P and S wave attenuation tomography of the Japan subduction zone

NASA Astrophysics Data System (ADS)

Wang, Zewei; Zhao, Dapeng; Liu, Xin; Chen, Chuanxu; Li, Xibing

2017-04-01

We determine the first high-resolution P and S wave attenuation (Q) tomography beneath the entire Japan Islands using a large number of high-quality t∗ data collected from P and S wave velocity spectra of 4222 local shallow and intermediate-depth earthquakes. The suboceanic earthquakes used in this study are relocated precisely using sP depth phases. Significant landward dipping high-Q zones are revealed clearly, which reflect the subducting Pacific slab beneath Hokkaido and Tohoku, and the subducting Philippine Sea (PHS) slab beneath SW Japan. Prominent low-Q zones are visible in the crust and mantle wedge beneath the active arc volcanoes in Hokkaido, Tohoku, and Kyushu, which reflect source zones of arc magmatism caused by fluids from the slab dehydration and corner flow in the mantle wedge. Our results also show that nonvolcanic low-frequency earthquakes (LFEs) in SW Japan mainly occur in the transition zone between a narrow low-Q belt and its adjacent high-Q zones right above the flat segment of the PHS slab. This feature suggests that the nonvolcanic LFEs are caused by not only fluid-affected slab interface but also specific conditions such as high pore pressure which is influenced by the overriding plate.

Dictionary-learning-based reconstruction method for electron tomography.

PubMed

Liu, Baodong; Yu, Hengyong; Verbridge, Scott S; Sun, Lizhi; Wang, Ge

2014-01-01

Electron tomography usually suffers from so-called “missing wedge” artifacts caused by limited tilt angle range. An equally sloped tomography (EST) acquisition scheme (which should be called the linogram sampling scheme) was recently applied to achieve 2.4-angstrom resolution. On the other hand, a compressive sensing inspired reconstruction algorithm, known as adaptive dictionary based statistical iterative reconstruction (ADSIR), has been reported for X-ray computed tomography. In this paper, we evaluate the EST, ADSIR, and an ordered-subset simultaneous algebraic reconstruction technique (OS-SART), and compare the ES and equally angled (EA) data acquisition modes. Our results show that OS-SART is comparable to EST, and the ADSIR outperforms EST and OS-SART. Furthermore, the equally sloped projection data acquisition mode has no advantage over the conventional equally angled mode in this context.

The inner zone electron model AE-5

NASA Technical Reports Server (NTRS)

Teague, M. J.; Vette, J. I.

1972-01-01

A description is given of the work performed in the development of the inner radiation zone electron model, AE-5. A complete description of the omnidirectional flux model is given for energy thresholds E sub T in the range 4.0 E sub T/(MeV) 0.04 and for L values in the range 2.8 L 1.2 for an epoch of October 1967. Confidence codes for certain regions of B-L space and certain energies are given based on data coverage and the assumptions made in the analysis. The electron model programs that can be supplied to a user are referred to. One of these, a program for accessing the model flux at arbitrary points in B-L space and arbitrary energies, includes the latest outer zone electron model and proton model. The model AE-5, is based on data from five satellites, OGO 1, OGO 3, 1963-38C, OV3-3, and Explorer 26, spanning the period December 1964 to December 1967.

Tomography experiment of an integrated circuit specimen using 3 MeV electrons in the transmission electron microscope.

PubMed

Zhang, Hai-Bo; Zhang, Xiang-Liang; Wang, Yong; Takaoka, Akio

2007-01-01

The possibility of utilizing high-energy electron tomography to characterize the micron-scale three dimensional (3D) structures of integrated circuits has been demonstrated experimentally. First, electron transmission through a tilted SiO(2) film was measured with an ultrahigh-voltage electron microscope (ultra-HVEM) and analyzed from the point of view of elastic scattering of electrons, showing that linear attenuation of the logarithmic electron transmission still holds valid for effective specimen thicknesses up to 5 microm under 2 MV accelerating voltages. Electron tomography of a micron-order thick integrated circuit specimen including the Cu/via interconnect was then tried with 3 MeV electrons in the ultra-HVEM. Serial projection images of the specimen tilted at different angles over the range of +/-90 degrees were acquired, and 3D reconstruction was performed with the images by means of the IMOD software package. Consequently, the 3D structures of the Cu lines, via and void, were revealed by cross sections and surface rendering.

Electron tomography and 3D molecular simulations of platinum nanocrystals

NASA Astrophysics Data System (ADS)

Florea, Ileana; Demortière, Arnaud; Petit, Christophe; Bulou, Hervé; Hirlimann, Charles; Ersen, Ovidiu

2012-07-01

This work reports on the morphology of individual platinum nanocrystals with sizes of about 5 nm. By using the electron tomography technique that gives 3D spatial selectivity, access to quantitative information in the real space was obtained. The morphology of individual nanoparticles was characterized using HAADF-STEM tomography and it was shown to be close to a truncated octahedron. Using molecular dynamics simulations, this geometrical shape was found to be the one minimizing the nanocrystal energy. Starting from the tomographic reconstruction, 3D crystallographic representations of the studied Pt nanocrystals were obtained at the nanometer scale, allowing the quantification of the relative amount of the crystallographic facets present on the particle surface.This work reports on the morphology of individual platinum nanocrystals with sizes of about 5 nm. By using the electron tomography technique that gives 3D spatial selectivity, access to quantitative information in the real space was obtained. The morphology of individual nanoparticles was characterized using HAADF-STEM tomography and it was shown to be close to a truncated octahedron. Using molecular dynamics simulations, this geometrical shape was found to be the one minimizing the nanocrystal energy. Starting from the tomographic reconstruction, 3D crystallographic representations of the studied Pt nanocrystals were obtained at the nanometer scale, allowing the quantification of the relative amount of the crystallographic facets present on the particle surface. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr30990d

Physically motivated global alignment method for electron tomography

DOE PAGES

Sanders, Toby; Prange, Micah; Akatay, Cem; ...

2015-04-08

Electron tomography is widely used for nanoscale determination of 3-D structures in many areas of science. Determining the 3-D structure of a sample from electron tomography involves three major steps: acquisition of sequence of 2-D projection images of the sample with the electron microscope, alignment of the images to a common coordinate system, and 3-D reconstruction and segmentation of the sample from the aligned image data. The resolution of the 3-D reconstruction is directly influenced by the accuracy of the alignment, and therefore, it is crucial to have a robust and dependable alignment method. In this paper, we develop amore » new alignment method which avoids the use of markers and instead traces the computed paths of many identifiable ‘local’ center-of-mass points as the sample is rotated. Compared with traditional correlation schemes, the alignment method presented here is resistant to cumulative error observed from correlation techniques, has very rigorous mathematical justification, and is very robust since many points and paths are used, all of which inevitably improves the quality of the reconstruction and confidence in the scientific results.« less

Computed Tomography Assessment of Ablation Zone Enhancement in Patients With Early-Stage Lung Cancer After Stereotactic Ablative Radiotherapy.

PubMed

Moore, William; Chaya, Yair; Chaudhry, Ammar; Depasquale, Britney; Glass, Samantha; Lee, Susan; Shin, James; Mikhail, George; Bhattacharji, Priya; Kim, Bong; Bilfinger, Thomas

2015-01-01

Stereotactic ablative radiotherapy (SABR) offers a curative treatment for lung cancer in patients who are marginal surgical candidates. However, unlike traditional surgery the lung cancer remains in place after treatment. Thus, imaging follow-up for evaluation of recurrence is of paramount importance. In this retrospective designed Institutional Review Board-approved study, follow-up contrast-enhanced computed tomography (CT) exams were performed on sixty one patients to evaluate enhancement pattern in the ablation zone at 1, 3, 6, and 12 months after SABR. Eleven patients had recurrence within the ablation zone after SABR. The postcontrast enhancement in the recurrence group showed a washin and washout phenomenon, whereas the radiation-induced lung injury group showed continuous enhancement suggesting an inflammatory process. The textural feature of the ablation zone of enhancement and perfusion as demonstrated in computed tomography nodule enhancement may allow early differentiation of recurrence from radiation-induced lung injury in patients' status after SABR or primary lung cancer.

Reductive dechlorination of trichloroethene DNAPL source zones: source zone architecture versus electron donor availability

NASA Astrophysics Data System (ADS)

Krol, M.; Kokkinaki, A.; Sleep, B.

2014-12-01

The persistence of dense-non-aqueous-phase liquids (DNAPLs) in the subsurface has led practitioners and regulatory agencies to turn towards low-maintenance, low-cost remediation methods. Biological degradation has been suggested as a possible solution, based on the well-proven ability of certain microbial species to break down dissolved chlorinated ethenes under favorable conditions. However, the biodegradation of pure phase chlorinated ethenes is subject to additional constraints: the continuous release of electron acceptor at a rate governed by mass transfer kinetics, and the temporal and spatial heterogeneity of DNAPL source zones which leads to spatially and temporally variable availability of the reactants for reductive dechlorination. In this work, we investigate the relationship between various DNAPL source zone characteristics and reaction kinetics using COMPSIM, a multiphase groundwater model that considers non-equilibrium mass transfer and Monod-type kinetics for reductive dechlorination. Numerical simulations are performed for simple, homogeneous trichloroethene DNAPL source zones to demonstrate the effect of single source zone characteristics, as well as for larger, more realistic heterogeneous source zones. It is shown that source zone size, and mass transfer kinetics may have a decisive effect on the predicted bio-enhancement. Finally, we evaluate the performance of DNAPL bioremediation for realistic, thermodynamically constrained, concentrations of electron donor. Our results indicate that the latter may be the most important limitation for the success of DNAPL bioremediation, leading to reduced bio-enhancement and, in many cases, comparable performance with water flooding.

Secondary signal imaging (SSI) electron tomography (SSI-ET): A new three-dimensional metrology for mesoscale specimens in transmission electron microscope.

PubMed

Han, Chang Wan; Ortalan, Volkan

2015-09-01

We have demonstrated a new electron tomography technique utilizing the secondary signals (secondary electrons and backscattered electrons) for ultra thick (a few μm) specimens. The Monte Carlo electron scattering simulations reveal that the amount of backscattered electrons generated by 200 and 300keV incident electrons is a monotonic function of the sample thickness and this causes the thickness contrast satisfying the projection requirement for the tomographic reconstruction. Additional contribution of the secondary electrons emitted from the edges of the specimens enhances the visibility of the surface features. The acquired SSI tilt series of the specimen having mesoscopic dimensions are successfully reconstructed verifying that this new technique, so called the secondary signal imaging electron tomography (SSI-ET), can directly be utilized for 3D structural analysis of mesoscale structures. Published by Elsevier Ltd.

Nanomaterial datasets to advance tomography in scanning transmission electron microscopy

DOE PAGES

Levin, Barnaby D. A.; Padgett, Elliot; Chen, Chien-Chun; ...

2016-06-07

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co 2 P nanocrystal, platinum nanoparticles on a carbonmore » nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.« less

Nanomaterial datasets to advance tomography in scanning transmission electron microscopy.

PubMed

Levin, Barnaby D A; Padgett, Elliot; Chen, Chien-Chun; Scott, M C; Xu, Rui; Theis, Wolfgang; Jiang, Yi; Yang, Yongsoo; Ophus, Colin; Zhang, Haitao; Ha, Don-Hyung; Wang, Deli; Yu, Yingchao; Abruña, Hector D; Robinson, Richard D; Ercius, Peter; Kourkoutis, Lena F; Miao, Jianwei; Muller, David A; Hovden, Robert

2016-06-07

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co2P nanocrystal, platinum nanoparticles on a carbon nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.

Nanomaterial datasets to advance tomography in scanning transmission electron microscopy

PubMed Central

Levin, Barnaby D.A.; Padgett, Elliot; Chen, Chien-Chun; Scott, M.C.; Xu, Rui; Theis, Wolfgang; Jiang, Yi; Yang, Yongsoo; Ophus, Colin; Zhang, Haitao; Ha, Don-Hyung; Wang, Deli; Yu, Yingchao; Abruña, Hector D.; Robinson, Richard D.; Ercius, Peter; Kourkoutis, Lena F.; Miao, Jianwei; Muller, David A.; Hovden, Robert

2016-01-01

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co2P nanocrystal, platinum nanoparticles on a carbon nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data. PMID:27272459

Electronic hardware design of electrical capacitance tomography systems.

PubMed

Saied, I; Meribout, M

2016-06-28

Electrical tomography techniques for process imaging are very prominent for industrial applications, such as the oil and gas industry and chemical refineries, owing to their ability to provide the flow regime of a flowing fluid within a relatively high throughput. Among the various techniques, electrical capacitance tomography (ECT) is gaining popularity due to its non-invasive nature and its capability to differentiate between different phases based on their permittivity distribution. In recent years, several hardware designs have been provided for ECT systems that have improved its resolution of measurements to be around attofarads (aF, 10(-18) F), or the number of channels, that is required to be large for some applications that require a significant amount of data. In terms of image acquisition time, some recent systems could achieve a throughput of a few hundred frames per second, while data processing time could be achieved in only a few milliseconds per frame. This paper outlines the concept and main features of the most recent front-end and back-end electronic circuits dedicated for ECT systems. In this paper, multiple-excitation capacitance polling, a front-end electronic technique, shows promising results for ECT systems to acquire fast data acquisition speeds. A highly parallel field-programmable gate array (FPGA) based architecture for a fast reconstruction algorithm is also described. This article is part of the themed issue 'Supersensing through industrial process tomography'. © 2016 The Author(s).

Selected-zone dark-field electron microscopy.

NASA Technical Reports Server (NTRS)

Heinemann, K.; Poppa, H.

1972-01-01

Description of a new method which makes it possible to reduce drastically the resolution-limiting influence of chromatic aberration, and thus to obtain high-quality images, by selecting the image-forming electrons that have passed through a small annular zone of an objective lens. In addition, the manufacture of special objective-lens aperture diaphragms that are needed for this method is also described.

Cryo-electron tomography of bacterial viruses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guerrero-Ferreira, Ricardo C.; Wright, Elizabeth R., E-mail: erwrigh@emory.edu

2013-01-05

Bacteriophage particles contain both simple and complex macromolecular assemblages and machines that enable them to regulate the infection process under diverse environmental conditions with a broad range of bacterial hosts. Recent developments in cryo-electron tomography (cryo-ET) make it possible to observe the interactions of bacteriophages with their host cells under native-state conditions at unprecedented resolution and in three-dimensions. This review describes the application of cryo-ET to studies of bacteriophage attachment, genome ejection, assembly and egress. Current topics of investigation and future directions in the field are also discussed.

Three-dimensional structural analysis of eukaryotic flagella/cilia by electron cryo-tomography

PubMed Central

Bui, Khanh Huy; Pigino, Gaia; Ishikawa, Takashi

2011-01-01

Electron cryo-tomography is a potential approach to analyzing the three-dimensional conformation of frozen hydrated biological macromolecules using electron microscopy. Since projections of each individual object illuminated from different orientations are merged, electron tomography is capable of structural analysis of such heterogeneous environments as in vivo or with polymorphism, although radiation damage and the missing wedge are severe problems. Here, recent results on the structure of eukaryotic flagella, which is an ATP-driven bending organelle, from green algae Chlamydomonas are presented. Tomographic analysis reveals asymmetric molecular arrangements, especially that of the dynein motor proteins, in flagella, giving insight into the mechanism of planar asymmetric bending motion. Methodological challenges to obtaining higher-resolution structures from this technique are also discussed. PMID:21169680

Formation of bimetallic clusters in superfluid helium nanodroplets analysed by atomic resolution electron tomography

PubMed Central

Haberfehlner, Georg; Thaler, Philipp; Knez, Daniel; Volk, Alexander; Hofer, Ferdinand; Ernst, Wolfgang E.; Kothleitner, Gerald

2015-01-01

Structure, shape and composition are the basic parameters responsible for properties of nanoscale materials, distinguishing them from their bulk counterparts. To reveal these in three dimensions at the nanoscale, electron tomography is a powerful tool. Advancing electron tomography to atomic resolution in an aberration-corrected transmission electron microscope remains challenging and has been demonstrated only a few times using strong constraints or extensive filtering. Here we demonstrate atomic resolution electron tomography on silver/gold core/shell nanoclusters grown in superfluid helium nanodroplets. We reveal morphology and composition of a cluster identifying gold- and silver-rich regions in three dimensions and we estimate atomic positions without using any prior information and with minimal filtering. The ability to get full three-dimensional information down to the atomic scale allows understanding the growth and deposition process of the nanoclusters and demonstrates an approach that may be generally applicable to all types of nanoscale materials. PMID:26508471

3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

PubMed

Ishikawa, Takashi

2013-01-01

Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex.

Energy-dependent dynamics of keV to MeV electrons in the inner zone, outer zone, and slot regions.

PubMed

Reeves, Geoffrey D; Friedel, Reiner H W; Larsen, Brian A; Skoug, Ruth M; Funsten, Herbert O; Claudepierre, Seth G; Fennell, Joseph F; Turner, Drew L; Denton, Mick H; Spence, Harlan E; Blake, J Bernard; Baker, Daniel N

2016-01-01

We present observations of the radiation belts from the Helium Oxygen Proton Electron and Magnetic Electron Ion Spectrometer particle detectors on the Van Allen Probes satellites that illustrate the energy dependence and L shell dependence of radiation belt enhancements and decays. We survey events in 2013 and analyze an event on 1 March in more detail. The observations show the following: (a) at all L shells, lower energy electrons are enhanced more often than higher energies; (b) events that fill the slot region are more common at lower energies; (c) enhancements of electrons in the inner zone are more common at lower energies; and (d) even when events do not fully fill the slot region, enhancements at lower energies tend to extend to lower L shells than higher energies. During enhancement events the outer zone extends to lower L shells at lower energies while being confined to higher L shells at higher energies. The inner zone shows the opposite with an outer boundary at higher L shells for lower energies. Both boundaries are nearly straight in log(energy) versus L shell space. At energies below a few 100 keV, radiation belt electron penetration through the slot region into the inner zone is commonplace, but the number and frequency of "slot filling" events decreases with increasing energy. The inner zone is enhanced only at energies that penetrate through the slot. Energy- and L shell-dependent losses (that are consistent with whistler hiss interactions) return the belts to more quiescent conditions.

Energy-dependent dynamics of keV to MeV electrons in the inner zone, outer zone, and slot regions

DOE PAGES

Reeves, Geoffrey D.; Friedel, Reiner H. W.; Larsen, Brian A.; ...

2016-01-28

Here, we present observations of the radiation belts from the Helium Oxygen Proton Electron and Magnetic Electron Ion Spectrometer particle detectors on the Van Allen Probes satellites that illustrate the energy dependence and L shell dependence of radiation belt enhancements and decays. We survey events in 2013 and analyze an event on 1 March in more detail. The observations show the following: (a) at all L shells, lower energy electrons are enhanced more often than higher energies; (b) events that fill the slot region are more common at lower energies; (c) enhancements of electrons in the inner zone are moremore » common at lower energies; and (d) even when events do not fully fill the slot region, enhancements at lower energies tend to extend to lower L shells than higher energies. During enhancement events the outer zone extends to lower L shells at lower energies while being confined to higher L shells at higher energies. The inner zone shows the opposite with an outer boundary at higher L shells for lower energies. Both boundaries are nearly straight in log(energy) versus L shell space. At energies below a few 100 keV, radiation belt electron penetration through the slot region into the inner zone is commonplace, but the number and frequency of “slot filling” events decreases with increasing energy. The inner zone is enhanced only at energies that penetrate through the slot. Energy- and L shell-dependent losses (that are consistent with whistler hiss interactions) return the belts to more quiescent conditions.« less

Energy‐dependent dynamics of keV to MeV electrons in the inner zone, outer zone, and slot regions

PubMed Central

Friedel, Reiner H. W.; Larsen, Brian A.; Skoug, Ruth M.; Funsten, Herbert O.; Claudepierre, Seth G.; Fennell, Joseph F.; Turner, Drew L.; Denton, Mick H.; Spence, Harlan E.; Blake, J. Bernard; Baker, Daniel N.

2016-01-01

Abstract We present observations of the radiation belts from the Helium Oxygen Proton Electron and Magnetic Electron Ion Spectrometer particle detectors on the Van Allen Probes satellites that illustrate the energy dependence and L shell dependence of radiation belt enhancements and decays. We survey events in 2013 and analyze an event on 1 March in more detail. The observations show the following: (a) at all L shells, lower energy electrons are enhanced more often than higher energies; (b) events that fill the slot region are more common at lower energies; (c) enhancements of electrons in the inner zone are more common at lower energies; and (d) even when events do not fully fill the slot region, enhancements at lower energies tend to extend to lower L shells than higher energies. During enhancement events the outer zone extends to lower L shells at lower energies while being confined to higher L shells at higher energies. The inner zone shows the opposite with an outer boundary at higher L shells for lower energies. Both boundaries are nearly straight in log(energy) versus L shell space. At energies below a few 100 keV, radiation belt electron penetration through the slot region into the inner zone is commonplace, but the number and frequency of “slot filling” events decreases with increasing energy. The inner zone is enhanced only at energies that penetrate through the slot. Energy‐ and L shell‐dependent losses (that are consistent with whistler hiss interactions) return the belts to more quiescent conditions. PMID:27818855

Automatic Segmentation and Quantification of Filamentous Structures in Electron Tomography

PubMed Central

Loss, Leandro A.; Bebis, George; Chang, Hang; Auer, Manfred; Sarkar, Purbasha; Parvin, Bahram

2016-01-01

Electron tomography is a promising technology for imaging ultrastructures at nanoscale resolutions. However, image and quantitative analyses are often hindered by high levels of noise, staining heterogeneity, and material damage either as a result of the electron beam or sample preparation. We have developed and built a framework that allows for automatic segmentation and quantification of filamentous objects in 3D electron tomography. Our approach consists of three steps: (i) local enhancement of filaments by Hessian filtering; (ii) detection and completion (e.g., gap filling) of filamentous structures through tensor voting; and (iii) delineation of the filamentous networks. Our approach allows for quantification of filamentous networks in terms of their compositional and morphological features. We first validate our approach using a set of specifically designed synthetic data. We then apply our segmentation framework to tomograms of plant cell walls that have undergone different chemical treatments for polysaccharide extraction. The subsequent compositional and morphological analyses of the plant cell walls reveal their organizational characteristics and the effects of the different chemical protocols on specific polysaccharides. PMID:28090597

Automatic Segmentation and Quantification of Filamentous Structures in Electron Tomography.

PubMed

Loss, Leandro A; Bebis, George; Chang, Hang; Auer, Manfred; Sarkar, Purbasha; Parvin, Bahram

2012-10-01

Electron tomography is a promising technology for imaging ultrastructures at nanoscale resolutions. However, image and quantitative analyses are often hindered by high levels of noise, staining heterogeneity, and material damage either as a result of the electron beam or sample preparation. We have developed and built a framework that allows for automatic segmentation and quantification of filamentous objects in 3D electron tomography. Our approach consists of three steps: (i) local enhancement of filaments by Hessian filtering; (ii) detection and completion (e.g., gap filling) of filamentous structures through tensor voting; and (iii) delineation of the filamentous networks. Our approach allows for quantification of filamentous networks in terms of their compositional and morphological features. We first validate our approach using a set of specifically designed synthetic data. We then apply our segmentation framework to tomograms of plant cell walls that have undergone different chemical treatments for polysaccharide extraction. The subsequent compositional and morphological analyses of the plant cell walls reveal their organizational characteristics and the effects of the different chemical protocols on specific polysaccharides.

Recovering fine details from under-resolved electron tomography data using higher order total variation ℓ 1 regularization

DOE PAGES

Sanders, Toby; Gelb, Anne; Platte, Rodrigo B.; ...

2017-01-03

Over the last decade or so, reconstruction methods using ℓ 1 regularization, often categorized as compressed sensing (CS) algorithms, have significantly improved the capabilities of high fidelity imaging in electron tomography. The most popular ℓ 1 regularization approach within electron tomography has been total variation (TV) regularization. In addition to reducing unwanted noise, TV regularization encourages a piecewise constant solution with sparse boundary regions. In this paper we propose an alternative ℓ 1 regularization approach for electron tomography based on higher order total variation (HOTV). Like TV, the HOTV approach promotes solutions with sparse boundary regions. In smooth regions however,more » the solution is not limited to piecewise constant behavior. We demonstrate that this allows for more accurate reconstruction of a broader class of images – even those for which TV was designed for – particularly when dealing with pragmatic tomographic sampling patterns and very fine image features. In conclusion, we develop results for an electron tomography data set as well as a phantom example, and we also make comparisons with discrete tomography approaches.« less

3D structure of eukaryotic flagella/cilia by cryo-electron tomography

PubMed Central

Ishikawa, Takashi

2013-01-01

Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex. PMID:27493552

75 FR 15413 - Approval for Processing Authority, Foreign-Trade Zone 196, ATC Logistics & Electronics (Personal...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-29

... DEPARTMENT OF COMMERCE Foreign-Trade Zones Board [Order No. 1671] Approval for Processing Authority, Foreign-Trade Zone 196, ATC Logistics & Electronics (Personal Navigation Devices), Fort Worth... & Electronics, an operator of Foreign-Trade Zone 196, has requested processing authority within FTZ 196 in Fort...

Robust membrane detection based on tensor voting for electron tomography.

PubMed

Martinez-Sanchez, Antonio; Garcia, Inmaculada; Asano, Shoh; Lucic, Vladan; Fernandez, Jose-Jesus

2014-04-01

Electron tomography enables three-dimensional (3D) visualization and analysis of the subcellular architecture at a resolution of a few nanometers. Segmentation of structural components present in 3D images (tomograms) is often necessary for their interpretation. However, it is severely hampered by a number of factors that are inherent to electron tomography (e.g. noise, low contrast, distortion). Thus, there is a need for new and improved computational methods to facilitate this challenging task. In this work, we present a new method for membrane segmentation that is based on anisotropic propagation of the local structural information using the tensor voting algorithm. The local structure at each voxel is then refined according to the information received from other voxels. Because voxels belonging to the same membrane have coherent structural information, the underlying global structure is strengthened. In this way, local information is easily integrated at a global scale to yield segmented structures. This method performs well under low signal-to-noise ratio typically found in tomograms of vitrified samples under cryo-tomography conditions and can bridge gaps present on membranes. The performance of the method is demonstrated by applications to tomograms of different biological samples and by quantitative comparison with standard template matching procedure. Copyright © 2014 Elsevier Inc. All rights reserved.

High-pressure freezing for scanning transmission electron tomography analysis of cellular organelles.

PubMed

Walther, Paul; Schmid, Eberhard; Höhn, Katharina

2013-01-01

Using an electron microscope's scanning transmission mode (STEM) for collection of tomographic datasets is advantageous compared to bright field transmission electron microscopic (TEM). For image formation, inelastic scattering does not cause chromatic aberration, since in STEM mode no image forming lenses are used after the beam has passed the sample, in contrast to regular TEM. Therefore, thicker samples can be imaged. It has been experimentally demonstrated that STEM is superior to TEM and energy filtered TEM for tomography of samples as thick as 1 μm. Even when using the best electron microscope, adequate sample preparation is the key for interpretable results. We adapted protocols for high-pressure freezing of cultivated cells from a physiological state. In this chapter, we describe optimized high-pressure freezing and freeze substitution protocols for STEM tomography in order to obtain high membrane contrast.

Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography

NASA Astrophysics Data System (ADS)

Zhang, Lei; Lei, Dongsheng; Smith, Jessica M.; Zhang, Meng; Tong, Huimin; Zhang, Xing; Lu, Zhuoyang; Liu, Jiankang; Alivisatos, A. Paul; Ren, Gang

2016-03-01

DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The control of DNA-mediated assembly depends crucially on a better understanding of three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Existing techniques do not allow for structural determination of these flexible and heterogeneous samples. Here we report cryo-electron microscopy and negative-staining electron tomography approaches to image, and three-dimensionally reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two 5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By individual-particle electron tomography reconstruction, we obtain 14 density maps at ~2-nm resolution. Using these maps as constraints, we derive 14 conformations of dsDNA by molecular dynamics simulations. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics.

Correlative cryo-fluorescence light microscopy and cryo-electron tomography of Streptomyces.

PubMed

Koning, Roman I; Celler, Katherine; Willemse, Joost; Bos, Erik; van Wezel, Gilles P; Koster, Abraham J

2014-01-01

Light microscopy and electron microscopy are complementary techniques that in a correlative approach enable identification and targeting of fluorescently labeled structures in situ for three-dimensional imaging at nanometer resolution. Correlative imaging allows electron microscopic images to be positioned in a broader temporal and spatial context. We employed cryo-correlative light and electron microscopy (cryo-CLEM), combining cryo-fluorescence light microscopy and cryo-electron tomography, on vitrified Streptomyces bacteria to study cell division. Streptomycetes are mycelial bacteria that grow as long hyphae and reproduce via sporulation. On solid media, Streptomyces subsequently form distinct aerial mycelia where cell division leads to the formation of unigenomic spores which separate and disperse to form new colonies. In liquid media, only vegetative hyphae are present divided by noncell separating crosswalls. Their multicellular life style makes them exciting model systems for the study of bacterial development and cell division. Complex intracellular structures have been visualized with transmission electron microscopy. Here, we describe the methods for cryo-CLEM that we applied for studying Streptomyces. These methods include cell growth, fluorescent labeling, cryo-fixation by vitrification, cryo-light microscopy using a Linkam cryo-stage, image overlay and relocation, cryo-electron tomography using a Titan Krios, and tomographic reconstruction. Additionally, methods for segmentation, volume rendering, and visualization of the correlative data are described. © 2014 Elsevier Inc. All rights reserved.

New hardware and workflows for semi-automated correlative cryo-fluorescence and cryo-electron microscopy/tomography.

PubMed

Schorb, Martin; Gaechter, Leander; Avinoam, Ori; Sieckmann, Frank; Clarke, Mairi; Bebeacua, Cecilia; Bykov, Yury S; Sonnen, Andreas F-P; Lihl, Reinhard; Briggs, John A G

2017-02-01

Correlative light and electron microscopy allows features of interest defined by fluorescence signals to be located in an electron micrograph of the same sample. Rare dynamic events or specific objects can be identified, targeted and imaged by electron microscopy or tomography. To combine it with structural studies using cryo-electron microscopy or tomography, fluorescence microscopy must be performed while maintaining the specimen vitrified at liquid-nitrogen temperatures and in a dry environment during imaging and transfer. Here we present instrumentation, software and an experimental workflow that improves the ease of use, throughput and performance of correlated cryo-fluorescence and cryo-electron microscopy. The new cryo-stage incorporates a specially modified high-numerical aperture objective lens and provides a stable and clean imaging environment. It is combined with a transfer shuttle for contamination-free loading of the specimen. Optimized microscope control software allows automated acquisition of the entire specimen area by cryo-fluorescence microscopy. The software also facilitates direct transfer of the fluorescence image and associated coordinates to the cryo-electron microscope for subsequent fluorescence-guided automated imaging. Here we describe these technological developments and present a detailed workflow, which we applied for automated cryo-electron microscopy and tomography of various specimens. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

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Whole-cell imaging of the budding yeast Saccharomyces cerevisiae by high-voltage scanning transmission electron tomography.

PubMed

Murata, Kazuyoshi; Esaki, Masatoshi; Ogura, Teru; Arai, Shigeo; Yamamoto, Yuta; Tanaka, Nobuo

2014-11-01

Electron tomography using a high-voltage electron microscope (HVEM) provides three-dimensional information about cellular components in sections thicker than 1 μm, although in bright-field mode image degradation caused by multiple inelastic scattering of transmitted electrons limit the attainable resolution. Scanning transmission electron microscopy (STEM) is believed to give enhanced contrast and resolution compared to conventional transmission electron microscopy (CTEM). Samples up to 1 μm in thickness have been analyzed with an intermediate-voltage electron microscope because inelastic scattering is not a critical limitation, and probe broadening can be minimized. Here, we employed STEM at 1 MeV high-voltage to extend the useful specimen thickness for electron tomography, which we demonstrate by a seamless tomographic reconstruction of a whole, budding Saccharomyces cerevisiae yeast cell, which is ~3 μm in thickness. High-voltage STEM tomography, especially in the bright-field mode, demonstrated sufficiently enhanced contrast and intensity, compared to CTEM tomography, to permit segmentation of major organelles in the whole cell. STEM imaging also reduced specimen shrinkage during tilt-series acquisition. The fidelity of structural preservation was limited by cytoplasmic extraction, and the spatial resolution was limited by the relatively large convergence angle of the scanning probe. However, the new technique has potential to solve longstanding problems of image blurring in biological specimens beyond 1 μm in thickness, and may facilitate new research in cellular structural biology. Copyright © 2014 Elsevier B.V. All rights reserved.

Variable pixel size ionospheric tomography

NASA Astrophysics Data System (ADS)

Zheng, Dunyong; Zheng, Hongwei; Wang, Yanjun; Nie, Wenfeng; Li, Chaokui; Ao, Minsi; Hu, Wusheng; Zhou, Wei

2017-06-01

A novel ionospheric tomography technique based on variable pixel size was developed for the tomographic reconstruction of the ionospheric electron density (IED) distribution. In variable pixel size computerized ionospheric tomography (VPSCIT) model, the IED distribution is parameterized by a decomposition of the lower and upper ionosphere with different pixel sizes. Thus, the lower and upper IED distribution may be very differently determined by the available data. The variable pixel size ionospheric tomography and constant pixel size tomography are similar in most other aspects. There are some differences between two kinds of models with constant and variable pixel size respectively, one is that the segments of GPS signal pay should be assigned to the different kinds of pixel in inversion; the other is smoothness constraint factor need to make the appropriate modified where the pixel change in size. For a real dataset, the variable pixel size method distinguishes different electron density distribution zones better than the constant pixel size method. Furthermore, it can be non-chided that when the effort is spent to identify the regions in a model with best data coverage. The variable pixel size method can not only greatly improve the efficiency of inversion, but also produce IED images with high fidelity which are the same as a used uniform pixel size method. In addition, variable pixel size tomography can reduce the underdetermined problem in an ill-posed inverse problem when the data coverage is irregular or less by adjusting quantitative proportion of pixels with different sizes. In comparison with constant pixel size tomography models, the variable pixel size ionospheric tomography technique achieved relatively good results in a numerical simulation. A careful validation of the reliability and superiority of variable pixel size ionospheric tomography was performed. Finally, according to the results of the statistical analysis and quantitative comparison, the

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En-face imaging of the ellipsoid zone in the retina from optical coherence tomography B-scans

NASA Astrophysics Data System (ADS)

Holmes, T.; Larkin, S.; Downing, M.; Csaky, K.

2015-03-01

It is generally believed that photoreceptor integrity is related to the ellipsoid zone appearance in optical coherence tomography (OCT) B-scans. Algorithms and software were developed for viewing and analyzing the ellipsoid zone. The software performs the following: (a), automated ellipsoid zone isolation in the B-scans, (b), en-face view of the ellipsoid-zone reflectance, (c), alignment and overlay of (b) onto reflectance images of the retina, and (d), alignment and overlay of (c) with microperimetry sensitivity points. Dataset groups were compared from normal and dry age related macular degeneration (DAMD) subjects. Scalar measurements for correlation against condition included the mean and standard deviation of the ellipsoid zone's reflectance. The imageprocessing techniques for automatically finding the ellipsoid zone are based upon a calculation of optical flow which tracks the edges of laminated structures across an image. Statistical significance was shown in T-tests of these measurements with the population pools separated as normal and DAMD subjects. A display of en-face ellipsoid-zone reflectance shows a clear and recognizable difference between any of the normal and DAMD subjects in that they show generally uniform and nonuniform reflectance, respectively, over the region near the macula. Regions surrounding points of low microperimetry (μP) sensitivity have nonregular and lower levels of ellipsoid-zone reflectance nearby. These findings support the idea that the photoreceptor integrity could be affecting both the ellipsoid-zone reflectance and the sensitivity measurements.

Electron microprobe study of lunar and planetary zoned plagioclase feldspars: An analytical and experimental study of zoning in plagioclase

NASA Technical Reports Server (NTRS)

Smith, R. K.; Lofgren, G. E.

1982-01-01

Natural and experimentally grown zoned plagioclase feldspars were examined by electron microprobe. The analyses revealed discontinuous, sector, and oscillary chemical zoning superimposed on continuous normal or reverse zoning trends. Postulated mechanisms for the origin of zoning are based on either physical changes external to the magma (P, T, H2O saturation) or kinetic changes internal to the magma (diffusion, supersaturation, growth rate). Comparison of microprobe data on natural zoned plagioclase with zoned plagioclase grown in controlled experiments show that it may be possible to distinguish zonal development resulting from physio-chemical changes to the bulk magma from local kinetic control on the growth of individual crystals.

Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography

DOE PAGES

Zhang, Lei; Lei, Dongsheng; Smith, Jessica M.; ...

2016-03-30

DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The control of DNA-mediated assembly depends crucially on a better understanding of three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Existing techniques do not allow for structural determination of these flexible and heterogeneous samples. Here we report cryo-electron microscopy and negative-staining electron tomography approaches to image, and three-dimensionally reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two 5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By individual-particle electron tomography reconstruction, we obtainmore » 14 density maps at ~ 2-nm resolution . Using these maps as constraints, we derive 14 conformations of dsDNA by molecular dynamics simulations. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics.« less

Automated discrete electron tomography - Towards routine high-fidelity reconstruction of nanomaterials.

PubMed

Zhuge, Xiaodong; Jinnai, Hiroshi; Dunin-Borkowski, Rafal E; Migunov, Vadim; Bals, Sara; Cool, Pegie; Bons, Anton-Jan; Batenburg, Kees Joost

2017-04-01

Electron tomography is an essential imaging technique for the investigation of morphology and 3D structure of nanomaterials. This method, however, suffers from well-known missing wedge artifacts due to a restricted tilt range, which limits the objectiveness, repeatability and efficiency of quantitative structural analysis. Discrete tomography represents one of the promising reconstruction techniques for materials science, potentially capable of delivering higher fidelity reconstructions by exploiting the prior knowledge of the limited number of material compositions in a specimen. However, the application of discrete tomography to practical datasets remains a difficult task due to the underlying challenging mathematical problem. In practice, it is often hard to obtain consistent reconstructions from experimental datasets. In addition, numerous parameters need to be tuned manually, which can lead to bias and non-repeatability. In this paper, we present the application of a new iterative reconstruction technique, named TVR-DART, for discrete electron tomography. The technique is capable of consistently delivering reconstructions with significantly reduced missing wedge artifacts for a variety of challenging data and imaging conditions, and can automatically estimate its key parameters. We describe the principles of the technique and apply it to datasets from three different types of samples acquired under diverse imaging modes. By further reducing the available tilt range and number of projections, we show that the proposed technique can still produce consistent reconstructions with minimized missing wedge artifacts. This new development promises to provide the electron microscopy community with an easy-to-use and robust tool for high-fidelity 3D characterization of nanomaterials. Copyright © 2017 Elsevier B.V. All rights reserved.

Zernike phase contrast cryo-electron tomography of whole bacterial cells.

PubMed

Guerrero-Ferreira, Ricardo C; Wright, Elizabeth R

2014-01-01

Cryo-electron tomography (cryo-ET) provides three-dimensional (3D) structural information of bacteria preserved in a native, frozen-hydrated state. The typical low contrast of tilt-series images, a result of both the need for a low electron dose and the use of conventional defocus phase-contrast imaging, is a challenge for high-quality tomograms. We show that Zernike phase-contrast imaging allows the electron dose to be reduced. This limits movement of gold fiducials during the tilt series, which leads to better alignment and a higher-resolution reconstruction. Contrast is also enhanced, improving visibility of weak features. The reduced electron dose also means that more images at more tilt angles could be recorded, further increasing resolution. Copyright © 2013 Elsevier Inc. All rights reserved.

Zernike phase contrast cryo-electron tomography of whole bacterial cells

PubMed Central

Guerrero-Ferreira, Ricardo C.; Wright, Elizabeth R.

2014-01-01

Cryo-electron tomography (cryo-ET) provides three-dimensional (3D) structural information of bacteria preserved in a native, frozen-hydrated state. The typical low contrast of tilt-series images, a result of both the need for a low electron dose and the use of conventional defocus phase-contrast imaging, is a challenge for high-quality tomograms. We show that Zernike phase-contrast imaging allows the electron dose to be reduced. This limits movement of gold fiducials during the tilt series, which leads to better alignment and a higher-resolution reconstruction. Contrast is also enhanced, improving visibility of weak features. The reduced electron dose also means that more images at more tilt angles could be recorded, further increasing resolution. PMID:24075950

CLASSIFICATION AND QUANTITATIVE ANALYSIS OF GEOGRAPHIC ATROPHY JUNCTIONAL ZONE USING SPECTRAL DOMAIN OPTICAL COHERENCE TOMOGRAPHY.

PubMed

Qu, Jinfeng; Velaga, Swetha Bindu; Hariri, Amir H; Nittala, Muneeswar Gupta; Sadda, Srinivas

2017-08-22

The junctional zone at the border of areas of geographic atrophy (GA) in eyes with nonneovascular age-related macular degeneration is an important target region for future therapeutic strategies. The goal of this study was to perform a detailed classification and quantitative characterization of the junctional zone using spectral domain optical coherence tomography. Spectral domain optical coherence tomography volume cube scans (Spectralis OCT, 1024 × 37, Automatic Real Time > 9) were obtained from 15 eyes of 11 patients with GA because of nonneovascular age-related macular degeneration. Volume optical coherence tomography data were imported into previously described validated grading software (3D-OCTOR), and manual segmentation of the retinal pigment epithelium (RPE) and photoreceptor layers was performed on all B-scans (total of 555). Retinal pigment epithelium and photoreceptor defect maps were produced for each case. The borders of the photoreceptor defect area and RPE defect area were delineated individually on separate annotation layers. The two outlines were then superimposed to compare the areas of overlap and nonoverlap. The perimeter of the RPE defect area was calculated by the software in pixels. The superimposed outline of the photoreceptor defect area and the RPE defect area was scrutinized to classify the overlap configuration of the junctional zone into one of three categories: Type 0, exact correspondence between the edge of the RPE defect and photoreceptor defect; Type 1, loss of photoreceptors outside and beyond the edge of the RPE defect; Type 2, preservation of photoreceptors beyond the edge of the RPE defect. The relative proportion of the various border configurations was expressed as a percentage of the perimeter of the RPE defect. Each configuration was then classified into four subgroups according to irregularity of the RPE band and the presence of debris. Fifteen eyes of 11 patients (mean age: 79.3 ± 4.3 years; range: 79-94 years) were

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Electron cryo-tomography captures macromolecular complexes in native environments.

PubMed

Baker, Lindsay A; Grange, Michael; Grünewald, Kay

2017-10-01

Transmission electron microscopy has a long history in cellular biology. Fixed and stained samples have been used for cellular imaging for over 50 years, but suffer from sample preparation induced artifacts. Electron cryo-tomography (cryoET) instead uses frozen-hydrated samples, without chemical modification, to determine the structure of macromolecular complexes in their native environment. Recent developments in electron microscopes and associated technologies have greatly expanded our ability to visualize cellular features and determine the structures of macromolecular complexes in situ. This review highlights the technological improvements and the new areas of biology these advances have made accessible. We discuss the potential of cryoET to reveal novel and significant biological information on the nanometer or subnanometer scale, and directions for further work. Copyright © 2017. Published by Elsevier Ltd.

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Quantitative Electron Tomography of Rubber Composites

NASA Astrophysics Data System (ADS)

Staniewicz, Lech; Vaudey, Thomas; Degrandcourt, Christophe; Couty, Marc; Gaboriaud, Fabien; Midgley, Paul

2014-06-01

Rubber composite materials have many applications, one example being tyre manufacture. The presence of a filler material in the composite (such as carbon black or silica) causes its mechanical properties to differ in several ways when compared to pure rubber such as viscoelastic behaviour (the Payne effect), increased tensile strength and improved wear resistance. To fully understand these properties, it is necessary to characterise how the filler material is organised on the nanoscale. Using composite materials representative of those found in tyres, this work illustrates the use of electron tomography and machine learning methods as tools to describe the percolation behaviour of the filler; in this case, we focus on the largest proportion of particles absorbed into one single object as a function of particle spacing.

A novel permeabilization protocol to obtain intracellular 3D immunolabeling for electron tomography.

PubMed

Jiménez, Nuria; Post, Jan A

2014-01-01

Electron tomography (ET) is a very important high-resolution tool for 3D imaging in cell biology. By combining the technique with immunolabeling, ET can provide essential insights into both cellular architecture and dynamics. We recently developed a protocol to achieve 3D immunolabeling of intracellular antigens without the need for uncontrolled permeabilization steps that cause random, extensive cell membrane disruption. Here we describe this novel method based on well-controlled permeabilization by targeted laser cell perforation. Mechanical permeabilization of the plasma membrane can be applied at specific sites without affecting other parts of the plasma membrane and intracellular membranes. Despite the relatively small opening created in the plasma membrane, the method allows specific 3D immunolocalization of cytoplasmic antigens in cultured cells by a pre-embedment protocol. The approach is unique and leads to a superior ultrastructural preservation for transmission electron microscopy and electron tomography.

Obtaining 3D Chemical Maps by Energy Filtered Transmission Electron Microscopy Tomography.

PubMed

Roiban, Lucian; Sorbier, Loïc; Hirlimann, Charles; Ersen, Ovidiu

2018-06-09

Energy filtered transmission electron microscopy tomography (EFTEM tomography) can provide three-dimensional (3D) chemical maps of materials at a nanometric scale. EFTEM tomography can separate chemical elements that are very difficult to distinguish using other imaging techniques. The experimental protocol described here shows how to create 3D chemical maps to understand the chemical distribution and morphology of a material. Sample preparation steps for data segmentation are presented. This protocol permits the 3D distribution analysis of chemical elements in a nanometric sample. However, it should be noted that currently, the 3D chemical maps can only be generated for samples that are not beam sensitive, since the recording of filtered images requires long exposure times to an intense electron beam. The protocol was applied to quantify the chemical distribution of the components of two different heterogeneous catalyst supports. In the first study, the chemical distribution of aluminum and titanium in titania-alumina supports was analyzed. The samples were prepared using the swing-pH method. In the second, the chemical distribution of aluminum and silicon in silica-alumina supports that were prepared using the sol-powder and mechanical mixture methods was examined.

Zone plate method for electronic holographic display using resolution redistribution technique.

PubMed

Takaki, Yasuhiro; Nakamura, Junya

2011-07-18

The resolution redistribution (RR) technique can increase the horizontal viewing-zone angle and screen size of electronic holographic display. The present study developed a zone plate method that would reduce hologram calculation time for the RR technique. This method enables calculation of an image displayed on a spatial light modulator by performing additions of the zone plates, while the previous calculation method required performing the Fourier transform twice. The derivation and modeling of the zone plate are shown. In addition, the look-up table approach was introduced for further reduction in computation time. Experimental verification using a holographic display module based on the RR technique is presented.

Mineral and organic matrix interaction in normally calcifying tendon visualized in three dimensions by high-voltage electron microscopic tomography and graphic image reconstruction

NASA Technical Reports Server (NTRS)

Landis, W. J.; Song, M. J.; Leith, A.; McEwen, L.; McEwen, B. F.

