve (e.g., logistic or S-shaped). A maximum-likelihood approach based on a logistic-mixture model, implemented with the EM algorithm, is developed to provide the estimates of QTL positions, QTL effects, and other model parameters responsible for growth trajectories. Logistic mapping displays a tremendous potential to increase the power of QTL detection, the precision of parameter estimation, and the resolution of QTL localization due to the small number of parameters to be estimated, the pleiotropic effect of a QTL on growth, and/or residual correlations of growth at different ages. More importantly, logistic mapping allows for testing numerous biologically important hypotheses concerning the genetic basis of quantitative variation, thus gaining an insight into the critical role of development in shaping plant and animal evolution and domestication. The power of logistic mapping is demonstrated by an example of a forest tree, in which one QTL affecting stem growth processes is detected on a linkage group using our method, whereas it cannot

  10. 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

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

    PubMed

    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.

  12. 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).

  13. A diffusive virus infection dynamic model with nonlinear functional response, absorption effect and chemotaxis

    NASA Astrophysics Data System (ADS)

    Wang, Wei; Ma, Wanbiao; Lai, Xiulan

    2017-01-01

    From a biological perspective, a diffusive virus infection dynamic model with nonlinear functional response, absorption effect and chemotaxis is proposed. In the model, the diffusion of virus consists of two parts, the random diffusion and the chemotactic movement. The chemotaxis flux of virus depends not only on their own density, but also on the density of infected cells, and the density gradient of infected cells. The well posedness of the proposed model is deeply investigated. For the proposed model, the linear stabilities of the infection-free steady state E0 and the infection steady state E* are extensively performed. We show that the threshold dynamics can be expressed by the basic reproduction number R0 of the model without chemotaxis. That is, the infection-free steady state E0 is globally asymptotically stable if R0 < 1, and the virus is uniformly persistent if R0 > 1. In addition, we use the cross iteration method and the Schauder's fixed point theorem to prove the existence of travelling wave solutions connecting the infection-free steady state E0 and the infection steady state E* by constructing a pair of upper-lower solutions. At last, numerical simulations are presented to confirm theoretical findings.

  14. 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.

  15. 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.

  16. 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.

  17. A global genetic interaction network maps a wiring diagram of cellular function.

    PubMed

    Costanzo, Michael; VanderSluis, Benjamin; Koch, Elizabeth N; Baryshnikova, Anastasia; Pons, Carles; Tan, Guihong; Wang, Wen; Usaj, Matej; Hanchard, Julia; Lee, Susan D; Pelechano, Vicent; Styles, Erin B; Billmann, Maximilian; van Leeuwen, Jolanda; van Dyk, Nydia; Lin, Zhen-Yuan; Kuzmin, Elena; Nelson, Justin; Piotrowski, Jeff S; Srikumar, Tharan; Bahr, Sondra; Chen, Yiqun; Deshpande, Raamesh; Kurat, Christoph F; Li, Sheena C; Li, Zhijian; Usaj, Mojca Mattiazzi; Okada, Hiroki; Pascoe, Natasha; San Luis, Bryan-Joseph; Sharifpoor, Sara; Shuteriqi, Emira; Simpkins, Scott W; Snider, Jamie; Suresh, Harsha Garadi; Tan, Yizhao; Zhu, Hongwei; Malod-Dognin, Noel; Janjic, Vuk; Przulj, Natasa; Troyanskaya, Olga G; Stagljar, Igor; Xia, Tian; Ohya, Yoshikazu; Gingras, Anne-Claude; Raught, Brian; Boutros, Michael; Steinmetz, Lars M; Moore, Claire L; Rosebrock, Adam P; Caudy, Amy A; Myers, Chad L; Andrews, Brenda; Boone, Charles

    2016-09-23

    We generated a global genetic interaction network for Saccharomyces cerevisiae, constructing more than 23 million double mutants, identifying about 550,000 negative and about 350,000 positive genetic interactions. This comprehensive network maps genetic interactions for essential gene pairs, highlighting essential genes as densely connected hubs. Genetic interaction profiles enabled assembly of a hierarchical model of cell function, including modules corresponding to protein complexes and pathways, biological processes, and cellular compartments. Negative interactions connected functionally related genes, mapped core bioprocesses, and identified pleiotropic genes, whereas positive interactions often mapped general regulatory connections among gene pairs, rather than shared functionality. The global network illustrates how coherent sets of genetic interactions connect protein complex and pathway modules to map a functional wiring diagram of the cell.