1993-01-01

To define the ultrastructural accommodation of mineral crystals by collagen fibrils and other organic matrix components during vertebrate calcification, electron microscopic 3-D reconstructions were generated from the normally mineralizing leg tendons from the domestic turkey, Meleagris gallopavo. Embedded specimens containing initial collagen mineralizing sites were cut into 0.5-micron-thick sections and viewed and photographed at 1.0 MV in the Albany AEI-EM7 high-voltage electron microscope. Tomographic 3-D reconstructions were computed from a 2 degree tilt series of micrographs taken over a minimum angular range of +/- 60 degrees. Reconstructions of longitudinal tendon profiles confirm the presence of irregularly shaped mineral platelets, whose crystallographic c-axes are oriented generally parallel to one another and directed along the collagen long axes. The reconstructions also corroborate observations of a variable crystal length (up to 170 nm measured along crystallographic c-axes), the presence of crystals initially in either the hole or overlap zones of collagen, and crystal growth in the c-axis direction beyond these zones into adjacent overlap and other hole regions. Tomography shows for the first time that crystal width varies (30-45 nm) but crystal thickness is uniform (approximately 4-6 nm at the resolution limit of tomography); more crystals are located in the collagen hole zones than in the overlap regions at the earliest stages of tendon mineralization; the crystallographic c-axes of the platelets lie within +/- 15-20 degrees of one another rather than being perfectly parallel; adjacent platelets are spatially separated by a minimum of 4.2 +/- 1.0 nm; crystals apparently fuse in coplanar alignment to form larger platelets; development of crystals in width occurs to dimensions beyond single collagen hole zones; and a thin envelope of organic origin may be present along or just beneath the surfaces of individual mineral platelets. Implicit in the

Exemplar-based inpainting as a solution to the missing wedge problem in electron tomography.

PubMed

Trampert, Patrick; Wang, Wu; Chen, Delei; Ravelli, Raimond B G; Dahmen, Tim; Peters, Peter J; Kübel, Christian; Slusallek, Philipp

2018-04-21

A new method for dealing with incomplete projection sets in electron tomography is proposed. The approach is inspired by exemplar-based inpainting techniques in image processing and heuristically generates data for missing projection directions. The method has been extended to work on three dimensional data. In general, electron tomography reconstructions suffer from elongation artifacts along the beam direction. These artifacts can be seen in the corresponding Fourier domain as a missing wedge. The new method synthetically generates projections for these missing directions with the help of a dictionary based approach that is able to convey both structure and texture at the same time. It constitutes a preprocessing step that can be combined with any tomographic reconstruction algorithm. The new algorithm was applied to phantom data, to a real electron tomography data set taken from a catalyst, as well as to a real dataset containing solely colloidal gold particles. Visually, the synthetic projections, reconstructions, and corresponding Fourier power spectra showed a decrease of the typical missing wedge artifacts. Quantitatively, the inpainting method is capable to reduce missing wedge artifacts and improves tomogram quality with respect to full width half maximum measurements. Copyright © 2018. Published by Elsevier B.V.

Comparisons Between Histology and Optical Coherence Tomography Angiography of the Periarterial Capillary-Free Zone.

PubMed

Balaratnasingam, Chandrakumar; An, Dong; Sakurada, Yoichi; Lee, Cecilia S; Lee, Aaron Y; McAllister, Ian L; Freund, K Bailey; Sarunic, Marinko; Yu, Dao-Yi

2018-05-01

To use the capillary-free zone along retinal arteries, a physiologic area of superficial avascularization, as an anatomic paradigm to investigate the reliability of optical coherence tomography angiography (OCTA) for visualizing the deep retinal circulation. Validity analysis and laboratory investigation. Five normal human donor eyes (mean age 69.8 years) were perfusion-labeled with endothelial antibodies and the capillary networks of the perifovea were visualized using confocal scanning laser microscopy. Regions of the capillary-free zone along the retinal artery were imaged using OCTA in 16 normal subjects (age range 24-51 years). Then, 3 × 3-mm scans were acquired using the RTVue XR Avanti (ver. 2016.1.0.26; Optovue, Inc, Fremont, California, USA), PLEX Elite 9000 (ver. 1.5.0.15909; Zeiss Meditec, Inc, Dublin, California, USA), Heidelberg Spectralis OCT2 (Family acquisition module 6.7.21.0; Heidelberg Engineering, Heidelberg, Germany), and DRI-OCT Triton (Ver. 1.1.1; Topcon Corp, Tokyo, Japan). Images of the superficial plexus, deep vascular plexus, and a slab containing all vascular plexuses were generated using manufacturer-recommended default settings. Comparisons between histology and OCTA were performed. Histologic analysis revealed that the capillary-free zone along the retinal artery was confined to the plane of the superficial capillary plexus and did not include the intermediate and deep capillary plexuses. Images derived from OCTA instruments demonstrated a prominent capillary-free zone along the retinal artery in slabs of the superficial plexus, deep plexus, and all capillary plexuses. The number of deep retinal capillaries seen in the capillary-free zone was significantly greater on histology than on OCTA (P < .001). Using the capillary-free zone as an anatomic paradigm, we show that the deep vascular beds of the retina are not completely visualized using OCTA. This may be a limitation of current OCTA techniques. Copyright © 2018 Elsevier Inc. All

Global Discontinuity Structure of the Mantle Transition Zone from Finite-Frequency Tomography of SS Precursors

NASA Astrophysics Data System (ADS)

Guo, Z.; Zhou, Y.

2017-12-01

We report global structure of the 410-km and 660-km discontinuities from finite-frequency tomography using frequency-dependent traveltime measurements of SS precursors recorded at the Global Seismological Network (GSN). Finite-frequency sensitivity kernels for discontinuity depth perturbations are calculated in the framework of traveling-wave mode coupling. We parametrize the global discontinuities using a set of spherical triangular grid points and solve the tomographic inverse problem based on singular value decomposition. Our global 410-km and 660-km discontinuity models reveal distinctly different characteristics beneath the oceans and subduction zones. In general, oceanic regions are associated with a thinner mantle transition zone and depth perturbations of the 410-km and 660-km discontinuities are anti-correlated, in agreement with a thermal origin and an overall warm and dry mantle beneath the oceans. The perturbations are not uniform throughout the oceans but show strong small-scale variations, indicating complex processes in the mantle transition zone. In major subduction zones (except for South America where data coverage is sparse), depth perturbations of the 410-km and 660-km discontinuities are correlated, with both the 410-km and the 660-km discontinuities occurring at greater depths. The distributions of the anomalies are consistent with cold stagnant slabs just above the 660-km discontinuity and ascending return flows in a superadiabatic upper mantle.

Electron tomography and computer visualisation of a three-dimensional 'photonic' crystal in a butterfly wing-scale.

PubMed

Argyros, A; Manos, S; Large, M C J; McKenzie, D R; Cox, G C; Dwarte, D M

2002-01-01

A combination of transmission electron tomography and computer modelling has been used to determine the three-dimensional structure of the photonic crystals found in the wing-scales of the Kaiser-I-Hind butterfly (Teinopalpus imperialis). These scales presented challenges for electron microscopy because the periodicity of the structure was comparable to the thickness of a section and because of the complex connectivity of the object. The structure obtained has been confirmed by taking slices of the three-dimensional computer model constructed from the tomography and comparing these with transmission electron microscope (TEM) images of microtomed sections of the actual scale. The crystal was found to have chiral tetrahedral repeating units packed in a triclinic lattice.

Structural relations between collagen and mineral in bone as determined by high voltage electron microscopic tomography

NASA Technical Reports Server (NTRS)

Landis, W. J.; Hodgens, K. J.; Arena, J.; Song, M. J.; McEwen, B. F.

1996-01-01

Aspects of the ultrastructural interaction between collagen and mineral crystals in embryonic chick bone have been examined by the novel technique of high voltage electron microscopic tomography to obtain three-dimensional information concerning extracellular calcification in this tissue. Newly mineralizing osteoid along periosteal surfaces of mid-diaphyseal regions from normal chick tibiae was embedded, cut into 0.25 microns thick sections, and documented at 1.0 MV in the Albany AEI-EM7 high voltage electron microscope. The areas of the tissue studied contained electron dense mineral crystals associated with collagen fibrils, some marked by crystals disposed along their cylindrically shaped lengths. Tomographic reconstructions of one site with two mineralizing fibrils were computed from a 5 degrees tilt series of micrographs over a +/- 60 degrees range. Reconstructions showed that the mineral crystals were platelets of irregular shape. Their sizes were variable, measured here up to 80 x 30 x 8 nm in length, width, and thickness, respectively. The longest crystal dimension, corresponding to the c-axis crystallographically, was generally parallel to the collagen fibril long axis. Individual crystals were oriented parallel to one another in each fibril examined. They were also parallel in the neighboring but apparently spatially separate fibrils. Crystals were periodically (approximately 67 nm repeat distance) arranged along the fibrils and their location appeared to correspond to collagen hole and overlap zones defined by geometrical imaging techniques. The crystals appeared to be continuously distributed along a fibril, their size and number increasing in a tapered fashion from a relatively narrow tip containing smaller and infrequent crystals to wider regions having more densely packed and larger crystals. Defined for the first time by direct visual 3D imaging, these data describe the size, shape, location, orientation, and development of early crystals in normal

Teleseismic Upper-mantle Tomography of the Tanlu Fault Zone in East China

NASA Astrophysics Data System (ADS)

Lei, J., Sr.; Zhao, D.; Du, M.; Mi, Q.; Lu, M.

2017-12-01

The Tanlu fault zone, NNE-SSW oriented with strike-slip motions, is the most significant active fault in East China. The great 1668 Tancheng earthquake (Ms 8.5) occurred on this fault zone, which is located above the stagnant Pacific slab in the mantle transition zone (MTZ). To the east of the Tancheng earthquake epicenter and under the southernmost Korean Peninsula to westernmost Japan, the subducting Pacific slab exhibits a sharp change in its geometry. However, the relationship between the Pacific slab and the great earthquake on the Tanlu fault is unclear. To address this issue, we conduct teleseismic P-wave tomography using 44,715 relative arrival times. These data are collected from high-quality seismograms of 838 teleseismic events (M > 5.5; epicenter distances of 30-90 degrees) recorded at 126 provincial seismic stations around the Tanlu fault zone in East China. Our results show that at depths < 150 km, high velocity (high-V) anomalies appear to the west of the Tanlu fault, whereas some low velocity (low-V) anomalies are visible to the east of the fault zone. Strong lateral heterogeneities are revealed along the fault zone. At depths of 230-470 km, to the northwest of the Tanlu fault, there are obvious low-V anomalies which may reflect hot and wet mantle upwelling, whereas to the east, some high-V anomalies are visible, which may reflect the detached Eurasian lithosphere. In the MTZ, both high-V and low-V anomalies are visible, and the widespread high-V anomalies may reflect the stagnant Pacific slab. Beneath the hypocenter of the 1668 Tancheng earthquake, a prominent low-V anomaly is revealed in the upper mantle down the MTZ depth, which may reflect upwelling flow of hot and wet materials. Fluids from the upwelling mantle flow may have played a key role in the generation of the Tancheng earthquake. Integrating with previous findings, our present results suggest that the Tancheng earthquake could be related to the sharp change in the Pacific slab geometry

Geometry and velocity structure of the northern Costa Rica seismogenic zone from 3D local earthquake tomography

NASA Astrophysics Data System (ADS)

Deshon, H. R.; Schwartz, S. Y.; Newman, A. V.; Dorman, L. M.; Protti, M.; Gonzalez, V.

2003-12-01

We present results of a 3D local earthquake tomography study of the Middle America Trench seismogenic zone in northern Costa Rica. Local earthquake tomography can provide constraints on the updip, downdip, and lateral variability of seismicity and P- and S-wave velocities; these constraints may in turn provide information on compositional and/or mechanical variability along the seismogenic zone. We use arrival time data recorded by the Nicoya Peninsula seismic array, part of the Costa Rica seismogenic zone experiment (CRSEIZE), a collaborative effort undertaken to better understand seismogenic behavior at the Costa Rica subduction zone using data from land and ocean bottom seismic arrays, oceanic fluid flux meters, and GPS receivers. We invert ˜10,000 P-wave and S-wave arrival times from 475 well-recorded local earthquakes (GAP < 180° , >8 P-wave arrivals) to solve for the best-fitting 1D P- and S-wave velocity models, station corrections, and hypocenters using the algorithm VELEST. These 1D velocity models are used as a starting models for 3D simultaneous inversion using the algorithm SIMULPS14. Preliminary P-wave inversions contain a positive velocity anomaly dipping beneath the Nicoya Peninsula, interpreted as the subducting Cocos Plate. Earthquakes occur in a narrow band along the slab-continent interface and are consistent with the results of Newman et al. (2002). The updip limit of seismicity occurs ˜5 km deeper and 5-10 km landward in the northern vs. the southern Nicoya Peninsula, and this shift spatially correlates to the change from Cocos-Nazca to East Pacific Rise derived oceanic plate. P-wave velocities in the upper 5-10 km of the model are consistent with the geology of the Nicoya Peninsula. We will correlate relocated microseismicity to previously noted variability in oceanic plate morphology, heat flow, fluid flow, and thermal structure and compare the resulting P- and S-wave velocity models to wide-angle refraction models and hypothesized mantle

Imaging of Fine Shallow Structure Beneath the Longmenshan Fault Zone from Ambient Noise Tomography

NASA Astrophysics Data System (ADS)

Zhao, P.; Campillo, M.; Chen, J.; Liu, Q.

2016-12-01

Short period seismic ambient noise group velocity dispersion curve, obtained from cross correlation of vertical component of 57 stations around the Longmenshan fault zone deployed after the Wenchuan earthquake and continuously observed for 1 year, is used to inverse the S wave velocity structure of the top 25 km of the central to northern part of Longmenshan fault zone. A iterative correction method based on 3-D simulation is proposed to reduce the influence of elevation. After 7 times of correction, a fine shllow S-wave velocity structure comes out. The results show that (1) Velocity structure above 10 km keeps good consistency with the surface fault system around Longmenshan, and controls the deep extension features of most major faults. Below the depth of 15 km, the velocity structure presents cross tectonic frame work along both Longmenshan and Minshan. The complex structure may have affected the rupture process of the Wenchuan earthquake. (2) The depth velocity structure profiles give good constraint for the deep geometry of main faults. The characteristics of the high angle, listric, reverse structure of the Longmenshan faults is further confirmed by our results.(3) At southern part of the study area, low-velocity structure is found at about 20km depth beneath the Pengguan massif, which is related to the low velocity layer in the middle crust of Songpan-Ganzi block. This may be an evidence for the existence of brittle-ductile transition zone in southern part of the rupture zone of the Wenchuan earthquake at the depth around 22km. Our results show the great potential of short period ambient noise tomography with data from densepassive seismic array in the study of fine velocity structure and fault zone imaging.

Evidence for a low permeability fluid trap in the Nový Kostel Seismic Zone, Czech Republic, using double-difference tomography

NASA Astrophysics Data System (ADS)

Alexandrakis, C.; Calo, M.; Vavrycuk, V.

2012-12-01

The West Bohemia/Vogtland region is the border area between the Czech Republic and Germany known for frequent occurrences of earthquake swarms. The most prominent earthquake swarms occurred recently in 1985/86, 1997, 2000 (Fischer and Horálek, 2003) and 2008 (Fischer et al., 2010). They comprised thousands of microearthquakes, their duration was between 2 weeks to 2 months, and the activity focused typically at depths ranging from 7 to 12 km. The seismic activity is concentrated mostly at the same epicentral area, called the Nový Kostel Zone. This zone is located on the edge of the Cheb Basin, Eger Rift, and at the junction of the Mariánské-Lázně Fault with the Počátky-Plesná Shear Zone. Numerous gas vents and mineral springs within and around the Cheb Basin indicate that uprising magmatic fluids may act as a swarm trigger. In this study, we apply double-difference tomography to investigate the structure within and around the Nový Kostel focal zone. We use data from the 2008 earthquake swarm, as it has been extensively analyzed, and focal mechanisms, principal faults, tectonic stress, source migration and other basic characteristics are known. We selected about 500 microearthquakes recorded at 22 local seismic stations of the West Bohemia Network (WEBNET). The events were inverted for the 3-D seismic structure using the TomoDD code (Zhang and Thurber, 2003) and post-processed using the Weighted Average Model method (Calò et al., 2011). The application of double-difference tomography is advantageous for this setting as swarm foci are closely spaced and form a dense cluster. The geometry of the focal zone and the WEBNET network configuration offer good raypath coverage in all directions. Applying double-difference tomography we produce and interpret 3-D models of the P and S velocities. In this work, we interpret 3-D models of the P velocity and P-to-S ratio in and around the focal zone. The P-to-S model was obtained by calculating directly the ratio

Electron tomography of HEK293T cells using scanning electron microscope-based scanning transmission electron microscopy.

PubMed

You, Yun-Wen; Chang, Hsun-Yun; Liao, Hua-Yang; Kao, Wei-Lun; Yen, Guo-Ji; Chang, Chi-Jen; Tsai, Meng-Hung; Shyue, Jing-Jong

2012-10-01

Based on a scanning electron microscope operated at 30 kV with a homemade specimen holder and a multiangle solid-state detector behind the sample, low-kV scanning transmission electron microscopy (STEM) is presented with subsequent electron tomography for three-dimensional (3D) volume structure. Because of the low acceleration voltage, the stronger electron-atom scattering leads to a stronger contrast in the resulting image than standard TEM, especially for light elements. Furthermore, the low-kV STEM yields less radiation damage to the specimen, hence the structure can be preserved. In this work, two-dimensional STEM images of a 1-μm-thick cell section with projection angles between ±50° were collected, and the 3D volume structure was reconstructed using the simultaneous iterative reconstructive technique algorithm with the TomoJ plugin for ImageJ, which are both public domain software. Furthermore, the cross-sectional structure was obtained with the Volume Viewer plugin in ImageJ. Although the tilting angle is constrained and limits the resulting structural resolution, slicing the reconstructed volume generated the depth profile of the thick specimen with sufficient resolution to examine cellular uptake of Au nanoparticles, and the final position of these nanoparticles inside the cell was imaged.

A cylindrical specimen holder for electron cryo-tomography

PubMed Central

Palmer, Colin M.; Löwe, Jan

2014-01-01

The use of slab-like flat specimens for electron cryo-tomography restricts the range of viewing angles that can be used. This leads to the “missing wedge” problem, which causes artefacts and anisotropic resolution in reconstructed tomograms. Cylindrical specimens provide a way to eliminate the problem, since they allow imaging from a full range of viewing angles around the tilt axis. Such specimens have been used before for tomography of radiation-insensitive samples at room temperature, but never for frozen-hydrated specimens. Here, we demonstrate the use of thin-walled carbon tubes as specimen holders, allowing the preparation of cylindrical frozen-hydrated samples of ribosomes, liposomes and whole bacterial cells. Images acquired from these cylinders have equal quality at all viewing angles, and the accessible tilt range is restricted only by the physical limits of the microscope. Tomographic reconstructions of these specimens demonstrate that the effects of the missing wedge are substantially reduced, and could be completely eliminated if a full tilt range was used. The overall quality of these tomograms is still lower than that obtained by existing methods, but improvements are likely in future. PMID:24275523

A cylindrical specimen holder for electron cryo-tomography.

PubMed

Palmer, Colin M; Löwe, Jan

2014-02-01

The use of slab-like flat specimens for electron cryo-tomography restricts the range of viewing angles that can be used. This leads to the "missing wedge" problem, which causes artefacts and anisotropic resolution in reconstructed tomograms. Cylindrical specimens provide a way to eliminate the problem, since they allow imaging from a full range of viewing angles around the tilt axis. Such specimens have been used before for tomography of radiation-insensitive samples at room temperature, but never for frozen-hydrated specimens. Here, we demonstrate the use of thin-walled carbon tubes as specimen holders, allowing the preparation of cylindrical frozen-hydrated samples of ribosomes, liposomes and whole bacterial cells. Images acquired from these cylinders have equal quality at all viewing angles, and the accessible tilt range is restricted only by the physical limits of the microscope. Tomographic reconstructions of these specimens demonstrate that the effects of the missing wedge are substantially reduced, and could be completely eliminated if a full tilt range was used. The overall quality of these tomograms is still lower than that obtained by existing methods, but improvements are likely in future. © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Micro 3D ERT tomography for data assimilation modelling of active root zone

NASA Astrophysics Data System (ADS)

Vanella, Daniela; Busato, Laura; Boaga, Jacopo; Cassiani, Giorgio; Binley, Andrew; Putti, Mario; Consoli, Simona

2016-04-01

Within the soil-plant-atmosphere system, root activity plays a fundamental role, as it connects different domains and allows a large part of the water and nutrient exchanges necessary for plant sustenance. The understanding of these processes is not only useful from an environmental point of view, making a fundamental contribution to the understanding of the critical zone dynamics, but also plays a pivotal role in precision agriculture, where the optimisation of water resources exploitation is mandatory and often carried out through deficit irrigation techniques. In this work, we present the results of non-invasive monitoring of the active root zone of two orange trees (Citrus sinensis, cv Tarocco Ippolito) located in an orange orchard in eastern Sicily (Italy) and drip irrigated with two different techniques: partial root drying and 100% crop evapotranspiration. The main goal of the monitoring activity is to assess possible differences between the developed root systems and the root water uptake between the two irrigation strategies. The monitoring is conducted using 3D micro-electrical resistivity tomography (ERT) based on an apparatus composed of a number of micro-boreholes (about 1.2 m deep) housing 12 electrodes each, plus a number of surface electrodes. Time-lapse measurements conducted both with long-term periodicity and short-term repetition before and after irrigation clearly highlight the presence and distribution of root water uptake zone both at shallow and larger depth, likely to correspond to zones utilized during the irrigation period (shallow) and during the time when the crop is not irrigated (deep). Subsidiary information is available in terms of precipitation, sap flow measurements and micrometeorological evapotranspiration estimates. This data ensemble lends itself to the assimilation into a variably saturated flow model, where both soil hydraulic parameters and root distribution shall be identified. Preliminary results in this directions show

Recent advances in the application of electron tomography to materials chemistry.

PubMed

Leary, Rowan; Midgley, Paul A; Thomas, John Meurig

2012-10-16

Nowadays, tomography plays a central role in pureand applied science, in medicine, and in many branches of engineering and technology. It entails reconstructing the three-dimensional (3D) structure of an object from a tilt series of two-dimensional (2D) images. Its origin goes back to 1917, when Radon showed mathematically how a series of 2D projection images could be converted to the 3D structural one. Tomographic X-ray and positron scanning for 3D medical imaging, with a resolution of ∼1 mm, is now ubiquitous in major hospitals. Electron tomography, a relatively new chemical tool, with a resolution of ∼1 nm, has been recently adopted by materials chemists as an invaluable aid for the 3D study of the morphologies, spatially-discriminating chemical compositions, and defect properties of nanostructured materials. In this Account, we review the advances that have been made in facilitating the recording of the required series of 2D electron microscopic images and the subsequent process of 3D reconstruction of specimens that are vulnerable, to a greater or lesser degree, to electron beam damage. We describe how high-fidelity 3D tomograms may be obtained from relatively few 2D images by incorporating prior structural knowledge into the reconstruction process. In particular, we highlight the vital role of compressed sensing, a recently developed procedure well-known to information theorists that exploits ideas of image compression and "sparsity" (that the important image information can be captured in a reduced data set). We also touch upon another promising approach, "discrete" tomography, which builds into the reconstruction process a prior assumption that the object can be described in discrete terms, such as the number of constituent materials and their expected densities. Other advances made recently that we outline, such as the availability of aberration-corrected electron microscopes, electron wavelength monochromators, and sophisticated specimen goniometers

Markov Random Field Based Automatic Image Alignment for ElectronTomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moussavi, Farshid; Amat, Fernando; Comolli, Luis R.

2007-11-30

Cryo electron tomography (cryo-ET) is the primary method for obtaining 3D reconstructions of intact bacteria, viruses, and complex molecular machines ([7],[2]). It first flash freezes a specimen in a thin layer of ice, and then rotates the ice sheet in a transmission electron microscope (TEM) recording images of different projections through the sample. The resulting images are aligned and then back projected to form the desired 3-D model. The typical resolution of biological electron microscope is on the order of 1 nm per pixel which means that small imprecision in the microscope's stage or lenses can cause large alignment errors.more » To enable a high precision alignment, biologists add a small number of spherical gold beads to the sample before it is frozen. These beads generate high contrast dots in the image that can be tracked across projections. Each gold bead can be seen as a marker with a fixed location in 3D, which provides the reference points to bring all the images to a common frame as in the classical structure from motion problem. A high accuracy alignment is critical to obtain a high resolution tomogram (usually on the order of 5-15nm resolution). While some methods try to automate the task of tracking markers and aligning the images ([8],[4]), they require user intervention if the SNR of the image becomes too low. Unfortunately, cryogenic electron tomography (or cryo-ET) often has poor SNR, since the samples are relatively thick (for TEM) and the restricted electron dose usually results in projections with SNR under 0 dB. This paper shows that formulating this problem as a most-likely estimation task yields an approach that is able to automatically align with high precision cryo-ET datasets using inference in graphical models. This approach has been packaged into a publicly available software called RAPTOR-Robust Alignment and Projection estimation for Tomographic Reconstruction.« less

3D Reconstruction of SPM Probes by Electron Tomography

NASA Astrophysics Data System (ADS)

Xu, X.; Peng, Y.; Saghi, Z.; Gay, R.; Inkson, B. J.; Möbus, G.

2007-04-01

Three-dimensional morphological and compositional structures of tungsten tips consisting of layered amorphous oxide shell and crystalline W core are reconstructed by electron tomography using both coherent and incoherent imaging modes. The fidelity of the reconstruction is dependent on three criteria, suppression of unwanted crystal orientation contrast in the crystalline core, nonlinear intensity-thickness relations above a certain thickness limit, and artefacts due to missing angular ranges when acquiring a tilt series of images. Annular dark field (ADF), and EDX chemical mapping are discussed as alternatives to standard bright field (BF) TEM imaging.

Preparation and Observation of Thick Biological Samples by Scanning Transmission Electron Tomography.

PubMed

Trépout, Sylvain; Bastin, Philippe; Marco, Sergio

2017-03-12

This report describes a protocol for preparing thick biological specimens for further observation using a scanning transmission electron microscope. It also describes an imaging method for studying the 3D structure of thick biological specimens by scanning transmission electron tomography. The sample preparation protocol is based on conventional methods in which the sample is fixed using chemical agents, treated with a heavy atom salt contrasting agent, dehydrated in a series of ethanol baths, and embedded in resin. The specific imaging conditions for observing thick samples by scanning transmission electron microscopy are then described. Sections of the sample are observed using a through-focus method involving the collection of several images at various focal planes. This enables the recovery of in-focus information at various heights throughout the sample. This particular collection pattern is performed at each tilt angle during tomography data collection. A single image is then generated, merging the in-focus information from all the different focal planes. A classic tilt-series dataset is then generated. The advantage of the method is that the tilt-series alignment and reconstruction can be performed using standard tools. The collection of through-focal images allows the reconstruction of a 3D volume that contains all of the structural details of the sample in focus.

Cryo-electron microscopy and cryo-electron tomography of nanoparticles.

PubMed

Stewart, Phoebe L

2017-03-01

Cryo-transmission electron microscopy (cryo-TEM or cryo-EM) and cryo-electron tomography (cryo-ET) offer robust and powerful ways to visualize nanoparticles. These techniques involve imaging of the sample in a frozen-hydrated state, allowing visualization of nanoparticles essentially as they exist in solution. Cryo-TEM grid preparation can be performed with the sample in aqueous solvents or in various organic and ionic solvents. Two-dimensional (2D) cryo-TEM provides a direct way to visualize the polydispersity within a nanoparticle preparation. Fourier transforms of cryo-TEM images can confirm the structural periodicity within a sample. While measurement of specimen parameters can be performed with 2D TEM images, determination of a three-dimensional (3D) structure often facilitates more spatially accurate quantization. 3D structures can be determined in one of two ways. If the nanoparticle has a homogeneous structure, then 2D projection images of different particles can be averaged using a computational process referred to as single particle reconstruction. Alternatively, if the nanoparticle has a heterogeneous structure, then a structure can be generated by cryo-ET. This involves collecting a tilt-series of 2D projection images for a defined region of the grid, which can be used to generate a 3D tomogram. Occasionally it is advantageous to calculate both a single particle reconstruction, to reveal the regular portions of a nanoparticle structure, and a cryo-electron tomogram, to reveal the irregular features. A sampling of 2D cryo-TEM images and 3D structures are presented for protein based, DNA based, lipid based, and polymer based nanoparticles. WIREs Nanomed Nanobiotechnol 2017, 9:e1417. doi: 10.1002/wnan.1417 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.

"No zone" approach in penetrating neck trauma reduces unnecessary computed tomography angiography and negative explorations.

PubMed

Ibraheem, Kareem; Khan, Muhammad; Rhee, Peter; Azim, Asad; O'Keeffe, Terence; Tang, Andrew; Kulvatunyou, Narong; Joseph, Bellal

2018-01-01

The most recent management guidelines advocate computed tomography angiography (CTA) for any suspected vascular or aero-digestive injuries in all zones and give zone II injuries special consideration. We hypothesized that physical examination can safely guide CTA use in a "no zone" approach. An 8-year retrospective analysis of all adult trauma patients with penetrating neck trauma (PNT) was performed. We included all patients in whom the platysma was violated. Patients were classified into three groups as follows: hard signs, soft signs, and asymptomatic. CTA use, positive CTA (contrast extravasation, dissection, or intimal flap) and operative details were reported. Primary outcomes were positive CTA and therapeutic neck exploration (TNE) (defined by repair of major vascular or aero-digestive injuries). A total of 337 patients with PNT met the inclusion criteria. Eighty-two patients had hard signs and all of them went to the operating room, of which 59 (72%) had TNE. One hundred fifty-six patients had soft signs, of which CTA was performed in 121 (78%), with positive findings in 12 (10%) patients. The remaining 35 (22%) underwent initial neck exploration, of which 14 (40%) were therapeutic yielding a high rate of negative exploration. Ninty-nine patients were asymptomatic, of which CTA was performed in 79 (80%), with positive findings in 3 (4%), however, none of these patients required TNE. On sub analysis based on symptoms, there was no difference in the rate of TNE between the neck zones in patients with hard signs (P = 0.23) or soft signs (P = 0.51). Regardless of the zone of injury, asymptomatic patients did not require a TNE. Physical examination regardless of the zone of injury should be the primary guide to CTA or TNE in patients with PNT. Following traditional zone-based guidelines can result in unnecessary negative explorations in patients with soft signs and may need rethinking. Copyright © 2017 Elsevier Inc. All rights reserved.

Transverse Phase Space Reconstruction and Emittance Measurement of Intense Electron Beams using a Tomography Technique

NASA Astrophysics Data System (ADS)

Stratakis, D.; Kishek, R. A.; Li, H.; Bernal, S.; Walter, M.; Tobin, J.; Quinn, B.; Reiser, M.; O'Shea, P. G.

2006-11-01

Tomography is the technique of reconstructing an image from its projections. It is widely used in the medical community to observe the interior of the human body by processing multiple x-ray images taken at different angles, A few pioneering researchers have adapted tomography to reconstruct detailed phase space maps of charged particle beams. Some questions arise regarding the limitations of tomography technique for space charge dominated beams. For instance is the linear space charge force a valid approximation? Does tomography equally reproduce phase space for complex, experimentally observed, initial particle distributions? Does tomography make any assumptions about the initial distribution? This study explores the use of accurate modeling with the particle-in-cell code WARP to address these questions, using a wide range of different initial distributions in the code. The study also includes a number of experimental results on tomographic phase space mapping performed on the University of Maryland Electron Ring (UMER).

Incorporating fault zone head wave and direct wave secondary arrival times into seismic tomography: Application at Parkfield, California

NASA Astrophysics Data System (ADS)

Bennington, N. L.; Thurber, C. H.; Zhang, H.; Peng, Z.; Zhao, P.

2011-12-01

Large crustal faults such as the San Andreas fault (SAF) often juxtapose rocks of significantly different elastic properties, resulting in well-defined bimaterial interfaces. A sharp material contrast across the fault interface is expected to generate fault zone head waves (FZHW's) that spend a large portion of their propagation paths refracting along the bimaterial interface (Ben-Zion 1989, 1990; Ben-Zion & Aki 1990). Because of this FZHW's provide a high-resolution tool for imaging the velocity contrast across the fault. Recently, Zhao et al. (2010) systematically analyzed large data sets of near-fault waveforms recorded by several permanent and temporary seismic networks along the Parkfield section of the SAF. The local-scale tomography study of Zhang et al. (2009) for a roughly 10 km3 volume centered on SAFOD and the more regional-scale study of Thurber et al. (2006) for a 130 km x 120 km x 20 km volume centered on the 2004 Parkfield earthquake rupture provide what are probably the best 3D images of the seismic velocity structure of the area. The former shows a low velocity zone associated with the SAF extending to significant depth, and both image the well-known velocity contrast across the fault. Seismic tomography generally uses just first P and/or S arrivals because of the relative simplicity of phase picking and ray tracing. Adding secondary arrivals such as FZHW's, however, can enhance the resolution of structure and strengthen constraints on earthquake locations and focal mechanisms. We present a model of 3D velocity structure for the Parkfield region that utilizes a combination of arrival times for FZHW's and the associated direct-wave secondary arrivals as well as existing P-wave arrival time data. The resulting image provides a higher-resolution model of the SAF at depth than previously published models. In addition, we plan to measure polarizations of the direct P and S waves and FZHW's and incorporate the data into our updated velocity tomography

In vivo examination of the cortical cytoskeleton in multiciliated cells using electron tomography.

PubMed

Clare, Daniel K; Dumoux, Maud; Delacour, Delphine

2015-01-01

Multiciliated cells are characterized by coordinated arrays of motile cilia. In the respiratory tract, the maintenance of this array is essential to ensure proper ciliary and mucus clearance. The establishment and the maintenance of the ciliary set are mediated by the correct positioning of basal bodies at the cell cortex. While microtubule and actin cytoskeletons have been reported to regulate basal body lattices, an understanding of their detailed organization was missing until recently. Here, we describe how electron tomography can highlight the arrangement of the cytoskeletal networks and their interplay with basal bodies in ciliated cells in their tissular environment. Thanks to this approach, information in fine detail on large parts of the cell, dense in organelles, is provided. In combination with other approaches, such as transgenic animal models, electron tomography constitutes a powerful technique giving an overview of tissues and cells concomitantly with acquisition of three-dimensional detail. Copyright © 2015 Elsevier Inc. All rights reserved.

Three-dimensional visualization of gammaherpesvirus life cycle in host cells by electron tomography.

PubMed

Peng, Li; Ryazantsev, Sergey; Sun, Ren; Zhou, Z Hong

2010-01-13

Gammaherpesviruses are etiologically associated with human tumors. A three-dimensional (3D) examination of their life cycle in the host is lacking, significantly limiting our understanding of the structural and molecular basis of virus-host interactions. Here, we report the first 3D visualization of key stages of the murine gammaherpesvirus 68 life cycle in NIH 3T3 cells, including viral attachment, entry, assembly, and egress, by dual-axis electron tomography. In particular, we revealed the transient processes of incoming capsids injecting viral DNA through nuclear pore complexes and nascent DNA being packaged into progeny capsids in vivo as a spool coaxial with the putative portal vertex. We discovered that intranuclear invagination of both nuclear membranes is involved in nuclear egress of herpesvirus capsids. Taken together, our results provide the structural basis for a detailed mechanistic description of gammaherpesvirus life cycle and also demonstrate the advantage of electron tomography in dissecting complex cellular processes of viral infection.

The Hidden Dynamics of Relativistic Electrons (0.7-1.5 MeV) in the Inner Zone and Slot Region

NASA Astrophysics Data System (ADS)

Claudepierre, S. G.; O'Brien, T. P., III; Blake, J. B.; Fennell, J. F.; Looper, M. D.; Roeder, J. L.; Clemmons, J. H.; Mazur, J. E.; Turner, D. L.; Reeves, G. D.; Spence, H. E.

2016-12-01

We present Van Allen Probes ECT/MagEIS observations of relativistic electrons (0.7-1.5 MeV) in the inner zone and slot region. We describe several approaches that are used to remove background contamination from the measurements, which in these regions is primarily due to very energetic inner zone protons. This careful analysis reveals that electrons with energies in excess of 1 MeV penetrated the slot region and into the inner zone following both the March and June 2015 geomagnetic storms. We also present evidence that electrons of these energies were present in the inner radiation belt region during earlier times in the Van Allen Probes era (e.g., in 2013). For both the March and June 2015 events, we examine pitch-angle distributions that shed light on the relevant physical processes responsible for the growth and decay of such relativistic electron enhancements in the inner zone and slot. We briefly discuss initial attempts to place an upper limit on the MeV electron flux intensity in the inner zone.

Preparation of cryofixed cells for improved 3D ultrastructure with scanning transmission electron tomography.

PubMed

Höhn, Katharina; Sailer, Michaela; Wang, Li; Lorenz, Myriam; Schneider, Marion E; Walther, Paul

2011-01-01

Scanning transmission electron tomography offers enhanced contrast compared to regular transmission electron microscopy, and thicker samples, up to 1 μm or more, can be analyzed, since the depth of focus and inelastic scattering are not limitations. In this study, we combine this novel imaging approach with state of the art specimen preparation by using novel light transparent sapphire specimen carrier for high-pressure freezing and a freeze substitution protocol for better contrast of membranes. This combination allows for imaging membranes and other subcellular structures with unsurpassed quality. This is demonstrated with mitochondria, where the inner and outer mitochondrial membranes as well as the membranes in the cristae appear in very close apposition with a minimal intermembrane space. These findings correspond well with old observations using freeze fracturing. In 880-nm thick sections of hemophagocytes, the three-dimensional structure of membrane sheets could be observed in the virtual sections of the tomogram. Microtubules, actin and intermediate filaments could be visualized within one sample. Intermediate filaments, however, could even be better observed in 3D using surface scanning electron tomography.

The hidden dynamics of relativistic electrons (0.7-1.5 MeV) in the inner zone and slot region

DOE Office of Scientific and Technical Information (OSTI.GOV)

Claudepierre, Seth G.; O'Brien, T. P.; Fennell, J. F.

We present measurements of relativistic electrons (0.7–1.5 MeV) in the inner zone and slot region obtained by the Magnetic Electron and Ion Spectrometer (MagEIS) instrument on Van Allen Probes. The data presented are corrected for background contamination, which is primarily due to inner-belt protons in these low-L regions. We find that ~1 MeV electrons were transported into the inner zone following the two largest geomagnetic storms of the Van Allen Probes era to date, the March and June 2015 events. As ~1 MeV electrons were not observed in Van Allen Probes data in the inner zone prior to these twomore » events, the injections created a new inner belt that persisted for at least 1.5 years. In contrast, we find that electrons injected into the slot region decay on much faster timescales, approximately tens of days. Furthermore, we find no evidence of >1.5 MeV electrons in the inner zone during the entire time interval considered (April 2013 through September 2016). The energies we examine thus span a transition range in the steeply falling inner zone electron spectrum, where modest intensities are observed at 0.7 MeV, and no electrons are observed at 1.5 MeV. To validate the results obtained from the background corrected flux measurements, we also present detailed pulse-height spectra from individual MagEIS detectors. These measurements confirm our results and also reveal low-intensity inner zone and slot region electrons that are not captured in the standard background corrected data product. Lastly, we briefly discuss efforts to refine the upper limit of inner zone MeV electron flux obtained in earlier work.« less

The hidden dynamics of relativistic electrons (0.7-1.5 MeV) in the inner zone and slot region

DOE PAGES

Claudepierre, Seth G.; O'Brien, T. P.; Fennell, J. F.; ...

2017-03-15

We present measurements of relativistic electrons (0.7–1.5 MeV) in the inner zone and slot region obtained by the Magnetic Electron and Ion Spectrometer (MagEIS) instrument on Van Allen Probes. The data presented are corrected for background contamination, which is primarily due to inner-belt protons in these low-L regions. We find that ~1 MeV electrons were transported into the inner zone following the two largest geomagnetic storms of the Van Allen Probes era to date, the March and June 2015 events. As ~1 MeV electrons were not observed in Van Allen Probes data in the inner zone prior to these twomore » events, the injections created a new inner belt that persisted for at least 1.5 years. In contrast, we find that electrons injected into the slot region decay on much faster timescales, approximately tens of days. Furthermore, we find no evidence of >1.5 MeV electrons in the inner zone during the entire time interval considered (April 2013 through September 2016). The energies we examine thus span a transition range in the steeply falling inner zone electron spectrum, where modest intensities are observed at 0.7 MeV, and no electrons are observed at 1.5 MeV. To validate the results obtained from the background corrected flux measurements, we also present detailed pulse-height spectra from individual MagEIS detectors. These measurements confirm our results and also reveal low-intensity inner zone and slot region electrons that are not captured in the standard background corrected data product. Lastly, we briefly discuss efforts to refine the upper limit of inner zone MeV electron flux obtained in earlier work.« less

Gas pressure and electron density at the level of the active zone of hollow cathode arc discharges

NASA Technical Reports Server (NTRS)

Minoo, M. H.

1984-01-01

A model for the longitudinal variations of the partial pressures of electrons, ions, and neutral particles is proposed as a result of an experimental study of pressure variations at the level of the active zone as a function of the various discharge parameters of a hollow cathode arc. The cathode region where the temperature passes through its maximum is called active zone. The proposed model embodies the very important variations which the partial electron and neutral particles pressures undergo at the level of the active zone.

Evaluating four-dimensional time-lapse electrical resistivity tomography for monitoring DNAPL source zone remediation.

PubMed

Power, Christopher; Gerhard, Jason I; Karaoulis, Marios; Tsourlos, Panagiotis; Giannopoulos, Antonios

2014-07-01

Practical, non-invasive tools do not currently exist for mapping the remediation of dense non-aqueous phase liquids (DNAPLs). Electrical resistivity tomography (ERT) exhibits significant potential but has not yet become a practitioner's tool due to challenges in interpreting the survey results at real sites. This study explores the effectiveness of recently developed four-dimensional (4D, i.e., 3D space plus time) time-lapse surface ERT to monitor DNAPL source zone remediation. A laboratory experiment demonstrated the approach for mapping a changing NAPL distribution over time. A recently developed DNAPL-ERT numerical model was then employed to independently simulate the experiment, providing confidence that the DNAPL-ERT model is a reliable tool for simulating real systems. The numerical model was then used to evaluate the potential for this approach at the field scale. Four DNAPL source zones, exhibiting a range of complexity, were initially simulated, followed by modeled time-lapse ERT monitoring of complete DNAPL remediation by enhanced dissolution. 4D ERT inversion provided estimates of the regions of the source zone experiencing mass reduction with time. Results show that 4D time-lapse ERT has significant potential to map both the outline and the center of mass of the evolving treated portion of the source zone to within a few meters in each direction. In addition, the technique can provide a reasonable, albeit conservative, estimate of the DNAPL volume remediated with time: 25% underestimation in the upper 2m and up to 50% underestimation at late time between 2 and 4m depth. The technique is less reliable for identifying cleanup of DNAPL stringers outside the main DNAPL body. Overall, this study demonstrates that 4D time-lapse ERT has potential for mapping where and how quickly DNAPL mass changes in real time during site remediation. Copyright © 2014 Elsevier B.V. All rights reserved.

Fully Mechanically Controlled Automated Electron Microscopic Tomography

DOE PAGES

Liu, Jinxin; Li, Hongchang; Zhang, Lei; ...

2016-07-11

Knowledge of three-dimensional (3D) structures of each individual particles of asymmetric and flexible proteins is essential in understanding those proteins' functions; but their structures are difficult to determine. Electron tomography (ET) provides a tool for imaging a single and unique biological object from a series of tilted angles, but it is challenging to image a single protein for three-dimensional (3D) reconstruction due to the imperfect mechanical control capability of the specimen goniometer under both a medium to high magnification (approximately 50,000-160,000×) and an optimized beam coherence condition. Here, we report a fully mechanical control method for automating ET data acquisitionmore » without using beam tilt/shift processes. This method could reduce the accumulation of beam tilt/shift that used to compensate the error from the mechanical control, but downgraded the beam coherence. Our method was developed by minimizing the error of the target object center during the tilting process through a closed-loop proportional-integral (PI) control algorithm. The validations by both negative staining (NS) and cryo-electron microscopy (cryo-EM) suggest that this method has a comparable capability to other ET methods in tracking target proteins while maintaining optimized beam coherence conditions for imaging.« less

3D Observation of GEMS by Electron Tomography

NASA Technical Reports Server (NTRS)

Matsuno, Junya; Miyake, Akira; Tsuchiyama, Akira; Nakamura-Messenger, Keiko; Messenger, Scott

2014-01-01

Amorphous silicates in chondritic porous interplanetary dust particles (CP-IDPs) coming from comets are dominated by glass with embedded metal and sulfides (GEMS). GEMS grains are submicron-sized rounded objects (typically 100-500) nm in diameter) with anaometer-sized (10-50 nm) Fe-Ni metal and sulfide grains embedded in an amorphous silicate matrix. Several formation processes for GEMS grains have been proposed so far, but these models are still being debated [2-5]. Bradley et al. proposed that GEMS grains are interstellar silicate dust that survived various metamorphism or alteration processes in the protoplanetary disk and that they are amorphiation products of crystalline silicates in the interstellar medium by sputter-deposition of cosmic ray irradiation, similar to space weathering [2,4]. This consideration is based on the observation of nano-sized crystals (approximately 10 nm) called relict grains in GEMS grains and their shapes are pseudomorphs to the host GEMS grains. On the other hand, Keller and Messenger proposed that most GEMS formed in the protoplanetary disk as condensates from high temperature gas [3,5]. This model is based on the fact that most GEMS grains have solar isotopic compositions and have extremely heterogeneous and non-solar elemental compositions. Keller and Messenger (2011) also reported that amorphous silicates in GEMS grains are surrounded by sulfide grains, which formed as sulfidization of metallic iron grains located on the GEMS surface. The previous studies were performed with 2D observation by using transmission electron microscopy (TEM) or scanning TEM (STEM). In order to understand the structure of GEMS grains described above more clearly, we observed 3D structure of GEMS grains by electron tomography using a TEM/STEM (JEM-2100F, JEOL) at Kyoto University. Electron tomography gives not only 3D structures but also gives higher spatial resolution (approximately a few nm) than that in conventional 2D image, which is restricted by

Electronic resistance tomography imaging of spatial moisture distribution, moisture distribution and movement in pavements

DOT National Transportation Integrated Search

1997-07-01

Electronic resistance tomography (ERT) was used to follow the infiltration of water into a pavement section at the UC Berkeley Richmond Field Station. A volume of pavement 1 m square and 1.29 m in depth was sampled by an ERT array consisting of elect...

Analytical electron tomography mapping of the SiCporeoxidation at the nanoscale

NASA Astrophysics Data System (ADS)

Florea, Ileana; Ersen, Ovidiu; Hirlimann, Charles; Roiban, Lucian; Deneuve, Adrien; Houllé, Matthieu; Janowska, Izabela; Nguyen, Patrick; Pham, Charlotte; Pham-Huu, Cuong

2010-12-01

Silicon carbide is a ceramic material that has been widely studied because of its potential applications, ranging from electronics to heterogeneous catalysis. Recently, a new type of SiC materials with a medium specific surface area and thermal conductivity, called β-SiC, has attracted overgrowing interest as a new class of catalyst support in several catalytic reactions. A primary electron tomography study, performed in usual mode, has revealed a dual surface structure defined by two types of porosities made of networks of connected channels with sizes larger than 50 nm and ink-bottled pores with sizes spanning from 4 to 50 nm. Depending on the solvent nature, metal nanoparticles could be selectively deposited inside one of the two porosities, a fact that illustrates a selective wetting titration of the two types of surfaces by different liquids. The explaining hypothesis that has been put forward was that this selectivity against solvents is related to the pore surface oxidation degree of the two types of pores. A new technique of analytical electron tomography, where the series of projections used to reconstruct the volume of an object is recorded in energy filtered mode (EFTEM), has been implemented to map the poreoxidation state and to correlate it with the morphology and the accessibility of the porous network. Applied, for the first time, at a nanoscale resolution, this technique allowed us to obtain 3D elemental maps of different elements present in the analysed porous grains, in particular oxygen; we found thus that the interconnected channelpores are more rapidly oxidized than the ink-bottled ones. Alternatively, our study highlights the great interest of this method that opens the way for obtaining precise information on the chemical composition of a 3D surface at a nanometer scale.Silicon carbide is a ceramic material that has been widely studied because of its potential applications, ranging from electronics to heterogeneous catalysis. Recently, a new

Localized heating of electrons in ionization zones: Going beyond the Penning-Thornton paradigm in magnetron sputtering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anders, Andre

2014-12-07

The fundamental question of how energy is supplied to a magnetron discharge is commonly answered by the Penning-Thornton paradigm invoking secondary electrons. Huo et al. (Plasma Sources Sci. Technol. 22, 045005, (2013)) used a global discharge model to show that electron heating in the electric field of the magnetic presheath is dominant. In this contribution, this concept is applied locally taking into account the electric potential structure of ionization zones. Images of ionization zones can and should be interpreted as diagrams of the localization of electric potential and related electron energy, where certain collisions promote or dampen their formation.

Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research

DOE PAGES

Ercius, Peter; Alaidi, Osama; Rames, Matthew J.; ...

2015-06-18

Three-dimensional (3D) structural analysis is essential to understand the relationship between the structure and function of an object. Many analytical techniques, such as X-ray diffraction, neutron spectroscopy, and electron microscopy imaging, are used to provide structural information. Transmission electron microscopy (TEM), one of the most popular analytic tools, has been widely used for structural analysis in both physical and biological sciences for many decades, in which 3D objects are projected into two-dimensional (2D) images. In many cases, 2D-projection images are insufficient to understand the relationship between the 3D structure and the function of nanoscale objects. Electron tomography (ET) is amore » technique that retrieves 3D structural information from a tilt series of 2D projections, and is gradually becoming a mature technology with sub-nanometer resolution. Distinct methods to overcome sample-based limitations have been separately developed in both physical and biological science, although they share some basic concepts of ET. Here, this review discusses the common basis for 3D characterization, and specifies difficulties and solutions regarding both hard and soft materials research. It is hoped that novel solutions based on current state-of-the-art techniques for advanced applications in hybrid matter systems can be motivated. Electron tomography produces quantitative 3D reconstructions for biological and physical sciences from sets of 2D projections acquired at different tilting angles in a transmission electron microscope. Finally, state-of-the-art techniques capable of producing 3D representations such as Pt-Pd core-shell nanoparticles and IgG1 antibody molecules are reviewed.« less

Adaptively Parameterized Tomography of the Western Hellenic Subduction Zone

NASA Astrophysics Data System (ADS)

Hansen, S. E.; Papadopoulos, G. A.

2017-12-01

The Hellenic subduction zone (HSZ) is the most seismically active region in Europe and plays a major role in the active tectonics of the eastern Mediterranean. This complicated environment has the potential to generate both large magnitude (M > 8) earthquakes and tsunamis. Situated above the western end of the HSZ, Greece faces a high risk from these geologic hazards, and characterizing this risk requires detailed understanding of the geodynamic processes occurring in this area. However, despite previous investigations, the kinematics of the HSZ are still controversial. Regional tomographic studies have yielded important information about the shallow seismic structure of the HSZ, but these models only image down to 150 km depth within small geographic areas. Deeper structure is constrained by global tomographic models but with coarser resolution ( 200-300 km). Additionally, current tomographic models focused on the HSZ were generated with regularly-spaced gridding, and this type of parameterization often over-emphasizes poorly sampled regions of the model or under-represents small-scale structure. Therefore, we are developing a new, high-resolution image of the mantle structure beneath the western HSZ using an adaptively parameterized seismic tomography approach. By combining multiple, regional travel-time datasets in the context of a global model, with adaptable gridding based on the sampling density of high-frequency data, this method generates a composite model of mantle structure that is being used to better characterize geodynamic processes within the HSZ, thereby allowing for improved hazard assessment. Preliminary results will be shown.

Bright-field electron tomography of individual inorganic fullerene-like structures

NASA Astrophysics Data System (ADS)

Bar Sadan, Maya; Wolf, Sharon G.; Houben, Lothar

2010-03-01

Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS2 or MoS2 fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties.Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS2 or MoS2 fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The

3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography

PubMed Central

Nicastro, Daniela; McIntosh, J. Richard; Baumeister, Wolfgang

2005-01-01

We have used cryo-electron tomography to investigate the 3D structure and macromolecular organization of intact, frozen-hydrated sea urchin sperm flagella in a quiescent state. The tomographic reconstructions provide information at a resolution better than 6 nm about the in situ arrangements of macromolecules that are key for flagellar motility. We have visualized the heptameric rings of the motor domains in the outer dynein arm complex and determined that they lie parallel to the plane that contains the axes of neighboring flagellar microtubules. Both the material associated with the central pair of microtubules and the radial spokes display a plane of symmetry that helps to explain the planar beat pattern of these flagella. Cryo-electron tomography has proven to be a powerful technique for helping us understand the relationships between flagellar structure and function and the design of macromolecular machines in situ. PMID:16246999

Tomography of the upper mantle beneath the African/Iberian collision zone

NASA Astrophysics Data System (ADS)

Mickael, B.; Nolet, G.; Villasenor, A.; Josep, G.; Thomas, C.

2013-12-01

During Cenozoic, geodynamics of the western Mediterranean domain has been characterized by a complex history of subduction of Mesozoic oceanic lithosphere. The final stage of these processes is proposed to have led to the development of the Calabria and Gibraltar arcs, whose formation is still under debate. In this study we take advantage of the dense broadband-station networks now available in Alborán Sea region, to develop a high-resolution 3D tomographic P velocity model of the upper mantle beneath the African/Iberian collision zone that will bring new constraints on the past dynamics of this zone. The model is based on 13200 teleseismic arrival times recorded between 2008 and 2012 at 279 stations for which cross-correlation delays are measured with a new technique in different frequency bands centered between 0.03 and 1.0 Hz, and interpreted using multiple frequency tomography. Our model shows, beneath Alborán Sea, a strong (~ 4%) fast vertically dipping anomaly observed to at least 650 km depth. The arched shape of this anomaly and its extent at depth are coherent with a lithospheric slab, thus favoring the hypothesis of a westward consumption of the Ligurian ocean slab by roll-back during Cenozoic. In addition to this fast anomaly in the deep upper-mantle, several high intensity slow anomalies are widely observed in the lithosphere and asthenosphere beneath Morocco and southern Spain. These anomalies are correlated at surface with the position of the orogens (Rif and Atlas) and with Cenozoic volcanic fields. We thus confirm the presence, beneath Morocco, of an anomalous (hot) upper mantle, with piece of evidence for a lateral connection with the Canary volcanic islands, likely indicating a lateral spreading of the Canary plume to the east.

Seismicity, Deformation, and Metamorphism in the Western Hellenic Subduction Zone: New Constraints From Tomography

NASA Astrophysics Data System (ADS)

Halpaap, Felix; Rondenay, Stéphane; Ottemöller, Lars

2018-04-01

The Western Hellenic Subduction Zone is characterized by a transition from oceanic to continental subduction. In the southern oceanic portion of the system, abundant seismicity reaches depths of 100 km to 190 km, while the northern continental portion rarely exhibits deep earthquakes. Our study investigates how this oceanic-continental transition affects fluid release and related seismicity along strike. We present results from local earthquake tomography and double-difference relocation in conjunction with published images based on scattered teleseismic waves. Our tomographic images recover both subducting oceanic and continental crusts as low-velocity layers on top of high-velocity mantle. Although the northern and southern trenches are offset along the Kephalonia Transform Fault, continental and oceanic subducting crusts appear to align at depth. This suggests a smooth transition between slab retreat in the south and slab convergence in the north. Relocated hypocenters outline a single-planed Wadati-Benioff Zone with significant along-strike variability in the south. Seismicity terminates abruptly north of the Kephalonia Transform Fault, likely reflecting the transition from oceanic to continental subducted crust. Near 90 km depth, the low-velocity signature of the subducting crust fades out and the Wadati-Benioff Zone thins and steepens, marking the outline of the basalt-eclogite transition. Subarc melting of the mantle is only observed in the southernmost sector of the oceanic subduction, below the volcanic part of the arc. Beneath the nonvolcanic part, the overriding crust appears to have undergone large-scale silica enrichment. This enrichment is observed as an anomalously low Vp/Vs ratio and requires massive transport of dehydration-derived fluids updip through the subducting crust.

Axial length variation impacts on retinal vessel density and foveal avascular zone area measurement using optical coherence tomography angiography

NASA Astrophysics Data System (ADS)

Sampson, Danuta M.; Gong, Peijun; An, Di; Menghini, Moreno; Hansen, Alex; Mackey, David A.; Sampson, David D.; Chen, Fred K.

2017-04-01

We examined the impact of axial length on superficial retinal vessel density (SRVD) and foveal avascular zone area (FAZA) measurement using optical coherence tomography angiography. The SRVD and FAZA were quantified before and after correction for magnification error associated with axial length variation. Although SRVD did not differ before and after correction for magnification error in the parafoveal region, change in foveal SRVD and FAZA were significant. This has implications for clinical trials outcome in diseased eyes where significant capillary dropout may occur in the parafovea.

Toward atomic-scale bright-field electron tomography for the study of fullerene-like nanostructures.

PubMed

Bar Sadan, Maya; Houben, Lothar; Wolf, Sharon G; Enyashin, Andrey; Seifert, Gotthard; Tenne, Reshef; Urban, Knut

2008-03-01

We present the advancement of electron tomography for three-dimensional structure reconstruction of fullerene-like particles toward atomic-scale resolution. The three-dimensional reconstruction of nested molybdenum disulfide nanooctahedra is achieved by the combination of low voltage operation of the electron microscope with aberration-corrected phase contrast imaging. The method enables the study of defects and irregularities in the three-dimensional structure of individual fullerene-like particles on the scale of 2-3 A. Control over shape, size, and atomic architecture is a key issue in synthesis and design of functional nanoparticles. Transmission electron microscopy (TEM) is the primary technique to characterize materials down to the atomic level, albeit the images are two-dimensional projections of the studied objects. Recent advancements in aberration-corrected TEM have demonstrated single atom sensitivity for light elements at subångström resolution. Yet, the resolution of tomographic schemes for three-dimensional structure reconstruction has not surpassed 1 nm3, preventing it from becoming a powerful tool for characterization in the physical sciences on the atomic scale. Here we demonstrate that negative spherical aberration imaging at low acceleration voltage enables tomography down to the atomic scale at reduced radiation damage. First experimental data on the three-dimensional reconstruction of nested molybdenum disulfide nanooctahedra is presented. The method is applicable to the analysis of the atomic architecture of a wide range of nanostructures where strong electron channeling is absent, in particular to carbon fullerenes and inorganic fullerenes.

Zernike Phase Contrast Electron Cryo-Tomography Applied to Marine Cyanobacteria Infected with Cyanophages

PubMed Central

Dai, Wei; Fu, Caroline; Khant, Htet A.; Ludtke, Steven J.; Schmid, Michael F.; Chiu, Wah

2015-01-01

Advances in electron cryo-tomography have provided a new opportunity to visualize the internal 3D structures of a bacterium. An electron microscope equipped with Zernike phase contrast optics produces images with dramatically increased contrast compared to images obtained by conventional electron microscopy. Here we describe a protocol to apply Zernike phase plate technology for acquiring electron tomographic tilt series of cyanophage-infected cyanobacterial cells embedded in ice, without staining or chemical fixation. We detail the procedures for aligning and assessing phase plates for data collection, and methods to obtain 3D structures of cyanophage assembly intermediates in the host, by subtomogram alignment, classification and averaging. Acquiring three to four tomographic tilt series takes approximately 12 h on a JEM2200FS electron microscope. We expect this time requirement to decrease substantially as the technique matures. Time required for annotation and subtomogram averaging varies widely depending on the project goals and data volume. PMID:25321408

Accelerating electron tomography reconstruction algorithm ICON with GPU.

PubMed

Chen, Yu; Wang, Zihao; Zhang, Jingrong; Li, Lun; Wan, Xiaohua; Sun, Fei; Zhang, Fa

2017-01-01

Electron tomography (ET) plays an important role in studying in situ cell ultrastructure in three-dimensional space. Due to limited tilt angles, ET reconstruction always suffers from the "missing wedge" problem. With a validation procedure, iterative compressed-sensing optimized NUFFT reconstruction (ICON) demonstrates its power in the restoration of validated missing information for low SNR biological ET dataset. However, the huge computational demand has become a major problem for the application of ICON. In this work, we analyzed the framework of ICON and classified the operations of major steps of ICON reconstruction into three types. Accordingly, we designed parallel strategies and implemented them on graphics processing units (GPU) to generate a parallel program ICON-GPU. With high accuracy, ICON-GPU has a great acceleration compared to its CPU version, up to 83.7×, greatly relieving ICON's dependence on computing resource.

Vectorization with SIMD extensions speeds up reconstruction in electron tomography.

PubMed

Agulleiro, J I; Garzón, E M; García, I; Fernández, J J

2010-06-01

Electron tomography allows structural studies of cellular structures at molecular detail. Large 3D reconstructions are needed to meet the resolution requirements. The processing time to compute these large volumes may be considerable and so, high performance computing techniques have been used traditionally. This work presents a vector approach to tomographic reconstruction that relies on the exploitation of the SIMD extensions available in modern processors in combination to other single processor optimization techniques. This approach succeeds in producing full resolution tomograms with an important reduction in processing time, as evaluated with the most common reconstruction algorithms, namely WBP and SIRT. The main advantage stems from the fact that this approach is to be run on standard computers without the need of specialized hardware, which facilitates the development, use and management of programs. Future trends in processor design open excellent opportunities for vector processing with processor's SIMD extensions in the field of 3D electron microscopy.

Imaging Subsurface Structure of Central Zagros Zone/Iran Using Ambient Noise Tomography

NASA Astrophysics Data System (ADS)

Vahidravesh, Shaghayegh; Pakzad, Mehrdad, ,, Dr.; Hatami, Mohammad Reza, ,, Dr.

2017-04-01

The Central Zagros zone, of west Iran & east Iraq, is surrounded by many active faults (including Main Zagros Reversed Fault, Main Recent Fault, High Zagros Fault, Zagros Fold, & Thrust Belt). Recent studies show that cross-correlation of a long-term ambient seismic noise data recorded in station-pair, includes important information regarding empirical Green's functions (EGFs) between stations. Hence, ambient seismic noise carries valuable information of the wave propagation path (which can be extracted). The 2D model of surface waves (Rayleigh & Love) velocities for the studied area is obtained by seismic ambient noise tomography (ANT) method. Throughout this research, we use continuous records of all three vertical, radial, and tangential components (obtained by rotation) recorded by IRSC (Iranian Seismological Center) and IIEES (International Institute of Earthquake Engineering) networks for this area of interest. The IRSC & IIEES networks are equipped by SS-1 kinematics and Guralp CMG-3T sensors respectively. Data of 20 stations were used for 12 months from 2014/Nov. to 2015/Nov. The performed data processing is similar to the one, put into words in detail by Bensen et al. (2007) including the processed daily base data. Mean, trend, and instrument response were removed and the data were decimated to 5 sps (sample per second) to reduce the amount of storage space and computational time required. We then applied merge to handle data gaps. One-bit time-domain normalization was also applied to suppress the influence of instrument irregularities and earthquake signals followed by spectral (frequency-domain) normalization between 0.05-0.2 Hz (period 5-20 sec). After cross-correlation (processing step), we perform rms stacking (new approach of stacking) to stack many cross-correlation functions based on the highest energy in a time interval which we accordingly anticipate to receive Rayleigh & Love waves fundamental modes. To evaluate quality of the stacking process

The quantitative measurements of foveal avascular zone using optical coherence tomography angiography in normal volunteers.

PubMed

Ghassemi, Fariba; Mirshahi, Reza; Bazvand, Fatemeh; Fadakar, Kaveh; Faghihi, Houshang; Sabour, Siamak

2017-12-01

To provide normative data of foveal avascular zone (FAZ) and thickness. In this cross-sectional study both eyes of each normal subject were scanned with optical coherence tomography angiography (OCTA) for foveal superficial and deep avascular zone (FAZ) and central foveal thickness (CFT) and parafoveal thickness (PFT). Out of a total of 224 eyes of 112 volunteers with a mean age of 37.03 (12-67) years, the mean superficial FAZ area was 0.27 mm 2 , and deep FAZ area was 0.35 mm 2 ( P  < 0.001), with no difference between both eyes. Females had a larger superficial (0.32 ± 0.11 mm 2 versus 0.23 ± 0.09 mm 2 ) and deep FAZ (0.40 ± 0.14 mm 2 versus 0.31 ± 0.10 mm 2 ) ( P  < 0.001) than males. By multivariate linear regression analysis, in normal eyes, superficial FAZ area varied significantly with the gender, CFT, and deep FAZ. Deep FAZ varied with the gender and CFT. The gender and CFT influence the size of normal superficial and deep FAZ of capillary network.

Cryo-Electron Tomography for Structural Characterization of Macromolecular Complexes

PubMed Central

Cope, Julia; Heumann, John; Hoenger, Andreas

2011-01-01

Cryo-electron tomography (cryo-ET) is an emerging 3-D reconstruction technology that combines the principles of tomographic 3-D reconstruction with the unmatched structural preservation of biological material embedded in vitreous ice. Cryo-ET is particularly suited to investigating cell-biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging-based 3-D reconstruction procedures. This unit aims to make cryo-ET accessible to newcomers and discusses the specialized equipment required, as well as the relevant advantages and hurdles associated with sample preparation by vitrification and cryo-ET. Protocols describe specimen preparation, data recording and 3-D data reconstruction for cryo-ET, with a special focus on macromolecular complexes. A step-by-step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt-series acquisition for cryo-ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo-tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal-to-noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions. PMID:21842467

Ultrastructure Features and Three-Dimensional Transmission Electron Tomography of Dhub Lizard (Uromastyx Aegyptia) Cornea and Its Adaptation to a Desert Environment.

PubMed

Akhtar, Saeed; Alkhalaf, Mousa; Khan, Adnan A; Almubrad, Turki M

2016-08-01

We report ultrastructural features and transmission electron tomography of the dhub lizard (Uromastyx aegyptia) cornea and its adaptation to hot and dry environments. Six corneas of dhub lizards were fixed in 2.5% glutaraldehyde and processed for electron microscopy and tomography. The ultrathin sections were observed with a JEOL 1400 transmission electron microscope. The cornea of the dhub lizard is very thin (~28-30 µm). The epithelium constitutes ~14% of the cornea, whereas the stroma constitutes 80% of the cornea. The middle stromal lamellae are significantly thicker than anterior and posterior stromal lamellae. Collagen fibril (CF) diameters in the anterior stroma are variable in size (25-75 nm). Proteoglycans (PGs) are very large in the middle and posterior stroma, whereas they are small in the anterior stroma. Three-dimensional electron tomography was carried out to understand the structure and arrangement of the PG and CFs. The presence of large PGs in the posterior and middle stroma might help the animal retain a large amount of water to protect it from dryness. The dhub corneal structure is equipped to adapt to the dry and hot desert environment.

Improved predictions of saturated and unsaturated zone drawdowns in a heterogeneous unconfined aquifer via transient hydraulic tomography: Laboratory sandbox experiments

NASA Astrophysics Data System (ADS)

Berg, Steven J.; Illman, Walter A.

2012-11-01

SummaryInterpretation of pumping tests in unconfined aquifers has largely been based on analytical solutions that disregard aquifer heterogeneity. In this study, we investigate whether the prediction of drawdown responses in a heterogeneous unconfined aquifer and the unsaturated zone above it with a variably saturated groundwater flow model can be improved by including information on hydraulic conductivity (K) and specific storage (Ss) from transient hydraulic tomography (THT). We also investigate whether these predictions are affected by the use of unsaturated flow parameters estimated through laboratory hanging column experiments or calibration of in situ drainage curves. To investigate these issues, we designed and conducted laboratory sandbox experiments to characterize the saturated and unsaturated properties of a heterogeneous unconfined aquifer. Specifically, we conducted pumping tests under fully saturated conditions and interpreted the drawdown responses by treating the medium to be either homogeneous or heterogeneous. We then conducted another pumping test and allowed the water table to drop, similar to a pumping test in an unconfined aquifer. Simulations conducted using a variably saturated flow model revealed: (1) homogeneous parameters in the saturated and unsaturated zones have a difficult time predicting the responses of the heterogeneous unconfined aquifer; (2) heterogeneous saturated hydraulic parameter distributions obtained via THT yielded significantly improved drawdown predictions in the saturated zone of the unconfined aquifer; and (3) considering heterogeneity of unsaturated zone parameters produced a minor improvement in predictions in the unsaturated zone, but not the saturated zone. These results seem to support the finding by Mao et al. (2011) that spatial variability in the unsaturated zone plays a minor role in the formation of the S-shape drawdown-time curve observed during pumping in an unconfined aquifer.

The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards

PubMed Central

Briegel, Ariane; Pilhofer, Martin; Mastronarde, David N.; Jensen, Grant J.

2013-01-01

The apparent handedness of an EM-tomography reconstruction depends on a number of conventions and can be confused in many ways. As the number of different hardware and software combinations being used for electron tomography continue to climb, and the reconstructions being produced reach higher and higher resolutions, the need to verify the hand of the results has increased. Here we enumerate various steps in a typical tomography experiment that affect handedness and show that DNA origami gold nanoparticle helices can be used as convenient and fail-safe handedness standards. PMID:23639902

A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law.

PubMed

Yan, Rui; Edwards, Thomas J; Pankratz, Logan M; Kuhn, Richard J; Lanman, Jason K; Liu, Jun; Jiang, Wen

2015-11-01

In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. Copyright © 2015 Elsevier Inc. All rights reserved.

A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law

PubMed Central

Yan, Rui; Edwards, Thomas J.; Pankratz, Logan M.; Kuhn, Richard J.; Lanman, Jason K.; Liu, Jun; Jiang, Wen

2015-01-01

In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. PMID:26455556

Hardening mechanisms in olivine single crystal deformed at 1090 °C: an electron tomography study

NASA Astrophysics Data System (ADS)

Mussi, Alexandre; Cordier, Patrick; Demouchy, Sylvie; Hue, Benoit

2017-11-01

The dislocation microstructures in a single crystal of olivine deformed experimentally in uniaxial compression at 1090 °C and under a confining pressure of 300 MPa, have been investigated by transmission electron tomography in order to better understand deformation mechanisms at the microscale relevant for lithospheric mantle deformations. Investigation by electron tomography reveals microstructures, which are more complex than previously described, composed of ? and ? dislocations commonly exhibiting 3D configurations. Numerous mechanisms such as climb, cross-slip, double cross-slip as well as interactions like junction formations and collinear annihilations are the source of this complexity. The diversity observed advocates for microscale deformation of olivine significantly less simple than classic dislocation creep reported in metals or ice close to melting temperature. Deciphering mechanism of hardening in olivine at temperatures where ionic diffusion is slow and is then expected to play very little role is crucial to better understand and thus model deformation at larger scale and at temperatures (900-1100 °C) highly relevant for the lithospheric mantle.

'Big Bang' tomography as a new route to atomic-resolution electron tomography.

PubMed

Van Dyck, Dirk; Jinschek, Joerg R; Chen, Fu-Rong

2012-06-13

Until now it has not been possible to image at atomic resolution using classical electron tomographic methods, except when the target is a perfectly crystalline nano-object imaged along a few zone axes. The main reasons are that mechanical tilting in an electron microscope with sub-ångström precision over a very large angular range is difficult, that many real-life objects such as dielectric layers in microelectronic devices impose geometrical constraints and that many radiation-sensitive objects such as proteins limit the total electron dose. Hence, there is a need for a new tomographic scheme that is able to deduce three-dimensional information from only one or a few projections. Here we present an electron tomographic method that can be used to determine, from only one viewing direction and with sub-ångström precision, both the position of individual atoms in the plane of observation and their vertical position. The concept is based on the fact that an experimentally reconstructed exit wave consists of the superposition of the spherical waves that have been scattered by the individual atoms of the object. Furthermore, the phase of a Fourier component of a spherical wave increases with the distance of propagation at a known 'phase speed'. If we assume that an atom is a point-like object, the relationship between the phase and the phase speed of each Fourier component is linear, and the distance between the atom and the plane of observation can therefore be determined by linear fitting. This picture has similarities with Big Bang cosmology, in which the Universe expands from a point-like origin such that the distance of any galaxy from the origin is linearly proportional to the speed at which it moves away from the origin (Hubble expansion). The proof of concept of the method has been demonstrated experimentally for graphene with a two-layer structure and it will work optimally for similar layered materials, such as boron nitride and molybdenum disulphide.

Using size-selected gold clusters on graphene oxide films to aid cryo-transmission electron tomography alignment

PubMed Central

Arkill, Kenton P.; Mantell, Judith M.; Plant, Simon R.; Verkade, Paul; Palmer, Richard E.

2015-01-01

A three-dimensional reconstruction of a nano-scale aqueous object can be achieved by taking a series of transmission electron micrographs tilted at different angles in vitreous ice: cryo-Transmission Electron Tomography. Presented here is a novel method of fine alignment for the tilt series. Size-selected gold clusters of ~2.7 nm (Au561 ± 14), ~3.2 nm (Au923 ± 22), and ~4.3 nm (Au2057 ± 45) in diameter were deposited onto separate graphene oxide films overlaying holes on amorphous carbon grids. After plunge freezing and subsequent transfer to cryo-Transmission Electron Tomography, the resulting tomograms have excellent (de-)focus and alignment properties during automatic acquisition. Fine alignment is accurate when the evenly distributed 3.2 nm gold particles are used as fiducial markers, demonstrated with a reconstruction of a tobacco mosaic virus. Using a graphene oxide film means the fiducial markers are not interfering with the ice bound sample and that automated collection is consistent. The use of pre-deposited size-selected clusters means there is no aggregation and a user defined concentration. The size-selected clusters are mono-dispersed and can be produced in a wide size range including 2–5 nm in diameter. The use of size-selected clusters on a graphene oxide films represents a significant technical advance for 3D cryo-electron microscopy. PMID:25783049

Characterisation of Fractures and Fracture Zones in a Carbonate Aquifer Using Electrical Resistivity Tomography and Pricking Probe Methodes

NASA Astrophysics Data System (ADS)

Szalai, Sandor; Kovacs, Attila; Kuslits, Lukács; Facsko, Gabor; Gribovszki, Katalin; Kalmar, Janos; Szarka, Laszlo

2018-04-01

Position, width and fragmentation level of fracture zones and position, significance and characteristic distance of fractures were aimed to determine in a carbonate aquifer. These are fundamental parameters, e.g. in hydrogeological modelling of aquifers, due to their role in subsurface water movements. The description of small scale fracture systems is however a challenging task. In the test area (Kádárta, Bakony Mts, Hungary), two methods proved to be applicable to get reasonable information about the fractures: Electrical Resistivity Tomography (ERT) and Pricking-Probe (PriP). PriP is a simple mechanical tool which has been successfully applied in archaeological investigations. ERT results demonstrated its applicability in this small scale fracture study. PriP proved to be a good verification tool both for fracture zone mapping and detecting fractures, but in certain areas, it produced different results than the ERT. The applicability of this method has therefore to be tested yet, although its problems most probably origin from human activity which reorganises the near-surface debris distribution. In the test site, both methods displayed fracture zones including a very characteristic one and a number of individual fractures and determined their characteristic distance and significance. Both methods prove to be able to produce hydrogeologically important parameters even individually, but their simultaneous application is recommended to decrease the possible discrepancies.

Slab narrowing in the Central Mediterranean: the Calabro-Ionian subduction zone as imaged by high resolution seismic tomography.

PubMed

Scarfì, L; Barberi, G; Barreca, G; Cannavò, F; Koulakov, I; Patanè, D

2018-03-26

A detailed 3D image of the Calabro-Ionian subduction system in the central Mediterranean was obtained by means of a seismic tomography, exploiting a large dataset of local earthquakes and computing algorithms able to build a dense grid of measure nodes. Results show that the slab is continuous below the southern sector of the Calabro-Peloritan Arc, but the deformation processes developing at its edges are leading to its progressive narrowing, influencing tectonics and magmatism at the surface, and with possible stress concentration in the tip zones. In the southwest, the deformation occurring at a free slab edge lead to propagation of a vertical lithospheric tear in the overriding plate, which extends along a NW-SE fault system (Aeolian-Tindari-Letojanni) up to about 30 km into the Ionian Sea; further southeast, the lithosphere appears only flexed and not broken yet. In the northeast, the slab seems to break progressively, parallel to the trench. Finally, northwest of Mt. Etna, the tomography highlights low V P that can be related to an upwelling of deep mantle material likely flowing laterally through a window opened by the complete slab detachment.

Refinement procedure for the image alignment in high-resolution electron tomography.

PubMed

Houben, L; Bar Sadan, M

2011-01-01

High-resolution electron tomography from a tilt series of transmission electron microscopy images requires an accurate image alignment procedure in order to maximise the resolution of the tomogram. This is the case in particular for ultra-high resolution where even very small misalignments between individual images can dramatically reduce the fidelity of the resultant reconstruction. A tomographic-reconstruction based and marker-free method is proposed, which uses an iterative optimisation of the tomogram resolution. The method utilises a search algorithm that maximises the contrast in tomogram sub-volumes. Unlike conventional cross-correlation analysis it provides the required correlation over a large tilt angle separation and guarantees a consistent alignment of images for the full range of object tilt angles. An assessment based on experimental reconstructions shows that the marker-free procedure is competitive to the reference of marker-based procedures at lower resolution and yields sub-pixel accuracy even for simulated high-resolution data. Copyright © 2011 Elsevier B.V. All rights reserved.

Visualizing Morphological Changes of Abscission Zone Cells in Arabidopsis by Scanning Electron Microscope.

PubMed

Shi, Chun-Lin; Butenko, Melinka A

2018-01-01

Scanning electron microscope (SEM) is a type of electron microscope which produces detailed images of surface structures. It has been widely used in plants and animals to study cellular structures. Here, we describe a detailed protocol to prepare samples of floral abscission zones (AZs) for SEM, as well as further image analysis. We show that it is a powerful tool to detect morphologic changes at the cellular level during the course of abscission in wild-type plants and to establish the details of phenotypic alteration in abscission mutants.

Cryo-Electron Tomography of Rubella Virus

PubMed Central

Battisti, Anthony J.; Yoder, Joshua D.; Plevka, Pavel; Winkler, Dennis C.; Mangala Prasad, Vidya; Kuhn, Richard J.; Frey, Teryl K.; Steven, Alasdair C.

2012-01-01

Rubella virus is the only member of the Rubivirus genus within the Togaviridae family and is the causative agent of the childhood disease known as rubella or German measles. Here, we report the use of cryo-electron tomography to examine the three-dimensional structure of rubella virions and compare their structure to that of Ross River virus, a togavirus belonging the genus Alphavirus. The ectodomains of the rubella virus glycoproteins, E1 and E2, are shown to be organized into extended rows of density, separated by 9 nm on the viral surface. We also show that the rubella virus nucleocapsid structure often forms a roughly spherical shell which lacks high density at its center. While many rubella virions are approximately spherical and have dimensions similar to that of the icosahedral Ross River virus, the present results indicate that rubella exhibits a large degree of pleomorphy. In addition, we used rotation function calculations and other analyses to show that approximately spherical rubella virions lack the icosahedral organization which characterizes Ross River and other alphaviruses. The present results indicate that the assembly mechanism of rubella virus, which has previously been shown to differ from that of the alphavirus assembly pathway, leads to an organization of the rubella virus structural proteins that is different from that of alphaviruses. PMID:22855483

Cryo-electron tomography of rubella virus.

PubMed

Battisti, Anthony J; Yoder, Joshua D; Plevka, Pavel; Winkler, Dennis C; Prasad, Vidya Mangala; Kuhn, Richard J; Frey, Teryl K; Steven, Alasdair C; Rossmann, Michael G

2012-10-01

Rubella virus is the only member of the Rubivirus genus within the Togaviridae family and is the causative agent of the childhood disease known as rubella or German measles. Here, we report the use of cryo-electron tomography to examine the three-dimensional structure of rubella virions and compare their structure to that of Ross River virus, a togavirus belonging the genus Alphavirus. The ectodomains of the rubella virus glycoproteins, E1 and E2, are shown to be organized into extended rows of density, separated by 9 nm on the viral surface. We also show that the rubella virus nucleocapsid structure often forms a roughly spherical shell which lacks high density at its center. While many rubella virions are approximately spherical and have dimensions similar to that of the icosahedral Ross River virus, the present results indicate that rubella exhibits a large degree of pleomorphy. In addition, we used rotation function calculations and other analyses to show that approximately spherical rubella virions lack the icosahedral organization which characterizes Ross River and other alphaviruses. The present results indicate that the assembly mechanism of rubella virus, which has previously been shown to differ from that of the alphavirus assembly pathway, leads to an organization of the rubella virus structural proteins that is different from that of alphaviruses.

Three-dimensional Organization of pKi-67: A Comparative Fluorescence and Electron Tomography Study Using Fluoronanogold

PubMed Central

Cheutin, Thierry; O'Donohue, Marie-Françoise; Beorchia, Adrien; Klein, Christophe; Kaplan, Hervé; Ploton, Dominique

2003-01-01

The monoclonal antibody (MAb) Ki-67 is routinely used in clinical studies to estimate the growth fraction of tumors. However, the role of pKi-67, the protein detected by the Ki-67 MAb, remains elusive, although some biochemical data strongly suggest that it might organize chromatin. To better understand the functional organization of pKi-67, we studied its three-dimensional distribution in interphase cells by confocal microscopy and electron tomography. FluoroNanogold, a single probe combining a dense marker with a fluorescent dye, was used to investigate pKi-67 organization at the optical and ultrastructural levels. Observation by confocal microscopy followed by 3D reconstruction showed that pKi-67 forms a shell around the nucleoli. Double labeling experiments revealed that pKi-67 co-localizes with perinucleolar heterochromatin. Electron microscopy studies confirmed this close association and demonstrated that pKi-67 is located neither in the fibrillar nor in the granular components of the nucleolus. Finally, spatial analyses by electron tomography showed that pKi-67 forms cords 250–300 nm in diameter, which are themselves composed of 30–50-nm-thick fibers. These detailed comparative in situ analyses strongly suggest the involvement of pKi-67 in the higher-order organization of perinucleolar chromatin. PMID:14566014

FPGA-Based Front-End Electronics for Positron Emission Tomography

PubMed Central

Haselman, Michael; DeWitt, Don; McDougald, Wendy; Lewellen, Thomas K.; Miyaoka, Robert; Hauck, Scott

2010-01-01

Modern Field Programmable Gate Arrays (FPGAs) are capable of performing complex discrete signal processing algorithms with clock rates above 100MHz. This combined with FPGA’s low expense, ease of use, and selected dedicated hardware make them an ideal technology for a data acquisition system for positron emission tomography (PET) scanners. Our laboratory is producing a high-resolution, small-animal PET scanner that utilizes FPGAs as the core of the front-end electronics. For this next generation scanner, functions that are typically performed in dedicated circuits, or offline, are being migrated to the FPGA. This will not only simplify the electronics, but the features of modern FPGAs can be utilizes to add significant signal processing power to produce higher resolution images. In this paper two such processes, sub-clock rate pulse timing and event localization, will be discussed in detail. We show that timing performed in the FPGA can achieve a resolution that is suitable for small-animal scanners, and will outperform the analog version given a low enough sampling period for the ADC. We will also show that the position of events in the scanner can be determined in real time using a statistical positioning based algorithm. PMID:21961085

Microscale reconstruction of biogeochemical substrates using multimode X-ray tomography and scanning electron microscopy

NASA Astrophysics Data System (ADS)

Miller, M.; Miller, E.; Liu, J.; Lund, R. M.; McKinley, J. P.

2012-12-01

X-ray computed tomography (CT), scanning electron microscopy (SEM), electron microprobe analysis (EMP), and computational image analysis are mature technologies used in many disciplines. Cross-discipline combination of these imaging and image-analysis technologies is the focus of this research, which uses laboratory and light-source resources in an iterative approach. The objective is to produce images across length scales, taking advantage of instrumentation that is optimized for each scale, and to unify them into a single compositional reconstruction. Initially, CT images will be collected using both x-ray absorption and differential phase contrast modes. The imaged sample will then be physically sectioned and the exposed surfaces imaged and characterized via SEM/EMP. The voxel slice corresponding to the physical sample surface will be isolated computationally, and the volumetric data will be combined with two-dimensional SEM images along CT image planes. This registration step will take advantage of the similarity between the X-ray absorption (CT) and backscattered electron (SEM) coefficients (both proportional to average atomic number in the interrogated volume) as well as the images' mutual information. Elemental and solid-phase distributions on the exposed surfaces, co-registered with SEM images, will be mapped using EMP. The solid-phase distribution will be propagated into three-dimensional space using computational methods relying on the estimation of compositional distributions derived from the CT data. If necessary, solid-phase and pore-space boundaries will be resolved using X-ray differential phase contrast tomography, x-ray fluorescence tomography, and absorption-edge microtomography at a light-source facility. Computational methods will be developed to register and model images collected over varying scales and data types. Image resolution, physically and dynamically, is qualitatively different for the electron microscopy and CT methodologies. Routine

3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xing; Zhang, Lei; Tong, Huimin

2015-05-05

Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, wemore » derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.« less

Bright-field electron tomography of individual inorganic fullerene-like structures.

PubMed

Bar Sadan, Maya; Wolf, Sharon G; Houben, Lothar

2010-03-01

Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS(2) or MoS(2) fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties.

CoCrMo cellular structures made by Electron Beam Melting studied by local tomography and finite element modelling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petit, Clémence; Maire, Eric, E-mail: eric.maire@insa-lyon.fr; Meille, Sylvain

The work focuses on the structural and mechanical characterization of Co-Cr-Mo cellular samples with cubic pore structure made by Electron Beam Melting (EBM). X-ray tomography was used to characterize the architecture of the sample. High resolution images were also obtained thanks to local tomography in which the specimen is placed close to the X-ray source. These images enabled to observe some defects due to the fabrication process: small pores in the solid phase, partially melted particles attached to the surface. Then, in situ compression tests were performed in the tomograph. The images of the deformed sample show a progressive bucklingmore » of the vertical struts leading to final fracture. The deformation initiated where the defects were present in the strut i.e. in regions with reduced local thickness. The finite element modelling confirmed the high stress concentrations of these weak points leading to the fracture of the sample. - Highlights: • CoCrMo samples fabricated by Electron Beam Melting (EBM) process are considered. • X-ray Computed Tomography is used to observe the structure of the sample. • The mechanical properties are tested thanks to an in situ test in the tomograph. • A finite element model is developed to model the mechanical behaviour.« less

Long streamer waveform tomography imaging of the Sanak Basin, Alaska subduction zone

NASA Astrophysics Data System (ADS)

Roche, Pierre-Henri; Delescluse, Matthias; Becel, Anne; Nedimovic, Mladen; Shillington, Donna; Webb, Spahr; Kuehn, Harold

2017-04-01

The Alaska subduction zone is prone to large megathrust earthquakes, including several large tsunamigenic events in the historical record (e.g. the 1964 Mw 9.2 and the 1946 Mw 8.6 earthquakes). Along the Alaska Peninsula trench, seismic coupling varies from fully locked to the east to weakly coupled to the West, with apparent aseismic slip in the Shumagin Gap and Unimak rupture zone. Overlapping the Shumagin gap and the Unimak area, the Sanak basin is a Miocene basin formed by a large-scale normal fault recently imaged by the ALEUT 2011 cruise and clearly rooting in the subduction interface at 30 km depth (Becel et al., submitted). Recent activity on this normal fault is detected at the seafloor of the Sanak Basin by a 5 m scarp in the multibeam bathymetry data. As this normal fault may be associated with faults involved in the 1946 tsunami earthquake, it is particularly important to try to decipher its history in the Sanak basin, where sediments record the fault activity. MCS data processing and interpretation shows evidence for the activity of the fault from Miocene to recent geological times. Very limited knowledge of the sedimentation rates and ages as well as complexities due to submarine landslides and channel depositions make it difficult to quantify the present day fault activity with respect to the Miocene fault activity. In addition, the mechanical behaviour of a normal splay fault system requires low to zero effective friction and probably involves fluids. High-resolution seismic velocity imaging can help with both the interpretation of complex sedimentary deposition and fluid detection. To obtain such a high resolution velocity field, we use two 45-km-long MCS profiles from the ALEUT 2011 cruise acquired with an 8-km-long streamer towed at 12 m depth to enhance low frequencies with shots fired from a large, tuned airgun array (6600 cu.in.). The two profiles extend from the shelf break to mid slope and encompass the normal splay fault emerging at 1 km

Atom-probe tomography and transmission electron microscopy of the kamacite-taenite interface in the fast-cooled Bristol IVA iron meteorite

NASA Astrophysics Data System (ADS)

Rout, Surya S.; Heck, Philipp R.; Isheim, Dieter; Stephan, Thomas; Zaluzec, Nestor J.; Miller, Dean J.; Davis, Andrew M.; Seidman, David N.

2017-12-01

We report the first combined atom-probe tomography (APT) and transmission electron microscopy (TEM) study of a kamacite-tetrataenite (K-T) interface region within an iron meteorite, Bristol (IVA). Ten APT nanotips were prepared from the K-T interface with focused ion beam scanning electron microscopy (FIB-SEM) and then studied using TEM followed by APT. Near the K-T interface, we found 3.8 ± 0.5 wt% Ni in kamacite and 53.4 ± 0.5 wt% Ni in tetrataenite. High-Ni precipitate regions of the cloudy zone (CZ) have 50.4 ± 0.8 wt% Ni. A region near the CZ and martensite interface has <10 nm sized Ni-rich precipitates with 38.4 ± 0.7 wt% Ni present within a low-Ni matrix having 25.5 ± 0.6 wt% Ni. We found that Cu is predominantly concentrated in tetrataenite, whereas Co, P, and Cr are concentrated in kamacite. Phosphorus is preferentially concentrated along the K-T interface. This study is the first precise measurement of the phase composition at high spatial resolution and in 3-D of the K-T interface region in a IVA iron meteorite and furthers our knowledge of the phase composition changes in a fast-cooled iron meteorite below 400 °C. We demonstrate that APT in conjunction with TEM is a useful approach to study the major, minor, and trace elemental composition of nanoscale features within fast-cooled iron meteorites.

Comparison of 3D cellular imaging techniques based on scanned electron probes: Serial block face SEM vs. Axial bright-field STEM tomography.

PubMed

McBride, E L; Rao, A; Zhang, G; Hoyne, J D; Calco, G N; Kuo, B C; He, Q; Prince, A A; Pokrovskaya, I D; Storrie, B; Sousa, A A; Aronova, M A; Leapman, R D

2018-06-01

Microscopies based on focused electron probes allow the cell biologist to image the 3D ultrastructure of eukaryotic cells and tissues extending over large volumes, thus providing new insight into the relationship between cellular architecture and function of organelles. Here we compare two such techniques: electron tomography in conjunction with axial bright-field scanning transmission electron microscopy (BF-STEM), and serial block face scanning electron microscopy (SBF-SEM). The advantages and limitations of each technique are illustrated by their application to determining the 3D ultrastructure of human blood platelets, by considering specimen geometry, specimen preparation, beam damage and image processing methods. Many features of the complex membranes composing the platelet organelles can be determined from both approaches, although STEM tomography offers a higher ∼3 nm isotropic pixel size, compared with ∼5 nm for SBF-SEM in the plane of the block face and ∼30 nm in the perpendicular direction. In this regard, we demonstrate that STEM tomography is advantageous for visualizing the platelet canalicular system, which consists of an interconnected network of narrow (∼50-100 nm) membranous cisternae. In contrast, SBF-SEM enables visualization of complete platelets, each of which extends ∼2 µm in minimum dimension, whereas BF-STEM tomography can typically only visualize approximately half of the platelet volume due to a rapid non-linear loss of signal in specimens of thickness greater than ∼1.5 µm. We also show that the limitations of each approach can be ameliorated by combining 3D and 2D measurements using a stereological approach. Copyright © 2018. Published by Elsevier Inc.

Electron tomography simulator with realistic 3D phantom for evaluation of acquisition, alignment and reconstruction methods.

PubMed

Wan, Xiaohua; Katchalski, Tsvi; Churas, Christopher; Ghosh, Sreya; Phan, Sebastien; Lawrence, Albert; Hao, Yu; Zhou, Ziying; Chen, Ruijuan; Chen, Yu; Zhang, Fa; Ellisman, Mark H

2017-05-01

Because of the significance of electron microscope tomography in the investigation of biological structure at nanometer scales, ongoing improvement efforts have been continuous over recent years. This is particularly true in the case of software developments. Nevertheless, verification of improvements delivered by new algorithms and software remains difficult. Current analysis tools do not provide adaptable and consistent methods for quality assessment. This is particularly true with images of biological samples, due to image complexity, variability, low contrast and noise. We report an electron tomography (ET) simulator with accurate ray optics modeling of image formation that includes curvilinear trajectories through the sample, warping of the sample and noise. As a demonstration of the utility of our approach, we have concentrated on providing verification of the class of reconstruction methods applicable to wide field images of stained plastic-embedded samples. Accordingly, we have also constructed digital phantoms derived from serial block face scanning electron microscope images. These phantoms are also easily modified to include alignment features to test alignment algorithms. The combination of more realistic phantoms with more faithful simulations facilitates objective comparison of acquisition parameters, alignment and reconstruction algorithms and their range of applicability. With proper phantoms, this approach can also be modified to include more complex optical models, including distance-dependent blurring and phase contrast functions, such as may occur in cryotomography. Copyright © 2017 Elsevier Inc. All rights reserved.

Correlated fluorescence microscopy and cryo-electron tomography of virus-infected or transfected mammalian cells

PubMed Central

Hampton, Cheri M; Strauss, Joshua D; Ke, Zunlong; Dillard, Rebecca S; Hammonds, Jason E; Alonas, Eric; Desai, Tanay M; Marin, Mariana; Storms, Rachel E; Leon, Fredrick; Melikyan, Gregory B; Santangelo, Philip J; Spearman, Paul W; Wright, Elizabeth R

2016-01-01

Correlative light and electron microscopy (CLEM) combines spatiotemporal information from fluorescence light microscopy (fLM) with high-resolution structural data from cryo-electron tomography (cryo-ET). These technologies provide opportunities to bridge knowledge gaps between cell and structural biology. Here we describe our protocol for correlated cryo-fLM, cryo-electron microscopy (cryo-EM), and cryo-ET (i.e., cryo-CLEM) of virus-infected or transfected mammalian cells. Mammalian-derived cells are cultured on EM substrates, using optimized conditions that ensure that the cells are spread thinly across the substrate and are not physically disrupted. The cells are then screened by fLM and vitrified before acquisition of cryo-fLM and cryo-ET images, which is followed by data processing. A complete session from grid preparation through data collection and processing takes 5–15 d for an individual experienced in cryo-EM. PMID:27977021

An electron beam linear scanning mode for industrial limited-angle nano-computed tomography.

PubMed

Wang, Chengxiang; Zeng, Li; Yu, Wei; Zhang, Lingli; Guo, Yumeng; Gong, Changcheng

2018-01-01

Nano-computed tomography (nano-CT), which utilizes X-rays to research the inner structure of some small objects and has been widely utilized in biomedical research, electronic technology, geology, material sciences, etc., is a high spatial resolution and non-destructive research technique. A traditional nano-CT scanning model with a very high mechanical precision and stability of object manipulator, which is difficult to reach when the scanned object is continuously rotated, is required for high resolution imaging. To reduce the scanning time and attain a stable and high resolution imaging in industrial non-destructive testing, we study an electron beam linear scanning mode of nano-CT system that can avoid mechanical vibration and object movement caused by the continuously rotated object. Furthermore, to further save the scanning time and study how small the scanning range could be considered with acceptable spatial resolution, an alternating iterative algorithm based on ℓ 0 minimization is utilized to limited-angle nano-CT reconstruction problem with the electron beam linear scanning mode. The experimental results confirm the feasibility of the electron beam linear scanning mode of nano-CT system.