  18. 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.

  19. Closures of the functional expansion hierarchy in the non-Markovian quantum state diffusion approach

    NASA Astrophysics Data System (ADS)

    Ritschel, Gerhard; Strunz, Walter T.; Eisfeld, Alexander

    2017-08-01

    To find a practical scheme to numerically solve the non-Markovian Quantum State Diffusion equation (NMQSD), one often uses a functional expansion of the functional derivative that appears in the general NMQSD equation. This expansion leads to a hierarchy of coupled operators. It turned out that if one takes only the zeroth order term into account, one has a very efficient method that agrees remarkably well with the exact results for many cases of interest. We denote this approach as zeroth order functional expansion (ZOFE). In the present work, we investigate two extensions of ZOFE. Firstly, we investigate how the hierarchy converges when taking higher orders into account (which, however, leads to a fast increase in numerical size). Secondly, we demonstrate that by using a terminator that approximates the higher order contributions, one can obtain significant improvement, at hardly any additional computational cost. We carry out our investigations for the case of absorption spectra of molecular aggregates.

  20. 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

  1. Simultaneously Extracting Multiple Parameters via Fitting One Single Autocorrelation Function Curve in Diffuse Correlation Spectroscopy

    PubMed Central

    Dong, Lixin; He, Lian; Lin, Yu; Shang, Yu; Yu, Guoqiang

    2015-01-01

    Near-infrared diffuse correlation spectroscopy (DCS) has recently been employed for noninvasive acquisition of blood flow information in deep tissues. Based on the established correlation diffusion equation, the light intensity autocorrelation function detected by DCS is determined by a blood flow index αDB, tissue absorption coefficient μa, reduced scattering coefficient μs’, and a coherence factor β. The present study is designed to investigate the possibility of extracting multiple parameters such as μa, μs’, β, and αDB through fitting one single autocorrelation function curve and evaluate the performance of different fitting methods. For this purpose, computer simulations, tissue-like phantom experiments and in-vivo tissue measurements were utilized. The results suggest that it is impractical to simultaneously fit αDB and μa or αDB and μs’ from one single autocorrelation function curve due to the large crosstalk between these paired parameters. However, simultaneously fitting β and αDB is feasible and generates more accurate estimation with smaller standard deviation compared to the conventional two-step fitting method (i.e., first calculating β and then fitting αDB). The outcomes from this study provide a crucial guidance for DCS data analysis. PMID:23193446

  2. 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.

  3. 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

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

    PubMed

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

    2014-10-07

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

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

    SciTech Connect

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

    2014-10-07

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

  6. Chronic kidney disease: Pathological and functional evaluation with intravoxel incoherent motion diffusion-weighted imaging.

    PubMed

    Mao, Wei; Zhou, Jianjun; Zeng, Mengsu; Ding, Yuqin; Qu, Lijie; Chen, Caizhong; Ding, Xiaoqiang; Wang, Yaqiong; Fu, Caixia

    2017-09-21

    Because chronic kidney disease (CKD) is a worldwide problem, accurate pathological and functional evaluation is required for planning treatment and follow-up. Intravoxel incoherent motion diffusion-weighted imaging (IVIM-DWI) can assess both capillary perfusion and tissue diffusion and may be helpful in evaluating renal function and pathology. To evaluate functional and pathological alterations in CKD by applying IVIM-DWI. Prospective study. In all, 72 CKD patients who required renal biopsy and 20 healthy volunteers. 1.5T. All subjects underwent IVIM-DWI of the kidneys, and image analysis was performed by two radiologists. The mean values of true diffusion coefficient (D), pseudo diffusion coefficient (D*), and perfusion fraction (f) were acquired from renal parenchyma. Correlation between IVIM-DWI parameters and estimated glomerular filtration rate (eGFR), as well as pathological damage, were assessed. One-way analysis of variance (ANOVA), paired sample t-test and Spearman correlation analysis. The paired sample t-test revealed that IVIM-DWI parameters were significantly lower in medulla than cortex for both patients and controls (P < 0.01). Regardless of whether eGFR was reduced, ANOVA revealed that f values of renal parenchyma were significantly lower in patients than controls (P < 0.05). Spearman correlation analysis revealed that there were positive correlations between eGFR and D (cortex, r = 0.466, P < 0.001; medulla, r = 0.491, P < 0.001), and between eGFR and f (cortex, r = 0.713, P < 0.001; medulla, r = 0.512, P < 0.001). Negative correlations were found between f and glomerular injury (cortex, r = -0.773, P < 0.001; medulla, r = -0.629, P < 0.001), and between f and tubulointerstitial lesion (cortex, r = -0.728, P < 0.001; medulla, r = -0.547, P < 0.001). IVIM-DWI might be feasible for noninvasive evaluation of renal function and pathology of CKD, especially in detection of renal insufficiency at an early stage. 1