An electron beam linear scanning mode for industrial limited-angle nano-computed tomography

NASA Astrophysics Data System (ADS)

Wang, Chengxiang; Zeng, Li; Yu, Wei; Zhang, Lingli; Guo, Yumeng; Gong, Changcheng

2018-01-01

Nano-computed tomography (nano-CT), which utilizes X-rays to research the inner structure of some small objects and has been widely utilized in biomedical research, electronic technology, geology, material sciences, etc., is a high spatial resolution and non-destructive research technique. A traditional nano-CT scanning model with a very high mechanical precision and stability of object manipulator, which is difficult to reach when the scanned object is continuously rotated, is required for high resolution imaging. To reduce the scanning time and attain a stable and high resolution imaging in industrial non-destructive testing, we study an electron beam linear scanning mode of nano-CT system that can avoid mechanical vibration and object movement caused by the continuously rotated object. Furthermore, to further save the scanning time and study how small the scanning range could be considered with acceptable spatial resolution, an alternating iterative algorithm based on ℓ0 minimization is utilized to limited-angle nano-CT reconstruction problem with the electron beam linear scanning mode. The experimental results confirm the feasibility of the electron beam linear scanning mode of nano-CT system.

Electron tomography study of isolated human centrioles.

PubMed

Ibrahim, Rana; Messaoudi, Cédric; Chichon, Francisco Javier; Celati, Claude; Marco, Sergio

2009-01-01

Centrioles are components of the centrosome, which is present in most eukaryotic cells (from protozoa to mammals). They organize the microtubule skeleton during interphase and the mitotic spindle during cell division. In ciliate cells, centrioles form basal bodies that are involved in cellular motility. Despite their important roles in biology, the detailed structure of centrioles remains obscure. This work contributes to a more complete model of centriole structure. The authors used electron tomography of isolated centrosomes from the human lymphoblast KE37 to explore the details of subdistal appendages and centriole lumen organization in mother centrioles. Their results reveal that each of the nine subdistal appendages is composed of two halves (20 nm diameter each) fused in a 40 nm tip that extends 100 nm from where it anchors to microtubules. The centriole lumen is filled at the distal domain by a 45 nm periodic stack of rings. Each ring has a 30 nm diameter, is 15 nm thick, and appears to be tilted at 53 degrees perpendicular to the centriole axis. The rings are anchored to microtubules by arms. Based on their results, the authors propose a model of the mother centriole distal structure. Copyright 2008 Wiley-Liss, Inc.

Three-dimensional organization of pKi-67: a comparative fluorescence and electron tomography study using FluoroNanogold.

PubMed

Cheutin, Thierry; O'Donohue, Marie-Françoise; Beorchia, Adrien; Klein, Christophe; Kaplan, Hervé; Ploton, Dominique

2003-11-01

The monoclonal antibody (MAb) Ki-67 is routinely used in clinical studies to estimate the growth fraction of tumors. However, the role of pKi-67, the protein detected by the Ki-67 MAb, remains elusive, although some biochemical data strongly suggest that it might organize chromatin. To better understand the functional organization of pKi-67, we studied its three-dimensional distribution in interphase cells by confocal microscopy and electron tomography. FluoroNanogold, a single probe combining a dense marker with a fluorescent dye, was used to investigate pKi-67 organization at the optical and ultrastructural levels. Observation by confocal microscopy followed by 3D reconstruction showed that pKi-67 forms a shell around the nucleoli. Double labeling experiments revealed that pKi-67 co-localizes with perinucleolar heterochromatin. Electron microscopy studies confirmed this close association and demonstrated that pKi-67 is located neither in the fibrillar nor in the granular components of the nucleolus. Finally, spatial analyses by electron tomography showed that pKi-67 forms cords 250-300 nm in diameter, which are themselves composed of 30-50-nm-thick fibers. These detailed comparative in situ analyses strongly suggest the involvement of pKi-67 in the higher-order organization of perinucleolar chromatin.

Insight into mitochondrial structure and function from electron tomography.

PubMed

Frey, T G; Renken, C W; Perkins, G A

2002-09-10

In recent years, electron tomography has provided detailed three-dimensional models of mitochondria that have redefined our concept of mitochondrial structure. The models reveal an inner membrane consisting of two components, the inner boundary membrane (IBM) closely apposed to the outer membrane and the cristae membrane that projects into the matrix compartment. These two components are connected by tubular structures of relatively uniform size called crista junctions. The distribution of crista junction sizes and shapes is predicted by a thermodynamic model based upon the energy of membrane bending, but proteins likely also play a role in determining the conformation of the inner membrane. Results of structural studies of mitochondria during apoptosis demonstrate that cytochrome c is released without detectable disruption of the outer membrane or extensive swelling of the mitochondrial matrix, suggesting the formation of an outer membrane pore large enough to allow passage of holo-cytochrome c. The possible compartmentation of inner membrane function between the IBM and the cristae membrane is also discussed.

Comparisons of ionospheric electron density distributions reconstructed by GPS computerized tomography, backscatter ionograms, and vertical ionograms

NASA Astrophysics Data System (ADS)

Zhou, Chen; Lei, Yong; Li, Bofeng; An, Jiachun; Zhu, Peng; Jiang, Chunhua; Zhao, Zhengyu; Zhang, Yuannong; Ni, Binbin; Wang, Zemin; Zhou, Xuhua

2015-12-01

Global Positioning System (GPS) computerized ionosphere tomography (CIT) and ionospheric sky wave ground backscatter radar are both capable of measuring the large-scale, two-dimensional (2-D) distributions of ionospheric electron density (IED). Here we report the spatial and temporal electron density results obtained by GPS CIT and backscatter ionogram (BSI) inversion for three individual experiments. Both the GPS CIT and BSI inversion techniques demonstrate the capability and the consistency of reconstructing large-scale IED distributions. To validate the results, electron density profiles obtained from GPS CIT and BSI inversion are quantitatively compared to the vertical ionosonde data, which clearly manifests that both methods output accurate information of ionopsheric electron density and thereby provide reliable approaches to ionospheric soundings. Our study can improve current understanding of the capability and insufficiency of these two methods on the large-scale IED reconstruction.

Digital retrospective motion-mode display and processing of electron beam cine-computed tomography and other cross-sectional cardiac imaging techniques

NASA Astrophysics Data System (ADS)

Reed, Judd E.; Rumberger, John A.; Buithieu, Jean; Behrenbeck, Thomas; Breen, Jerome F.; Sheedy, Patrick F., II

1995-05-01

Electron beam computed tomography is unparalleled in its ability to consistently produce high quality dynamic images of the human heart. Its use in quantification of left ventricular dynamics is well established in both clinical and research applications. However, the image analysis tools supplied with the scanners offer a limited number of analysis options. They are based on embedded computer systems which have not been significantly upgraded since the scanner was introduced over a decade ago in spite of the explosive improvements in available computer power which have occured during this period. To address these shortcomings, a workstation-based ventricular analysis system has been developed at our institution. This system, which has been in use for over five years, is based on current workstation technology and therefore has benefited from the periodic upgrades in processor performance available to these systems. The dynamic image segmentation component of this system is an interactively supervised, semi-automatic surface identification and tracking system. It characterizes the endocardial and epicardial surfaces of the left ventricle as two concentric 4D hyper-space polyhedrons. Each of these polyhedrons have nearly ten thousand vertices which are deposited into a relational database. The right ventricle is also processed in a similar manner. This database is queried by other custom components which extract ventricular function parameters such as regional ejection fraction and wall stress. The interactive tool which supervises dynamic image segmentation has been enhanced with a temporal domain display. The operator interactively chooses the spatial location of the endpoints of a line segment while the corresponding space/time image is displayed. These images, with content resembling M-Mode echocardiography, benefit form electron beam computed tomography's high spatial and contrast resolution. The segmented surfaces are displayed along with the imagery. These

Electron heating within interaction zones of simple high-speed solar wind streams

NASA Technical Reports Server (NTRS)

Feldman, W. C.; Asbridge, J. R.; Bame, S. J.; Gosling, J. T.; Lemons, D. S.

1978-01-01

In the present paper, electron heating within the high-speed portions of three simple stream-stream interaction zones is studied to further our understanding of the physics of heat flux regulation in interplanetary space. To this end, the thermal signals present in the compressions at the leading edges of the simple high-speed streams are analyzed, showing that the data are inconsistent with the Spitzer conductivity. Instead, a polynomial law is found to apply. Its implication concerning the mechanism of interplanetary heat conduction is discussed, and the results of applying this conductivity law to high-speed flows inside of 1 AU are studied. A self-consistent model of the radial evolution of electrons in the high-speed solar wind is proposed.

Lyman alpha line shapes from electron impact H2 dissociative processes in the Jovian auroral zone

NASA Technical Reports Server (NTRS)

Waite, J. H., Jr.; Gladstone, G. R.

1992-01-01

Over the past two years several Lyman alpha line profile spectra of Jupiter were obtained using the International Ultraviolet Explorer (IUE) telescope. Several different regions of the planet were observed including the auroral zone, the low and mid latitudes, and the equatorial region which includes the Lyman alpha bulge region. These results have presented a very interesting picture of atomic hydrogen on Jupiter with explanations that range from ion outflow in the auroral zone to large thermospheric winds at low and mid latitudes. New data are needed to address the outstanding questions. Almost certainly, high resolution spectra from the Hubble Space Telescope will play a role in new observations. Better data also require better models, and better models require new laboratory data as inputs. The purpose of this program is two-fold: (1) to introduce a method by which new laboratory electron impact measurements of H2 dissociation can be used to calculate both the slow and fast H(S-2) and H(P-2) fragments in an H2 atmosphere; and (2) to determine the predicted Lyman alpha line shape that would result from electron impact production of these dissociative fragments in the Jovian auroral zone.

Continuous cropping of endangered therapeutic plants via electron beam soil-treatment and neutron tomography.

PubMed

Sim, Cheul Muu; Seong, Bong Jae; Kim, Dong Won; Kim, Yong Bum; Wi, Seung Gon; Kim, Gyuil; Oh, Hwasuk; Kim, TaeJoo; Chung, Byung Yeoup; Song, Jeong Young; Kim, Hong Gi; Oh, Sang-Keun; Shin, Young Dol; Seok, Jea Hwan; Kang, Min Young; Lee, Yunhee; Radebe, Mabuti Jacob; Kardjilov, Nikolay; Honermeier, Bernd

2018-02-01

Various medicinal plants are threatened with extinction owing to their over-exploitation and the prevalence of soil borne pathogens. In this study, soils infected with root-rot pathogens, which prevent continuous-cropping, were treated with an electron beam. The level of soil-borne fungus was reduced to ≤0.01% by soil electron beam treatment without appreciable effects on the levels of antagonistic microorganism or on the physicochemical properties of the soil. The survival rate of 4-year-old plant was higher in electron beam-treated soil (81.0%) than in fumigated (62.5%), virgin (78%), or untreated-replanting soil (0%). Additionally, under various soils conditions, neutron tomography permitted the monitoring of plant health and the detection of root pathological changes over a period of 4-6 years by quantitatively measuring root water content in situ. These methods allow continual cropping on the same soil without pesticide treatment. This is a major step toward the environmentally friendly production of endangered therapeutic herbs.

Progress and opportunities in EELS and EDS tomography.

PubMed

Collins, Sean M; Midgley, Paul A

2017-09-01

Electron tomography using energy loss and X-ray spectroscopy in the electron microscope continues to develop in rapidly evolving and diverse directions, enabling new insight into the three-dimensional chemistry and physics of nanoscale volumes. Progress has been made recently in improving reconstructions from EELS and EDS signals in electron tomography by applying compressed sensing methods, characterizing new detector technologies in detail, deriving improved models of signal generation, and exploring machine learning approaches to signal processing. These disparate threads can be brought together in a cohesive framework in terms of a model-based approach to analytical electron tomography. Models incorporate information on signal generation and detection as well as prior knowledge of structures in the spectrum image data. Many recent examples illustrate the flexibility of this approach and its feasibility for addressing challenges in non-linear or limited signals in EELS and EDS tomography. Further work in combining multiple imaging and spectroscopy modalities, developing synergistic data acquisition, processing, and reconstruction approaches, and improving the precision of quantitative spectroscopic tomography will expand the frontiers of spatial resolution, dose limits, and maximal information recovery. Copyright © 2017 Elsevier B.V. All rights reserved.

Subduction Zone Dewatering at the Southern End of New Zealand's Hikurangi Margin - Insights from 2D Seismic Tomography

NASA Astrophysics Data System (ADS)

Crutchley, G. J.; Klaeschen, D.

2016-12-01

The southern end of New Zealand's Hikurangi subduction margin is characterised by highly-oblique convergence as it makes a southward transition into a right-lateral transform plate boundary. Long-offset seismic data that cross part of the offshore portion of this transition zone give new insight into the nature of the margin. We have carried out two-dimensional pre-stack depth migrations with an iterative reflection tomography to update the velocity field on two seismic lines in this area. The depth-migrated sections show much-improved imaging of faulting within the wedge, and the seismic velocities themselves give clues about the distribution of gas and/or overpressured regions at the plate boundary and within the overlying wedge. A fascinating observation is a major splay fault that has been (or continues to be) a preferred dewatering pathway through the wedge, evidenced by a thermal anomaly that has left its mark on the overlying gas hydrate layer. Another interesting observation is a thick and laterally extensive low velocity zone beneath the subduction interface, which might have important implications for the long-term mechanical stability of the interface. Our on-going work on these data is focused on amplitude versus offset analysis in an attempt to better understand the nature of the subduction interface and also the shallower gas hydrate system. This study is an example of how distinct disturbances of the gas hydrate system can provide insight into subduction zone fluid flow processes that are important for understanding wedge stability and ultimately earthquake hazard.

Three-dimensional fine structure of the organization of microtubules in neurite varicosities by ultra-high voltage electron microscope tomography.

PubMed

Nishida, Tomoki; Yoshimura, Ryoichi; Endo, Yasuhisa

2017-09-01

Neurite varicosities are highly specialized compartments that are involved in neurotransmitter/ neuromodulator release and provide a physiological platform for neural functions. However, it remains unclear how microtubule organization contributes to the form of varicosity. Here, we examine the three-dimensional structure of microtubules in varicosities of a differentiated PC12 neural cell line using ultra-high voltage electron microscope tomography. Three-dimensional imaging showed that a part of the varicosities contained an accumulation of organelles that were separated from parallel microtubule arrays. Further detailed analysis using serial sections and whole-mount tomography revealed microtubules running in a spindle shape of swelling in some other types of varicosities. These electron tomographic results showed that the structural diversity and heterogeneity of microtubule organization supported the form of varicosities, suggesting that a different distribution pattern of microtubules in varicosities is crucial to the regulation of varicosities development.

Electron tomography reveals the fibril structure and lipid interactions in amyloid deposits

PubMed Central

Kollmer, Marius; Meinhardt, Katrin; Haupt, Christian; Liberta, Falk; Wulff, Melanie; Linder, Julia; Handl, Lisa; Heinrich, Liesa; Loos, Cornelia; Schmidt, Matthias; Syrovets, Tatiana; Simmet, Thomas; Westermark, Per; Westermark, Gunilla T.; Horn, Uwe; Schmidt, Volker; Walther, Paul; Fändrich, Marcus

2016-01-01

Electron tomography is an increasingly powerful method to study the detailed architecture of macromolecular complexes or cellular structures. Applied to amyloid deposits formed in a cell culture model of systemic amyloid A amyloidosis, we could determine the structural morphology of the fibrils directly in the deposit. The deposited fibrils are arranged in different networks, and depending on the relative fibril orientation, we can distinguish between fibril meshworks, fibril bundles, and amyloid stars. These networks are frequently infiltrated by vesicular lipid inclusions that may originate from the death of the amyloid-forming cells. Our data support the role of nonfibril components for constructing fibril deposits and provide structural views of different types of lipid–fibril interactions. PMID:27140609

Electrical Resistivity Tomography monitoring reveals groundwater storage in a karst vadose zone

NASA Astrophysics Data System (ADS)

Watlet, A.; Kaufmann, O.; Van Camp, M. J.; Triantafyllou, A.; Cisse, M. F.; Quinif, Y.; Meldrum, P.; Wilkinson, P. B.; Chambers, J. E.

2016-12-01

Karst systems are among the most difficult aquifers to characterize, due to their high heterogeneity. In particular, temporary groundwater storage that occurs in the unsaturated zone and the discharge to deeper layers are difficult processes to identify and estimate with in-situ measurements. Electrical Resistivity Tomography (ERT) monitoring is meant to track changes in the electrical properties of the subsurface and has proved to be applicable to evidence and quantify hydrological processes in several types of environments. Applied to karst systems, it has particularly highlighted the challenges in linking electrical resistivity changes to groundwater content with usual approaches of petrophysical relationships, given the high heterogeneity of the subsurface. However, taking up the challenge, we undertook an ERT monitoring at the Rochefort Cave Laboratory (Belgium) lasting from Spring 2014 to Winter 2016. This includes 3 main periods of several months with daily measurements, from which seasonal groundwater content changes in the first meters of the vadose zone were successfully imaged. The monitoring concentrates on a 48 electrodes profile that goes from a limestone plateau to the bottom of a sinkhole. 3D UAV photoscans of the surveyed sinkhole and of the main chamber of the nearby cave were performed. Combined with lithological observations from a borehole drilled next to the ERT profile, the 3D information made it possible to project karstified layers visible in the cave to the surface and assess their potential locations along the ERT profile. Overall, this helped determining more realistic local petrophysical properties in the surveyed area, and improving the ERT data inversion by adding structural constraints. Given a strong air temperature gradient in the sinkhole, we also developed a new approach of temperature correction of the raw ERT data. This goes through the solving (using pyGIMLI package) of the 2D ground temperature field and its temporal

Developing a denoising filter for electron microscopy and tomography data in the cloud.

PubMed

Starosolski, Zbigniew; Szczepanski, Marek; Wahle, Manuel; Rusu, Mirabela; Wriggers, Willy

2012-09-01

The low radiation conditions and the predominantly phase-object image formation of cryo-electron microscopy (cryo-EM) result in extremely high noise levels and low contrast in the recorded micrographs. The process of single particle or tomographic 3D reconstruction does not completely eliminate this noise and is even capable of introducing new sources of noise during alignment or when correcting for instrument parameters. The recently developed Digital Paths Supervised Variance (DPSV) denoising filter uses local variance information to control regional noise in a robust and adaptive manner. The performance of the DPSV filter was evaluated in this review qualitatively and quantitatively using simulated and experimental data from cryo-EM and tomography in two and three dimensions. We also assessed the benefit of filtering experimental reconstructions for visualization purposes and for enhancing the accuracy of feature detection. The DPSV filter eliminates high-frequency noise artifacts (density gaps), which would normally preclude the accurate segmentation of tomography reconstructions or the detection of alpha-helices in single-particle reconstructions. This collaborative software development project was carried out entirely by virtual interactions among the authors using publicly available development and file sharing tools.

FIB-SEM cathodoluminescence tomography: practical and theoretical considerations.

PubMed

De Winter, D A M; Lebbink, M N; Wiggers De Vries, D F; Post, J A; Drury, M R

2011-09-01

Focused ion beam-scanning electron microscope (FIB-SEM) tomography is a powerful application in obtaining three-dimensional (3D) information. The FIB creates a cross section and subsequently removes thin slices. The SEM takes images using secondary or backscattered electrons, or maps every slice using X-rays and/or electron backscatter diffraction patterns. The objective of this study is to assess the possibilities of combining FIB-SEM tomography with cathodoluminescence (CL) imaging. The intensity of CL emission is related to variations in defect or impurity concentrations. A potential problem with FIB-SEM CL tomography is that ion milling may change the defect state of the material and the CL emission. In addition the conventional tilted sample geometry used in FIB-SEM tomography is not compatible with conventional CL detectors. Here we examine the influence of the FIB on CL emission in natural diamond and the feasibility of FIB-SEM CL tomography. A systematic investigation establishes that the ion beam influences CL emission of diamond, with a dependency on both the ion beam and electron beam acceleration voltage. CL emission in natural diamond is enhanced particularly at low ion beam and electron beam voltages. This enhancement of the CL emission can be partly explained by an increase in surface defects induced by ion milling. CL emission enhancement could be used to improve the CL image quality. To conduct FIB-SEM CL tomography, a recently developed novel specimen geometry is adopted to enable sequential ion milling and CL imaging on an untilted sample. We show that CL imaging can be manually combined with FIB-SEM tomography with a modified protocol for 3D microstructure reconstruction. In principle, automated FIB-SEM CL tomography should be feasible, provided that dedicated CL detectors are developed that allow subsequent milling and CL imaging without manual intervention, as the current CL detector needs to be manually retracted before a slice can be milled

Cryo-Electron Tomography of Marburg Virus Particles and Their Morphogenesis within Infected Cells

PubMed Central

Kolesnikova, Larissa; Welsch, Sonja; Krähling, Verena; Davey, Norman; Parsy, Marie-Laure; Becker, Stephan; Briggs, John A. G.

2011-01-01

Several major human pathogens, including the filoviruses, paramyxoviruses, and rhabdoviruses, package their single-stranded RNA genomes within helical nucleocapsids, which bud through the plasma membrane of the infected cell to release enveloped virions. The virions are often heterogeneous in shape, which makes it difficult to study their structure and assembly mechanisms. We have applied cryo-electron tomography and sub-tomogram averaging methods to derive structures of Marburg virus, a highly pathogenic filovirus, both after release and during assembly within infected cells. The data demonstrate the potential of cryo-electron tomography methods to derive detailed structural information for intermediate steps in biological pathways within intact cells. We describe the location and arrangement of the viral proteins within the virion. We show that the N-terminal domain of the nucleoprotein contains the minimal assembly determinants for a helical nucleocapsid with variable number of proteins per turn. Lobes protruding from alternate interfaces between each nucleoprotein are formed by the C-terminal domain of the nucleoprotein, together with viral proteins VP24 and VP35. Each nucleoprotein packages six RNA bases. The nucleocapsid interacts in an unusual, flexible “Velcro-like” manner with the viral matrix protein VP40. Determination of the structures of assembly intermediates showed that the nucleocapsid has a defined orientation during transport and budding. Together the data show striking architectural homology between the nucleocapsid helix of rhabdoviruses and filoviruses, but unexpected, fundamental differences in the mechanisms by which the nucleocapsids are then assembled together with matrix proteins and initiate membrane envelopment to release infectious virions, suggesting that the viruses have evolved different solutions to these conserved assembly steps. PMID:22110401

DYNAMICS OF NASCENT AND ACTIVE ZONE ULTRASTRUCTURE AS SYNAPSES ENLARGE DURING LTP IN MATURE HIPPOCAMPUS

PubMed Central

Bell, Maria Elizabeth; Bourne, Jennifer N.; Chirillo, Michael A.; Mendenhall, John M.; Kuwajima, Masaaki; Harris, Kristen M.

2014-01-01

Nascent zones and active zones are adjacent synaptic regions that share a postsynaptic density, but nascent zones lack the presynaptic vesicles found at active zones. Here dendritic spine synapses were reconstructed through serial section electron microscopy (3DEM) and EM tomography to investigate nascent zone dynamics during long-term potentiation (LTP) in mature rat hippocampus. LTP was induced with theta-burst stimulation and comparisons were made to control stimulation in the same hippocampal slices at 5 minutes, 30 minutes, and 2 hours post-induction and to perfusion-fixed hippocampus in vivo. Nascent zones were present at the edges of ~35% of synapses in perfusion-fixed hippocampus and as many as ~50% of synapses in some hippocampal slice conditions. By 5 minutes, small dense core vesicles known to transport active zone proteins moved into more presynaptic boutons. By 30 minutes, nascent zone area decreased without significant change in synapse area, suggesting that presynaptic vesicles were recruited to pre-existing nascent zones. By 2 hours, both nascent and active zones were enlarged. Immunogold labeling revealed that glutamate receptors can be found in nascent zones; however, average distances from nascent zones to docked presynaptic vesicles ranged from 170±5 nm in perfusion-fixed hippocampus to 251±4 nm at enlarged synapses by 2 hours during LTP. Prior stochastic modeling suggests that falloff in glutamate concentration reduces the probability of glutamate receptor activation from 0.4 at the center of release to 0.1 just 200 nm away. Thus, conversion of nascent zones to functional active zones likely requires the recruitment of presynaptic vesicles during LTP. PMID:25043676

Dual-color STED microscopy reveals a sandwich structure of Bassoon and Piccolo in active zones of adult and aged mice.

PubMed

Nishimune, Hiroshi; Badawi, Yomna; Mori, Shuuichi; Shigemoto, Kazuhiro

2016-06-20

Presynaptic active zones play a pivotal role as synaptic vesicle release sites for synaptic transmission, but the molecular architecture of active zones in mammalian neuromuscular junctions (NMJs) at sub-diffraction limited resolution remains unknown. Bassoon and Piccolo are active zone specific cytosolic proteins essential for active zone assembly in NMJs, ribbon synapses, and brain synapses. These proteins are thought to colocalize and share some functions at active zones. Here, we report an unexpected finding of non-overlapping localization of these two proteins in mouse NMJs revealed using dual-color stimulated emission depletion (STED) super resolution microscopy. Piccolo puncta sandwiched Bassoon puncta and aligned in a Piccolo-Bassoon-Piccolo structure in adult NMJs. P/Q-type voltage-gated calcium channel (VGCC) puncta colocalized with Bassoon puncta. The P/Q-type VGCC and Bassoon protein levels decreased significantly in NMJs from aged mouse. In contrast, the Piccolo levels in NMJs from aged mice were comparable to levels in adult mice. This study revealed the molecular architecture of active zones in mouse NMJs at sub-diffraction limited resolution, and described the selective degeneration mechanism of active zone proteins in NMJs from aged mice. Interestingly, the localization pattern of active zone proteins described herein is similar to active zone structures described using electron microscope tomography.

The E-Only Tipping Point for Journals: What's Ahead in the Print-to-Electronic Transition Zone

ERIC Educational Resources Information Center

Johnson, Richard K.; Luther, Judy

2007-01-01

This report examines the issues associated with moves toward electronic-only publication of journals, based on interviews with academic librarians and journal publishers. Noting that publishers and libraries today find themselves in an extended transition zone between print-only and e-only journals, the report investigates forces driving change…

IPET and FETR: Experimental Approach for Studying Molecular Structure Dynamics by Cryo-Electron Tomography of a Single-Molecule Structure

PubMed Central

Zhang, Lei; Ren, Gang

2012-01-01

The dynamic personalities and structural heterogeneity of proteins are essential for proper functioning. Structural determination of dynamic/heterogeneous proteins is limited by conventional approaches of X-ray and electron microscopy (EM) of single-particle reconstruction that require an average from thousands to millions different molecules. Cryo-electron tomography (cryoET) is an approach to determine three-dimensional (3D) reconstruction of a single and unique biological object such as bacteria and cells, by imaging the object from a series of tilting angles. However, cconventional reconstruction methods use large-size whole-micrographs that are limited by reconstruction resolution (lower than 20 Å), especially for small and low-symmetric molecule (<400 kDa). In this study, we demonstrated the adverse effects from image distortion and the measuring tilt-errors (including tilt-axis and tilt-angle errors) both play a major role in limiting the reconstruction resolution. Therefore, we developed a “focused electron tomography reconstruction” (FETR) algorithm to improve the resolution by decreasing the reconstructing image size so that it contains only a single-instance protein. FETR can tolerate certain levels of image-distortion and measuring tilt-errors, and can also precisely determine the translational parameters via an iterative refinement process that contains a series of automatically generated dynamic filters and masks. To describe this method, a set of simulated cryoET images was employed; to validate this approach, the real experimental images from negative-staining and cryoET were used. Since this approach can obtain the structure of a single-instance molecule/particle, we named it individual-particle electron tomography (IPET) as a new robust strategy/approach that does not require a pre-given initial model, class averaging of multiple molecules or an extended ordered lattice, but can tolerate small tilt-errors for high-resolution single �

Radial and Azimuthal Anisotropy Tomography of the NE Japan Subduction Zone: Implications for the Pacific Slab and Mantle Wedge Dynamics

NASA Astrophysics Data System (ADS)

Ishise, Motoko; Kawakatsu, Hitoshi; Morishige, Manabu; Shiomi, Katsuhiko

2018-05-01

We investigate slab and mantle structure of the NE Japan subduction zone from P wave azimuthal and radial anisotropy using travel time tomography. Trench normal E-W-trending azimuthal anisotropy (AA) and radial anisotropy (RA) with VPV > VPH are found in the mantle wedge, which supports the existence of small-scale convection in the mantle wedge with flow-induced LPO of mantle minerals. In the subducting Pacific slab, trench parallel N-S-trending AA and RA with VPH > VPV are obtained. Considering the effect of dip of the subducting slab on apparent anisotropy, we suggest that both characteristics can be explained by the presence of laminar structure, in addition to AA frozen-in in the subducting plate prior to subduction.

Structural analysis of vimentin and keratin intermediate filaments by cryo-electron tomography.

PubMed

Norlén, Lars; Masich, Sergej; Goldie, Kenneth N; Hoenger, Andreas

2007-06-10

Intermediate filaments are a large and structurally diverse group of cellular filaments that are classified into five different groups. They are referred to as intermediate filaments (IFs) because they are intermediate in diameter between the two other cytoskeletal filament systems that is filamentous actin and microtubules. The basic building block of IFs is a predominantly alpha-helical rod with variable length globular N- and C-terminal domains. On the ultra-structural level there are two major differences between IFs and microtubules or actin filaments: IFs are non-polar, and they do not exhibit large globular domains. IF molecules associate via a coiled-coil interaction into dimers and higher oligomers. Structural investigations into the molecular building plan of IFs have been performed with a variety of biophysical and imaging methods such as negative staining and metal-shadowing electron microscopy (EM), mass determination by scanning transmission EM, X-ray crystallography on fragments of the IF stalk and low-angle X-ray scattering. The actual packing of IF dimers into a long filament varies between the different families. Typically the dimers form so called protofibrils that further assemble into a filament. Here we introduce new cryo-imaging methods for structural investigations of IFs in vitro and in vivo, i.e., cryo-electron microscopy and cryo-electron tomography, as well as associated techniques such as the preparation and handling of vitrified sections of cellular specimens.

Spatial localization of the Ebola virus glycoprotein mucin-like domain determined by cryo-electron tomography.

PubMed

Tran, Erin E H; Simmons, James A; Bartesaghi, Alberto; Shoemaker, Charles J; Nelson, Elizabeth; White, Judith M; Subramaniam, Sriram

2014-09-01

The Ebola virus glycoprotein mucin-like domain (MLD) is implicated in Ebola virus cell entry and immune evasion. Using cryo-electron tomography of Ebola virus-like particles, we determined a three-dimensional structure for the full-length glycoprotein in a near-native state and compared it to that of a glycoprotein lacking the MLD. Our results, which show that the MLD is located at the apex and the sides of each glycoprotein monomer, provide a structural template for analysis of MLD function. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research

PubMed Central

Alaidi, Osama; Rames, Matthew J.

2016-01-01

Three-dimensional (3D) structural analysis is essential to understand the relationship between the structure and function of an object. Many analytical techniques, such as X-ray diffraction, neutron spectroscopy, and electron microscopy imaging, are used to provide structural information. Transmission electron microscopy (TEM), one of the most popular analytic tools, has been widely used for structural analysis in both physical and biological sciences for many decades, in which 3D objects are projected into two-dimensional (2D) images. In many cases, 2D-projection images are insufficient to understand the relationship between the 3D structure and the function of nanoscale objects. Electron tomography (ET) is a technique that retrieves 3D structural information from a tilt series of 2D projections, and is gradually becoming a mature technology with sub-nanometer resolution. Distinct methods to overcome sample-based limitations have been separately developed in both physical and biological science, although they share some basic concepts of ET. This review discusses the common basis for 3D characterization, and specifies difficulties and solutions regarding both hard and soft materials research. It is hoped that novel solutions based on current state-of-the-art techniques for advanced applications in hybrid matter systems can be motivated. PMID:26087941

Electron tomography and nano-diffraction enabling the investigation of individual magnetic nanoparticles inside fibers of MR visible implants

NASA Astrophysics Data System (ADS)

Slabu, I.; Wirch, N.; Caumanns, T.; Theissmann, R.; Krüger, M.; Schmitz-Rode, T.; Weirich, T. E.

2017-08-01

Superparamagnetic iron oxide nanoparticles (SPIONPs) incorporated into the base material of implants are used as contrast agents in magnetic resonance imaging for the delineation of the implants from the surrounding tissue. However, the delineation quality is strongly related to the structural characteristics of the incorporated SPIONPs and their interparticle interaction as well as their interaction with the polymer matrix of the implant. Consequently, a profound knowledge of the formation of aggregates inside the polymer matrix, which are responsible for strong interparticle interactions, and of their structural characteristics, is required for controlling the magnetic resonance image quality of the implants. In this work, transmission electron microscopy methods such as electron tomography and nano-electron diffraction were used to depict SPIONP aggregates inside the melt-spin polyvinylidene fluoride fibers used for the assembly of implants and to determine the crystal structure of individual nanocrystals inside these aggregates, respectively. Using these techniques it was possible for the first time to characterize the aggregates inside the fibers of implants and to validate the magnetization measurements that have been previously used to assess the interaction phenomena inside the fibers of implants. With electron tomography, inhomogeneously sized distributed aggregates were delineated and 3D models of these aggregates were constructed. Furthermore, the distribution of the aggregates inside the fibers was verified by means of magnetic force microscopy. With nano-diffraction measurements, the SPIONP crystal structure inside the fibers of the implant could not be clearly assigned to that of magnetite (Fe3O4) or maghemite (γ-Fe2O3). Therefore, additional electron energy loss spectroscopy measurements were performed, which revealed the presence of both phases of Fe3O4 and γ-Fe2O3, probably caused by oxidation processes during the manufacture of the fibers by

Sampling limits for electron tomography with sparsity-exploiting reconstructions.

PubMed

Jiang, Yi; Padgett, Elliot; Hovden, Robert; Muller, David A

2018-03-01

Electron tomography (ET) has become a standard technique for 3D characterization of materials at the nano-scale. Traditional reconstruction algorithms such as weighted back projection suffer from disruptive artifacts with insufficient projections. Popularized by compressed sensing, sparsity-exploiting algorithms have been applied to experimental ET data and show promise for improving reconstruction quality or reducing the total beam dose applied to a specimen. Nevertheless, theoretical bounds for these methods have been less explored in the context of ET applications. Here, we perform numerical simulations to investigate performance of ℓ 1 -norm and total-variation (TV) minimization under various imaging conditions. From 36,100 different simulated structures, our results show specimens with more complex structures generally require more projections for exact reconstruction. However, once sufficient data is acquired, dividing the beam dose over more projections provides no improvements-analogous to the traditional dose-fraction theorem. Moreover, a limited tilt range of ±75° or less can result in distorting artifacts in sparsity-exploiting reconstructions. The influence of optimization parameters on reconstructions is also discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Organization of organelles within hyphae of Ashbya gossypii revealed by electron tomography.

PubMed

Gibeaux, Romain; Hoepfner, Dominic; Schlatter, Ivan; Antony, Claude; Philippsen, Peter

2013-11-01

Ashbya gossypii grows as multinucleated and constantly elongating hyphae. Nuclei are in continuous forward and backward motion, also move during mitosis, and frequently bypass each other. Whereas these nuclear movements are well documented, comparatively little is known about the density and morphology of organelles which very likely influence these movements. To understand the three-dimensional subcellular organization of hyphae at high resolution, we performed large-scale electron tomography of the tip regions in A. gossypii. Here, we present a comprehensive space-filling model in which most membrane-limited organelles including nuclei, mitochondria, endosomes, multivesicular bodies, vacuoles, autophagosomes, peroxisomes, and vesicles are modeled. Nuclei revealed different morphologies and protrusions filled by the nucleolus. Mitochondria are very abundant and form a tubular network with a polarized spherical fraction. The organelles of the degradative pathways show a clustered organization. By analyzing vesicle-like bodies, we identified three size classes of electron-dense vesicles (∼200, ∼150, and ∼100 nm) homogeneously distributed in the cytoplasm which most likely represent peroxisomes. Finally, coated and uncoated vesicles with approximately 40-nm diameters show a polarized distribution toward the hyphal tip with the coated vesicles preferentially localizing at the hyphal periphery.

Retinal nerve fiber layer thickness measured with optical coherence tomography is related to visual function in glaucomatous eyes.

PubMed

El Beltagi, Tarek A; Bowd, Christopher; Boden, Catherine; Amini, Payam; Sample, Pamela A; Zangwill, Linda M; Weinreb, Robert N

2003-11-01

To determine the relationship between areas of glaucomatous retinal nerve fiber layer thinning identified by optical coherence tomography and areas of decreased visual field sensitivity identified by standard automated perimetry in glaucomatous eyes. Retrospective observational case series. Forty-three patients with glaucomatous optic neuropathy identified by optic disc stereo photographs and standard automated perimetry mean deviations >-8 dB were included. Participants were imaged with optical coherence tomography within 6 months of reliable standard automated perimetry testing. The location and number of optical coherence tomography clock hour retinal nerve fiber layer thickness measures outside normal limits were compared with the location and number of standard automated perimetry visual field zones outside normal limits. Further, the relationship between the deviation from normal optical coherence tomography-measured retinal nerve fiber layer thickness at each clock hour and the average pattern deviation in each visual field zone was examined by using linear regression (R(2)). The retinal nerve fiber layer areas most frequently outside normal limits were the inferior and inferior temporal regions. The least sensitive visual field zones were in the superior hemifield. Linear regression results (R(2)) showed that deviation from the normal retinal nerve fiber layer thickness at optical coherence tomography clock hour positions 6 o'clock, 7 o'clock, and 8 o'clock (inferior and inferior temporal) was best correlated with standard automated perimetry pattern deviation in visual field zones corresponding to the superior arcuate and nasal step regions (R(2) range, 0.34-0.57). These associations were much stronger than those between clock hour position 6 o'clock and the visual field zone corresponding to the inferior nasal step region (R(2) = 0.01). Localized retinal nerve fiber layer thinning, measured by optical coherence tomography, is topographically related to

Computed Tomography Perfusion, Magnetic Resonance Imaging, and Histopathological Findings After Laparoscopic Renal Cryoablation: An In Vivo Pig Model.

PubMed

Nielsen, Tommy Kjærgaard; Østraat, Øyvind; Graumann, Ole; Pedersen, Bodil Ginnerup; Andersen, Gratien; Høyer, Søren; Borre, Michael

2017-08-01

The present study investigates how computed tomography perfusion scans and magnetic resonance imaging correlates with the histopathological alterations in renal tissue after cryoablation. A total of 15 pigs were subjected to laparoscopic-assisted cryoablation on both kidneys. After intervention, each animal was randomized to a postoperative follow-up period of 1, 2, or 4 weeks, after which computed tomography perfusion and magnetic resonance imaging scans were performed. Immediately after imaging, open bilateral nephrectomy was performed allowing for histopathological examination of the cryolesions. On computed tomography perfusion and magnetic resonance imaging examinations, rim enhancement was observed in the transition zone of the cryolesion 1week after laparoscopic-assisted cryoablation. This rim enhancement was found to subside after 2 and 4 weeks of follow-up, which was consistent with the microscopic examinations revealing of fibrotic scar tissue formation in the peripheral zone of the cryolesion. On T2 magnetic resonance imaging sequences, a thin hypointense rim surrounded the cryolesion, separating it from the adjacent renal parenchyma. Microscopic examinations revealed hemorrhage and later hemosiderin located in the peripheral zone. No nodular or diffuse contrast enhancement was found in the central zone of the cryolesions at any follow-up stage on neither computed tomography perfusion nor magnetic resonance imaging. On microscopic examinations, the central zone was found to consist of coagulative necrosis 1 week after laparoscopic-assisted cryoablation, which was partially replaced by fibrotic scar tissue 4 weeks following laparoscopic-assisted cryoablation. Both computed tomography perfusion and magnetic resonance imaging found the renal collecting system to be involved at all 3 stages of follow-up, but on microscopic examination, the urothelium was found to be intact in all cases. In conclusion, cryoablation effectively destroyed renal parenchyma

Nanoroses of nickel oxides: synthesis, electron tomography study, and application in CO oxidation and energy storage.

PubMed

Fihri, Aziz; Sougrat, Rachid; Rakhi, Raghavan Baby; Rahal, Raed; Cha, Dongkyu; Hedhili, Mohamed Nejib; Bouhrara, Mohamed; Alshareef, Husam N; Polshettiwar, Vivek

2012-07-01

Nickel oxide and mixed-metal oxide structures were fabricated by using microwave irradiation in pure water. The nickel oxide self-assembled into unique rose-shaped nanostructures. These nickel oxide roses were studied by performing electron tomography with virtual cross-sections through the particles to understand their morphology from their interior to their surface. These materials exhibited promising performance as nanocatalysts for CO oxidation and in energy storage devices. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fast auto-acquisition tomography tilt series by using HD video camera in ultra-high voltage electron microscope.

PubMed

Nishi, Ryuji; Cao, Meng; Kanaji, Atsuko; Nishida, Tomoki; Yoshida, Kiyokazu; Isakozawa, Shigeto

2014-11-01

The ultra-high voltage electron microscope (UHVEM) H-3000 with the world highest acceleration voltage of 3 MV can observe remarkable three dimensional microstructures of microns-thick samples[1]. Acquiring a tilt series of electron tomography is laborious work and thus an automatic technique is highly desired. We proposed the Auto-Focus system using image Sharpness (AFS)[2,3] for UHVEM tomography tilt series acquisition. In the method, five images with different defocus values are firstly acquired and the image sharpness are calculated. The sharpness are then fitted to a quasi-Gaussian function to decide the best focus value[3]. Defocused images acquired by the slow scan CCD (SS-CCD) camera (Hitachi F486BK) are of high quality but one minute is taken for acquisition of five defocused images.In this study, we introduce a high-definition video camera (HD video camera; Hamamatsu Photonics K. K. C9721S) for fast acquisition of images[4]. It is an analog camera but the camera image is captured by a PC and the effective image resolution is 1280×1023 pixels. This resolution is lower than that of the SS-CCD camera of 4096×4096 pixels. However, the HD video camera captures one image for only 1/30 second. In exchange for the faster acquisition the S/N of images are low. To improve the S/N, 22 captured frames are integrated so that each image sharpness is enough to become lower fitting error. As countermeasure against low resolution, we selected a large defocus step, which is typically five times of the manual defocus step, to discriminate different defocused images.By using HD video camera for autofocus process, the time consumption for each autofocus procedure was reduced to about six seconds. It took one second for correction of an image position and the total correction time was seven seconds, which was shorter by one order than that using SS-CCD camera. When we used SS-CCD camera for final image capture, it took 30 seconds to record one tilt image. We can obtain a tilt

Electron microscopy of Drosophila garland cell nephrocytes: Optimal preparation, immunostaining and STEM tomography.

PubMed

Hochapfel, Florian; Denk, Lucia; Maaßen, Christine; Zaytseva, Yulia; Rachel, Reinhard; Witzgall, Ralph; Krahn, Michael P

2018-01-29

Due to its structural and molecular similarities to mammalian podocytes, the Drosophila nephrocyte emerged as a model system to study podocyte development and associated diseases. Similar to podocytes, nephrocytes establish a slit diaphragm between foot process-like structures in order to filter the hemolymph. One major obstacle in nephrocyte research is the distinct visualization of this subcellular structure to assess its integrity. Therefore, we developed a specialized dissection and fixation protocol, including high pressure freezing and freeze substitution techniques, to improve the preservation of the intricate ultrastructural details necessary for electron microscopic assessment. By means of scanning transmission electron microscopy (STEM) tomography, a three-dimensional dataset was generated to further understand the complex architecture of the nephrocyte channel system. Moreover, a staining protocol for immunolabeling of ultrathin sections of Epon-embedded nephrocytes is discussed, which allows the reliable detection of GFP-tagged fusion proteins combined with superior sample preservation. Due to the growing number of available GFP-trap fly lines, this approach is widely applicable for high resolution localization studies in wild type and mutant nephrocytes. © 2018 Wiley Periodicals, Inc.

Analysis of inner and outer zone: OGO-1 and OGO-2 electron spectrometer and ion chamber data

NASA Technical Reports Server (NTRS)

Pfitzer, K. A.

1972-01-01

The dynamic processes governing the acceleration and loss of electrons in the radiation zones are investigated. The radial diffusion coefficient was determined for a McIlwain parameter between 1.6 and 2.2 for electrons having a first adiabatic invariant of 12 MeV/gauss. The coefficient is larger than earlier values and suggests that there exists a lower limit to the fluxes in the inner zone. The agreement between observed and calculated magnetic fields and particle fluxes is improved by using solar wind pressure as input to the magnetic field models. Changes in the plasma pressure can cause apparent local time asymmetries in particle flux. A comparison of the magnetic field models with observed location of the trapping boundary also indicates the need for including distributed currents within the magnetosphere. The high latitude trapping boundary is only weakly dependent on A sub p, and the trapping boundary data are improved by including in the models a stand-off distance which varies with the plasma pressure.

HAADF-STEM atom counting in atom probe tomography specimens: Towards quantitative correlative microscopy.

PubMed

Lefebvre, W; Hernandez-Maldonado, D; Moyon, F; Cuvilly, F; Vaudolon, C; Shinde, D; Vurpillot, F

2015-12-01

The geometry of atom probe tomography tips strongly differs from standard scanning transmission electron microscopy foils. Whereas the later are rather flat and thin (<20 nm), tips display a curved surface and a significantly larger thickness. As far as a correlative approach aims at analysing the same specimen by both techniques, it is mandatory to explore the limits and advantages imposed by the particular geometry of atom probe tomography specimens. Based on simulations (electron probe propagation and image simulations), the possibility to apply quantitative high angle annular dark field scanning transmission electron microscopy to of atom probe tomography specimens has been tested. The influence of electron probe convergence and the benefice of deconvolution of electron probe point spread function electron have been established. Atom counting in atom probe tomography specimens is for the first time reported in this present work. It is demonstrated that, based on single projections of high angle annular dark field imaging, significant quantitative information can be used as additional input for refining the data obtained by correlative analysis of the specimen in APT, therefore opening new perspectives in the field of atomic scale tomography. Copyright © 2015 Elsevier B.V. All rights reserved.

Three dimensional X-ray Diffraction Contrast Tomography Reconstruction of Polycrystalline Strontium Titanate during Sintering and Electron Backscatter Diffraction Validation

NASA Astrophysics Data System (ADS)

Syha, M.; Rheinheimer, W.; Loedermann, B.; Graff, A.; Trenkle, A.; Baeurer, M.; Weygand, D.; Ludwig, W.; Gumbsch, P.

The microstructural evolution of polycrystalline strontium titanate was investigated in three dimensions (3D) using X-ray diffraction contrast tomography (DCT) before and after ex-situ annealing at 1600°C. Post-annealing, the specimen was additionally subjected to phase contrast tomography (PCT) in order to finely resolve the porosities. The resulting microstructure reconstructions were studied with special emphasis on morphology and interface orientation during microstructure evolution. Subsequently, cross-sections of the specimen were studied using electron backscatter diffraction (EBSD). Corresponding cross-sections through the 3D reconstruction were identified and the quality of the reconstruction is validated with special emphasis on the spatial resolution at the grain boundaries, the size and location of pores contained in the material and the accuracy of the orientation determination.

Hydrogeophysical imaging of deposit heterogeneity and groundwater chemistry changes during DNAPL source zone bioremediation.

PubMed

Chambers, J E; Wilkinson, P B; Wealthall, G P; Loke, M H; Dearden, R; Wilson, R; Allen, D; Ogilvy, R D

2010-10-21

Robust characterization and monitoring of dense nonaqueous phase liquid (DNAPL) source zones is essential for designing effective remediation strategies, and for assessing the efficacy of treatment. In this study high-resolution cross-hole electrical resistivity tomography (ERT) was evaluated as a means of monitoring a field-scale in-situ bioremediation experiment, in which emulsified vegetable oil (EVO) electron donor was injected into a trichloroethene source zone. Baseline ERT scans delineated the geometry of the interface between the contaminated alluvial aquifer and the underlying mudstone bedrock, and also the extent of drilling-induced physical heterogeneity. Time-lapse ERT images revealed major preferential flow pathways in the source and plume zones, which were corroborated by multiple lines of evidence, including geochemical monitoring and hydraulic testing using high density multilevel sampler arrays within the geophysical imaging planes. These pathways were shown to control the spatial distribution of the injected EVO, and a bicarbonate buffer introduced into the cell for pH control. Resistivity signatures were observed within the preferential flow pathways that were consistent with elevated chloride levels, providing tentative evidence from ERT of the biodegradation of chlorinated solvents. Copyright © 2010 S. Yamamoto. Published by Elsevier B.V. All rights reserved.

Correlative Tomography

PubMed Central

Burnett, T. L.; McDonald, S. A.; Gholinia, A.; Geurts, R.; Janus, M.; Slater, T.; Haigh, S. J.; Ornek, C.; Almuaili, F.; Engelberg, D. L.; Thompson, G. E.; Withers, P. J.

2014-01-01

Increasingly researchers are looking to bring together perspectives across multiple scales, or to combine insights from different techniques, for the same region of interest. To this end, correlative microscopy has already yielded substantial new insights in two dimensions (2D). Here we develop correlative tomography where the correlative task is somewhat more challenging because the volume of interest is typically hidden beneath the sample surface. We have threaded together x-ray computed tomography, serial section FIB-SEM tomography, electron backscatter diffraction and finally TEM elemental analysis all for the same 3D region. This has allowed observation of the competition between pitting corrosion and intergranular corrosion at multiple scales revealing the structural hierarchy, crystallography and chemistry of veiled corrosion pits in stainless steel. With automated correlative workflows and co-visualization of the multi-scale or multi-modal datasets the technique promises to provide insights across biological, geological and materials science that are impossible using either individual or multiple uncorrelated techniques. PMID:24736640

Attenuation tomography of the main volcanic regions of the Campanian Plain.

NASA Astrophysics Data System (ADS)

de Siena, Luca; Del Pezzo, Edoardo; Bianco, Francesca

2010-05-01

Passive, high resolution attenuation tomography is used to image the geological structure in the first upper 4 km of shallow crust beneath the Campanian Plain. Images were produced by two separate attenuation tomography studies of the main volcanic regions of the Campanian Plain, Southern Italy, Mt. Vesuvius volcano and Campi Flegrei caldera. The three-dimensional S wave attenuation tomography of Mt. Vesuvius has been obtained with multiple measurements of coda-normalized S-wave spectra of local small magnitude earthquakes. P-wave attenuation tomography was performed using classical spectral methods. The images were obtained inverting the spectral data with a multiple resolution approach expressively designed for attenuation tomography. This allowed to obtain a robust attenuation image of the volumes under the central cone at a maximum resolution of 300 m. The same approach was applied to a data set recorded in the Campi Flegrei area during the 1982-1984 seismic crisis. Inversion ensures a minimum cell size resolution of 500 meters in the zones with sufficient ray coverage, and 1000 meters outside these zones. The study of the resolution matrix as well as the synthetic tests guarantee an optimal reproduction of the input anomalies in the center of the caldera, between 0 and 3.5 km in depth. Results allowed an unprecedented view of several features of the medium, like the residual part of solidified magma from the last eruption, under the central cone of Mt. Vesuvius, and the feeding systems and top of the carbonate basement, 3 km depth below both volcanic areas. Vertical Q contrast image important fault zones, such as the La Starza fault, as well as high attenuation structures that correspond to gas or fluid reservoirs, and reveal the upper part of gas bearing conduits connecting these high attenuation volumes with the magma sill revealed at about 7 km in depth by passive travel-time tomography under the whole Campanian Plain.

Differentiation and Characterization of Excitatory and Inhibitory Synapses by Cryo-electron Tomography and Correlative Microscopy

PubMed Central

Sun, Rong; Zhang, Bin; Qi, Lei; Shivakoti, Sakar; Tian, Chong-Li; Lau, Pak-Ming

2018-01-01

As key functional units in neural circuits, different types of neuronal synapses play distinct roles in brain information processing, learning, and memory. Synaptic abnormalities are believed to underlie various neurological and psychiatric disorders. Here, by combining cryo-electron tomography and cryo-correlative light and electron microscopy, we distinguished intact excitatory and inhibitory synapses of cultured hippocampal neurons, and visualized the in situ 3D organization of synaptic organelles and macromolecules in their native state. Quantitative analyses of >100 synaptic tomograms reveal that excitatory synapses contain a mesh-like postsynaptic density (PSD) with thickness ranging from 20 to 50 nm. In contrast, the PSD in inhibitory synapses assumes a thin sheet-like structure ∼12 nm from the postsynaptic membrane. On the presynaptic side, spherical synaptic vesicles (SVs) of 25–60 nm diameter and discus-shaped ellipsoidal SVs of various sizes coexist in both synaptic types, with more ellipsoidal ones in inhibitory synapses. High-resolution tomograms obtained using a Volta phase plate and electron filtering and counting reveal glutamate receptor-like and GABAA receptor-like structures that interact with putative scaffolding and adhesion molecules, reflecting details of receptor anchoring and PSD organization. These results provide an updated view of the ultrastructure of excitatory and inhibitory synapses, and demonstrate the potential of our approach to gain insight into the organizational principles of cellular architecture underlying distinct synaptic functions. SIGNIFICANCE STATEMENT To understand functional properties of neuronal synapses, it is desirable to analyze their structure at molecular resolution. We have developed an integrative approach combining cryo-electron tomography and correlative fluorescence microscopy to visualize 3D ultrastructural features of intact excitatory and inhibitory synapses in their native state. Our approach shows

Differentiation and Characterization of Excitatory and Inhibitory Synapses by Cryo-electron Tomography and Correlative Microscopy.

PubMed

Tao, Chang-Lu; Liu, Yun-Tao; Sun, Rong; Zhang, Bin; Qi, Lei; Shivakoti, Sakar; Tian, Chong-Li; Zhang, Peijun; Lau, Pak-Ming; Zhou, Z Hong; Bi, Guo-Qiang

2018-02-07

As key functional units in neural circuits, different types of neuronal synapses play distinct roles in brain information processing, learning, and memory. Synaptic abnormalities are believed to underlie various neurological and psychiatric disorders. Here, by combining cryo-electron tomography and cryo-correlative light and electron microscopy, we distinguished intact excitatory and inhibitory synapses of cultured hippocampal neurons, and visualized the in situ 3D organization of synaptic organelles and macromolecules in their native state. Quantitative analyses of >100 synaptic tomograms reveal that excitatory synapses contain a mesh-like postsynaptic density (PSD) with thickness ranging from 20 to 50 nm. In contrast, the PSD in inhibitory synapses assumes a thin sheet-like structure ∼12 nm from the postsynaptic membrane. On the presynaptic side, spherical synaptic vesicles (SVs) of 25-60 nm diameter and discus-shaped ellipsoidal SVs of various sizes coexist in both synaptic types, with more ellipsoidal ones in inhibitory synapses. High-resolution tomograms obtained using a Volta phase plate and electron filtering and counting reveal glutamate receptor-like and GABA A receptor-like structures that interact with putative scaffolding and adhesion molecules, reflecting details of receptor anchoring and PSD organization. These results provide an updated view of the ultrastructure of excitatory and inhibitory synapses, and demonstrate the potential of our approach to gain insight into the organizational principles of cellular architecture underlying distinct synaptic functions. SIGNIFICANCE STATEMENT To understand functional properties of neuronal synapses, it is desirable to analyze their structure at molecular resolution. We have developed an integrative approach combining cryo-electron tomography and correlative fluorescence microscopy to visualize 3D ultrastructural features of intact excitatory and inhibitory synapses in their native state. Our approach shows

Three-dimensional morphology of GaP-GaAs nanowires revealed by transmission electron microscopy tomography.

PubMed

Verheijen, Marcel A; Algra, Rienk E; Borgström, Magnus T; Immink, George; Sourty, Erwan; Enckevort, Willem J P van; Vlieg, Elias; Bakkers, Erik P A M

2007-10-01

We have investigated the morphology of heterostructured GaP-GaAs nanowires grown by metal-organic vapor-phase epitaxy as a function of growth temperature and V/III precursor ratio. The study of heterostructured nanowires with transmission electron microscopy tomography allowed the three-dimensional morphology to be resolved, and discrimination between the effect of axial (core) and radial (shell) growth on the morphology. A temperature- and precursor-dependent structure diagram for the GaP nanowire core morphology and the evolution of the different types of side facets during GaAs and GaP shell growth were constituted.

A Closed-Loop Proportional-Integral (PI) Control Software for Fully Mechanically Controlled Automated Electron Microscopic Tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

REN, GANG; LIU, JINXIN; LI, HONGCHANG

A closed-loop proportional-integral (PI) control software is provided for fully mechanically controlled automated electron microscopic tomography. The software is developed based on Gatan DigitalMicrograph, and is compatible with Zeiss LIBRA 120 transmission electron microscope. However, it can be expanded to other TEM instrument with modification. The software consists of a graphical user interface, a digital PI controller, an image analyzing unit, and other drive units (i.e.: image acquire unit and goniometer drive unit). During a tomography data collection process, the image analyzing unit analyzes both the accumulated shift and defocus value of the latest acquired image, and provides the resultsmore » to the digital PI controller. The digital PI control compares the results with the preset values and determines the optimum adjustments of the goniometer. The goniometer drive unit adjusts the spatial position of the specimen according to the instructions given by the digital PI controller for the next tilt angle and image acquisition. The goniometer drive unit achieves high precision positioning by using a backlash elimination method. The major benefits of the software are: 1) the goniometer drive unit keeps pre-aligned/optimized beam conditions unchanged and achieves position tracking solely through mechanical control; 2) the image analyzing unit relies on only historical data and therefore does not require additional images/exposures; 3) the PI controller enables the system to dynamically track the imaging target with extremely low system error.« less

Three-dimensional Architecture of Hair-bundle Linkages Revealed by Electron-microscopic Tomography

PubMed Central

Auer, Manfred; Koster, Abrahram J.; Ziese, Ulrike; Bajaj, Chandrajit; Volkmann, Niels; Wang, Da Neng

2008-01-01

The senses of hearing and balance rest upon mechanoelectrical transduction by the hair bundles of hair cells in the inner ear. Located at the apical cellular surface, each hair bundle comprises several tens of stereocilia and a single kinocilium that are interconnected by extracellular proteinaceous links. Using electron-microscopic tomography of bullfrog saccular sensory epithelia, we examined the three-dimensional structures of basal links, kinociliary links, and tip links. We observed significant differences in the appearances and dimensions of these three structures and found two distinct populations of tip links suggestive of the involvement of different proteins, splice variants, or protein–protein interactions. We noted auxiliary links connecting the upper portions of tip links to the taller stereocilia. Tip links and auxiliary links show a tendency to adopt a globular conformation when disconnected from the membrane surface. PMID:18421501

Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research.

PubMed

Ercius, Peter; Alaidi, Osama; Rames, Matthew J; Ren, Gang

2015-10-14

Three-dimensional (3D) structural analysis is essential to understand the relationship between the structure and function of an object. Many analytical techniques, such as X-ray diffraction, neutron spectroscopy, and electron microscopy imaging, are used to provide structural information. Transmission electron microscopy (TEM), one of the most popular analytic tools, has been widely used for structural analysis in both physical and biological sciences for many decades, in which 3D objects are projected into two-dimensional (2D) images. In many cases, 2D-projection images are insufficient to understand the relationship between the 3D structure and the function of nanoscale objects. Electron tomography (ET) is a technique that retrieves 3D structural information from a tilt series of 2D projections, and is gradually becoming a mature technology with sub-nanometer resolution. Distinct methods to overcome sample-based limitations have been separately developed in both physical and biological science, although they share some basic concepts of ET. This review discusses the common basis for 3D characterization, and specifies difficulties and solutions regarding both hard and soft materials research. It is hoped that novel solutions based on current state-of-the-art techniques for advanced applications in hybrid matter systems can be motivated. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Near surface structure of the North Anatolian Fault Zone near 30°E from Rayleigh and Love wave tomography using ambient seismic noise.

NASA Astrophysics Data System (ADS)

Taylor, G.; Rost, S.; Houseman, G. A.; Hillers, G.

2017-12-01

By utilising short period surface waves present in the noise field, we can construct images of shallow structure in the Earth's upper crust: a depth-range that is usually poorly resolved in earthquake tomography. Here, we use data from a dense seismic array (Dense Array for Northern Anatolia - DANA) deployed across the North Anatolian Fault Zone (NAFZ) in the source region of the 1999 magnitude 7.6 Izmit earthquake in western Turkey. The NAFZ is a major strike-slip system that extends 1200 km across northern Turkey and continues to pose a high level of seismic hazard, in particular to the mega-city of Istanbul. We obtain maps of group velocity variation using surface wave tomography applied to short period (1- 6 s) Rayleigh and Love waves to construct high-resolution images of SV and SH-wave velocity in the upper 5 km of a 70 km x 35 km region centred on the eastern end of the fault segment that ruptured in the 1999 Izmit earthquake. The average Rayleigh wave group velocities in the region vary between 1.8 km/s at 1.5 s period, to 2.2 km/s at 6 s period. The NAFZ bifurcates into northern and southern strands in this region; both are active but only the northern strand ruptured in the 1999 event. The signatures of both the northern and southern branches of the NAFZ are clearly associated with strong gradients in seismic velocity that also denote the boundaries of major tectonic units. This observation implies that the fault zone exploits the pre-existing structure of the Intra-Pontide suture zone. To the north of the NAFZ, we observe low S-wave velocities ( 2.0 km/s) associated with the unconsolidated sediments of the Adapazari basin, and blocks of weathered terrigenous clastic sediments. To the south of the northern branch of the NAFZ in the Armutlu block, we detect higher velocities ( 2.9 km/s) associated with a shallow crystalline basement, in particular a block of metamorphosed schists and marbles that bound the northern branch of the NAFZ.

High resolution IVEM tomography of biological specimens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sedat, J.W.; Agard, D.A.

Electron tomography is a powerful tool for elucidating the three-dimensional architecture of large biological complexes and subcellular organelles. The introduction of intermediate voltage electron microscopes further extended the technique by providing the means to examine very large and non-symmetrical subcellular organelles, at resolutions beyond what would be possible using light microscopy. Recent studies using electron tomography on a variety of cellular organelles and assemblies such as centrosomes, kinetochores, and chromatin have clearly demonstrated the power of this technique for obtaining 3D structural information on non-symmetric cell components. When combined with biochemical and molecular observations, these 3D reconstructions have provided significantmore » new insights into biological function.« less

New trend in electron holography

NASA Astrophysics Data System (ADS)

Tanigaki, Toshiaki; Harada, Ken; Murakami, Yasukazu; Niitsu, Kodai; Akashi, Tetsuya; Takahashi, Yoshio; Sugawara, Akira; Shindo, Daisuke

2016-06-01

Electron holography using a coherent electron wave is a promising technique for high-resolution visualization of electromagnetic fields in and around objects. The capability of electron holography has been enhanced by the development of new technologies and has thus become an even more powerful tool for exploring scientific frontiers. This review introduces these technologies including split-illumination electron holography and vector-field electron tomography. Split-illumination electron holography, which uses separated coherent waves, overcomes the limits imposed by the lateral coherence requirement for electron waves in electron holography. Areas that are difficult to observe using conventional electron holography are now observable. Exemplified applications include observing a singular magnetic domain wall in electrical steel sheets, local magnetizations at anti-phase boundaries, and electrostatic potentials in metal-oxide-semiconductor field-effect transistors. Vector-field electron tomography can be used to visualize magnetic vectors in three dimensions. Two components of the vectors are reconstructed using dual-axis tomography, and the remaining one is calculated using div B   =  0. A high-voltage electron microscope can be used to achieve precise magnetic reconstruction. For example, magnetic vortices have been visualized using a 1 MV holography electron microscope.

Noninvasive coronary artery angiography using electron beam computed tomography

NASA Astrophysics Data System (ADS)

Rumberger, John A.; Rensing, Benno J.; Reed, Judd E.; Ritman, Erik L.; Sheedy, Patrick F., II

1996-04-01

Electron beam computed tomography (EBCT), also known as ultrafast-CT or cine-CT, uses a unique scanning architecture which allows for multiple high spatial resolution electrocardiographic triggered images of the beating heart. A recent study has demonstrated the feasibility of qualitative comparisons between EBCT derived 3D coronary angiograms and invasive angiography. Stenoses of the proximal portions of the left anterior descending and right coronary arteries were readily identified, but description of atherosclerotic narrowing in the left circumflex artery (and distal epicardial disease) was not possible with any degree of confidence. Although these preliminary studies support the notion that this approach has potential, the images overall were suboptimal for clinical application as an adjunct to invasive angiography. Furthermore, these studies did not examine different methods of EBCT scan acquisition, tomographic slice thicknesses, extent of scan overlap, or other segmentation, thresholding, and interpolation algorithms. Our laboratory has initiated investigation of these aspects and limitations of EBCT coronary angiography. Specific areas of research include defining effects of cardiac orientation; defining the effects of tomographic slice thickness and intensity (gradient) versus positional (shaped based) interpolation; and defining applicability of imaging each of the major epicardial coronary arteries for quantitative definition of vessel size, cross-sectional area, taper, and discrete vessel narrowing.

Imaging of osteo-odonto-keratoprosthesis by electron beam tomography

PubMed Central

Fong, K C S; Ferrett, C G; Tandon, R; Paul, B; Herold, J; Liu, C S C

2005-01-01

Aim: To describe the experience of using electron beam tomography (EBT) in imaging of osteo-odonto-keratoprosthesis (OOKP) to identify early bone and dentine loss which may threaten the viability of the eye. Methods: Seven patients with an OOKP in one eye underwent EBT. The OOKP lamina dimensions were measured on EBT and compared to the manual measurements at the time of surgery. Results: There was a high degree of resolution of the OOKP lamina noted with EBT. In particular, it identified three patients with a marked degree of thinning of the lamina edges. Two of these patients had OOKP that were allografts. The mean time from surgery to examination was 3.6 years (range 1.2–5 years) while the mean age of the patients was 56 years (range 31–79 years). Conclusions: It is important to monitor regularly the dimensions and stability of the OOKP lamina as it will help detect cases that are at risk of extrusion of the optical cylinder and consequent endophthalmitis. Prophylactic measures can then be taken to prevent such serious complications from occurring. In this series, the authors found EBT to have excellent resolution and speed and they would support regular scanning of the OOKP lamina in all patients. PMID:16024842

Imaging of osteo-odonto-keratoprosthesis by electron beam tomography.

PubMed

Fong, K C S; Ferrett, C G; Tandon, R; Paul, B; Herold, J; Liu, C S C

2005-08-01

To describe the experience of using electron beam tomography (EBT) in imaging of osteo-odonto-keratoprosthesis (OOKP) to identify early bone and dentine loss which may threaten the viability of the eye. Seven patients with an OOKP in one eye underwent EBT. The OOKP lamina dimensions were measured on EBT and compared to the manual measurements at the time of surgery. There was a high degree of resolution of the OOKP lamina noted with EBT. In particular, it identified three patients with a marked degree of thinning of the lamina edges. Two of these patients had OOKP that were allografts. The mean time from surgery to examination was 3.6 years (range 1.2-5 years) while the mean age of the patients was 56 years (range 31-79 years). It is important to monitor regularly the dimensions and stability of the OOKP lamina as it will help detect cases that are at risk of extrusion of the optical cylinder and consequent endophthalmitis. Prophylactic measures can then be taken to prevent such serious complications from occurring. In this series, the authors found EBT to have excellent resolution and speed and they would support regular scanning of the OOKP lamina in all patients.

Multiple mantle upwellings in the transition zone beneath the northern East-African Rift system from relative P-wave travel-time tomography

NASA Astrophysics Data System (ADS)

Civiero, Chiara; Hammond, James O. S.; Goes, Saskia; Fishwick, Stewart; Ahmed, Abdulhakim; Ayele, Atalay; Doubre, Cecile; Goitom, Berhe; Keir, Derek; Kendall, J.-Michael; Leroy, Sylvie; Ogubazghi, Ghebrebrhan; Rümpker, Georg; Stuart, Graham W.

2015-09-01

Mantle plumes and consequent plate extension have been invoked as the likely cause of East African Rift volcanism. However, the nature of mantle upwelling is debated, with proposed configurations ranging from a single broad plume connected to the large low-shear-velocity province beneath Southern Africa, the so-called African Superplume, to multiple lower-mantle sources along the rift. We present a new P-wave travel-time tomography model below the northern East-African, Red Sea, and Gulf of Aden rifts and surrounding areas. Data are from stations that span an area from Madagascar to Saudi Arabia. The aperture of the integrated data set allows us to image structures of ˜100 km length-scale down to depths of 700-800 km beneath the study region. Our images provide evidence of two clusters of low-velocity structures consisting of features with diameter of 100-200 km that extend through the transition zone, the first beneath Afar and a second just west of the Main Ethiopian Rift, a region with off-rift volcanism. Considering seismic sensitivity to temperature, we interpret these features as upwellings with excess temperatures of 100 ± 50 K. The scale of the upwellings is smaller than expected for lower mantle plume sources. This, together with the change in pattern of the low-velocity anomalies across the base of the transition zone, suggests that ponding or flow of deep-plume material below the transition zone may be spawning these upper mantle upwellings. This article was corrected on 28 SEP 2015. See the end of the full text for details.

Application of δ recycling to electron automated diffraction tomography data from inorganic crystalline nanovolumes.

PubMed

Rius, Jordi; Mugnaioli, Enrico; Vallcorba, Oriol; Kolb, Ute

2013-07-01

δ Recycling is a simple procedure for directly extracting phase information from Patterson-type functions [Rius (2012). Acta Cryst. A68, 399-400]. This new phasing method has a clear theoretical basis and was developed with ideal single-crystal X-ray diffraction data. On the other hand, introduction of the automated diffraction tomography (ADT) technique has represented a significant advance in electron diffraction data collection [Kolb et al. (2007). Ultramicroscopy, 107, 507-513]. When combined with precession electron diffraction, it delivers quasi-kinematical intensity data even for complex inorganic compounds, so that single-crystal diffraction data of nanometric volumes are now available for structure determination by direct methods. To check the tolerance of δ recycling to missing data-collection corrections and to deviations from kinematical behaviour of ADT intensities, δ recycling has been applied to differently shaped nanocrystals of various inorganic materials. The results confirm that it can phase ADT data very efficiently. In some cases even more complete structure models than those derived from conventional direct methods and least-squares refinement have been found. During this study it has been demonstrated that the Wilson-plot scaling procedure is largely insensitive to sample thickness variations and missing absorption corrections affecting electron ADT intensities.

Effective grain pinning revealed by nanoscale electron tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Y. Q.; Tang, W.; Dennis, K. W.

2011-03-21

The grain pinning behavior of TiC particles in a rapidly solidified MRE-Fe-B (MRE = Nd + Y + Dy) nanocrystalline hard magnet was studied using electron tomography (ET). The 3D reconstruction overcomes the inherent 2D nature of conventional transmission electronmicroscopy (TEM) to reveal how this grain boundary phase controls the nanoscale structure in the rapidly solidified alloy. The 3D reconstruction was performed on the optimally annealed alloy (750 C/15 min) with hard magnetic properties of M{sub r} = 8.1 kGs, H{sub c} = 6.2 kOe, (BH){sub max} = 11.2 MGOe measured at 300 k. The sampled volume, 425 x 425more » x 92.5 nm{sup 3}, contains more than 20 grains of the RE2-14-1 phase and more than 70 TiC nanoparticles. The TiC grains shapes depend on their sizes and locations along the grain boundary. Most of the TiC particles are oval or short rod like shapes and range from 5 nm to 10 nm. TiC particles less than 10 nm formed between adjacent 2-14-1 grains, while the largest ones formed at triple junctions. There are -1.7 x 10{sup 8} TiC particles within a 1 mm{sup 3} volume in the alloy. This accounts for the strong grain boundary pinning effect, which limits grain growth during annealing.« less

Electron Tomography Reveals the Steps in Filovirus Budding

PubMed Central

Welsch, Sonja; Kolesnikova, Larissa; Krähling, Verena; Riches, James D.; Becker, Stephan; Briggs, John A. G.

2010-01-01

The filoviruses, Marburg and Ebola, are non-segmented negative-strand RNA viruses causing severe hemorrhagic fever with high mortality rates in humans and nonhuman primates. The sequence of events that leads to release of filovirus particles from cells is poorly understood. Two contrasting mechanisms have been proposed, one proceeding via a “submarine-like” budding with the helical nucleocapsid emerging parallel to the plasma membrane, and the other via perpendicular “rocket-like” protrusion. Here we have infected cells with Marburg virus under BSL-4 containment conditions, and reconstructed the sequence of steps in the budding process in three dimensions using electron tomography of plastic-embedded cells. We find that highly infectious filamentous particles are released at early stages in infection. Budding proceeds via lateral association of intracellular nucleocapsid along its whole length with the plasma membrane, followed by rapid envelopment initiated at one end of the nucleocapsid, leading to a protruding intermediate. Scission results in local membrane instability at the rear of the virus. After prolonged infection, increased vesiculation of the plasma membrane correlates with changes in shape and infectivity of released viruses. Our observations demonstrate a cellular determinant of virus shape. They reconcile the contrasting models of filovirus budding and allow us to describe the sequence of events taking place during budding and release of Marburg virus. We propose that this represents a general sequence of events also followed by other filamentous and rod-shaped viruses. PMID:20442788

Viewing Golgi structure and function from a different perspective--insights from electron tomography.

PubMed

Marsh, Brad J; Pavelka, Margit

2013-01-01

Historically, ultrastructural investigations, which have focused on elucidating the biological idiosyncrasies of the Golgi apparatus, have tended towards oversimplified or fallacious hypotheses when postulating how the Golgi apparatus reorganizes itself both structurally and functionally to fulfill the plethora of cellular processes underpinned by this complex organelle. Key questions are still unanswered with regard to how changes in Golgi architecture correlate so reproducibly to changes in its functional priorities under different physiological conditions or experimental perturbations. This fact alone serves to highlight how the technical limitations associated with conventional two-dimensional imaging approaches employed in the past failed to adequately capture the extraordinary complexity of the Golgi's three-dimensional (3D) structure-now a hallmark of this challenging organelle. Consequently, this has hampered progress towards developing a clear understanding of how changes in its structure and function typically occur in parallel. In this chapter, we highlight but a few of the significant new insights regarding variations in the Golgi's structure-function relationships that have been afforded over recent years through advanced electron microscopic techniques for 3D image reconstruction, commonly referred to as electron tomography. Copyright © 2013 Elsevier Inc. All rights reserved.

Correlative tomography at the cathode/electrolyte interfaces of solid oxide fuel cells

NASA Astrophysics Data System (ADS)

Wankmüller, Florian; Szász, Julian; Joos, Jochen; Wilde, Virginia; Störmer, Heike; Gerthsen, Dagmar; Ivers-Tiffée, Ellen

2017-08-01

This paper introduces a correlative tomography technique. It visualizes the spatial organization of primary and secondary phases at the interface of La0.58Sr0.4Co0.2Fe0.8O3-δ cathode/10 mol% Gadolinia doped Ceria/8 mol% Yttria stabilized Zirconia electrolyte. It uses focused ion beam/scanning electron microscope tomography (FIB/SEM), and combines data sets from Everhart-Thornley and Inlens detector differentiating four primary and two secondary material phases. In addition, grayscale information is correlated to elemental distribution gained by energy dispersive X-ray spectroscopy in a scanning transmission electron microscope. Interdiffusion of GDC into YSZ and SrZrO3 as secondary phases depend (in both amount and spatial organization) on the varied co-sintering temperature of the GDC/YSZ electrolyte. The ion-blocking SrZrO3 forms a continuous layer on top of the temperature-dependent GDC/YSZ interdiffusion zone (ID) at and below a co-sintering temperature of 1200 °C; above it becomes intermittent. 2D FIB/SEM images of primary and secondary phases at 1100, 1200, 1300 and 1400 °C were combined with a 3D FIB/SEM reconstruction (1300 °C). This reveals that ;preferred; oxygen ion transport pathways from the LSCF cathode through GDC and the ID into the YSZ electrolyte only exist in samples sintered above 1200 °C. The applied correlative technique expands our understanding of this multiphase cathode/electrolyte interface region.

Holography and tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Howells, M.

This session includes a collection of outlines of pertinent information, diagrams, graphs, electron micrographs, and color photographs pertaining to historical aspects and recent advances in the development of X-ray Gabor Holography. Many of the photographs feature or pertain to instrumentation used in holography, tomography, and cryo-holography.

Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lei, Dongsheng; Marras, Alexander E.; Liu, Jianfang

Scaffolded DNA origami has proven to be a powerful and efficient technique to fabricate functional nanomachines by programming the folding of a single-stranded DNA template strand into three-dimensional (3D) nanostructures, designed to be precisely motion-controlled. Although two-dimensional (2D) imaging of DNA nanomachines using transmission electron microscopy and atomic force microscopy suggested these nanomachines are dynamic in 3D, geometric analysis based on 2D imaging was insufficient to uncover the exact motion in 3D. In this paper, we use the individual-particle electron tomography method and reconstruct 129 density maps from 129 individual DNA origami Bennett linkage mechanisms at ~6-14 nm resolution. The statisticalmore » analyses of these conformations lead to understanding the 3D structural dynamics of Bennett linkage mechanisms. Moreover, our effort provides experimental verification of a theoretical kinematics model of DNA origami, which can be used as feedback to improve the design and control of motion via optimized DNA sequences and routing.« less

Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography

DOE PAGES

Lei, Dongsheng; Marras, Alexander E.; Liu, Jianfang; ...

2018-02-09

Scaffolded DNA origami has proven to be a powerful and efficient technique to fabricate functional nanomachines by programming the folding of a single-stranded DNA template strand into three-dimensional (3D) nanostructures, designed to be precisely motion-controlled. Although two-dimensional (2D) imaging of DNA nanomachines using transmission electron microscopy and atomic force microscopy suggested these nanomachines are dynamic in 3D, geometric analysis based on 2D imaging was insufficient to uncover the exact motion in 3D. In this paper, we use the individual-particle electron tomography method and reconstruct 129 density maps from 129 individual DNA origami Bennett linkage mechanisms at ~6-14 nm resolution. The statisticalmore » analyses of these conformations lead to understanding the 3D structural dynamics of Bennett linkage mechanisms. Moreover, our effort provides experimental verification of a theoretical kinematics model of DNA origami, which can be used as feedback to improve the design and control of motion via optimized DNA sequences and routing.« less

Danger zone analysis using cone beam computed tomography after apical enlargement with K3 and K3XF in a manikin model

PubMed Central

Olivier, Juan-Gonzalo; García-Font, Marc; Gonzalez-Sanchez, Jose-Antonio; Roig-Cayon, Miguel

2016-01-01

Background The objective of the study was to evaluate and compare how apical enlargement with K3 and K3XF nickel-titanium (NiTi) rotary instruments reduces the root thickness in the danger zone and affects canal transportation and centering ability in mandibular molar mesial canals in a manikin extracted tooth model. Material and Methods Seventy-two mesial root canals of first mandibular molars were instrumented. Initial and post-instrumentation Cone Beam Computed Tomography scans were performed after root canal preparation up to size 25, 30, 35 and 40 files. Canal transportation, canal centering and remaining root dentin thickness toward the danger zone were calculated in sections 1, 2 and 3 mm under the furcation level. Data were analyzed using non-parametric Kruskal-Wallis analysis of variance at a significance level of P < 0.05. Results K3 instruments removed more dentin toward the danger zone compared with K3XF instruments (P< .05) and significant differences in dentin thickness were found when canal enlargement was performed to a #35-40 with both systems (P< 0.05). No significant differences in canal transportation and centering ability were found between systems, except when canal enlargement was performed to a #40 (P = 0,0136). No differences were observed when comparing the number of uses in both systems (P> 0.05). Conclusions Under the conditions of this study K3 removed a significant amount of dentin at the furcation level compared with the R-Phase K3XF rotary system in curved root canals. Enlargement to a 35-40/04 file removed significantly more dentin with both systems. Key words:K3, K3XF, R-phase, center ability, canal transportation, dentin thickness, increased apical enlargement, danger zone, dentin thickness. PMID:27703602

ICON: 3D reconstruction with 'missing-information' restoration in biological electron tomography.

PubMed

Deng, Yuchen; Chen, Yu; Zhang, Yan; Wang, Shengliu; Zhang, Fa; Sun, Fei

2016-07-01

Electron tomography (ET) plays an important role in revealing biological structures, ranging from macromolecular to subcellular scale. Due to limited tilt angles, ET reconstruction always suffers from the 'missing wedge' artifacts, thus severely weakens the further biological interpretation. In this work, we developed an algorithm called Iterative Compressed-sensing Optimized Non-uniform fast Fourier transform reconstruction (ICON) based on the theory of compressed-sensing and the assumption of sparsity of biological specimens. ICON can significantly restore the missing information in comparison with other reconstruction algorithms. More importantly, we used the leave-one-out method to verify the validity of restored information for both simulated and experimental data. The significant improvement in sub-tomogram averaging by ICON indicates its great potential in the future application of high-resolution structural determination of macromolecules in situ. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Electrodeposition of Highly Porous Pt Nanoparticles Studied by Quantitative 3D Electron Tomography: Influence of Growth Mechanisms and Potential Cycling on the Active Surface Area.

PubMed

Ustarroz, Jon; Geboes, Bart; Vanrompay, Hans; Sentosun, Kadir; Bals, Sara; Breugelmans, Tom; Hubin, Annick

2017-05-17

Nanoporous Pt nanoparticles (NPs) are promising fuel cell catalysts due to their large surface area and increased electrocatalytic activity toward the oxygen reduction reaction (ORR). Herein, we report on the influence of the growth mechanisms on the surface properties of electrodeposited Pt dendritic NPs with large surface areas. The electrochemically active surface was studied by hydrogen underpotential deposition (H UPD) and compared for the first time to high-angle annular dark field scanning transmission electron microscopy (HAADF-STEM) quantitative 3D electron tomography of individual nanoparticles. Large nucleation overpotential leads to a large surface coverage of roughened spheroids, which provide a large roughness factor (R f ) but low mass-specific electrochemically active surface area (EASA). Lowering the nucleation overpotential leads to highly porous Pt NPs with pores stretching to the center of the structure. At the expense of smaller R f , the obtained EASA values of these structures are in the range of those of large surface area supported fuel cell catalysts. The active surface area of the Pt dendritic NPs was measured by electron tomography, and it was found that the potential cycling in the H adsorption/desorption and Pt oxidation/reduction region, which is generally performed to determine the EASA, leads to a significant reduction of that surface area due to a partial collapse of their dendritic and porous morphology. Interestingly, the extrapolation of the microscopic tomography results in macroscopic electrochemical parameters indicates that the surface properties measured by H UPD are comparable to the values measured on individual NPs by electron tomography after the degradation caused by the H UPD measurement. These results highlight that the combination of electrochemical and quantitative 3D surface analysis techniques is essential to provide insights into the surface properties, the electrochemical stability, and, hence, the

Applications of emerging transmission electron microscopy technology in PCD research and diagnosis.

PubMed

Shoemark, Amelia

2017-01-01

Primary Ciliary Dyskinesia (PCD) is a heterogeneous genetic condition characterized by dysfunction of motile cilia. Patients suffer from chronic infection and inflammation of the upper and lower respiratory tract. Diagnosis of PCD is confirmed by identification of a hallmark defect of ciliary ultrastructure or by identification of biallelic pathogenic mutations in a known PCD gene. Since the first description of PCD in 1976, assessment of ciliary ultrastructure by transmission electron microscopy (TEM) has been central to diagnosis and research. Electron tomography is a technique whereby a series of transmission electron micrographs are collected at different angles and reconstructed into a single 3D model of a specimen. Electron tomography provides improved spatial information and resolution compared to a single micrograph. Research by electron tomography has revealed new insight into ciliary ultrastructure and consequently ciliary function at a molecular and cellular level. Gene discovery studies in PCD have utilized electron tomography to define the structural consequences of variants in cilia genes. Modern transmission electron microscopes capable of electron tomography are increasingly being installed in clinical laboratories. This presents the possibility for the use of tomography technique in a diagnostic setting. This review describes the electron tomography technique, the contribution tomography has made to the understanding of basic cilia structure and function and finally the potential of the technique for use in PCD diagnosis.

Teleseismic P-wave tomography of the Sunda-Banda Arc subduction zone

NASA Astrophysics Data System (ADS)

Harris, C. W.; Miller, M. S.; Widiyantoro, S.; Supendi, P.; O'Driscoll, L.; Roosmawati, N.; Porritt, R.

2017-12-01

The Sunda-Banda Arc is the site of multiple ongoing tectonic deformation processes and is perhaps the best example of the transition from subduction of oceanic lithosphere to an active arc-continent collision. Investigating the mantle structure that has resulted from the collision of continental Australia, as well as the concurrent phenomena of continental subduction, slab-rollback, lithospheric tearing, and subduction polarity reversal is possible through seismic tomography. While both regional scale and global tomographic models have previously been constructed to study the tectonics this region, here we use 250 seismic stations that span the length of this convergent margin to invert for P-wave velocity perturbations in the upper mantle. We combine data from a temporary deployment of 30 broadband instruments as part of the NSF-funded Banda Arc Project, along with data from permanent broadband stations maintained by the Meteorological, Climatological, and Geophysical Agency of Indonesia (BMKG) to image mantle structure, in particular the subducted Indo-Australian plate. The BMKG dataset spans 2009-2017 and includes >200 broadband seismometers. The Banda Arc array (network YS) adds coverage and resolution to southeastern Indonesia and Timor-Leste, where few permanent seismometers are located but the Australian continent-Banda Arc collision is most advanced. The preliminary model was computed using 50,000 teleseismic P-wave travel-time residuals and 3D finite frequency sensitivity kernels. Results from the inversion of the combined dataset are presented as well as resolution tests to assess the quality of the model. The velocity model shows an arcuate Sunda-Banda slab with morphological changes along strike that correlate with the tectonic collision. The model also features the double-sided Molucca Sea slab and regions of high velocity below the bottom of the transition zone. The resolution added by the targeted USC deployment is clear when comparing models that

Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography.

PubMed

Galaz-Montoya, Jesús G; Hecksel, Corey W; Baldwin, Philip R; Wang, Eryu; Weaver, Scott C; Schmid, Michael F; Ludtke, Steven J; Chiu, Wah

2016-06-01

Single particle cryo-electron tomography (cryoSPT) extracts features from cryo-electron tomograms, followed by 3D classification, alignment and averaging to generate improved 3D density maps of such features. Robust methods to correct for the contrast transfer function (CTF) of the electron microscope are necessary for cryoSPT to reach its resolution potential. Many factors can make CTF correction for cryoSPT challenging, such as lack of eucentricity of the specimen stage, inherent low dose per image, specimen charging, beam-induced specimen motions, and defocus gradients resulting both from specimen tilting and from unpredictable ice thickness variations. Current CTF correction methods for cryoET make at least one of the following assumptions: that the defocus at the center of the image is the same across the images of a tiltseries, that the particles all lie at the same Z-height in the embedding ice, and/or that the specimen, the cryo-electron microscopy (cryoEM) grid and/or the carbon support are flat. These experimental conditions are not always met. We have developed a CTF correction algorithm for cryoSPT without making any of the aforementioned assumptions. We also introduce speed and accuracy improvements and a higher degree of automation to the subtomogram averaging algorithms available in EMAN2. Using motion-corrected images of isolated virus particles as a benchmark specimen, recorded with a DE20 direct detection camera, we show that our CTF correction and subtomogram alignment routines can yield subtomogram averages close to 4/5 Nyquist frequency of the detector under our experimental conditions. Copyright © 2016 Elsevier Inc. All rights reserved.

Electron precipitation in the post midnight sector of the auroral zones. [on the Explorer 40 satellite

NASA Technical Reports Server (NTRS)

Frank, L. A.; Saflekos, N. A.; Ackerson, K. L.

1975-01-01

Comprehensive measurements of the angular distributions and energy spectra of electron intensities with electrostatic analyzer arrays on board the low-altitude satellite Injun 5 are reported. These are for the post-midnight sector of the auroral zones during the high-intensity events accompanying magnetic substorms. Precipitation features on closed terrestrial field lines well equatorward of the trapping boundary for energetic electrons with E greater than 45 keV were examined. No evidences of maxima in the differential energy spectra or of strongly field-aligned currents which are indicative of quasi-static electric fields aligned parallel to the geomagnetic field were found. Precipitation of low-energy electron intensities fluctuated on time scales greater than 2 seconds as viewed at the satellite position. This precipitation was characterized by isotropy for all pitch angles outside the atmospheric backscatter cone.

Characterization of electrical properties in axial Si-Ge nanowire heterojunctions using off-axis electron holography and atom-probe tomography

DOE PAGES

Gan, Zhaofeng; Perea, Daniel E.; Yoo, Jinkyoung; ...

2016-09-13

Doped Si-Ge nanowire (NW) heterojunctions were grown using the vapor-liquid-solid method with AuGa and Au catalyst particles. Transmission electron microscopy and off-axis electron holography (EH) were used to characterize the nanostructure and to measure the electrostatic potential profile across the junction resulting from electrically active dopants, while atom-probe tomography (APT) was used to determine the Si, Ge and total (active and inactive) dopant concentration profiles. A comparison of the measured potential profile with simulations indicated that Ga dopants unintentionally introduced during AuGa catalyst growth were electronically inactive despite APT results that showed considerable amounts of Ga in the Si region.more » 10% P in Ge and 100% B in Si were estimated to be activated, which was corroborated by in situ electron-holography biasing experiments. This combination of EH, APT, in situ biasing and simulations allows a better knowledge and understanding of the electrically active dopant distributions in NWs.« less

Protein secondary structure determination by constrained single-particle cryo-electron tomography.

PubMed

Bartesaghi, Alberto; Lecumberry, Federico; Sapiro, Guillermo; Subramaniam, Sriram

2012-12-05

Cryo-electron microscopy (cryo-EM) is a powerful technique for 3D structure determination of protein complexes by averaging information from individual molecular images. The resolutions that can be achieved with single-particle cryo-EM are frequently limited by inaccuracies in assigning molecular orientations based solely on 2D projection images. Tomographic data collection schemes, however, provide powerful constraints that can be used to more accurately determine molecular orientations necessary for 3D reconstruction. Here, we propose "constrained single-particle tomography" as a general strategy for 3D structure determination in cryo-EM. A key component of our approach is the effective use of images recorded in tilt series to extract high-resolution information and correct for the contrast transfer function. By incorporating geometric constraints into the refinement to improve orientational accuracy of images, we reduce model bias and overrefinement artifacts and demonstrate that protein structures can be determined at resolutions of ∼8 Å starting from low-dose tomographic tilt series. Copyright © 2012 Elsevier Ltd. All rights reserved.

Examination of Scanning Electron Microscope and Computed Tomography Images of PICA

NASA Technical Reports Server (NTRS)

Lawson, John W.; Stackpoole, Margaret M.; Shklover, Valery

2010-01-01

Micrographs of PICA (Phenolic Impregnated Carbon Ablator) taken using a Scanning Electron Microscope (SEM) and 3D images taken with a Computed Tomography (CT) system are examined. PICA is a carbon fiber based composite (Fiberform ) with a phenolic polymer matrix. The micrographs are taken at different surface depths and at different magnifications in a sample after arc jet testing and show different levels of oxidative removal of the charred matrix (Figs 1 though 13). CT scans, courtesy of Xradia, Inc. of Concord CA, were captured for samples of virgin PICA, charred PICA and raw Fiberform (Fig. 14). We use these images to calculate the thermal conductivity (TC) of these materials using correlation function (CF) methods. CF methods give a mathematical description of how one material is embedded in another and is thus ideally suited for modeling composites like PICA. We will evaluate how the TC of the materials changes as a function of surface depth. This work is in collaboration with ETH-Zurich, which has expertise in high temperature materials and TC modeling (including CF methods).

Progressive Stochastic Reconstruction Technique (PSRT) for cryo electron tomography.

PubMed

Turoňová, Beata; Marsalek, Lukas; Davidovič, Tomáš; Slusallek, Philipp

2015-03-01

Cryo Electron Tomography (cryoET) plays an essential role in Structural Biology, as it is the only technique that allows to study the structure of large macromolecular complexes in their close to native environment in situ. The reconstruction methods currently in use, such as Weighted Back Projection (WBP) or Simultaneous Iterative Reconstruction Technique (SIRT), deliver noisy and low-contrast reconstructions, which complicates the application of high-resolution protocols, such as Subtomogram Averaging (SA). We propose a Progressive Stochastic Reconstruction Technique (PSRT) - a novel iterative approach to tomographic reconstruction in cryoET based on Monte Carlo random walks guided by Metropolis-Hastings sampling strategy. We design a progressive reconstruction scheme to suit the conditions present in cryoET and apply it successfully to reconstructions of macromolecular complexes from both synthetic and experimental datasets. We show how to integrate PSRT into SA, where it provides an elegant solution to the region-of-interest problem and delivers high-contrast reconstructions that significantly improve template-based localization without any loss of high-resolution structural information. Furthermore, the locality of SA is exploited to design an importance sampling scheme which significantly speeds up the otherwise slow Monte Carlo approach. Finally, we design a new memory efficient solution for the specimen-level interior problem of cryoET, removing all associated artifacts. Copyright © 2015 Elsevier Inc. All rights reserved.

THE RELATIONSHIP BETWEEN FOVEAL AVASCULAR ZONE AREA, VESSEL DENSITY, AND CYSTOID CHANGES IN DIABETIC RETINOPATHY, AN OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY STUDY.

PubMed

Tarassoly, Kia; Miraftabi, Arezoo; Soltan Sanjari, Mostafa; Parvaresh, Mohammad Mehdi

2017-06-29

To measure the foveal avascular zone (FAZ) areas and vessel densities of patients with diabetic retinopathy and to study their relationship with diabetic cystoid changes and retinal thickness. Prospective case series of 51 eyes of 31 patients with diabetic retinopathy. The eyes were grouped based on the presence or absence of cystoid edema and evaluated using optical coherence tomography angiography. The FAZ areas and vessel density were compared. The FAZ area at the superficial capillary plexus level was equal between the eyes with and without cystoid edema. Vessel density did not differ as well. There was no correlation with retinal thickness. In eyes with cystoid changes, FAZ area changes at the deep capillary plexus level were difficult to interpret. The FAZ area and vessel density at the superficial capillary plexus level are reproducible and independent of the presence of cystoid edema.

CAPILLARY NETWORK ANOMALIES IN BRANCH RETINAL VEIN OCCLUSION ON OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY.