  7. Mapping the royal road and other hierarchical functions.

    PubMed

    Wiles, Janet; Tonkes, Bradley

    2003-01-01

    In this paper we present a technique for visualising hierarchical and symmetric, multi-modal fitness functions that have been investigated in the evolutionary computation literature. The focus of this technique is on landscapes in moderate-dimensional, binary spaces (i.e., fitness functions defined over [0,1](n), for n < or = 16). The visualisation approach involves an unfolding of the hyperspace into a two-dimensional graph, whose layout represents the topology of the space using a recursive relationship, and whose shading defines the shape of the cost surface defined on the space. Using this technique we present case-study explorations of three fitness functions: royal road, hierarchical-if-and-only-if (H-IFF), and hierarchically decomposable functions (HDF). The visualisation approach provides an insight into the properties of these functions, particularly with respect to the size and shape of the basins of attraction around each of the local optima.

  8. Large scale mapping of forests with a protection function against rockfall and avalanches

    NASA Astrophysics Data System (ADS)

    Toe, David; Berger, Fréderic

    2014-05-01

    On mountain slopes, forest can play an important role to protect human lives and facilities against natural hazards. Silvicultural strategies and interventions to maintain or improve protection forest structures are of first interest. Up to now no large scale mapping of forest with a protection function against rockfalls and snow avalanches exist in France. The objectives of the study is to develop decision support tools for rockfall protection forest management. Two Geographic Information System based models which automatically map forests with a protection function against rockfalls and snow avalanches have been developed. These devices have been used to map forest with protection function in the French Alps. The first model, RollFree, calculates the maximum rockfall run out zone using the energy line principle. Forest with protection function are mapped crossing data on rockfall hazard, the forest cover and the socio-economical issues of a county. The second model, AvaLine, mapped the maximum run out zones of snow avalanches. Forests located in a departure zone of an avalanche that endangered an issue are mapped as protection forests. Results showed that forests with a protection function against rockfall can represent up to 30 percents of the forest cover in a county. In addition, forests with a protection function against avalanches can represent up to 7 percents of the total forested area. The two models developed present the advantages of a fast computational time and need only few input parameters such as a DEM, a map of the issues and a map of the forest cover. However it remain difficult to estimate precisely the error on the area mapped as protection forest on the all county. A first campaign of validation was done in the Vercor Regional natural park for forest with a protection function against rockfall. The study show that the model can overestimate the protection forest mapping up to 12 percent. Up to now no similar study was done for protection

  9. 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.

  10. Influence of mapping function parameters on global GPS network analyses: Comparisons between NMF and IMF

    NASA Astrophysics Data System (ADS)

    Vey, S.; Dietrich, R.; Fritsche, M.; Rülke, A.; Rothacher, M.; Steigenberger, P.

    2006-01-01

    One major part in the error budget of GPS measurements is the imperfect modeling of the tropospheric delay. By processing a global network of 195 stations we have compared two different mapping techniques: (1) the commonly used Niell hydrostatic mapping function (NMF) and (2) the isobaric hydrostatic mapping function (IMF) based on numerical weather fields. The two solutions reveal significant differences in the derived zenith total delay (ZTD) parameters and site positions. The largest differences occur in Antarctica, where the annual mean heights differ by up to 15 mm. We infer that the significant differences are related to model deficiencies in NMF since a) IMF improves the repeatability in station heights in high southern latitudes significantly, and b) using IMF reduces the dependence of the solution on the elevation cut-off angle by about 20%. In conclusion, the use of mapping function (MF) parameters based on meteorological data is strongly recommended for global GPS analyses.

  11. Diffusion in an expanding medium: Fokker-Planck equation, Green's function, and first-passage properties