PubMed

Rispoli, Marco; Savastano, Maria Cristina; Lumbroso, Bruno

2015-11-01

To analyze the foveal microvasculature features in eyes with branch retinal vein occlusion (BRVO) using optical coherence tomography angiography based on split spectrum amplitude decorrelation angiography technology. A total of 10 BRVO eyes (mean age 64.2 ± 8.02 range between 52 years and 76 years) were evaluated by optical coherence tomography angiography (XR-Avanti; Optovue). The macular angiography scan protocol covered a 3 mm × 3 mm area. The focus of angiography analysis were two retinal layers: superficial vascular network and deep vascular network. The following vascular morphological congestion parameters were assessed in the vein occlusion area in both the superficial and deep networks: foveal avascular zone enlargement, capillary non-perfusion occurrence, microvascular abnormalities appearance, and vascular congestion signs. Image analyses were performed by 2 masked observers and interobserver agreement of image analyses was 0.90 (κ = 0.225, P < 0.01). In both superficial and deep network of BRVO, a decrease in capillary density with foveal avascular zone enlargement, capillary non-perfusion occurrence, and microvascular abnormalities appearance was observed (P < 0.01). The deep network showed the main vascular congestion at the boundary between healthy and nonperfused retina. Optical coherence tomography angiography in BRVO allows to detect foveal avascular zone enlargement, capillary nonperfusion, microvascular abnormalities, and vascular congestion signs both in the superficial and deep capillary network in all eyes. Optical coherence tomography angiography technology is a potential clinical tool for BRVO diagnosis and follow-up, providing stratigraphic vascular details that have not been previously observed by standard fluorescein angiography. The normal retinal vascular nets and areas of nonperfusion and congestion can be identified at various retinal levels. Optical coherence tomography angiography provides noninvasive images of the retinal

Structure of junctions of multiwalled carbon nanotubes with tetragonal cross section and flattened nanotubes revealed by electron-beam tomography

NASA Astrophysics Data System (ADS)

Nagano, Yuta; Kohno, Hideo

2017-11-01

Multiwalled carbon nanotubes with tetragonal cross section frequently form junctions with flattened multi-walled carbon nanotubes, a kind of carbon nanoribbon. The three-dimensional structure of the junctions is revealed by transmission-electron-microscopy-based tomography. Two types of junction, parallel and diagonal, are found. The formation mechanism of these two types of junction is discussed in terms of the origami mechanism that was previously proposed to explain the formation of carbon nanoribbons and nanotetrahedra.

Three-dimensional structure of basal body triplet revealed by electron cryo-tomography

PubMed Central

Li, Sam; Fernandez, Jose-Jesus; Marshall, Wallace F; Agard, David A

2012-01-01

Basal bodies and centrioles play central roles in microtubule (MT)-organizing centres within many eukaryotes. They share a barrel-shaped cylindrical structure composed of nine MT triplet blades. Here, we report the structure of the basal body triplet at 33 Å resolution obtained by electron cryo-tomography and 3D subtomogram averaging. By fitting the atomic structure of tubulin into the EM density, we built a pseudo-atomic model of the tubulin protofilaments at the core of the triplet. The 3D density map reveals additional densities that represent non-tubulin proteins attached to the triplet, including a large inner circular structure in the basal body lumen, which functions as a scaffold to stabilize the entire basal body barrel. We found clear longitudinal structural variations along the basal body, suggesting a sequential and coordinated assembly mechanism. We propose a model in which δ-tubulin and other components participate in the assembly of the basal body. PMID:22157822

Using quantum process tomography to characterize decoherence in an analog electronic device

NASA Astrophysics Data System (ADS)

Ostrove, Corey; La Cour, Brian; Lanham, Andrew; Ott, Granville

The mathematical structure of a universal gate-based quantum computer can be emulated faithfully on a classical electronic device using analog signals to represent a multi-qubit state. We describe a prototype device capable of performing a programmable sequence of single-qubit and controlled two-qubit gate operations on a pair of voltage signals representing the real and imaginary parts of a two-qubit quantum state. Analog filters and true-RMS voltage measurements are used to perform unitary and measurement gate operations. We characterize the degradation of the represented quantum state with successive gate operations by formally performing quantum process tomography to estimate the equivalent decoherence channel. Experimental measurements indicate that the performance of the device may be accurately modeled as an equivalent quantum operation closely resembling a depolarizing channel with a fidelity of over 99%. This work was supported by the Office of Naval Research under Grant No. N00014-14-1-0323.

Vadose Zone Transport Field Study: Status Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gee, Glendon W.; Ward, Anderson L.

2001-11-30

Studies were initiated at the Hanford Site to evaluate the process controlling the transport of fluids in the vadose zone and to develop a reliable database upon which vadose-zone transport models can be calibrated. These models are needed to evaluate contaminant migration through the vadose zone to underlying groundwaters at Hanford. A study site that had previously been extensively characterized using geophysical monitoring techniques was selected in the 200 E Area. Techniques used previously included neutron probe for water content, spectral gamma logging for radionuclide tracers, and gamma scattering for wet bulk density. Building on the characterization efforts of themore » past 20 years, the site was instrumented to facilitate the comparison of nine vadose-zone characterization methods: advanced tensiometers, neutron probe, electrical resistance tomography (ERT), high-resolution resistivity (HRR), electromagnetic induction imaging (EMI), cross-borehole radar (XBR), and cross-borehole seismic (XBS). Soil coring was used to obtain soil samples for analyzing ionic and isotopic tracers.« less

Characterizing the Three-Dimensional Structure of Block Copolymers via Sequential Infiltration Synthesis and Scanning Transmission Electron Tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Segal-Peretz, Tamar; Winterstein, Jonathan; Doxastakis, Manolis

Understanding and controlling the three-dimensional structure of block copolymer (BCP) thin films is critical for utilizing these materials for sub-20 nm nanopatterning in semiconductor devices, as well as in membranes and solar cell applications. Combining an atomic layer deposition (ALD) based technique for enhancing the contrast of BCPs in transmission electron microscopy (TEM) together with scanning TEM (STEM) tomography reveals and characterizes the three-dimensional structures of poly(styrene-block-methyl methacrylate) (PS-b-PMMA) thin films with great clarity. Sequential infiltration synthesis (SIS), a block-selective technique for growing inorganic materials in BCPs films in ALD, and an emerging tool for enhancing the etch contrast ofmore » BCPs, was harnessed to significantly enhance the high-angle scattering from the polar domains of BCP films in the TEM. The power of combining SIS and STEM tomography for three dimensional (3D) characterization of BCPs films was demonstrated with the following cases: self-assembled cylindrical, lamellar, and spherical PS-PMMA thin films. In all cases, STEM tomography has revealed 3D structures that were hidden underneath the surface, including: 1) the 3D structure of defects in cylindrical and lamellar phases, 2) non-perpendicular 3D surface of grain boundaries in the cylindrical phase, and 3) the 3D arrangement of spheres in body centered cubic (BCC) and hexagonal closed pack (HCP) morphologies in the spherical phase. The 3D data of the spherical morphologies was compared to coarse-grained simulations and assisted in validating the simulations’ parameters. STEM tomography of SIS-treated BCP films enables the characterization of the exact structure used for pattern transfer, and can lead to better understating of the physics which is utilized in BCP lithography.« less

Structure resolution by electron diffraction tomography of the complex layered iron-rich Fe-2234-type Sr{sub 5}Fe{sub 6}O{sub 15.4}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lepoittevin, Christophe, E-mail: christophe.lepoittevin@neel.cnrs.fr

2016-10-15

The crystal structure of the strontium ferrite Sr{sub 5}Fe{sub 6}O{sub 15.4}, was solved by direct methods on electron diffraction tomography data acquired on a transmission electron microscope. The refined cell parameters are a=27.4047(3) Å, b=5.48590(7) Å and c=42.7442(4) Å in Fm2m symmetry. Its structure is built up from the intergrowth sequence between a quadruple perovskite-type layer with a complex rock-salt (RS)-type block. In the latter iron atoms are found in two different environments : tetragonal pyramid and tetrahedron. The structural model was refined by Rietveld method based on the powder X-ray diffraction pattern. - Highlights: • Complex structure of Sr{submore » 5}Fe{sub 6}O{sub 15.4} solved by electron diffraction tomography. • Observed Fourier maps allow determining missing oxygen atoms in the structure. • Structural model refined from powder X-ray diffraction data. • Intergrowth between quadruple perovskite layer with double rock-salt-type layer.« less

Near-surface high resolution imaging of a metallogenic zone in the northern fringe of Dalma volcanics in eastern India using electrical resistivity tomography

NASA Astrophysics Data System (ADS)

Adhikari, P. K.; Srivastava, Shalivahan; Maurya, Ved P.; Tripathi, Anurag; Singh, Roshan K.; Bage, Ashish K.

2017-06-01

Electrical resistivity tomography (ERT) is a useful tool to map near-surface conducting anomalies. The detailed ERT survey was taken over an already defined conducting zone on a regional scale through a magnetotelluric (MT) survey, in order to provide better resolution of the subsurface structure within the study area. The survey lines were carried out crossing the delineated conducting zone through MT giving a dense coverage over the area. The ERT survey were carried out along 15 lines covering an area of ~1 km2 with a line spacing of ~50 m in the northern fringe of the Dalma volcanics (DVs). The study utilised the 61-channel cum 64-electrode resistivity equipment, FlashRES-Universal ERT multi-electrode data acquisition system, developed by ZZ Resistivity Imaging, Australia. Data has been acquired both through conventional arrays i.e. Wenner, Schlumberger and ZZ unconventional arrays. Inversion of the data set have been performed using 2.5D finite element conjugate gradient algorithm after performing the quality check. Resistivity models along all the lines were obtained using Wenner, Schlumberger and combination of Wenner, Schlumberger and ZZ arrays. Resistivity models resolved four major zones: (1) resistivity less than 1 Ωm (2) resistivity 1-10 Ωm (3) resistivity 10-100 Ωm and (4) resistivity more than 100 Ωm . The resistivity results corroborate well with the geological succession from the drilling data. The conducting zones with resistivity values ranging from 1-10 Ωm correlates with the Lower Dalma volcanics while the Upper Dalma volcanics corresponds to the regions with resistivity values of less than 1 Ωm. The Upper Dalma volcanics corresponds to the metallogeny while the depth to the top of the ore body is ~25 m.

Rayleigh-Wave Group-Velocity Tomography of Saudi Arabia

NASA Astrophysics Data System (ADS)

Tang, Zheng; Mai, P. Martin; Chang, Sung-Joon; Zahran, Hani

2017-04-01

We use surface-wave tomography to investigate the lithospheric structure of the Arabian plate, which is traditionally divided into the Arabian shield in the west and the Arabian platform in the east. The Arabian shield is a complicated mélange of crustal material, composed of several Proterozoic terrains separated by ophiolite-bearing suture zones and dotted by outcropping Cenozoic volcanic rocks. The Arabian platform is primarily covered by very thick Paleozoic, Mesozoic and Cenozoic sediments. We develop high-resolution tomographic images from fundamental-mode Rayleigh-wave group-velocities across Saudi Arabia, utilizing the teleseismic data recorded by the permanent Saudi National Seismic Network (SNSN). Our study extends previous efforts on surface wave work by increasing ray path density and improving spatial resolution. Good quality dispersion measurements for roughly 3000 Rayleigh-wave paths have been obtained and utilized for the group-velocity tomography. We have applied the Fast Marching Surface Tomography (FMST) scheme of Rawlinson (2005) to obtain Rayleigh-wave group-velocity images for periods from 8 s to 40 s on a 0.8° 0.8° grid and at resolutions approaching 2.5° based on the checkerboard tests. Our results indicate that short-period group-velocity maps (8-15 s) correlate well with surface geology, with slow velocities delineating the main sedimentary features including the Arabian platform, the Persian Gulf and Mesopotamia. For longer periods (20-40 s), the velocity contrast is due to the differences in crustal thickness and subduction/collision zones. The lower velocities are sensitive to the thicker continental crust beneath the eastern Arabia and the subduction/collision zones between the Arabian and Eurasian plate, while the higher velocities in the west infer mantle velocity.

Upper crustal structure of the North Anatolian Fault Zone from ambient seismic noise Rayleigh and Love wave tomography

NASA Astrophysics Data System (ADS)

Taylor, George; Rost, Sebastian; Houseman, Gregory; Hillers, Gregor

2017-04-01

By utilising short period surface waves present in the noise field, we can construct images of shallow structure in the Earth's upper crust: a region that is usually poorly resolved in earthquake tomography. Here, we use data from a dense seismic array (Dense Array for Northern Anatolia - DANA) deployed across the North Anatolian Fault Zone (NAFZ) in the region of the 1999 magnitude 7.6 Izmit earthquake in western Turkey. The NAFZ is a major strike-slip system that extends ˜1200 km across northern Turkey and continues to pose a high level of seismic hazard, in particular to the mega-city of Istanbul. We obtain maps of group velocity variation using surface wave tomography applied to short period (1- 6 s) Rayleigh and Love waves to construct high-resolution images of the upper 5 km of a 70 km x 35 km region centred on the eastern end of the fault segment that ruptured in the 1999 Izmit earthquake. The average Rayleigh wave group velocities in the region vary between 1.8 km/s at 1.5 s period, to 2.2 km/s at 6 s period. The NAFZ bifurcates into northern and southern strands in this region; both are active but only the northern strand moved in the 1999 event. The signatures of both the northern and southern branches of the NAFZ are clearly associated with strong gradients in surface wave group velocity. To the north of the NAFZ, we observe low Rayleigh wave group velocities ( 1.2 km/s) associated with the unconsolidated sediments of the Adapazari basin, and blocks of weathered terrigenous clastic sediments. To the south of the northern branch of the NAFZ, we detect high velocities ( 2.5 km/s) associated with a shallow crystalline basement, in particular a block of metamorphosed schists and marbles that bound the northern branch of the NAFZ.

Electron Microscopy Imaging of Zinc Soaps Nucleation in Oil Paint.

PubMed

Hermans, Joen; Osmond, Gillian; van Loon, Annelies; Iedema, Piet; Chapman, Robyn; Drennan, John; Jack, Kevin; Rasch, Ronald; Morgan, Garry; Zhang, Zhi; Monteiro, Michael; Keune, Katrien

2018-06-04

Using the recently developed techniques of electron tomography, we have explored the first stages of disfiguring formation of zinc soaps in modern oil paintings. The formation of complexes of zinc ions with fatty acids in paint layers is a major threat to the stability and appearance of many late 19th and early 20th century oil paintings. Moreover, the occurrence of zinc soaps in oil paintings leading to defects is disturbingly common, but the chemical reactions and migration mechanisms leading to large zinc soap aggregates or zones remain poorly understood. State-of-the-art scanning (SEM) and transmission (TEM) electron microscopy techniques, primarily developed for biological specimens, have enabled us to visualize the earliest stages of crystalline zinc soap growth in a reconstructed zinc white (ZnO) oil paint sample. In situ sectioning techniques and sequential imaging within the SEM allowed three-dimensional tomographic reconstruction of sample morphology. Improvements in the detection and discrimination of backscattered electrons enabled us to identify local precipitation processes with small atomic number contrast. The SEM images were correlated to low-dose and high-sensitivity TEM images, with high-resolution tomography providing unprecedented insight into the structure of nucleating zinc soaps at the molecular level. The correlative approach applied here to study phase separation, and crystallization processes specific to a problem in art conservation creates possibilities for visualization of phase formation in a wide range of soft materials.

3D imaging of nanomaterials by discrete tomography.

PubMed

Batenburg, K J; Bals, S; Sijbers, J; Kübel, C; Midgley, P A; Hernandez, J C; Kaiser, U; Encina, E R; Coronado, E A; Van Tendeloo, G

2009-05-01

The field of discrete tomography focuses on the reconstruction of samples that consist of only a few different materials. Ideally, a three-dimensional (3D) reconstruction of such a sample should contain only one grey level for each of the compositions in the sample. By exploiting this property in the reconstruction algorithm, either the quality of the reconstruction can be improved significantly, or the number of required projection images can be reduced. The discrete reconstruction typically contains fewer artifacts and does not have to be segmented, as it already contains one grey level for each composition. Recently, a new algorithm, called discrete algebraic reconstruction technique (DART), has been proposed that can be used effectively on experimental electron tomography datasets. In this paper, we propose discrete tomography as a general reconstruction method for electron tomography in materials science. We describe the basic principles of DART and show that it can be applied successfully to three different types of samples, consisting of embedded ErSi(2) nanocrystals, a carbon nanotube grown from a catalyst particle and a single gold nanoparticle, respectively.

Tomography Reconstruction of Ionospheric Electron Density with Empirical Orthonormal Functions Using Korea GNSS Network

NASA Astrophysics Data System (ADS)

Hong, Junseok; Kim, Yong Ha; Chung, Jong-Kyun; Ssessanga, Nicholas; Kwak, Young-Sil

2017-03-01

In South Korea, there are about 80 Global Positioning System (GPS) monitoring stations providing total electron content (TEC) every 10 min, which can be accessed through Korea Astronomy and Space Science Institute (KASI) for scientific use. We applied the computerized ionospheric tomography (CIT) algorithm to the TEC dataset from this GPS network for monitoring the regional ionosphere over South Korea. The algorithm utilizes multiplicative algebraic reconstruction technique (MART) with an initial condition of the latest International Reference Ionosphere-2016 model (IRI-2016). In order to reduce the number of unknown variables, the vertical profiles of electron density are expressed with a linear combination of empirical orthonormal functions (EOFs) that were derived from the IRI empirical profiles. Although the number of receiver sites is much smaller than that of Japan, the CIT algorithm yielded reasonable structure of the ionosphere over South Korea. We verified the CIT results with NmF2 from ionosondes in Icheon and Jeju and also with GPS TEC at the center of South Korea. In addition, the total time required for CIT calculation was only about 5 min, enabling the exploration of the vertical ionospheric structure in near real time.

Methodological accuracy of image-based electron density assessment using dual-energy computed tomography.

PubMed

Möhler, Christian; Wohlfahrt, Patrick; Richter, Christian; Greilich, Steffen

2017-06-01

Electron density is the most important tissue property influencing photon and ion dose distributions in radiotherapy patients. Dual-energy computed tomography (DECT) enables the determination of electron density by combining the information on photon attenuation obtained at two different effective x-ray energy spectra. Most algorithms suggested so far use the CT numbers provided after image reconstruction as input parameters, i.e., are imaged-based. To explore the accuracy that can be achieved with these approaches, we quantify the intrinsic methodological and calibration uncertainty of the seemingly simplest approach. In the studied approach, electron density is calculated with a one-parametric linear superposition ('alpha blending') of the two DECT images, which is shown to be equivalent to an affine relation between the photon attenuation cross sections of the two x-ray energy spectra. We propose to use the latter relation for empirical calibration of the spectrum-dependent blending parameter. For a conclusive assessment of the electron density uncertainty, we chose to isolate the purely methodological uncertainty component from CT-related effects such as noise and beam hardening. Analyzing calculated spectrally weighted attenuation coefficients, we find universal applicability of the investigated approach to arbitrary mixtures of human tissue with an upper limit of the methodological uncertainty component of 0.2%, excluding high-Z elements such as iodine. The proposed calibration procedure is bias-free and straightforward to perform using standard equipment. Testing the calibration on five published data sets, we obtain very small differences in the calibration result in spite of different experimental setups and CT protocols used. Employing a general calibration per scanner type and voltage combination is thus conceivable. Given the high suitability for clinical application of the alpha-blending approach in combination with a very small methodological

Alignment Algorithms and Per-Particle CTF Correction for Single Particle Cryo-Electron Tomography

PubMed Central

Galaz-Montoya, Jesús G.; Hecksel, Corey W.; Baldwin, Philip R.; Wang, Eryu; Weaver, Scott C.; Schmid, Michael F.; Ludtke, Steven J.; Chiu, Wah

2016-01-01

Single particle cryo-electron tomography (cryoSPT) extracts features from cryo-electron tomograms, followed by 3D classification, alignment and averaging to generate improved 3D density maps of such features. Robust methods to correct for the contrast transfer function (CTF) of the electron microscope are necessary for cryoSPT to reach its resolution potential. Many factors can make CTF correction for cryoSPT challenging, such as lack of eucentricity of the specimen stage, inherent low dose per image, specimen charging, beam-induced specimen motions, and defocus gradients resulting both from specimen tilting and from unpredictable ice thickness variations. Current CTF correction methods for cryoET make at least one of the following assumptions: that the defocus at the center of the image is the same across the images of a tiltseries, that the particles all lie at the same Z-height in the embedding ice, and/or that the specimen grid and carbon support are flat. These experimental conditions are not always met. We have developed a CTF correction algorithm for cryoSPT without making any of the aforementioned assumptions. We also introduce speed and accuracy improvements and a higher degree of automation to the subtomogram averaging algorithms available in EMAN2. Using motion-corrected images of isolated virus particles as a benchmark specimen, recorded with a DE20 direct detection camera, we show that our CTF correction and subtomogram alignment routines can yield subtomogram averages close to 4/5 Nyquist frequency of the detector under our experimental conditions. PMID:27016284

Structural analysis of the PSD-95 cluster by electron tomography and CEMOVIS: a proposal for the application of the genetically encoded metallothionein tag.

PubMed

Hirabayashi, Ai; Fukunaga, Yuko; Miyazawa, Atsuo

2014-06-01

Postsynaptic density-95 (PSD-95) accumulates at excitatory postsynapses and plays important roles in the clustering and anchoring of numerous proteins at the PSD. However, a detailed ultrastructural analysis of clusters exclusively consisting of PSD-95 has never been performed. Here, we employed a genetically encoded tag, three tandem repeats of metallothionein (3MT), to study the structure of PSD-95 clusters in cells by electron tomography and cryo-electron microscopy of vitreous sections. We also performed conventional transmission electron microscopy (TEM). Cultured hippocampal neurons expressing a fusion protein of PSD-95 coupled to 3MT (PDS-95-3MT) were incubated with CdCl2 to result in the formation of Cd-bound PSD-95-3MT. Two types of electron-dense deposits composed of Cd-bound PSD-95-3MT were observed in these cells by TEM, as reported previously. Electron tomography revealed the presence of membrane-shaped structures representing PSD-95 clusters at the PSD and an ellipsoidal structure located in the non-synaptic cytoplasm. By TEM, the PSD-95 clusters appeared to be composed of a number of dense cores. In frozen hydrated sections, these dense cores were also found beneath the postsynaptic membrane. Taken together, our findings suggest that dense cores of PSD-95 aggregate to form the larger clusters present in the PSD and the non-synaptic cytoplasm. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Ultra-structural study of insulin granules in pancreatic β-cells of db/db mouse by scanning transmission electron microscopy tomography.

PubMed

Xue, Yanhong; Zhao, Wei; Du, Wen; Zhang, Xiang; Ji, Gang; Ying, Wang; Xu, Tao

2012-07-01

Insulin granule trafficking is a key step in the secretion of glucose-stimulated insulin from pancreatic β-cells. The main feature of type 2 diabetes (T2D) is the failure of pancreatic β-cells to secrete sufficient amounts of insulin to maintain normal blood glucose levels. In this work, we developed and applied tomography based on scanning transmission electron microscopy (STEM) to image intact insulin granules in the β-cells of mouse pancreatic islets. Using three-dimensional (3D) reconstruction, we found decreases in both the number and the grey level of insulin granules in db/db mouse pancreatic β-cells. Moreover, insulin granules were closer to the plasma membrane in diabetic β-cells than in control cells. Thus, 3D ultra-structural tomography may provide new insights into the pathology of insulin secretion in T2D.

Creep cavitation can establish a dynamic granular fluid pump in ductile shear zones.

PubMed

Fusseis, F; Regenauer-Lieb, K; Liu, J; Hough, R M; De Carlo, F

2009-06-18

The feedback between fluid migration and rock deformation in mid-crustal shear zones is acknowledged as being critical for earthquake nucleation, the initiation of subduction zones and the formation of mineral deposits. The importance of this poorly understood feedback is further highlighted by evidence for shear-zone-controlled advective flow of fluids in the ductile lower crust and the recognition that deformation-induced grain-scale porosity is a key to large-scale geodynamics. Fluid migration in the middle crust cannot be explained in terms of classical concepts. The environment is considered too hot for a dynamic fracture-sustained permeability as in the upper crust, and fluid pathways are generally too deformed to be controlled by equilibrium wetting angles that apply to hotter, deeper environments. Here we present evidence that mechanical and chemical potentials control a syndeformational porosity generation in mid-crustal shear zones. High-resolution synchrotron X-ray tomography and scanning electron microscopy observations allow us to formulate a model for fluid migration in shear zones where a permeable porosity is dynamically created by viscous grain-boundary sliding, creep cavitation, dissolution and precipitation. We propose that syndeformational fluid migration in our 'granular fluid pump' model is a self-sustained process controlled by the explicit role of the rate of entropy production of the underlying irreversible mechanical and chemical microprocesses. The model explains fluid transfer through the middle crust, where strain localization in the creep regime is required for plate tectonics, the formation of giant ore deposits, mantle degassing and earthquake nucleation. Our findings provide a key component for the understanding of creep instabilities in the middle crust.

CAPILLARY NETWORK ALTERATIONS IN X-LINKED RETINOSCHISIS IMAGED ON OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY.

PubMed

Romano, Francesco; Arrigo, Alessandro; Chʼng, Soon Wai; Battaglia Parodi, Maurizio; Manitto, Maria Pia; Martina, Elisabetta; Bandello, Francesco; Stanga, Paulo E

2018-06-05

To assess foveal and parafoveal vasculature at the superficial capillary plexus, deep capillary plexus, and choriocapillaris of patients with X-linked retinoschisis by means of optical coherence tomography angiography. Six patients with X-linked retinoschisis (12 eyes) and seven healthy controls (14 eyes) were recruited and underwent complete ophthalmologic examination, including best-corrected visual acuity, dilated fundoscopy, and 3 × 3-mm optical coherence tomography angiography macular scans (DRI OCT Triton; Topcon Corp). After segmentation and quality review, optical coherence tomography angiography slabs were imported into ImageJ 1.50 (NIH; Bethesda) and digitally binarized. Quantification of vessel density was performed after foveal avascular zone area measurement and exclusion. Patients were additionally divided into "responders" and "nonresponders" to dorzolamide therapy. Foveal avascular zone area resulted markedly enlarged at the deep capillary plexus (P < 0.001), particularly in nonresponders. Moreover, patients disclosed a significant deep capillary plexus rarefaction, when compared with controls (P: 0.04); however, a subanalysis revealed that this damage was limited to the fovea (P: 0.006). Finally, the enlargement of foveal avascular zone area positively correlated with a decline in best-corrected visual acuity (P: 0.01). Prominent foveal vascular impairment is detectable in the deep capillary plexus of patients with X-linked retinoschisis. Our results correlate with functional outcomes, suggesting a possible vascular role in X-linked retinoschisis clinical manifestations.

Structure of the Cascadia Subduction Zone Imaged Using Surface Wave Tomography

NASA Astrophysics Data System (ADS)

Schaeffer, A. J.; Audet, P.

2017-12-01

Studies of the complete structure of the Cascadia subduction zone from the ridge to the arc have historically been limited by the lack of offshore ocean bottom seismograph (OBS) infrastructure. On land, numerous dense seismic deployments have illuminated detailed structures and dynamics associated with the interaction between the subducting oceanic plate and the overriding continental plate, including cycling of fluids, serpentinization of the overlying forearc mantle wedge, and the location of the upper surface of the Juan de Fuca plate as it subducts beneath the Pacific Northwest. In the last half-decade, the Cascadia Initiative (CI), along with Neptune (ONC) and several other OBS initiatives, have instrumented both the continental shelf and abyssal plains off shore of the Cascadia subduction zone, facilitating the construction of a complete picture of the subduction zone from ridge to trench and volcanic arc. In this study, we present a preliminary azimuthally anisotropic surface-wave phase-velocity based model of the complete system, capturing both the young, unaltered Juan de Fuca plate from the ridge, to its alteration as it enters the subduction zone, in addition to the overlying continent. This model is constructed from a combination of ambient noise cross-correlations and teleseismic two station interferometry, and combines together concurrently running offshore OBS and onshore stations. We furthermore perform a number of representative 1D depth inversions for shear velocity to categorize the pristine oceanic, subducted oceanic, and continental crust and lithospheric structure. In the future the dispersion dataset will be jointly inverted with receiver functions to constrain a 3D shear-velocity model of the complete region.

Ab initio structure determination and quantitative disorder analysis on nanoparticles by electron diffraction tomography.

PubMed

Krysiak, Yaşar; Barton, Bastian; Marler, Bernd; Neder, Reinhard B; Kolb, Ute

2018-03-01

Nanoscaled porous materials such as zeolites have attracted substantial attention in industry due to their catalytic activity, and their performance in sorption and separation processes. In order to understand the properties of such materials, current research focuses increasingly on the determination of structural features beyond the averaged crystal structure. Small particle sizes, various types of disorder and intergrown structures render the description of structures at atomic level by standard crystallographic methods difficult. This paper reports the characterization of a strongly disordered zeolite structure, using a combination of electron exit-wave reconstruction, automated diffraction tomography (ADT), crystal disorder modelling and electron diffraction simulations. Zeolite beta was chosen for a proof-of-principle study of the techniques, because it consists of two different intergrown polymorphs that are built from identical layer types but with different stacking sequences. Imaging of the projected inner Coulomb potential of zeolite beta crystals shows the intergrowth of the polymorphs BEA and BEB. The structures of BEA as well as BEB could be extracted from one single ADT data set using direct methods. A ratio for BEA/BEB = 48:52 was determined by comparison of the reconstructed reciprocal space based on ADT data with simulated electron diffraction data for virtual nanocrystals, built with different ratios of BEA/BEB. In this way, it is demonstrated that this smart interplay of the above-mentioned techniques allows the elaboration of the real structures of functional materials in detail - even if they possess a severely disordered structure.

Direct atomic-scale imaging of hydrogen and oxygen interstitials in pure niobium using atom-probe tomography and aberration-corrected scanning transmission electron microscopy.

PubMed

Kim, Yoon-Jun; Tao, Runzhe; Klie, Robert F; Seidman, David N

2013-01-22

Imaging the three-dimensional atomic-scale structure of complex interfaces has been the goal of many recent studies, due to its importance to technologically relevant areas. Combining atom-probe tomography and aberration-corrected scanning transmission electron microscopy (STEM), we present an atomic-scale study of ultrathin (~5 nm) native oxide layers on niobium (Nb) and the formation of ordered niobium hydride phases near the oxide/Nb interface. Nb, an elemental type-II superconductor with the highest critical temperature (T(c) = 9.2 K), is the preferred material for superconducting radio frequency (SRF) cavities in next-generation particle accelerators. Nb exhibits high solubilities for oxygen and hydrogen, especially within the RF-field penetration depth, which is believed to result in SRF quality factor losses. STEM imaging and electron energy-loss spectroscopy followed by ultraviolet laser-assisted local-electrode atom-probe tomography on the same needle-like sample reveals the NbO(2), Nb(2)O(5), NbO, Nb stacking sequence; annular bright-field imaging is used to visualize directly hydrogen atoms in bulk β-NbH.

Secondary electron ion source neutron generator

DOEpatents

Brainard, John P.; McCollister, Daryl R.

1998-01-01

A neutron generator employing an electron emitter, an ion source bombarded by the electrons from the electron emitter, a plasma containment zone, and a target situated between the plasma containment zone and the electron emitter. The target contains occluded deuterium, tritium, or a mixture thereof

Cryo-electron tomography investigation of serum albumin-camouflaged tobacco mosaic virus nanoparticles.

PubMed

Gulati, Neetu M; Pitek, Andrzej S; Steinmetz, Nicole F; Stewart, Phoebe L

2017-03-09

Nanoparticles offer great potential in drug delivery and imaging, but shielding strategies are necessary to increase circulation time and performance. Structure-function studies are required to define the design rules to achieve effective shielding. With several formulations reaching clinical testing and approval, the ability to assess and detail nanoparticle formulations at the single particle level is becoming increasingly important. To address this need, we use cryo-electron tomography (cryo-ET) to investigate stealth-coated nanoparticles. As a model system, we studied the soft matter nanotubes formed by tobacco mosaic virus (TMV) coated with human serum albumin (SA) stealth proteins. Cryo-ET and subtomogram averaging allow for visualization of individual SA molecules and determination of their orientations relative to the TMV surface, and also for measurement of the surface coverage provided by added stealth proteins. This information fills a critical gap in the understanding of the structural morphology of stealth-coated nanoparticles, and therefore cryo-ET may play an important role in guiding the development of future nanoparticle-based therapeutics.

Three-dimensional coordinates of individual atoms in materials revealed by electron tomography

DOE PAGES

Xu, Rui; Chen, Chien-Chun; Wu, Li; ...

2015-09-21

Crystallography, the primary method for determining the 3D atomic positions in crystals, has been fundamental to the development of many fields of science. However, the atomic positions obtained from crystallography represent a global average of many unit cells in a crystal. In this paper, we report, for the first time, the determination of the 3D coordinates of thousands of individual atoms and a point defect in a material by electron tomography with a precision of ~19 pm, where the crystallinity of the material is not assumed. From the coordinates of these individual atoms, we measure the atomic displacement field andmore » the full strain tensor with a 3D resolution of ~1 nm 3 and a precision of ~10 -3, which are further verified by density functional theory calculations and molecular dynamics simulations. Finally, the ability to precisely localize the 3D coordinates of individual atoms in materials without assuming crystallinity is expected to find important applications in materials science, nanoscience, physics, chemistry and biology.« less

Three-dimensional coordinates of individual atoms in materials revealed by electron tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Rui; Chen, Chien-Chun; Wu, Li

Crystallography, the primary method for determining the 3D atomic positions in crystals, has been fundamental to the development of many fields of science. However, the atomic positions obtained from crystallography represent a global average of many unit cells in a crystal. In this paper, we report, for the first time, the determination of the 3D coordinates of thousands of individual atoms and a point defect in a material by electron tomography with a precision of ~19 pm, where the crystallinity of the material is not assumed. From the coordinates of these individual atoms, we measure the atomic displacement field andmore » the full strain tensor with a 3D resolution of ~1 nm 3 and a precision of ~10 -3, which are further verified by density functional theory calculations and molecular dynamics simulations. Finally, the ability to precisely localize the 3D coordinates of individual atoms in materials without assuming crystallinity is expected to find important applications in materials science, nanoscience, physics, chemistry and biology.« less

Optimization of a solid-state electron spin qubit using Gate Set Tomography

DOE PAGES

Dehollain, Juan P.; Muhonen, Juha T.; Blume-Kohout, Robin J.; ...

2016-10-13

Here, state of the art qubit systems are reaching the gate fidelities required for scalable quantum computation architectures. Further improvements in the fidelity of quantum gates demands characterization and benchmarking protocols that are efficient, reliable and extremely accurate. Ideally, a benchmarking protocol should also provide information on how to rectify residual errors. Gate Set Tomography (GST) is one such protocol designed to give detailed characterization of as-built qubits. We implemented GST on a high-fidelity electron-spin qubit confined by a single 31P atom in 28Si. The results reveal systematic errors that a randomized benchmarking analysis could measure but not identify, whereasmore » GST indicated the need for improved calibration of the length of the control pulses. After introducing this modification, we measured a new benchmark average gate fidelity of 99.942(8)%, an improvement on the previous value of 99.90(2)%. Furthermore, GST revealed high levels of non-Markovian noise in the system, which will need to be understood and addressed when the qubit is used within a fault-tolerant quantum computation scheme.« less

Atom probe tomography of lithium-doped network glasses.

PubMed

Greiwe, Gerd-Hendrik; Balogh, Zoltan; Schmitz, Guido

2014-06-01

Li-doped silicate and borate glasses are electronically insulating, but provide considerable ionic conductivity. Under measurement conditions of laser-assisted atom probe tomography, mobile Li ions are redistributed in response to high electric fields. In consequence, the direct interpretation of measured composition profiles is prevented. It is demonstrated that composition profiles are nevertheless well understood by a complex model taking into account the electronic structure of dielectric materials, ionic mobility and field screening. Quantitative data on band bending and field penetration during measurement are derived which are important in understanding laser-assisted atom probe tomography of dielectric materials. Copyright © 2014 Elsevier B.V. All rights reserved.

Research on ionospheric tomography based on variable pixel height

NASA Astrophysics Data System (ADS)

Zheng, Dunyong; Li, Peiqing; He, Jie; Hu, Wusheng; Li, Chaokui

2016-05-01

A novel ionospheric tomography technique based on variable pixel height was developed for the tomographic reconstruction of the ionospheric electron density distribution. The method considers the height of each pixel as an unknown variable, which is retrieved during the inversion process together with the electron density values. In contrast to conventional computerized ionospheric tomography (CIT), which parameterizes the model with a fixed pixel height, the variable-pixel-height computerized ionospheric tomography (VHCIT) model applies a disturbance to the height of each pixel. In comparison with conventional CIT models, the VHCIT technique achieved superior results in a numerical simulation. A careful validation of the reliability and superiority of VHCIT was performed. According to the results of the statistical analysis of the average root mean square errors, the proposed model offers an improvement by 15% compared with conventional CIT models.

Secondary electron ion source neutron generator

DOEpatents

Brainard, J.P.; McCollister, D.R.

1998-04-28

A neutron generator employing an electron emitter, an ion source bombarded by the electrons from the electron emitter, a plasma containment zone, and a target situated between the plasma containment zone and the electron emitter is disclosed. The target contains occluded deuterium, tritium, or a mixture thereof. 4 figs.

STEM Tomography Imaging of Hypertrophied Golgi Stacks in Mucilage-Secreting Cells.

PubMed

Kang, Byung-Ho

2016-01-01

Because of the weak penetrating power of electrons, the signal-to-noise ratio of a transmission electron micrograph (TEM) worsens as section thickness increases. This problem is alleviated by the use of the scanning transmission electron microscopy (STEM). Tomography analyses using STEM of thick sections from yeast and mammalian cells are of higher quality than are bright-field (BF) images. In this study, we compared regular BF tomograms and STEM tomograms from 500-nm thick sections from hypertrophied Golgi stacks of alfalfa root cap cells. Due to their thickness and intense heavy metal staining, BF tomograms of the thick sections suffer from poor contrast and high noise levels. We were able to mitigate these drawbacks by using STEM tomography. When we performed STEM tomography of densely stained chloroplasts of Arabidopsis cotyledon, we observed similar improvements relative to BF tomograms. A longer time is required to collect a STEM tilt series than similar BF TEM images, and dynamic autofocusing required for STEM imaging often fails at high tilt angles. Despite these limitations, STEM tomography is a powerful method for analyzing structures of large or dense organelles of plant cells.

Cellular uptake mechanisms of functionalised multi-walled carbon nanotubes by 3D electron tomography imaging

NASA Astrophysics Data System (ADS)

Al-Jamal, Khuloud T.; Nerl, Hannah; Müller, Karin H.; Ali-Boucetta, Hanene; Li, Shouping; Haynes, Peter D.; Jinschek, Joerg R.; Prato, Maurizio; Bianco, Alberto; Kostarelos, Kostas; Porter, Alexandra E.

2011-06-01

Carbon nanotubes (CNTs) are being investigated for a variety of biomedical applications. Despite numerous studies, the pathways by which carbon nanotubes enter cells and their subsequent intracellular trafficking and distribution remain poorly determined. Here, we use 3-D electron tomography techniques that offer optimum enhancement of contrast between carbon nanotubes and the plasma membrane to investigate the mechanisms involved in the cellular uptake of shortened, functionalised multi-walled carbon nanotubes (MWNT-NH3+). Both human lung epithelial (A549) cells, that are almost incapable of phagocytosis and primary macrophages, capable of extremely efficient phagocytosis, were used. We observed that MWNT-NH3+ were internalised in both phagocytic and non-phagocytic cells by any one of three mechanisms: (a) individually via membrane wrapping; (b) individually by direct membrane translocation; and (c) in clusters within vesicular compartments. At early time points following intracellular translocation, we noticed accumulation of nanotube material within various intracellular compartments, while a long-term (14-day) study using primary human macrophages revealed that MWNT-NH3+ were able to escape vesicular (phagosome) entrapment by translocating directly into the cytoplasm.Carbon nanotubes (CNTs) are being investigated for a variety of biomedical applications. Despite numerous studies, the pathways by which carbon nanotubes enter cells and their subsequent intracellular trafficking and distribution remain poorly determined. Here, we use 3-D electron tomography techniques that offer optimum enhancement of contrast between carbon nanotubes and the plasma membrane to investigate the mechanisms involved in the cellular uptake of shortened, functionalised multi-walled carbon nanotubes (MWNT-NH3+). Both human lung epithelial (A549) cells, that are almost incapable of phagocytosis and primary macrophages, capable of extremely efficient phagocytosis, were used. We observed

Ionospheric tomography using ADS-B signals

NASA Astrophysics Data System (ADS)

Cushley, A. C.; Noël, J.-M.

2014-07-01

Numerical modeling has demonstrated that Automatic Dependent Surveillance Broadcast (ADS-B) signals can be used to reconstruct two-dimensional (2-D) electron density maps of the ionosphere using techniques for computerized tomography. Ray tracing techniques were used to determine the characteristics of individual waves, including the wave path and the state of polarization at the satellite receiver. The modeled Faraday rotation was computed and converted to total electron content (TEC) along the raypaths. The resulting TEC was used as input for computerized ionospheric tomography (CIT) using algebraic reconstruction technique. This study concentrated on reconstructing mesoscale structures 25-100 km in horizontal extent. The primary scientific interest of this study was to show that ADS-B signals can be used as a new source of data for CIT to image the ionosphere and to obtain a better understanding of magneto-ionic wave propagation.

Correlating Atom Probe Tomography with Atomic-Resolved Scanning Transmission Electron Microscopy: Example of Segregation at Silicon Grain Boundaries.

PubMed

Stoffers, Andreas; Barthel, Juri; Liebscher, Christian H; Gault, Baptiste; Cojocaru-Mirédin, Oana; Scheu, Christina; Raabe, Dierk

2017-04-01

In the course of a thorough investigation of the performance-structure-chemistry interdependency at silicon grain boundaries, we successfully developed a method to systematically correlate aberration-corrected scanning transmission electron microscopy and atom probe tomography. The correlative approach is conducted on individual APT and TEM specimens, with the option to perform both investigations on the same specimen in the future. In the present case of a Σ9 grain boundary, joint mapping of the atomistic details of the grain boundary topology, in conjunction with chemical decoration, enables a deeper understanding of the segregation of impurities observed at such grain boundaries.

An Application of Computerized Axial Tomography (CAT) Technology to Mass Raid Tracking

DTIC Science & Technology

1989-08-01

ESD-TR-89-305 MTR-10542 An Application of Computerized Axial Tomography ( CAT ) Technology to Mass Raid Tracking By John K. Barr August 1989...NO 11. TITLE (Include Security Classification) An Application of Computerized Axial Tomography ( CAT ) Technology to Mass Raid Tracking 12...by block number) Computerized Axial Tomography ( CAT ) Scanner Electronic Support Measures (ESM) Fusion (continued) 19. ABSTRACT (Continue on

Fluid flow and permeabilities in basement fault zones

NASA Astrophysics Data System (ADS)

Hollinsworth, Allan; Koehn, Daniel

2017-04-01

rocks, and younger Mesozoic age faults may provide analogues for the West Shetland basin. Samples have been collected from both of these localities, and will be examined by optical and scanning electron microscopy. X-Ray micro-tomography will also be used to analyse the permeability characteristics of the fault rocks. Our understanding of fault zone permeability is crucial for a number of research areas, including earthquake geoscience, economic mineral formation, and hydrocarbon systems. As a result, this research has relevance to a variety of industry sectors, including oil and gas (and ccs), nuclear waste disposal, geothermal and mining.

Positron Emission Tomography - Computed Tomography (PET/CT)

MedlinePlus

... A-Z Positron Emission Tomography - Computed Tomography (PET/CT) Positron emission tomography (PET) uses small amounts of ... What is Positron Emission Tomography – Computed Tomography (PET/CT) Scanning? Positron emission tomography, also called PET imaging ...

EEL spectroscopic tomography: towards a new dimension in nanomaterials analysis.

PubMed

Yedra, Lluís; Eljarrat, Alberto; Arenal, Raúl; Pellicer, Eva; Cabo, Moisés; López-Ortega, Alberto; Estrader, Marta; Sort, Jordi; Baró, Maria Dolors; Estradé, Sònia; Peiró, Francesca

2012-11-01

Electron tomography is a widely spread technique for recovering the three dimensional (3D) shape of nanostructured materials. Using a spectroscopic signal to achieve a reconstruction adds a fourth chemical dimension to the 3D structure. Up to date, energy filtering of the images in the transmission electron microscope (EFTEM) is the usual spectroscopic method even if most of the information in the spectrum is lost. Unlike EFTEM tomography, the use of electron energy-loss spectroscopy (EELS) spectrum images (SI) for tomographic reconstruction retains all chemical information, and the possibilities of this new approach still remain to be fully exploited. In this article we prove the feasibility of EEL spectroscopic tomography at low voltages (80 kV) and short acquisition times from data acquired using an aberration corrected instrument and data treatment by Multivariate Analysis (MVA), applied to Fe(x)Co((3-x))O(4)@Co(3)O(4) mesoporous materials. This approach provides a new scope into materials; the recovery of full EELS signal in 3D. Copyright © 2012 Elsevier B.V. All rights reserved.

Energy Filtering Transmission Electron Tomography (EFTET) of Bacteria-Mineral Associations within the Deep sea Hydrothermal Vent Shrimp Rimicaris exoculata.

NASA Astrophysics Data System (ADS)

Anderson, L. M.; Halary, S.; Lechaire, J.; Frébourg, G.; Boudier, T.; Zbinden, M.; Laval, J.; Marco, S.; Gaill, F.

2007-12-01

The chemical and temperature conditions around deep sea hydrothermal vents are both dynamic and extreme, yet the shrimp Rimicaris exoculata flourishes around these environments on the Mid--Atlantic Ridge (MAR). Epibiotic bacteria and minerals found within the branchial chamber (BC) of the shrimp are of great interest in the search for a chemical model for the Rainbow MAR hydrothermal vent site. Here we examine the close, three-- dimensional (3D) relationship between bacteria (on the inner surface of the BC wall) and the minerals that surround them. The morphology and chemistry of the minerals were analysed by Energy filtering Transmission Electron Microscopy (EFTEM, on a LEO--912 microscope) and X-ray Nano-analysis (EDXN, on a JEOL--2010 FEG microscope) respectively, and the 3D organization was determined by Transmission Electron Tomography (TET) and EFTET. Consecutive thin and semi--thin sections of 50--80nm (for EFTEM and EDXN) and 200--250nm (for TEM and EFTET) were cut through the BC cuticle and mounted on standard microscope grids. Sections were observed initially for morphology, to find broad relationships between bacteria and minerals. EFTET series acquisition was performed under cryo-conditions (-175°C) using a LEO-912 microscope. At each position of interest four tilt series were taken at two degree increments between -55° and +55° at various energy--losses: 1) zero--loss (ref); 2) 720 eV, 3) 690 eV and 4) 670 eV, to reconstruct the 3D location of iron. Tilted series were obtained using the ESIvision program (Soft--Imaging Software, Münster, Germany) with additional in--house scripts for automated acquisition. The 3D EFTET reconstruction volume was produced from the four tilted series using recently developed EFTET--J software (http://www.snv.jussieu.fr/~wboudier/softs.html). In many cases the observed minerals exhibit a sharp boundary against the bacteria, often with a substantial void between bacterial membrane/cell wall and mineral boundary. Mineral

Seismic Velocity Structure of the San Jacinto Fault Zone from Double-Difference Tomography and Expected Distribution of Head Waves

NASA Astrophysics Data System (ADS)

Allam, A. A.; Ben-Zion, Y.

2010-12-01

We present initial results of double-difference tomographic images for the velocity structure of the San Jacinto Fault Zone (SJFZ), and related 3D forward calculations of waves in the immediate vicinity of the SJFZ. We begin by discretizing the SJFZ region with a uniform grid spacing of 500 m, extending 140 km by 80 km and down to 25 km depth. We adopt the layered 1D model of Dreger & Helmberger (1993) as a starting model for this region, and invert for 3D distributions of VP and VS with the double-difference tomography of Zhang & Thurber (2003), which makes use of absolute event-station travel times as well as relative travel times for phases from nearby event pairs. Absolute arrival times of over 78,000 P- and S-wave phase picks generated by 1127 earthquakes and recorded at 70 stations near the SJFZ are used. Only data from events with Mw greater than 2.2 are used. Though ray coverage is limited at shallow depths, we obtain relatively high-resolution images from 4 to 13 km which show a clear contrast in velocity across the NW section of the SJFZ. To the SE, in the so-called trifurcation area, the structure is more complicated, though station coverage is poorest in this region. Using the obtained image, the current event locations, and the 3D finite-difference code of Olsen (1994), we estimate the likely distributions of fault zone head waves as a tool for future deployment of instrument. We plan to conduct further studies by including more travel time picks, including those from newly-deployed stations in the SJFZ area, in order to gain a more accurate image of the velocity structure.

Slip Zone versus Damage Zone Micromechanics, Arima-Takasuki Tectonic Line, Japan

NASA Astrophysics Data System (ADS)

White, J. C.; Lin, A.

2017-12-01

The Arima-Takasuki Tectonic Line (ATTL) of southern Honshu, Japan is defined by historically active faults and multiple splays producing M7 earthquakes. The damage zone of the ATTL comprises a broad zone of crushed, comminuted and pulverized granite/rhyolite1,2containing cm-scale slip zones and highly comminuted injection veins. In this presentation, prior work on the ATTL fault rocks is extending to include microstructural characterization by transmission electron microscopy (TEM) from recent trenching of the primary slip zone, as well as secondary slip zones. This is necessary to adequately characterize the extremely fine-grained material (typically less than 1mm) in both damage and core zones. Damage zone material exhibits generally random textures3 whereas slip zones are macroscopically foliated, and compositionally layered, notwithstanding a fairly homogeneous protolith. The latter reflects fluid-rock interaction during both coseismic and interseismic periods. The slip zones are microstructurally heterogeneous at all scales, comprising not only cataclasites and phyllosilicate (clay)-rich gouge zones, but Fe/Mn pellets or clasts that are contained within gouge. These structures appear to have rolled and would suggest rapid recrystallization and/or growth. A central question related to earthquake recurrence along existing faults is the nature of the gouge. In both near-surface exposures and ongoing drilling at depth, "plastic" or "viscous" gouge zones comprise ultra-fine-grained clay-siliciclastic particles that would not necessarily respond in a simple frictional manner. Depending on whether the plastic nature of these slip zones develops during or after slip, subsequent focusing of slip within them could be complicated. 1 Mitchell, T.A., Ben-Zion, Y., Shimamoto, T., 2011. Ear. Planet. Sci. Lett. 308, 284-297. 2 Lin, A., Yamashita, K, Tanaka, M. J., 2013. Struc. Geol. 48, 3-13. 3 White, J.C., Lin, A. 2016. Proc. AGU Fall Mtg., T42-02 San Francisco.

Patency of cavopulmonary connection studied by single phase electron beam computed tomography.

PubMed

Choi, Byoung Wook; Park, Young Hwan; Lee, Jong Kyun; Kim, Dong Joon; Kim, Min Jung; Choe, Kyu Ok

2003-10-01

The shunt patency and anatomic alteration of central PA after cavopulmonary connection was assessed by one phase electron-beam computed tomography (EBCT) METHODS: Thirteen patients that received a bi-directional cavo-pulmonary shunt (BCPS, n = 7) or total cavo-pulmonary connection (TCPC, n = 6) were included. The patency of the shunt and the anatomy of intra-pericardial PA were evaluated by EBCT, and compared by angiography and echocardiography. EBCT accurately evaluated shunt patency and the anatomy of the intra-pericardial PA, except for the incorrect diagnosis of SVC-PA shunt patency and peripheral pulmonary stenosis in two TCPC patients. Both of these patients had bilateral SVC and received either bilateral BCPS or ligation of the left SVC respectively. The baffle between the IVC and PA was partly opacified through a fenestration of the baffle, but was not opacified in two patients without fenestration. EBCT accurately evaluated shunt patency and the anatomy of central PA, however, the accuracy was limited in two cases with bilateral SVC. The opacification of the intra-atrial baffle was insufficient in TCPC cases. Multi-phase CT angiography may overcome this limitation in this patient subset.

Electron coherent diffraction tomography of a nanocrystal

NASA Astrophysics Data System (ADS)

Dronyak, Roman; Liang, Keng S.; Tsai, Jin-Sheng; Stetsko, Yuri P.; Lee, Ting-Kuo; Chen, Fu-Rong

2010-05-01

Coherent diffractive imaging (CDI) with electron or x-ray sources is a promising technique for investigating the structure of nanoparticles down to the atomic scale. In electron CDI, a two-dimensional reconstruction is demonstrated using highly coherent illumination from a field-emission gun as a source of electrons. In a three-dimensional (3D) electron CDI, we experimentally determine the morphology of a single MgO nanocrystal using the Bragg diffraction geometry. An iterative algorithm is applied to invert the 3D diffraction pattern about a (200) reflection of the nanoparticle measured at an angular range of 1.8°. The results reveal a 3D image of the sample at ˜8 nm resolution, and agree with a simulation. Our work demonstrates an alternative approach to obtain the 3D structure of nanocrystals with an electron microscope.

Complex deformation in western Tibet revealed by anisotropic tomography

NASA Astrophysics Data System (ADS)

Zhang, Heng; Zhao, Junmeng; Zhao, Dapeng; Yu, Chunquan; Liu, Hongbing; Hu, Zhaoguo

2016-10-01

The mechanism and pattern of deformation beneath western Tibet are still an issue of debate. In this work we present 3-D P- and S-wave velocity tomography as well as P-wave radial and azimuthal anisotropy along the ANTILOPE-I profile and surrounding areas in western Tibet, which are determined by using a large number of P and S arrival-time data of local earthquakes and teleseismic events. Our results show that low-velocity (low-V) zones exist widely in the middle crust, whereas low-V zones are only visible in the lower crust beneath northwestern Tibet, indicating the existence of significant heterogeneities and complex flow there. In the upper mantle, a distinct low-V gap exists between the Indian and Asian plates. Considering the P- and S-wave tomography and P-wave azimuthal and radial anisotropy results, we interpret the gap to be caused mainly by shear heating. Depth-independent azimuthal anisotropy and high-velocity zones exist beneath the northern part of the study region, suggesting a vertically coherent deformation beneath the Tarim Basin. In contrast, tomographic and anisotropic features change with depth beneath the central and southern parts of the study region, which reflects depth-dependent (or decoupled) deformations there. At the northern edge of the Indian lithospheric mantle (ILM), P-wave azimuthal anisotropy shows a nearly east-west fast-velocity direction, suggesting that the ILM was re-built by mantle materials flowing to the north.

A method and example of seismically imaging near‐surface fault zones in geologically complex areas using Vp, Vs, and their ratios

USGS Publications Warehouse

Catchings, Rufus D.; Rymer, Michael J.; Goldman, Mark R.; Sickler, Robert R.; Criley, Coyn J.

2014-01-01

The determination of near‐surface (vadose zone and slightly below) fault locations and geometries is important because assessment of ground rupture, strong shaking, geologic slip rates, and rupture histories occurs at shallow depths. However, seismic imaging of fault zones at shallow depths can be difficult due to near‐surface complexities, such as weathering, groundwater saturation, massive (nonlayered) rocks, and vertically layered strata. Combined P‐ and S‐wave seismic‐refraction tomography data can overcome many of the near‐surface, fault‐zone seismic‐imaging problems because of differences in the responses of elastic (bulk and shear) moduli of P and S waves to shallow‐depth, fault‐zone properties. We show that high‐resolution refraction tomography images of P‐ to S‐wave velocity ratios (VP/VS) can reliably identify near‐surface faults. We demonstrate this method using tomography images of the San Andreas fault (SAF) surface‐rupture zone associated with the 18 April 1906 ∼M 7.9 San Francisco earthquake on the San Francisco peninsula in California. There, the SAF cuts through Franciscan mélange, which consists of an incoherent assemblage of greywacke, chert, greenstone, and serpentinite. A near‐vertical zone (∼75° northeast dip) of high P‐wave velocities (up to 3000  m/s), low S‐wave velocities (∼150–600  m/s), high VP/VS ratios (4–8.8), and high Poisson’s ratios (0.44–0.49) characterizes the main surface‐rupture zone to a depth of about 20 m and is consistent with nearby trench observations. We suggest that the combined VP/VSimaging approach can reliably identify most near‐surface fault zones in locations where many other seismic methods cannot be applied.

Structure of the Sumatra-Andaman subduction zone

NASA Astrophysics Data System (ADS)

Pesicek, Jeremy Dale

We have conducted studies of the Sumatra-Andaman subduction zone using newly available teleseismic data resulting from the aftershock sequences of the 2004, 2005, and 2007 great earthquakes that occurred offshore of the island of Sumatra. In order to better exploit the new data, existing methodologies have been adapted and advanced in several ways to obtain results at a level of precision not previously possible from teleseismic data. Seismic tomography studies of the mantle were conducted using an improved iterative technique that accounts for fine-scale three-dimensional (3-D) velocity variations inside the study region and coarser global velocity variations outside the region. More precise earthquake locations were determined using a double-difference technique that has been extended to teleseismic distances using spherical ray tracing through the nested 3-D regional-global velocity models. Earthquake relocation was included in the iterative tomography scheme and was found to significantly enhance the recovery of slab velocity anomalies. Finally, because crustal structure is poorly constrained by the teleseismic data, 3-D density modeling of the crust was conducted using newly available satellite gravity data and a spherical prism gravity algorithm. The results of these studies better constrain the structure of the Sumatra-Andaman subduction zone, including the geometry of the mantle slab, position of the megathrust, and structural features of the downgoing plate. Tomography results reveal continuous upper mantle slab anomalies with significant variations in dip throughout the region. Broad curvature of the fast anomalies beneath northern Sumatra, similar to curvature of the trench and volcanic arc at the surface, is interpreted as folding of the upper mantle slab. Earthquake relocations show systematic shifts of the hypocenters to the northeast and to shallower depths, each with average changes of 5 km. Reduced scatter in the relocations better constrain the

Compensation of missing wedge effects with sequential statistical reconstruction in electron tomography.

PubMed

Paavolainen, Lassi; Acar, Erman; Tuna, Uygar; Peltonen, Sari; Moriya, Toshio; Soonsawad, Pan; Marjomäki, Varpu; Cheng, R Holland; Ruotsalainen, Ulla

2014-01-01

Electron tomography (ET) of biological samples is used to study the organization and the structure of the whole cell and subcellular complexes in great detail. However, projections cannot be acquired over full tilt angle range with biological samples in electron microscopy. ET image reconstruction can be considered an ill-posed problem because of this missing information. This results in artifacts, seen as the loss of three-dimensional (3D) resolution in the reconstructed images. The goal of this study was to achieve isotropic resolution with a statistical reconstruction method, sequential maximum a posteriori expectation maximization (sMAP-EM), using no prior morphological knowledge about the specimen. The missing wedge effects on sMAP-EM were examined with a synthetic cell phantom to assess the effects of noise. An experimental dataset of a multivesicular body was evaluated with a number of gold particles. An ellipsoid fitting based method was developed to realize the quantitative measures elongation and contrast in an automated, objective, and reliable way. The method statistically evaluates the sub-volumes containing gold particles randomly located in various parts of the whole volume, thus giving information about the robustness of the volume reconstruction. The quantitative results were also compared with reconstructions made with widely-used weighted backprojection and simultaneous iterative reconstruction technique methods. The results showed that the proposed sMAP-EM method significantly suppresses the effects of the missing information producing isotropic resolution. Furthermore, this method improves the contrast ratio, enhancing the applicability of further automatic and semi-automatic analysis. These improvements in ET reconstruction by sMAP-EM enable analysis of subcellular structures with higher three-dimensional resolution and contrast than conventional methods.

Coronary artery screening by electron beam computed tomography. Facts, controversy, and future.

PubMed

Wong, N D; Detrano, R C; Abrahamson, D; Tobis, J M; Gardin, J M

1995-08-01

Coronary calcium as detected by electron beam computed tomography always signifies at least some atherosclerosis, appears to be correlated with coronary risk factors, cardiac history, and overall angiographic severity of disease, but is inconsistently related to degree of atherosclerotic lesion stenosis in a given artery. Increasing evidence, however, suggests an association between coronary artery calcium, atherosclerosis, and coronary risk. But atherosclerosis is a very common condition, its prevalence increasing with age. No fully validated method for determining the quantity of coronary calcium is available, and we do not know whether the amount of calcium is a consistently accurate reflection of the amount of atherosclerosis or whether the amount of atherosclerosis reflects the degree of risk. Furthermore, the prognostic significance of coronary calcium in any given atherosclerotic lesion is not yet established. What is clear from cohort studies, however, is that at least three quarters of asymptomatic individuals, at least half of whom would have "positive" coronary calcium electron beam computed tomographic scans, will live for at least 10 years without cardiac problems of any kind. Investigation is needed to determine whether medical intervention may impact the clinical outcome of the rest of those identified with a positive scan but destined to suffer future clinical events. Despite lack of validation, this test has widespread appeal, both to the public as a means of being able to find out the condition of their coronary arteries "without injections or dye" and to hospitals and private medical groups who view this both as an innovation in cardiovascular diagnosis and as a potentially profitable diagnostic procedure.(ABSTRACT TRUNCATED AT 250 WORDS)

Native architecture of the Chlamydomonas chloroplast revealed by in situ cryo-electron tomography

PubMed Central

Engel, Benjamin D; Schaffer, Miroslava; Kuhn Cuellar, Luis; Villa, Elizabeth; Plitzko, Jürgen M; Baumeister, Wolfgang

2015-01-01

Chloroplast function is orchestrated by the organelle's intricate architecture. By combining cryo-focused ion beam milling of vitreous Chlamydomonas cells with cryo-electron tomography, we acquired three-dimensional structures of the chloroplast in its native state within the cell. Chloroplast envelope inner membrane invaginations were frequently found in close association with thylakoid tips, and the tips of multiple thylakoid stacks converged at dynamic sites on the chloroplast envelope, implicating lipid transport in thylakoid biogenesis. Subtomogram averaging and nearest neighbor analysis revealed that RuBisCO complexes were hexagonally packed within the pyrenoid, with ∼15 nm between their centers. Thylakoid stacks and the pyrenoid were connected by cylindrical pyrenoid tubules, physically bridging the sites of light-dependent photosynthesis and light-independent carbon fixation. Multiple parallel minitubules were bundled within each pyrenoid tubule, possibly serving as conduits for the targeted one-dimensional diffusion of small molecules such as ATP and sugars between the chloroplast stroma and the pyrenoid matrix. DOI: http://dx.doi.org/10.7554/eLife.04889.001 PMID:25584625

Assessment of Systematic Measurement Errors for Acoustic Travel-Time Tomography of the Atmosphere

DTIC Science & Technology

2013-01-01

measurements include assess- ment of the time delays in electronic circuits and mechanical hardware (e.g., drivers and microphones) of a tomography array ...hardware and electronic circuits of the tomography array and errors in synchronization of the transmitted and recorded signals. For example, if...coordinates can be as large as 30 cm. These errors are equivalent to the systematic errors in the travel times of 0.9 ms. Third, loudspeakers which are used

Visualization of bacteriophage P1 infection by cryo-electron tomography of tiny Escherichia coli

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu Jun, E-mail: Jun.Liu.1@uth.tmc.edu; Chen Chengyen; Shiomi, Daisuke

2011-09-01

Bacteriophage P1 has a contractile tail that targets the conserved lipopolysaccharide on the outer membrane surface of the host for initial adsorption. The mechanism by which P1 DNA enters the host cell is not well understood, mainly because the transient molecular interactions between bacteriophage and bacteria have been difficult to study by conventional approaches. Here, we engineered tiny E. coli host cells so that the initial stages of P1-host interactions could be captured in unprecedented detail by cryo-electron tomography. Analysis of three-dimensional reconstructions of frozen-hydrated specimens revealed three predominant configurations: an extended tail stage with DNA present in the phagemore » head, a contracted tail stage with DNA, and a contracted tail stage without DNA. Comparative analysis of various conformations indicated that there is uniform penetration of the inner tail tube into the E. coli periplasm and a significant movement of the baseplate away from the outer membrane during tail contraction.« less

ACUTE ZONAL OCCULT OUTER RETINOPATHY: Structural and Functional Analysis Across the Transition Zone Between Healthy and Diseased Retina.

PubMed

Duncker, Tobias; Lee, Winston; Jiang, Fan; Ramachandran, Rithambara; Hood, Donald C; Tsang, Stephen H; Sparrow, Janet R; Greenstein, Vivienne C

2018-01-01

To assess structure and function across the transition zone (TZ) between relatively healthy and diseased retina in acute zonal occult outer retinopathy. Six patients (6 eyes; age 22-71 years) with acute zonal occult outer retinopathy were studied. Spectral-domain optical coherence tomography, fundus autofluorescence, near-infrared reflectance, color fundus photography, and fundus perimetry were performed and images were registered to each other. The retinal layers of the spectral-domain optical coherence tomography scans were segmented and the thicknesses of two outer retinal layers, that is, the total receptor and outer segment plus layers, and the retinal nerve fiber layer were measured. All eyes showed a TZ on multimodal imaging. On spectral-domain optical coherence tomography, the TZ was in the nasal retina at varying distances from the fovea. For all eyes, it was associated with loss of the ellipsoid zone band, significant thinning of the two outer retinal layers, and in three eyes with thickening of the retinal nerve fiber layer. On fundus autofluorescence, all eyes had a clearly demarcated peripapillary area of abnormal fundus autofluorescence delimited by a border of high autofluorescence; the latter was associated with loss of the ellipsoid zone band and with a change from relatively normal to markedly decreased or nonrecordable visual sensitivity on fundus perimetry. The results of multimodal imaging clarified the TZ in acute zonal occult outer retinopathy. The TZ was outlined by a distinct high autofluorescence border that correlated with loss of the ellipsoid zone band on spectral-domain optical coherence tomography. However, in fundus areas that seemed healthy on fundus autofluorescence, thinning of the outer retinal layers and thickening of the retinal nerve fiber layer were observed near the TZ. The TZ was also characterized by a decrease in visual sensitivity.

Seismicity and structure of Nazca Plate subduction zone in southern Peru

NASA Astrophysics Data System (ADS)

Lim, H.; Kim, Y.; Clayton, R. W.; Thurber, C. H.

2016-12-01

We define subducting plate geometries in the Nazca subduction zone by (re)locating intra-slab earthquakes in southern Peru (2-18°S) and taking previously published converted phase analysis results, to clarify the slab geometry and inferred relationships to the seismicity. We also provide both P- and S-wave velocities of the subducting Nazca Plate and mantle wedge portions close to the slab using double-difference tomography (Zhang and Thurber, 2003) to understand upper plate volcanism and subduction process. A total of 492 regional earthquakes from August 2008 to February 2013 recorded from the dense seismic array (PeruSE, 2013) are selected for the relocation and tomography. The relocated seismicity shows a smooth contortion in the slab-dip transition zone for 400 km between the shallow (25°)-to-flat dipping interface in the north and 40°-dipping interface in the south. We find a significant slab-dip difference (up to 10°) between our results and previously published slab models along the profile region sampling the normal-dip slab at depth (>100 km). Robust features in both P- and S-wave tomography inversions are dipping low-velocity slabs down to 100 km transitioning to higher-velocities at 100-140 km in both flat slab and dipping slab regions. Differences in the velocities of the mantle wedge between the two regions may indicate different hydration states in the wedge.

The Electron Density Features Revealed by the GNSS-Based Radio Tomography in the Different Latitudinal and Longitudinal Sectors of the Ionosphere

NASA Astrophysics Data System (ADS)

Andreeva, Elena; Tereshchenko, Evgeniy; Nazarenko, Marina; Nesterov, Ivan; Kozharin, Maksim; Padokhin, Artem; Tumanova, Yulia

2016-04-01

The ionospheric radio tomography is an efficient method for electron density imaging in the different geographical regions of the world under different space weather conditions. The input for the satellite-based ionospheric radio tomography is provided by the signals that are transmitted from the navigational satellites and recorded by the chains or networks of ground receivers. The low-orbiting (LO) radio tomography employs the 150/400 MHz radio transmissions from the Earth's orbiters (like the Russian Tsikada/Parus and American Transit) flying at a height of ~1000 km above the Earth in the nearly polar orbits. The phases of the signals from a moving satellite which are recorded by the chains of ground receivers oriented along the satellite path form the families of linear integrals of electron density along the satellite-receiver rays that are used as the input data for LORT. The LO tomographic inversion of these data by phase difference method yields the 2D distributions of the ionospheric plasma in the vertical plane containing the receiving chain and the satellite path. LORT provides vertical resolution of 20-30 km and horizontal resolution of 30-40 km. The high-orbiting (HO) radio tomography employs the radio transmissions from the GPS/GLONASS satellites and enables 4D imaging of the ionosphere (3 spatial coordinates and time). HORT has a much wider spatial coverage (almost worldwide) and provides continuous time series of the reconstructions. However, the spatial resolution of HORT is lower (~100 km horizontally with a time step 60-20 min). In the regions with dense receiving networks (Europe, USA, Alaska, Japan), the resolution can be increased to 30-50 km with a time interval of 30-10 min. To date, the extensive RT data collected from the existing RT chains and networks enable a thorough analysis of both the regular and sporadic ionospheric features which are observed systematically or appear spontaneously, whose origin is fairly well understood or

High-resolution x-ray tomography using laboratory sources

NASA Astrophysics Data System (ADS)

Tkachuk, Andrei; Feser, Michael; Cui, Hongtao; Duewer, Fred; Chang, Hauyee; Yun, Wenbing

2006-08-01

X-ray computed tomography (XCT) is a powerful nondestructive 3D imaging technique, which enables the visualization of the three dimensional structure of complex, optically opaque samples. High resolution XCT using Fresnel zone plate lenses has been confined in the past to synchrotron radiation centers due to the need for a bright and intense source of x-rays. This confinement severely limits the availability and accessibility of x-ray microscopes and the wide proliferation of this methodology. We are describing a sub-50nm resolution XCT system operating at 8 keV in absorption and Zernike phase contrast mode based on a commercially available laboratory x-ray source. The system utilizes high-efficiency Fresnel zone plates with an outermost zone width of 35 nm and 700 nm structure height resulting in a current spatial resolution better than 50 nm. In addition to the technical description of the system and specifications, we present application examples in the semiconductor field.

Degradation of metallic materials studied by correlative tomography

NASA Astrophysics Data System (ADS)

Burnett, T. L.; Holroyd, N. J. H.; Lewandowski, J. J.; Ogurreck, M.; Rau, C.; Kelley, R.; Pickering, E. J.; Daly, M.; Sherry, A. H.; Pawar, S.; Slater, T. J. A.; Withers, P. J.

2017-07-01

There are a huge array of characterization techniques available today and increasingly powerful computing resources allowing for the effective analysis and modelling of large datasets. However, each experimental and modelling tool only spans limited time and length scales. Correlative tomography can be thought of as the extension of correlative microscopy into three dimensions connecting different techniques, each providing different types of information, or covering different time or length scales. Here the focus is on the linking of time lapse X-ray computed tomography (CT) and serial section electron tomography using the focussed ion beam (FIB)-scanning electron microscope to study the degradation of metals. Correlative tomography can provide new levels of detail by delivering a multiscale 3D picture of key regions of interest. Specifically, the Xe+ Plasma FIB is used as an enabling tool for large-volume high-resolution serial sectioning of materials, and also as a tool for preparation of microscale test samples and samples for nanoscale X-ray CT imaging. The exemplars presented illustrate general aspects relating to correlative workflows, as well as to the time-lapse characterisation of metal microstructures during various failure mechanisms, including ductile fracture of steel and the corrosion of aluminium and magnesium alloys. Correlative tomography is already providing significant insights into materials behaviour, linking together information from different instruments across different scales. Multiscale and multifaceted work flows will become increasingly routine, providing a feed into multiscale materials models as well as illuminating other areas, particularly where hierarchical structures are of interest.

3D Electrical resistivity tomography monitoring of an artificial tracer injected within the hyporheic zone

NASA Astrophysics Data System (ADS)

Houzé, Clémence; Pessel, Marc; Durand, Veronique

2016-04-01

Due to the high complexity level of hyporheic flow paths, hydrological and biogeochemical processes which occur in this mixing place are not fully understood yet. Some previous studies made in flumes show that hyporheic flow is strongly connected to the streambed morphology and sediment heterogeneity . There is still a lack of practical field experiment considering a natural environment and representation of natural streambed heterogeneities will be always limited in laboratories. The purpose of this project is to propose an innovative method using 3D Electrical Resistivity Tomography (ERT) monitoring of an artificial tracer injection directly within the streambed sediments in order to visualize the water pathways within the hyporheic zone. Field experiment on a small stream was conducted using a plastic tube as an injection piezometer and home-made electrodes strips arranged in a rectangular form made of 180 electrodes (15 strips of 12 electrodes each). The injection of tracer (NaCl) lasted approximatively 90 minutes, and 24h monitoring with increasing step times was performed. The physical properties of the water are controlled by CTD probes installed upstream and downstream within the river. Inverse time-lapse tomographs show development and persistence of a conductive water plume around the injection point. Due to the low hydraulic conductivity of streambed sediments (clay and overlying loess), the tracer movement is barely visible, as it dilutes gradually in the pore water. Impact of boundary conditions on inversion results can lead to significant differences on images, especially in the shallow part of the profiles. Preferential paths of transport are not highlighted here, but this experiment allows to follow spatially and temporarily the evolution of the tracer in a complex natural environment .

Assessment of liver ablation using cone beam computed tomography.

PubMed

Abdel-Rehim, Mohamed; Ronot, Maxime; Sibert, Annie; Vilgrain, Valérie

2015-01-14

To investigate the feasibility and accuracy of cone beam computed tomography (CBCT) in assessing the ablation zone after liver tumor ablation. Twenty-three patients (17 men and 6 women, range: 45-85 years old, mean age 65 years) with malignant liver tumors underwent ultrasound-guided percutaneous tumor ablation [radiofrequency (n = 14), microwave (n = 9)] followed by intravenous contrast-enhanced CBCT. Baseline multidetector computed tomography (MDCT) and peri-procedural CBCT images were compared. CBCT image quality was assessed as poor, good, or excellent. Image fusion was performed to assess tumor coverage, and quality of fusion was rated as bad, good, or excellent. Ablation zone volumes on peri-procedural CBCT and post-procedural MDCT were compared using the non-parametric paired Wilcoxon t-test. Rate of primary ablation effectiveness was 100%. There were no complications related to ablation. Local tumor recurrence and new liver tumors were found 3 mo after initial treatment in one patient (4%). The ablation zone was identified in 21/23 (91.3%) patients on CBCT. The fusion of baseline MDCT and peri-procedural CBCT images was feasible in all patients and showed satisfactory tumor coverage (at least 5-mm margin). CBCT image quality was poor, good, and excellent in 2 (9%), 8 (35%), and 13 (56%), patients respectively. Registration quality between peri-procedural CBCT and post-procedural MDCT images was good to excellent in 17/23 (74%) patients. The median ablation volume on peri-procedural CBCT and post-procedural MDCT was 30 cm(3) (range: 4-95 cm(3)) and 30 cm(3) (range: 4-124 cm(3)), respectively (P-value > 0.2). There was a good correlation (r = 0.79) between the volumes of the two techniques. Contrast-enhanced CBCT after tumor ablation of the liver allows early assessment of the ablation zone.

Tomography and the Herglotz-Wiechert inverse formulation

NASA Astrophysics Data System (ADS)

Nowack, Robert L.

1990-04-01

In this paper, linearized tomography and the Herglotz-Wiechert inverse formulation are compared. Tomographic inversions for 2-D or 3-D velocity structure use line integrals along rays and can be written in terms of Radon transforms. For radially concentric structures, Radon transforms are shown to reduce to Abel transforms. Therefore, for straight ray paths, the Abel transform of travel-time is a tomographic algorithm specialized to a one-dimensional radially concentric medium. The Herglotz-Wiechert formulation uses seismic travel-time data to invert for one-dimensional earth structure and is derived using exact ray trajectories by applying an Abel transform. This is of historical interest since it would imply that a specialized tomographic-like algorithm has been used in seismology since the early part of the century (see Herglotz, 1907; Wiechert, 1910). Numerical examples are performed comparing the Herglotz-Wiechert algorithm and linearized tomography along straight rays. Since the Herglotz-Wiechert algorithm is applicable under specific conditions, (the absence of low velocity zones) to non-straight ray paths, the association with tomography may prove to be useful in assessing the uniqueness of tomographic results generalized to curved ray geometries.

DETECTION OF MICROVASCULAR CHANGES IN EYES OF PATIENTS WITH DIABETES BUT NOT CLINICAL DIABETIC RETINOPATHY USING OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY.

PubMed

de Carlo, Talisa E; Chin, Adam T; Bonini Filho, Marco A; Adhi, Mehreen; Branchini, Lauren; Salz, David A; Baumal, Caroline R; Crawford, Courtney; Reichel, Elias; Witkin, Andre J; Duker, Jay S; Waheed, Nadia K

2015-11-01

To evaluate the ability of optical coherence tomography angiography to detect early microvascular changes in eyes of diabetic individuals without clinical retinopathy. Prospective observational study of 61 eyes of 39 patients with diabetes mellitus and 28 control eyes of 22 age-matched healthy subjects that received imaging using optical coherence tomography angiography between August 2014 and March 2015. Eyes with concomitant retinal, optic nerve, and vitreoretinal interface diseases and/or poor-quality images were excluded. Foveal avascular zone size and irregularity, vessel beading and tortuosity, capillary nonperfusion, and microaneurysm were evaluated. Foveal avascular zone size measured 0.348 mm² (0.1085-0.671) in diabetic eyes and 0.288 mm² (0.07-0.434) in control eyes (P = 0.04). Foveal avascular zone remodeling was seen more often in diabetic than control eyes (36% and 11%, respectively; P = 0.01). Capillary nonperfusion was noted in 21% of diabetic eyes and 4% of control eyes (P = 0.03). Microaneurysms and venous beading were noted in less than 10% of both diabetic and control eyes. Both diabetic and healthy control eyes demonstrated tortuous vessels in 21% and 25% of eyes, respectively. Optical coherence tomography angiography was able to image foveal microvascular changes that were not detected by clinical examination in diabetic eyes. Changes to the foveal avascular zone and capillary nonperfusion were more prevalent in diabetic eyes, whereas vessel tortuosity was observed with a similar frequency in normal and diabetic eyes. Optical coherence tomography angiography may be able to detect diabetic eyes at risk of developing retinopathy and to screen for diabetes quickly and noninvasively before the systemic diagnosis is made.

A new apparatus for electron tomography in the scanning electron microscope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morandi, V., E-mail: morandi@bo.imm.cnr.it; Maccagnani, P.; Masini, L.

2015-06-23

The three-dimensional reconstruction of a microscopic specimen has been obtained by applying the tomographic algorithm to a set of images acquired in a Scanning Electron Microscope. This result was achieved starting from a series of projections obtained by stepwise rotating the sample under the beam raster. The Scanning Electron Microscope was operated in the scanning-transmission imaging mode, where the intensity of the transmitted electron beam is a monotonic function of the local mass-density and thickness of the specimen. The detection strategy has been implemented and tailored in order to maintain the projection requirement over the large tilt range, as requiredmore » by the tomographic workflow. A Si-based electron detector and an eucentric-rotation specimen holder have been specifically developed for the purpose.« less

Float-zone processing in a weightless environment

NASA Technical Reports Server (NTRS)

Fowle, A. A.; Haggerty, J. S.; Perron, R. R.; Strong, P. F.; Swanson, J. L.

1976-01-01

The results were reported of investigations to: (1) test the validity of analyses which set maximum practical diameters for Si crystals that can be processed by the float zone method in a near weightless environment, (2) determine the convective flow patterns induced in a typical float zone, Si melt under conditions perceived to be advantageous to the crystal growth process using flow visualization techniques applied to a dimensionally scaled model of the Si melt, (3) revise the estimates of the economic impact of space produced Si crystal by the float zone method on the U.S. electronics industry, and (4) devise a rational plan for future work related to crystal growth phenomena wherein low gravity conditions available in a space site can be used to maximum benefit to the U.S. electronics industry.

Electron Beam-Induced Deposition for Atom Probe Tomography Specimen Capping Layers.

PubMed

Diercks, David R; Gorman, Brian P; Mulders, Johannes J L

2017-04-01

Six precursors were evaluated for use as in situ electron beam-induced deposition capping layers in the preparation of atom probe tomography specimens with a focus on near-surface features where some of the deposition is retained at the specimen apex. Specimens were prepared by deposition of each precursor onto silicon posts and shaped into sub-70-nm radii needles using a focused ion beam. The utility of the depositions was assessed using several criteria including composition and uniformity, evaporation behavior and evaporation fields, and depth of Ga+ ion penetration. Atom probe analyses through depositions of methyl cyclopentadienyl platinum trimethyl, palladium hexafluoroacetylacetonate, and dimethyl-gold-acetylacetonate [Me2Au(acac)] were all found to result in tip fracture at voltages exceeding 3 kV. Examination of the deposition using Me2Au(acac) plus flowing O2 was inconclusive due to evaporation of surface silicon from below the deposition under all analysis conditions. Dicobalt octacarbonyl [Co2(CO)8] and diiron nonacarbonyl [Fe2(CO)9] depositions were found to be effective as in situ capping materials for the silicon specimens. Their very different evaporation fields [36 V/nm for Co2(CO)8 and 21 V/nm for Fe2(CO)9] provide options for achieving reasonably close matching of the evaporation field between the capping material and many materials of interest.

The Eastern Tennessee Seismic Zone: Reactivation of an Ancient Continent-Continent Suture Zone

NASA Astrophysics Data System (ADS)

Powell, C. A.

2014-12-01

The eastern Tennessee seismic zone (ETSZ) may represent reactivation of an ancient shear zone that accommodated left-lateral, transpressive motion of the Amazon craton during the Grenville orogeny. Several different lines of evidence support this concept including velocity models for the crust, earthquake hypocenter alignments, focal mechanism solutions, potential field anomalies, paleomagnetic pole positions, and isotopic geochemical studies. The ETSZ trends NE-SW for about 300 km and displays remarkable correlation with the prominent New York - Alabama (NY-AL) aeromagnetic lineament. Vp and Vs models for the crust derived from a local ETSZ earthquake tomography study reveal the presence of a narrow, NE-SW trending, steeply dipping zone of low velocities that extends to a depth of at least 24 km and is associated with the vertical projection of the NY-AL aeromagnetic lineament. The low velocity zone is interpreted as a major basement fault. The recent Mw 4.2 Perry County eastern Kentucky earthquake occurred north of the ETSZ but has a focal depth and mechanism that are similar to those for ETSZ earthquakes. We investigate the possibility that the proposed ancient shear zone extends into eastern Kentucky using Bouguer and aeromagnetic maps. The southern end of the ETSZ is characterized by hypocenters that align along planes dipping at roughly 45 degrees and focal mechanisms that contain large normal faulting components. The NY-AL aeromagnetic lineament also changes trend in the southern end of the ETSZ and the exact location of the lineament is ambiguous. We suggest that the southern portion of the ETSZ involves reactivation of reverse faults (now as normal faults) that mark the ancient transition between a collisional to a more transpressive boundary between Amazonia and Laurentia during the formation of the super continent Rodinia.

75 FR 17691 - Foreign-Trade Zone 196 - Fort Worth, Texas, Application for Temporary/Interim Manufacturing...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-07

... DEPARTMENT OF COMMERCE Foreign-Trade Zones Board [Docket T-2-2010] Foreign-Trade Zone 196 - Fort Worth, Texas, Application for Temporary/Interim Manufacturing Authority, ATC Logistics & Electronics... Executive Secretary of the Foreign-Trade Zones Board (the Board) by ATC Logistics & Electronics, operator of...

FIB-SEM tomography in biology.

PubMed

Kizilyaprak, Caroline; Bittermann, Anne Greet; Daraspe, Jean; Humbel, Bruno M

2014-01-01

Three-dimensional information is much easier to understand than a set of two-dimensional images. Therefore a layman is thrilled by the pseudo-3D image taken in a scanning electron microscope (SEM) while, when seeing a transmission electron micrograph, his imagination is challenged. First approaches to gain insight in the third dimension were to make serial microtome sections of a region of interest (ROI) and then building a model of the object. Serial microtome sectioning is a tedious and skill-demanding work and therefore seldom done. In the last two decades with the increase of computer power, sophisticated display options, and the development of new instruments, an SEM with a built-in microtome as well as a focused ion beam scanning electron microscope (FIB-SEM), serial sectioning, and 3D analysis has become far easier and faster.Due to the relief like topology of the microtome trimmed block face of resin-embedded tissue, the ROI can be searched in the secondary electron mode, and at the selected spot, the ROI is prepared with the ion beam for 3D analysis. For FIB-SEM tomography, a thin slice is removed with the ion beam and the newly exposed face is imaged with the electron beam, usually by recording the backscattered electrons. The process, also called "slice and view," is repeated until the desired volume is imaged.As FIB-SEM allows 3D imaging of biological fine structure at high resolution of only small volumes, it is crucial to perform slice and view at carefully selected spots. Finding the region of interest is therefore a prerequisite for meaningful imaging. Thin layer plastification of biofilms offers direct access to the original sample surface and allows the selection of an ROI for site-specific FIB-SEM tomography just by its pronounced topographic features.

Medium-scale traveling ionospheric disturbances by three-dimensional ionospheric GPS tomography

NASA Astrophysics Data System (ADS)

Chen, C. H.; Saito, A.; Lin, C. H.; Yamamoto, M.; Suzuki, S.; Seemala, G. K.

2016-02-01

In this study, we develop a three-dimensional ionospheric tomography with the ground-based global position system (GPS) total electron content observations. Because of the geometric limitation of GPS observation path, it is difficult to solve the ill-posed inverse problem for the ionospheric electron density. Different from methods given by pervious studies, we consider an algorithm combining the least-square method with a constraint condition, in which the gradient of electron density tends to be smooth in the horizontal direction and steep in the vicinity of the ionospheric F2 peak. This algorithm is designed to be independent of any ionospheric or plasmaspheric electron density models as the initial condition. An observation system simulation experiment method is applied to evaluate the performance of the GPS ionospheric tomography in detecting ionospheric electron density perturbation at the scale size of around 200 km in wavelength, such as the medium-scale traveling ionospheric disturbances.

Telocytes and putative stem cells in the lungs: electron microscopy, electron tomography and laser scanning microscopy.

PubMed

Popescu, Laurentiu M; Gherghiceanu, Mihaela; Suciu, Laura C; Manole, Catalin G; Hinescu, Mihail E

2011-09-01

This study describes a novel type of interstitial (stromal) cell - telocytes (TCs) - in the human and mouse respiratory tree (terminal and respiratory bronchioles, as well as alveolar ducts). TCs have recently been described in pleura, epicardium, myocardium, endocardium, intestine, uterus, pancreas, mammary gland, etc. (see www.telocytes.com ). TCs are cells with specific prolongations called telopodes (Tp), frequently two to three per cell. Tp are very long prolongations (tens up to hundreds of μm) built of alternating thin segments known as podomers (≤ 200 nm, below the resolving power of light microscope) and dilated segments called podoms, which accommodate mitochondria, rough endoplasmic reticulum and caveolae. Tp ramify dichotomously, making a 3-dimensional network with complex homo- and heterocellular junctions. Confocal microscopy reveals that TCs are c-kit- and CD34-positive. Tp release shed vesicles or exosomes, sending macromolecular signals to neighboring cells and eventually modifying their transcriptional activity. At bronchoalveolar junctions, TCs have been observed in close association with putative stem cells (SCs) in the subepithelial stroma. SCs are recognized by their ultrastructure and Sca-1 positivity. Tp surround SCs, forming complex TC-SC niches (TC-SCNs). Electron tomography allows the identification of bridging nanostructures, which connect Tp with SCs. In conclusion, this study shows the presence of TCs in lungs and identifies a TC-SC tandem in subepithelial niches of the bronchiolar tree. In TC-SCNs, the synergy of TCs and SCs may be based on nanocontacts and shed vesicles.

Three-dimensional Upper Crustal Velocity and Attenuation Structures of the Central Tibetan Plateau from Local Earthquake Tomography

NASA Astrophysics Data System (ADS)

Zhou, B.; Liang, X.; Lin, G.; Tian, X.; Zhu, G.; Mechie, J.; Teng, J.

2017-12-01

A series of V-shaped conjugate strike-slip faults are the most spectacular geologic features in the central Tibetan plateau. A previous study suggested that this conjugate strike-slip fault system accommodates the east-west extension and coeval north-south contraction. Another previous study suggested that the continuous convergence between the Indian and Eurasian continents and the eastward asthenospheric flow generated lithospheric paired general-shear (PGS) deformation, which then caused the development of conjugate strike-slip faults in central Tibet. Local seismic tomography can image three dimensional upper-crustal velocity and attenuation structures in central Tibet, which will provide us with more information about the spatial distribution of physical properties and compositional variations around the conjugate strike-slip fault zone. Ultimately, this information could improve our understanding of the development mechanism of the conjugate strike-slip fault system. In this study, we collected 6,809 Pg and 2,929 Sg arrival times from 414 earthquakes recorded by the temporary SANDWICH and permanent CNSN networks from November 2013 to November 2015. We also included 300 P and 17 S arrival times from 12 shots recorded by the INDEPTH III project during the summer of 1998 in the velocity tomography. We inverted for preliminary Vp and Vp/Vs models using the SIMUL2000 tomography algorithm, and then relocated the earthquakes with these preliminary velocity models. After that, we inverted for the final velocity models with these improved source locations and origin times. After the velocity inversion, we performed local attenuation tomography using t* measurements from the same dataset with an already existing approach. There are correlated features in the velocity and attenuation structures. From the surface to 10 km depth, the study area is dominated by high Vp and Qp anomalies. However, from 10 km to 20 km depth, there is a low Vp and Qp zone distributed along the

Advanced prior modeling for 3D bright field electron tomography

NASA Astrophysics Data System (ADS)

Sreehari, Suhas; Venkatakrishnan, S. V.; Drummy, Lawrence F.; Simmons, Jeffrey P.; Bouman, Charles A.

2015-03-01

Many important imaging problems in material science involve reconstruction of images containing repetitive non-local structures. Model-based iterative reconstruction (MBIR) could in principle exploit such redundancies through the selection of a log prior probability term. However, in practice, determining such a log prior term that accounts for the similarity between distant structures in the image is quite challenging. Much progress has been made in the development of denoising algorithms like non-local means and BM3D, and these are known to successfully capture non-local redundancies in images. But the fact that these denoising operations are not explicitly formulated as cost functions makes it unclear as to how to incorporate them in the MBIR framework. In this paper, we formulate a solution to bright field electron tomography by augmenting the existing bright field MBIR method to incorporate any non-local denoising operator as a prior model. We accomplish this using a framework we call plug-and-play priors that decouples the log likelihood and the log prior probability terms in the MBIR cost function. We specifically use 3D non-local means (NLM) as the prior model in the plug-and-play framework, and showcase high quality tomographic reconstructions of a simulated aluminum spheres dataset, and two real datasets of aluminum spheres and ferritin structures. We observe that streak and smear artifacts are visibly suppressed, and that edges are preserved. Also, we report lower RMSE values compared to the conventional MBIR reconstruction using qGGMRF as the prior model.

Electron tomography and cryo-SEM characterization reveals novel ultrastructural features of host-parasite interaction during Chlamydia abortus infection.

PubMed

Wilkat, M; Herdoiza, E; Forsbach-Birk, V; Walther, P; Essig, A

2014-08-01

Chlamydia (C.) abortus is a widely spread pathogen among ruminants that can be transmitted to women during pregnancy leading to severe systemic infection with consecutive abortion. As a member of the Chlamydiaceae, C. abortus shares the characteristic feature of an obligate intracellular biphasic developmental cycle with two morphological forms including elementary bodies (EBs) and reticulate bodies (RBs). In contrast to other chlamydial species, C. abortus ultrastructure has not been investigated yet. To do so, samples were fixed by high-pressure freezing and processed by different electron microscopic methods. Freeze-substituted samples were analysed by transmission electron microscopy, scanning transmission electron microscopical tomography and immuno-electron microscopy, and freeze-fractured samples were analysed by cryo-scanning electron microscopy. Here, we present three ultrastructural features of C. abortus that have not been reported up to now. Firstly, the morphological evidence that C. abortus is equipped with the type three secretion system. Secondly, the accumulation and even coating of whole inclusion bodies by membrane complexes consisting of multiple closely adjacent membranes which seems to be a C. abortus specific feature. Thirdly, the formation of small vesicles in the periplasmic space of RBs in the second half of the developmental cycle. Concerning the time point of their formation and the fact that they harbour chlamydial components, these vesicles might be morphological correlates of an intermediate step during the process of redifferentiation of RBs into EBs. As this feature has also been shown for C. trachomatis and C. pneumoniae, it might be a common characteristic of the family of Chlamydiaceae.

Image the heterogeneous structure of Colima volcano complex using ambient noise and teleseismic tomography

NASA Astrophysics Data System (ADS)

Dai, Y.; Yang, T.

2017-12-01

As one of the most active stratovolcano in present world, Colima volcano has aroused extensive researches about its structure and mechanism. Preceded studies have described the deep internal structure of Jalisco subduction zone and attributed the surface volcanism to the subduction of Rivera plate and Cocos plate here, but the image of crustal structure remains vague. Thus our work aims to depict the lithosphere structure and magma system, trying to understand the material transportation of Colima volcano. Two dense networks of temporary stations, CODEX and MARS, were deployed in the studying area during 2006-2007, collected adequate seismic data for tomography. We used ambient noise tomography to obtain both the phase velocity maps and azimuthal anisotropic character of crust. Those results show a shallow magma chamber right beneath the Colima volcano reaching a depth of 8km and its azimuthal anisotropic character ,which is of larger magnitude and northeast-ward in the connection part, indicates the material probably flow from central Mexico volcanic zone in the superficial crust. Hereafter, we combine the ambient noise tomography with surface wave tomography which corresponding to deeper structure. Phase velocity information from two methods are then used to invert a 3D heterogeneous model, which well presents the complex lithosphere structure of this area and shows the connection between the mantle window and magma chamber, giving the clues of how the magma materials transport from source to surface to support the constant eruption of Colima volcano.

Human cardiac telocytes: 3D imaging by FIB-SEM tomography

PubMed Central

Cretoiu, D; Hummel, E; Zimmermann, H; Gherghiceanu, M; Popescu, L M

2014-01-01

Telocyte (TC) is a newly identified type of cell in the cardiac interstitium (www.telocytes.com). TCs are described by classical transmission electron microscopy as cells with very thin and long telopodes (Tps; cellular prolongations) having podoms (dilations) and podomers (very thin segments). TCs’ three-dimensional (3D) morphology is still unknown. Cardiac TCs seem to be particularly involved in long and short distance intercellular signalling and, therefore, their 3D architecture is important for understanding their spatial connections. Using focused ion beam scanning electron microscopy (FIB-SEM) we show, for the first time, the whole ultrastructural anatomy of cardiac TCs. 3D reconstruction of cardiac TCs by FIB-SEM tomography confirms that they have long, narrow but flattened (ribbon-like) telopodes, with humps generated by the podoms. FIB-SEM tomography also confirms the network made by TCs in the cardiac interstitium through adherens junctions. This study provides the first FIB-SEM tomography of a human cell type. PMID:25327290

FIB–SEM tomography of 4th generation PWA 1497 superalloy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ziętara, Maciej, E-mail: zietara@agh.edu.pl; Kruk, Adam, E-mail: kruczek@agh.edu.pl; Gruszczyński, Adam, E-mail: gruszcz@agh.edu.pl

2014-01-15

The effect of creep deformation on the microstructure of the PWA 1497 single crystal Ni-base superalloy developed for turbine blade applications was investigated. The aim of the present study was to characterize quantitatively a superalloy microstructure and subsequent development of rafted γ′ precipitates in the PWA 1497 during creep deformation at 982 °C and 248 MPa up to rupture. The PWA1497 microstructure was characterized by scanning electron microscopy and FIB–SEM electron tomography. The 3D reconstruction of the PWA1497 microstructure is presented and discussed. - Highlights: • The microstructure of PWA1497 superalloy was examined using FIB–SEM tomography. • In case ofmore » modern single crystal superalloys, measurements of A{sub A} are adequate for V{sub V}. • During creep the γ channel width increases from 65 to 193 nm for ruptured specimen. • Tomography is a useful technique for quantitative studies of material microstructure.« less

A neural network approach for image reconstruction in electron magnetic resonance tomography.

PubMed

Durairaj, D Christopher; Krishna, Murali C; Murugesan, Ramachandran

2007-10-01

An object-oriented, artificial neural network (ANN) based, application system for reconstruction of two-dimensional spatial images in electron magnetic resonance (EMR) tomography is presented. The standard back propagation algorithm is utilized to train a three-layer sigmoidal feed-forward, supervised, ANN to perform the image reconstruction. The network learns the relationship between the 'ideal' images that are reconstructed using filtered back projection (FBP) technique and the corresponding projection data (sinograms). The input layer of the network is provided with a training set that contains projection data from various phantoms as well as in vivo objects, acquired from an EMR imager. Twenty five different network configurations are investigated to test the ability of the generalization of the network. The trained ANN then reconstructs two-dimensional temporal spatial images that present the distribution of free radicals in biological systems. Image reconstruction by the trained neural network shows better time complexity than the conventional iterative reconstruction algorithms such as multiplicative algebraic reconstruction technique (MART). The network is further explored for image reconstruction from 'noisy' EMR data and the results show better performance than the FBP method. The network is also tested for its ability to reconstruct from limited-angle EMR data set.

Internal Structure of Taiwan Chelungpu Fault Zone Gouges

NASA Astrophysics Data System (ADS)

Song, Y.; Song, S.; Tang, M.; Chen, F.; Chen, Y.

2005-12-01

Gouge formation is found to exist in brittle faults at all scale (1). This fine-grain gouge is thought to control earthquake instability. And thus investigating the gouge textures and compositions is very important to an understanding of the earthquake process. Employing the transmission electron microscope (TEM) and a new transmission X-ray microscope (TXM), we study the internal structure of fault zone gouges from the cores of the Taiwan Chelungpu-fault Drilling Project (TCDP), which drilled in the fault zone of 1999 Chi-Chi earthquake. This X-ray microscope have installed at beamline BL01B of the Taiwan Light Source, National Synchrotron Radiation Research Center (NSRRC). It provides 2D imaging and 3D tomography at energy 8-11 keV with a spatial resolution of 25-60 nm, and is equipped with the Zernike-phase contrast capability for imaging light materials. In this work, we show the measurements of gouge texture, particle size distribution and 3D structure of the ultracataclasite in fault gouges within 12 cm about 1111.29 m depth. These characterizations in transition from the fault core to damage zone are related to the comminuting and the fracture energy in the earthquake faulting. The TXM data recently shows the particle size distributions of the ultracataclasite are between 150 nm and 900 nm in diameter. We will keep analyzing the characterization of particle size distribution, porosity and 3D structure of the fault zone gouges in transition from the fault core to damage zone to realize the comminuting and fracture surface energy in the earthquake faulting(2-5).The results may ascertain the implication of the nucleation, growth, transition, structure and permeability of the fault zones(6-8). Furthermore, it may be possible to infer the mechanism of faulting, the physical and chemical property of the fault, and the nucleation of the earthquake. References 1) B. Wilson, T. Dewerw, Z. Reches and J. Brune, Nature, 434 (2005) 749. 2) S. E. Schulz and J. P. Evans

A methodology for finding the optimal iteration number of the SIRT algorithm for quantitative Electron Tomography.

PubMed

Okariz, Ana; Guraya, Teresa; Iturrondobeitia, Maider; Ibarretxe, Julen

2017-02-01

The SIRT (Simultaneous Iterative Reconstruction Technique) algorithm is commonly used in Electron Tomography to calculate the original volume of the sample from noisy images, but the results provided by this iterative procedure are strongly dependent on the specific implementation of the algorithm, as well as on the number of iterations employed for the reconstruction. In this work, a methodology for selecting the iteration number of the SIRT reconstruction that provides the most accurate segmentation is proposed. The methodology is based on the statistical analysis of the intensity profiles at the edge of the objects in the reconstructed volume. A phantom which resembles a a carbon black aggregate has been created to validate the methodology and the SIRT implementations of two free software packages (TOMOJ and TOMO3D) have been used. Copyright © 2016 Elsevier B.V. All rights reserved.

Collagen Fibrils and Proteoglycans of Macular Dystrophy Cornea: Ultrastructure and 3D Transmission Electron Tomography.

PubMed

Akhtar, Saeed; Alkatan, Hind M; Kirat, Omar; Khan, Adnan A; Almubrad, Turki

2015-06-01

We report the ultrastructure and 3D transmission electron tomography of collagen fibrils (CFs), proteoglycans (PGs), and microfibrils within the CF of corneas of patients with macular corneal dystrophy (MCD). Three normal corneas and three MCD corneas from three Saudi patients (aged 25, 31, and 49 years, respectively) were used for this study. The corneas were processed for light and electron microscopy studies. 3D images were composed from a set of 120 ultrastructural images using the program "Composer" and visualized using the program "Visuliser Kai". 3D image analysis of MCD cornea showed a clear organization of PGs around the CF at very high magnification and degeneration of the microfibrils within the CF. Within the MCD cornea, the PG area in the anterior stroma was significantly larger than in the middle and posterior stroma. The PG area in the MCD cornea was significantly larger compared with the PG area in the normal cornea. The CF diameter and inter-fibrillar spacing of the MCD cornea were significantly smaller compared with those of the normal cornea. Ultrastructural 3D imaging showed that the production of unsulfated keratin sulfate (KS) may lead to the degeneration of micro-CFs within the CFs. The effect of the unsulfated KS was higher in the anterior stroma compared with the posterior stroma.

Electron Beam "Writes" Silicon On Sapphire

NASA Technical Reports Server (NTRS)

Heinemann, Klaus

1988-01-01

Method of growing silicon on sapphire substrate uses beam of electrons to aid growth of semiconductor material. Silicon forms as epitaxial film in precisely localized areas in micron-wide lines. Promising fabrication method for fast, densely-packed integrated circuits. Silicon deposited preferentially in contaminated substrate zones and in clean zone irradiated by electron beam. Electron beam, like surface contamination, appears to stimulate decomposition of silane atmosphere.

Reservoir Structure and Wastewater-Induced Seismicity at the Val d'Agri Oilfield (Italy) Shown by Three-Dimensional Vp and Vp/Vs Local Earthquake Tomography

NASA Astrophysics Data System (ADS)

Improta, L.; Bagh, S.; De Gori, P.; Valoroso, L.; Pastori, M.; Piccinini, D.; Chiarabba, C.; Anselmi, M.; Buttinelli, M.

2017-11-01

Wastewater injection into a high-rate well in the Val d'Agri oilfield, the largest in onshore Europe, has induced swarm microseismicity since the initiation of disposal in 2006. To investigate the reservoir structure and to track seismicity, we performed a high-spatial resolution local earthquake tomography using 1,281 natural and induced earthquakes recorded by local networks. The properties of the carbonate reservoir (rock fracturing, pore fluid pressure) and inherited faults control the occurrence and spatiotemporal distribution of seismicity. A low-Vp, high-Vp/Vs region under the well represents a fluid saturated fault zone ruptured by induced seismicity. High-Vp, high-Vp/Vs bumps match reservoir culminations indicating saturated liquid-bearing zones, whereas a very low Vp, low Vp/Vs anomaly might represent a strongly fractured and depleted zone of the hydrocarbon reservoir characterized by significant fluid withdrawal. The comprehensive picture of the injection-linked seismicity obtained by integrating reservoir-scale tomography, high-precision earthquake locations, and geophysical and injection data suggests that the driving mechanism is the channeling of pore pressure perturbations through a high permeable fault damage zone within the reservoir. The damage zone surrounds a Pliocene reverse fault optimally oriented in the current extensional stress field. The ruptured damage zone measures 2 km along strike and 3 km along dip and is confined between low permeability ductile formations. Injection pressure is the primary parameter controlling seismicity rate. Our study underlines that local earthquake tomography also using wastewater-induced seismicity can give useful insights into the physical mechanism leading to these earthquakes.

3D Structure Determination of Native Mammalian Cells using Cryo-FIB and Cryo-electron Tomography

PubMed Central

Wang, Ke; Strunk, Korrinn; Zhao, Gongpu; Gray, Jennifer L.; Zhang, Peijun

2012-01-01

Cryo-electron tomography (cryo-ET) has enabled high resolution three-dimensional (3D) structural analysis of virus and host cell interactions and many cell signaling events; these studies, however, have largely been limited to very thin, peripheral regions of eukaryotic cells or to small prokaryotic cells. Recent efforts to make thin, vitreous sections using cryo-ultramicrotomy have been successful, however, this method is technically very challenging and with many artifacts. Here, we report a simple and robust method for creating in situ, frozen-hydrated cell lamellas using a focused ion beam at cryogenic temperature (cryo-FIB), allowing access to any interior cellular regions of interest. We demonstrate the utility of cryo-FIB with high resolution 3D cellular structures from both bacterial cells and large mammalian cells. The method will not only facilitate high-throughput 3D structural analysis of biological specimens, but is also broadly applicable to sample preparation of thin films and surface materials without the need for FIB “lift-out”. PMID:22796867

Improved specimen reconstruction by Hilbert phase contrast tomography.

PubMed

Barton, Bastian; Joos, Friederike; Schröder, Rasmus R

2008-11-01

The low signal-to-noise ratio (SNR) in images of unstained specimens recorded with conventional defocus phase contrast makes it difficult to interpret 3D volumes obtained by electron tomography (ET). The high defocus applied for conventional tilt series generates some phase contrast but leads to an incomplete transfer of object information. For tomography of biological weak-phase objects, optimal image contrast and subsequently an optimized SNR are essential for the reconstruction of details such as macromolecular assemblies at molecular resolution. The problem of low contrast can be partially solved by applying a Hilbert phase plate positioned in the back focal plane (BFP) of the objective lens while recording images in Gaussian focus. Images recorded with the Hilbert phase plate provide optimized positive phase contrast at low spatial frequencies, and the contrast transfer in principle extends to the information limit of the microscope. The antisymmetric Hilbert phase contrast (HPC) can be numerically converted into isotropic contrast, which is equivalent to the contrast obtained by a Zernike phase plate. Thus, in-focus HPC provides optimal structure factor information without limiting effects of the transfer function. In this article, we present the first electron tomograms of biological specimens reconstructed from Hilbert phase plate image series. We outline the technical implementation of the phase plate and demonstrate that the technique is routinely applicable for tomography. A comparison between conventional defocus tomograms and in-focus HPC volumes shows an enhanced SNR and an improved specimen visibility for in-focus Hilbert tomography.

On spinodal decomposition in alnico - A transmission electron microscopy and atom probe tomography study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Lin; Guo, Wei; Poplawsky, J. D.

Here, alnico is a prime example of a finely tuned nanostructure whose magnetic properties are intimately connected to magnetic annealing (MA) during spinodal transformation and subsequent lower temperature annealing (draw) cycles. Using a combination of transmission electron microscopy and atom probe tomography, we show how these critical processing steps affect the local composition and nanostructure evolution with impact on magnetic properties. The nearly 2-fold increase of intrinsic coercivity (H ci) during the draw cycle is not adequately explained by chemical refinement of the spinodal phases. Instead, increased Fe-Co phase (α 1) isolation, development of Cu-rich spheres/rods/blades and additional α 1more » rod precipitation that occurs during the MA and draw, likely play a key role in Hci enhancement. Chemical ordering of the Al-Ni-phase (α 2) and formation of Ni-rich (α 3) may also contribute. Unraveling of the subtle effect of these nano-scaled features is crucial to understanding on how to improve shape anisotropy in alnico magnets.« less

On spinodal decomposition in alnico - A transmission electron microscopy and atom probe tomography study

DOE PAGES

Zhou, Lin; Guo, Wei; Poplawsky, J. D.; ...

2018-04-26

Here, alnico is a prime example of a finely tuned nanostructure whose magnetic properties are intimately connected to magnetic annealing (MA) during spinodal transformation and subsequent lower temperature annealing (draw) cycles. Using a combination of transmission electron microscopy and atom probe tomography, we show how these critical processing steps affect the local composition and nanostructure evolution with impact on magnetic properties. The nearly 2-fold increase of intrinsic coercivity (H ci) during the draw cycle is not adequately explained by chemical refinement of the spinodal phases. Instead, increased Fe-Co phase (α 1) isolation, development of Cu-rich spheres/rods/blades and additional α 1more » rod precipitation that occurs during the MA and draw, likely play a key role in Hci enhancement. Chemical ordering of the Al-Ni-phase (α 2) and formation of Ni-rich (α 3) may also contribute. Unraveling of the subtle effect of these nano-scaled features is crucial to understanding on how to improve shape anisotropy in alnico magnets.« less

Nicotinic receptor transduction zone: invariant arginine couples to multiple electron-rich residues.

PubMed

Mukhtasimova, Nuriya; Sine, Steven M

2013-01-22

Gating of the muscle-type acetylcholine receptor (AChR) channel depends on communication between the ACh-binding site and the remote ion channel. A key region for this communication is located within the structural transition zone between the ligand-binding and pore domains. Here, stemming from β-strand 10 of the binding domain, the invariant αArg209 lodges within the hydrophobic interior of the subunit and is essential for rapid and efficient channel gating. Previous charge-reversal experiments showed that the contribution of αArg209 to channel gating depends strongly on αGlu45, also within this region. Here we determine whether the contribution of αArg209 to channel gating depends on additional anionic or electron-rich residues in this region. Also, to reconcile diverging findings in the literature, we compare the dependence of αArg209 on αGlu45 in AChRs from different species, and compare the full agonist ACh with the weak agonist choline. Our findings reveal that the contribution of αArg209 to channel gating depends on additional nearby electron-rich residues, consistent with both electrostatic and steric contributions. Furthermore, αArg209 and αGlu45 show a strong interdependence in both human and mouse AChRs, whereas the functional consequences of the mutation αE45R depend on the agonist. The emerging picture shows a multifaceted network of interdependent residues that are required for communication between the ligand-binding and pore domains. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A novel fully automatic scheme for fiducial marker-based alignment in electron tomography.

PubMed

Han, Renmin; Wang, Liansan; Liu, Zhiyong; Sun, Fei; Zhang, Fa

2015-12-01

Although the topic of fiducial marker-based alignment in electron tomography (ET) has been widely discussed for decades, alignment without human intervention remains a difficult problem. Specifically, the emergence of subtomogram averaging has increased the demand for batch processing during tomographic reconstruction; fully automatic fiducial marker-based alignment is the main technique in this process. However, the lack of an accurate method for detecting and tracking fiducial markers precludes fully automatic alignment. In this paper, we present a novel, fully automatic alignment scheme for ET. Our scheme has two main contributions: First, we present a series of algorithms to ensure a high recognition rate and precise localization during the detection of fiducial markers. Our proposed solution reduces fiducial marker detection to a sampling and classification problem and further introduces an algorithm to solve the parameter dependence of marker diameter and marker number. Second, we propose a novel algorithm to solve the tracking of fiducial markers by reducing the tracking problem to an incomplete point set registration problem. Because a global optimization of a point set registration occurs, the result of our tracking is independent of the initial image position in the tilt series, allowing for the robust tracking of fiducial markers without pre-alignment. The experimental results indicate that our method can achieve an accurate tracking, almost identical to the current best one in IMOD with half automatic scheme. Furthermore, our scheme is fully automatic, depends on fewer parameters (only requires a gross value of the marker diameter) and does not require any manual interaction, providing the possibility of automatic batch processing of electron tomographic reconstruction. Copyright © 2015 Elsevier Inc. All rights reserved.

Using Local Event Tomography to Image Changes in the Rock Mass in the Kiirunavaara Iron Ore Mine, Northern Sweden

NASA Astrophysics Data System (ADS)

Lund, B.; Berglund, K.; Tryggvason, A.; Dineva, S.; Jonsson, L.

2017-12-01

Although induced seismic events in a mining environment are a potential hazard, they can be used to gain information about the rock mass in the mine which otherwise would be very difficult to obtain. In this study we use approximately 1.2 million mining induced seismic events in the Kiirunavaara iron ore mine in northernmost Sweden to image the rock mass using local event travel-time tomography. The Kiirunavaara mine is the largest underground iron ore mine in the world. The ore body is a magnetite sheet of 4 km length, with an average thickness of 80 m, which dips approximately 55° to the east. The events are of various origins such as shear slip on fractures, non-shear events and blasts, with magnitudes of up to 2.5. We use manually picked P- and S-wave arrival times from the routine processing in the tomography and we require that both phases are present at at least five geophones. For the tomography we use the 3D local earthquake tomography code PStomo_eq (Tryggvason et al., 2002), which we adjusted to the mining scale. The tomographic images show clearly defined regions of high and low velocities. Prominent low S-velocity zones are associated with mapped clay zones. Regions of ore where mining is ongoing and the near-ore tunnel infrastructure in the foot-wall also show generally low P- and S-velocities. The ore at depths below the current mining levels is imaged both as a low S-velocity zone but even more pronounced as a high Vp/Vs ratio zone. The tomography shows higher P- and S-velocities in the foot-wall away from the areas of mine infrastructure. We relocate all 1.2 million events in the new 3D velocity model. The relocation significantly enhances the clarity of the event distribution in space and we can much more easily identify seismically active structures, such as e.g. the deformation of the ore passes. The large number of events makes it possible to do detailed studies of the temporal evolution of stability in the mine. We present preliminary results

Electron Tomography of Cryofixed, Isometrically Contracting Insect Flight Muscle Reveals Novel Actin-Myosin Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Shenping; Liu, Jun; Reedy, Mary C.

2010-10-22

Isometric muscle contraction, where force is generated without muscle shortening, is a molecular traffic jam in which the number of actin-attached motors is maximized and all states of motor action are trapped with consequently high heterogeneity. This heterogeneity is a major limitation to deciphering myosin conformational changes in situ. We used multivariate data analysis to group repeat segments in electron tomograms of isometrically contracting insect flight muscle, mechanically monitored, rapidly frozen, freeze substituted, and thin sectioned. Improved resolution reveals the helical arrangement of F-actin subunits in the thin filament enabling an atomic model to be built into the thin filamentmore » density independent of the myosin. Actin-myosin attachments can now be assigned as weak or strong by their motor domain orientation relative to actin. Myosin attachments were quantified everywhere along the thin filament including troponin. Strong binding myosin attachments are found on only four F-actin subunits, the 'target zone', situated exactly midway between successive troponin complexes. They show an axial lever arm range of 77{sup o}/12.9 nm. The lever arm azimuthal range of strong binding attachments has a highly skewed, 127{sup o} range compared with X-ray crystallographic structures. Two types of weak actin attachments are described. One type, found exclusively in the target zone, appears to represent pre-working-stroke intermediates. The other, which contacts tropomyosin rather than actin, is positioned M-ward of the target zone, i.e. the position toward which thin filaments slide during shortening. We present a model for the weak to strong transition in the myosin ATPase cycle that incorporates azimuthal movements of the motor domain on actin. Stress/strain in the S2 domain may explain azimuthal lever arm changes in the strong binding attachments. The results support previous conclusions that the weak attachments preceding force generation are very

Laser-Assisted Atom Probe Tomography of Deformed Minerals: A Zircon Case Study.

PubMed

La Fontaine, Alexandre; Piazolo, Sandra; Trimby, Patrick; Yang, Limei; Cairney, Julie M

2017-04-01

The application of atom probe tomography to the study of minerals is a rapidly growing area. Picosecond-pulsed, ultraviolet laser (UV-355 nm) assisted atom probe tomography has been used to analyze trace element mobility within dislocations and low-angle boundaries in plastically deformed specimens of the nonconductive mineral zircon (ZrSiO4), a key material to date the earth's geological events. Here we discuss important experimental aspects inherent in the atom probe tomography investigation of this important mineral, providing insights into the challenges in atom probe tomography characterization of minerals as a whole. We studied the influence of atom probe tomography analysis parameters on features of the mass spectra, such as the thermal tail, as well as the overall data quality. Three zircon samples with different uranium and lead content were analyzed, and particular attention was paid to ion identification in the mass spectra and detection limits of the key trace elements, lead and uranium. We also discuss the correlative use of electron backscattered diffraction in a scanning electron microscope to map the deformation in the zircon grains, and the combined use of transmission Kikuchi diffraction and focused ion beam sample preparation to assist preparation of the final atom probe tip.

An electron tomography algorithm for reconstructing 3D morphology using surface tangents of projected scattering interfaces

NASA Astrophysics Data System (ADS)

Petersen, T. C.; Ringer, S. P.

2010-03-01

Upon discerning the mere shape of an imaged object, as portrayed by projected perimeters, the full three-dimensional scattering density may not be of particular interest. In this situation considerable simplifications to the reconstruction problem are possible, allowing calculations based upon geometric principles. Here we describe and provide an algorithm which reconstructs the three-dimensional morphology of specimens from tilt series of images for application to electron tomography. Our algorithm uses a differential approach to infer the intersection of projected tangent lines with surfaces which define boundaries between regions of different scattering densities within and around the perimeters of specimens. Details of the algorithm implementation are given and explained using reconstruction calculations from simulations, which are built into the code. An experimental application of the algorithm to a nano-sized Aluminium tip is also presented to demonstrate practical analysis for a real specimen. Program summaryProgram title: STOMO version 1.0 Catalogue identifier: AEFS_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFS_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 2988 No. of bytes in distributed program, including test data, etc.: 191 605 Distribution format: tar.gz Programming language: C/C++ Computer: PC Operating system: Windows XP RAM: Depends upon the size of experimental data as input, ranging from 200 Mb to 1.5 Gb Supplementary material: Sample output files, for the test run provided, are available. Classification: 7.4, 14 External routines: Dev-C++ ( http://www.bloodshed.net/devcpp.html) Nature of problem: Electron tomography of specimens for which conventional back projection may fail and/or data for which there is a limited angular

Time-lapse 3D electrical resistivity tomography to monitor soil-plant interactions

NASA Astrophysics Data System (ADS)

Boaga, Jacopo; Rossi, Matteo; Cassiani, Giorgio; Putti, Mario

2013-04-01

In this work we present the application of time-lapse non-invasive 3D micro- electrical tomography (ERT) to monitor soil-plant interactions in the root zone in the framework of the FP7 Project CLIMB (Climate Induced Changes on the Hydrology of Mediterranean Basins). The goal of the study is to gain a better understanding of the soil-vegetation interactions by the use of non-invasive techniques. We designed, built and installed a 3D electrical tomography apparatus for the monitoring of the root zone of a single apple tree in an orchard located in the Trentino region, Northern Italy. The micro-ERT apparatus consists of 48 buried electrodes on 4 instrumented micro boreholes plus 24 mini-electrodes on the surface spaced 0.1 m on a square grid. We collected repeated ERT and TDR soil moisture measurements for one year and performed two different controlled irrigation tests: one during a very dry Summer and one during a very wet and highly dynamic plant growing Spring period. We also ran laboratory analyses on soil specimens, in order to evaluate the electrical response at different saturation steps. The results demonstrate that 3D micro-ERT is capable of characterizing subsoil conditions and monitoring root zone activities, especially in terms of root zone suction regions. In particular, we note that in very dry conditions, 3D micro ERT can image water plumes in the shallow subsoil produced by a drip irrigation system. In the very dynamic growing season, under abundant irrigation, micro 3D ERT can detect the main suction zones caused by the tree root activity. Even though the quantitative use of this technique for moisture content balance suffers from well-known inversion difficulties, even the pure imaging of the active root zone is a valuable contribution. However the integration of the measurements in a fully coupled hydrogeophysical inversion is the way forward for a better understanding of subsoil interactions between biomass, hydrosphere and atmosphere.

Upper crustal structure beneath East Java from ambient noise tomography: A preliminary result

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martha, Agustya Adi; Graduate Research on Earthquakes and Active Tectonics, Institut Teknologi Bandung, Bandung; Widiyantoro, Sri

East Java has a fairly complex geological structure. Physiographically East Java can be divided into three zones, i.e. the Southern Mountains zone in the southern part, the Kendeng zone in the middle part, and the Rembang zone in the northern part. Most of the seismic hazards in this region are due to processes in the upper crust. In this study, the Ambient Noise Tomography (ANT) method is used to image the upper crustal structure beneath East Java. We have used seismic waveform data recorded by 8Meteorological, Climatological and Geophysical Agency (BMKG) stationary seismographic stations and 16 portable seismographs installed formore » 2 to 8 weeks. The data were processed to obtain waveforms fromnoise cross-correlation between pairs of seismographic stations. Our preliminary results indicate that the Kendeng zone, an area of low gravity anomaly, is associated with a low velocity zone. On the other hand, the southern mountain range, which has a high gravity anomaly, is related to a high velocity anomaly as shown by our tomographic images.« less

Three dimensional rock microstructures: insights from FIB-SEM tomography

NASA Astrophysics Data System (ADS)

Drury, Martyn; Pennock, Gill; de Winter, Matthijs

2016-04-01

Most studies of rock microstructures investigate two-dimensional sections or thin slices of three dimensional grain structures. With advances of X-ray and electron tomography methods the 3-D microstructure can be(relatively) routinely investigated on scales from a few microns to cm. 3D studies are needed to investigate the connectivity of microstructures and to test the assumptions we use to calculate 3D properties from 2D sections. We have used FIB-SEM tomography to study the topology of melts in synthetic olivine rocks, 3D crystal growth microstructures, pore networks and subgrain structures. The technique uses a focused ion beam to make serial sections with a spacing of tens to hundreds of nanometers. Each section is then imaged or mapped using the electron beam. The 3D geometry of grains and subgrains can be investigated using orientation contrast or EBSD mapping. FIB-SEM tomography of rocks and minerals can be limited by charging of the uncoated surfaces exposed by the ion beam. The newest generation of FIB-SEMs have much improved low voltage imaging capability allowing high resolution charge free imaging. Low kV FIB-SEM tomography is now widely used to study the connectivity of pore networks. In-situ fluids can also be studied using cryo-FIB-SEM on frozen samples, although special freezing techniques are needed to avoid artifacts produced by ice crystallization. FIB-SEM tomography is complementary, in terms of spatial resolution and sampled volume, to TEM tomography and X-ray tomography, and the combination of these methods can cover a wide range of scales. Our studies on melt topology in synthetic olivine rocks with a high melt content show that many grain boundaries are wetted by nanometre scale melt layers that are too thin to resolve by X-ray tomography. A variety of melt layer geometries occur consistent with several mechanisms of melt layer formation. The nature of melt geometries along triple line junctions and quadruple points can be resolved

Type 1a endoleak following Zone 1 and Zone 2 thoracic endovascular aortic repair: effect of bird-beak configuration.

PubMed

Kudo, Tomoaki; Kuratani, Toru; Shimamura, Kazuo; Sakamoto, Tomohiko; Kin, Keiwa; Masada, Kenta; Shijo, Takayuki; Torikai, Kei; Maeda, Koichi; Sawa, Yoshiki

2017-10-01

Type 1a endoleak is one of the most severe complications after thoracic endovascular aortic repair (TEVAR), because it carries the risk of aortic rupture. The association between bird-beak configuration and Type 1a endoleak remains unclear. The purpose of this study was to analyse the predictors of Type 1a endoleak following Zone 1 and Zone 2 TEVAR, with a particular focus on the effect of bird-beak configuration. From April 2008 to July 2015, 105 patients (mean age 68.6 years) who underwent Zone 1 and 2 landing TEVAR were enrolled, with a mean follow-up period of 4.3 years. The patients were categorized into 2 groups, according to the presence (Group B, n = 32) or the absence (Group N, n = 73) of bird-beak configuration on the first postoperative multidetector computed tomography. The Kaplan-Meier event-free rate curve showed that Type 1a endoleak and bird-beak progression occurred less frequently in Group N than in Group B. Five-year freedom from Type 1a endoleak rates were 79.7% and 100% for Groups B and N, respectively (P = 0.007). Multivariable logistic regression analysis showed that dissecting aortic aneurysm (odds ratio 3.72, 95% confidence interval 1.30-11.0; P = 0.014) and shorter radius of inner curvature (odds ratio 1.09, 95% confidence interval 0.85-0.99; P = 0.025) were significant risk factors for bird-beak configuration. Multivariable Cox proportional hazard regression showed that Z-type stent graft (hazard ratio 2.69, 95% confidence interval 1.11-6.51; P = 0.030) was a significant risk factor for bird-beak progression. Appropriate stent grafts need to be chosen carefully to prevent Type 1a endoleak and bird-beak configuration after landing Zone 1 and 2 TEVAR. Patients with bird-beak configuration on early postoperative multidetector computed tomography require closer follow-up to screen for Type 1a endoleak. © The Author 2017. Published by Oxford University Press on behalf of the European Association for Cardio

Nicotinic Receptor Transduction Zone: Invariant Arginine Couples to Multiple Electron-Rich Residues

PubMed Central

Mukhtasimova, Nuriya; Sine, Steven M.

2013-01-01

Summary Gating of the muscle-type acetylcholine receptor (AChR) channel depends on communication between the ACh-binding site and the remote ion channel. A key region for this communication is located within the structural transition zone between the ligand-binding and pore domains. Here, stemming from β-strand 10 of the binding domain, the invariant αArg209 lodges within the hydrophobic interior of the subunit and is essential for rapid and efficient channel gating. Previous charge-reversal experiments showed that the contribution of αArg209 to channel gating depends strongly on αGlu45, also within this region. Here we determine whether the contribution of αArg209 to channel gating depends on additional anionic or electron-rich residues in this region. Also, to reconcile diverging findings in the literature, we compare the dependence of αArg209 on αGlu45 in AChRs from different species, and compare the full agonist ACh with the weak agonist choline. Our findings reveal that the contribution of αArg209 to channel gating depends on additional nearby electron-rich residues, consistent with both electrostatic and steric contributions. Furthermore, αArg209 and αGlu45 show a strong interdependence in both human and mouse AChRs, whereas the functional consequences of the mutation αE45R depend on the agonist. The emerging picture shows a multifaceted network of interdependent residues that are required for communication between the ligand-binding and pore domains. PMID:23442857

Human cardiac telocytes: 3D imaging by FIB-SEM tomography.

PubMed

Cretoiu, D; Hummel, E; Zimmermann, H; Gherghiceanu, M; Popescu, L M

2014-11-01

Telocyte (TC) is a newly identified type of cell in the cardiac interstitium (www.telocytes.com). TCs are described by classical transmission electron microscopy as cells with very thin and long telopodes (Tps; cellular prolongations) having podoms (dilations) and podomers (very thin segments). TCs' three-dimensional (3D) morphology is still unknown. Cardiac TCs seem to be particularly involved in long and short distance intercellular signalling and, therefore, their 3D architecture is important for understanding their spatial connections. Using focused ion beam scanning electron microscopy (FIB-SEM) we show, for the first time, the whole ultrastructural anatomy of cardiac TCs. 3D reconstruction of cardiac TCs by FIB-SEM tomography confirms that they have long, narrow but flattened (ribbon-like) telopodes, with humps generated by the podoms. FIB-SEM tomography also confirms the network made by TCs in the cardiac interstitium through adherens junctions. This study provides the first FIB-SEM tomography of a human cell type. © 2014 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

Assessment of β-zone peripapillary atrophy by optical coherence tomography and scanning laser ophthalmoscopy imaging in glaucoma patients

PubMed Central

Seidensticker, Florian; Reznicek, Lukas; Mann, Thomas; Hübert, Irene; Kampik, Anselm; Ulbig, Michael; Hirneiss, Christoph; Neubauer, Aljoscha S; Kernt, Marcus

2014-01-01

Purpose To assess β-zone peripapillary atrophy (β-PPA) using spectral domain optical coherence tomography (SD-OCT), scanning laser ophthalmoscopy (SLO), and fundus auto-fluorescence (FAF) imaging in patients with primary open-angle glaucoma with advanced glaucomatous visual field defects. Methods A consecutive, prospective series of 82 study eyes with primary open-angle glaucoma were included in this study. All study participants underwent a full ophthalmic examination followed by SD-OCT, wide-field SLO, and FAF imaging of the optic nerve head and the peripapillary region. Results Eighty-four glaucomatous eyes were included in our prospective study. Correlation analyses for horizontally and vertically obtained β-PPA for all three imaging modalities (color SLO, FAF, and SD-OCT) revealed highest correlations between FAF and color SLO (Pearson correlation coefficient: 0.904 [P<0.001] for horizontal β-PPA and 0.786 [P<0.001] for vertical β-PPA). Bland–Altman plotting revealed highest agreements between color SLO and FAF, with −2.1 pixels ±1.96 standard deviation (SD) for horizontal β-PPA, SD: 10.5 pixels and 2.4 pixels ±1.96 SD for vertical β-PPA. Conclusion β-PPA can be assessed using en-face SLO and cross-sectional SD-OCT imaging. Correlation analyses revealed highest correlations between color SLO and FAF imaging, while correlations between SLO and SD-OCT were weak. A more precise structural definition of β-PPA is needed. PMID:25061270

Nonlinear electron-acoustic rogue waves in electron-beam plasma system with non-thermal hot electrons

NASA Astrophysics Data System (ADS)

Elwakil, S. A.; El-hanbaly, A. M.; Elgarayh, A.; El-Shewy, E. K.; Kassem, A. I.

2014-11-01

The properties of nonlinear electron-acoustic rogue waves have been investigated in an unmagnetized collisionless four-component plasma system consisting of a cold electron fluid, non-thermal hot electrons obeying a non-thermal distribution, an electron beam and stationary ions. It is found that the basic set of fluid equations is reduced to a nonlinear Schrodinger equation. The dependence of rogue wave profiles on the electron beam and energetic population parameter are discussed. The results of the present investigation may be applicable in auroral zone plasma.

On the longitudinal distribution of electric field in the acceleration zones of plasma accelerators and thrusters with closed electron drift

NASA Astrophysics Data System (ADS)

Kim, V. P.

2017-04-01

The long-term experience in controlling the electric field distribution in the discharge gaps of plasma accelerators and thrusters with closed electron drift and the key ideas determining the concepts of these devices and tendencies of their development are analyzed. It is shown that an electrostatic mechanism of ion acceleration in plasma by an uncompensated space charge of the cloud of magnetized electrons "kept" to the magnetic field takes place in the acceleration zones and that the electric field distribution can be controlled by varying the magnetic field in the discharge gap. The role played by the space charge makes the mechanism of ion acceleration in this type of thrusters is fundamentally different from the acceleration mechanism operating in purely electrostatic thrusters.

Computed tomography in the evaluation of penetrating neck trauma: a preliminary study.

PubMed

Gracias, V H; Reilly, P M; Philpott, J; Klein, W P; Lee, S Y; Singer, M; Schwab, C W

2001-11-01

Penetrating neck trauma has traditionally been evaluated by surgical exploration and/or invasive diagnostic studies. We hypothesized that computed tomography (CT), used as an early diagnostic tool to accurately determine trajectory, would direct or eliminate further studies or procedures in stable patients with penetrating neck trauma. Retrospective case series. Academic, urban, level I trauma center. Hemodynamically stable patients without hard signs of vascular injury or aerodigestive violation who had sustained penetrating trauma to the neck. Patients underwent a spiral CT as an initial diagnostic study after initial evaluation in the trauma bay. Further invasive studies were directed by CT findings. Number of invasive studies performed. Twenty-three patients were identified during the 30-month period. Nineteen patients sustained gunshot wounds; 3, shotgun wounds; and 1, a stab wound. One patient died of a cranial gunshot wound. Three isolated zone I, 1 isolated zone II, 9 isolated zone III, and 10 multiple neck zone trajectories were evaluated. Thirteen patients were identified by CT to have trajectories remote from vital structures and required no further evaluation. Ten patients underwent angiography. Only 2 underwent bronchoscopy and esophagoscopy. Four patients were discharged from the emergency department; 7 other patients were discharged within 24 hours. No adverse patient events occurred before, during, or after CT scan. Computed tomography in stable selected patients with penetrating neck trauma appears safe. Invasive studies can often be eliminated from the diagnostic algorithm when CT demonstrates trajectories remote from vital structures. As a result, efficient evaluation and early discharge from the trauma bay or emergency department can be realized. Further prospective study of CT scan after penetrating neck trauma is needed.

Unique thylakoid membrane architecture of a unicellular N2-fixing cyanobacterium revealed by electron tomography.

PubMed

Liberton, Michelle; Austin, Jotham R; Berg, R Howard; Pakrasi, Himadri B

2011-04-01

Cyanobacteria, descendants of the endosymbiont that gave rise to modern-day chloroplasts, are vital contributors to global biological energy conversion processes. A thorough understanding of the physiology of cyanobacteria requires detailed knowledge of these organisms at the level of cellular architecture and organization. In these prokaryotes, the large membrane protein complexes of the photosynthetic and respiratory electron transport chains function in the intracellular thylakoid membranes. Like plants, the architecture of the thylakoid membranes in cyanobacteria has direct impact on cellular bioenergetics, protein transport, and molecular trafficking. However, whole-cell thylakoid organization in cyanobacteria is not well understood. Here we present, by using electron tomography, an in-depth analysis of the architecture of the thylakoid membranes in a unicellular cyanobacterium, Cyanothece sp. ATCC 51142. Based on the results of three-dimensional tomographic reconstructions of near-entire cells, we determined that the thylakoids in Cyanothece 51142 form a dense and complex network that extends throughout the entire cell. This thylakoid membrane network is formed from the branching and splitting of membranes and encloses a single lumenal space. The entire thylakoid network spirals as a peripheral ring of membranes around the cell, an organization that has not previously been described in a cyanobacterium. Within the thylakoid membrane network are areas of quasi-helical arrangement with similarities to the thylakoid membrane system in chloroplasts. This cyanobacterial thylakoid arrangement is an efficient means of packing a large volume of membranes in the cell while optimizing intracellular transport and trafficking.

On the electron density localization in elemental cubic ceramic and FCC transition metals by means of a localized electrons detector.

PubMed

Aray, Yosslen; Paredes, Ricardo; Álvarez, Luis Javier; Martiz, Alejandro

2017-06-14

The electron density localization in insulator and semiconductor elemental cubic materials with diamond structure, carbon, silicon, germanium, and tin, and good metallic conductors with face centered cubic structure such as α-Co, Ni, Cu, Rh, Pd, Ag, Ir, Pt, and Au, was studied using a localized electrons detector defined in the local moment representation. Our results clearly show an opposite pattern of the electron density localization for the cubic ceramic and transition metal materials. It was found that, for the elemental ceramic materials, the zone of low electron localization is very small and is mainly localized on the atomic basin edges. On the contrary, for the transition metals, there are low-valued localized electrons detector isocontours defining a zone of highly delocalized electrons that extends throughout the material. We have found that the best conductors are those in which the electron density at this low-value zone is the lowest.

New Radiation Zones on Jupiter

NASA Image and Video Library

2017-12-11

This graphic shows a new radiation zone surrounding Jupiter, located just above the atmosphere near the equator, that has been discovered by NASA's Juno mission. The new radiation zone is depicted here as a glowing blue area around the planet's middle. This radiation zone includes energetic hydrogen, oxygen and sulfur ions moving at close to the speed of light (referred to as "relativistic" speeds). It resides inside Jupiter's previously known radiation belts. The zone was identified by the mission's Jupiter Energetic Particle Detector Instrument (JEDI), enabled by Juno's unique close approach to the planet during the spacecraft's science flybys (2,100 miles or 3,400 kilometers from the cloud tops). Juno scientists believe the particles creating this region of intense radiation are derived from energetic neutral atoms -- that is, fast-moving atoms without an electric charge -- coming from the tenuous gas around Jupiter's moons Io and Europa. The neutral atoms then become ions -- atoms with an electric charge -- as their electrons are stripped away by interaction with the planet's upper atmosphere. (This discovery is discussed further in an issue of the journal Geophysical Research Letters [Kollmann et al. (2017), Geophys. Res. Lett., 44, 5259-5268].) Juno also has detected signatures of a population of high-energy, heavy ions in the inner edges of Jupiter's relativistic electron radiation belt. This radiation belt was previously understood to contain mostly electrons moving at near light speed. The signatures of the heavy ions are observed at high latitude locations within the electron belt -- a region not previously explored by spacecraft. The origin and exact species of these heavy ions is not yet understood. Juno's Stellar Reference Unit (SRU-1) star camera detects the signatures of this population as extremely high noise in images collected as part of the mission's radiation monitoring investigation. The locations where the heavy ions were detected are

Atom Probe Tomography Studies on the Cu(In,Ga)Se2 Grain Boundaries

PubMed Central

Cojocaru-Mirédin, Oana; Schwarz, Torsten; Choi, Pyuck-Pa; Herbig, Michael; Wuerz, Roland; Raabe, Dierk

2013-01-01

Compared with the existent techniques, atom probe tomography is a unique technique able to chemically characterize the internal interfaces at the nanoscale and in three dimensions. Indeed, APT possesses high sensitivity (in the order of ppm) and high spatial resolution (sub nm). Considerable efforts were done here to prepare an APT tip which contains the desired grain boundary with a known structure. Indeed, site-specific sample preparation using combined focused-ion-beam, electron backscatter diffraction, and transmission electron microscopy is presented in this work. This method allows selected grain boundaries with a known structure and location in Cu(In,Ga)Se2 thin-films to be studied by atom probe tomography. Finally, we discuss the advantages and drawbacks of using the atom probe tomography technique to study the grain boundaries in Cu(In,Ga)Se2 thin-film solar cells. PMID:23629452

Lymph node detection in IASLC-defined zones on PET/CT images

NASA Astrophysics Data System (ADS)

Song, Yihua; Udupa, Jayaram K.; Odhner, Dewey; Tong, Yubing; Torigian, Drew A.

2016-03-01

Lymph node detection is challenging due to the low contrast between lymph nodes as well as surrounding soft tissues and the variation in nodal size and shape. In this paper, we propose several novel ideas which are combined into a system to operate on positron emission tomography/ computed tomography (PET/CT) images to detect abnormal thoracic nodes. First, our previous Automatic Anatomy Recognition (AAR) approach is modified where lymph node zones predominantly following International Association for the Study of Lung Cancer (IASLC) specifications are modeled as objects arranged in a hierarchy along with key anatomic anchor objects. This fuzzy anatomy model built from diagnostic CT images is then deployed on PET/CT images for automatically recognizing the zones. A novel globular filter (g-filter) to detect blob-like objects over a specified range of sizes is designed to detect the most likely locations and sizes of diseased nodes. Abnormal nodes within each automatically localized zone are subsequently detected via combined use of different items of information at various scales: lymph node zone model poses found at recognition indicating the geographic layout at the global level of node clusters, g-filter response which hones in on and carefully selects node-like globular objects at the node level, and CT and PET gray value but within only the most plausible nodal regions for node presence at the voxel level. The models are built from 25 diagnostic CT scans and refined for an object hierarchy based on a separate set of 20 diagnostic CT scans. Node detection is tested on an additional set of 20 PET/CT scans. Our preliminary results indicate node detection sensitivity and specificity at around 90% and 85%, respectively.

Microstructure of Reaction Zone Formed During Diffusion Bonding of TiAl with Ni/Al Multilayer

NASA Astrophysics Data System (ADS)

Simões, Sónia; Viana, Filomena; Koçak, Mustafa; Ramos, A. Sofia; Vieira, M. Teresa; Vieira, Manuel F.

2012-05-01

In this article, the characterization of the interfacial structure of diffusion bonding a TiAl alloy is presented. The joining surfaces were modified by Ni/Al reactive multilayer deposition as an alternative approach to conventional diffusion bonding. TiAl substrates were coated with alternated Ni and Al nanolayers. The nanolayers were deposited by dc magnetron sputtering with 14 nm of period (bilayer thickness). Joining experiments were performed at 900 °C for 30 and 60 min with a pressure of 5 MPa. Cross sections of the joints were prepared for characterization of their interfaces by scanning electron microscopy (SEM), transmission electron microscopy (TEM), scanning transmission electron microscopy (STEM), high resolution TEM (HRTEM), energy dispersive x-ray spectroscopy (EDS), and electron backscatter diffraction (EBSD). Several intermetallic compounds form at the interface, assuring the bonding of the TiAl. The interface can be divided into three distinct zones: zone 1 exhibits elongated nanograins, very small equiaxed grains are observed in zone 2, while zone 3 has larger equiaxed grains. EBSD analysis reveals that zone 1 corresponds to the intermetallic Al2NiTi and AlNiTi, and zones 2 and 3 to NiAl.

78 FR 35801 - Safety and Security Zones, San Juan Captain of the Port Zone

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-14

... Rico and U. S. Virgin Island port communities. This action would modify existing safety zones... federal holidays. The telephone number is 202-366-9329. See the ``Public Participation and Request for..., except federal holidays. 3. Privacy Act Anyone can search the electronic form of comments received into...

FIB-SEM tomography of human skin telocytes and their extracellular vesicles

PubMed Central

Cretoiu, Dragos; Gherghiceanu, Mihaela; Hummel, Eric; Zimmermann, Hans; Simionescu, Olga; Popescu, Laurentiu M

2015-01-01

We have shown in 2012 the existence of telocytes (TCs) in human dermis. TCs were described by transmission electron microscopy (TEM) as interstitial cells located in non-epithelial spaces (stroma) of many organs (see www.telocytes.com). TCs have very long prolongations (tens to hundreds micrometers) named Telopodes (Tps). These Tps have a special conformation with dilated portions named podoms (containing mitochondria, endoplasmic reticulum and caveolae) and very thin segments (below resolving power of light microscopy), called podomers. To show the real 3D architecture of TC network, we used the most advanced available electron microscope technology: focused ion beam scanning electron microscopy (FIB-SEM) tomography. Generally, 3D reconstruction of dermal TCs by FIB-SEM tomography revealed the existence of Tps with various conformations: (i) long, flattened irregular veils (ribbon-like segments) with knobs, corresponding to podoms, and (ii) tubular structures (podomers) with uneven calibre because of irregular dilations (knobs) – the podoms. FIB-SEM tomography also showed numerous extracellular vesicles (diameter 438.6 ± 149.1 nm, n = 30) released by a human dermal TC. Our data might be useful for understanding the role(s) of TCs in intercellular signalling and communication, as well as for comprehension of pathologies like scleroderma, multiple sclerosis, psoriasis, etc. PMID:25823591

Polyhedral 3D structure of human plasma very low density lipoproteins by individual particle cryo-electron tomography

DOE PAGES

Yu, Yadong; Kuang, Yu-Lin; Lei, Dongsheng; ...

2016-08-18

Human VLDLs assembled in the liver and secreted into the circulation supply energy to peripheral tissues. VLDL lipolysis yields atherogenic LDLs and VLDL remnants that strongly correlate with CVD. Although the composition of VLDL particles has been well-characterized, their 3D structure is elusive because of their variations in size, heterogeneity in composition, structural flexibility, and mobility in solution. Here, we employed cryo-electron microscopy and individual-particle electron tomography to study the 3D structure of individual VLDL particles (without averaging) at both below and above their lipid phase transition temperatures. The 3D reconstructions of VLDL and VLDL bound to antibodies revealed anmore » unexpected polyhedral shape, in contrast to the generally accepted model of a spherical emulsion-like particle. The smaller curvature of surface lipids compared with HDL may also reduce surface hydrophobicity, resulting in lower binding affinity to the hydrophobic distal end of the N-terminal β-barrel domain of cholesteryl ester transfer protein (CETP) compared with HDL. The directional binding of CETP to HDL and VLDL may explain the function of CETP in transferring TGs and cholesteryl esters between these particles. This first visualization of the 3D structure of VLDL could improve our understanding of the role of VLDL in atherogenesis.« less

External cervical resorption: an analysis using cone beam and microfocus computed tomography and scanning electron microscopy.

PubMed

Gunst, V; Mavridou, A; Huybrechts, B; Van Gorp, G; Bergmans, L; Lambrechts, P

2013-09-01

To provide a three-dimensional representation of external cervical resorption (ECR) with microscopy, stereo microscopy, cone beam computed tomography (CT), microfocus CT and scanning electron microscopy (SEM). External cervical resorption is an aggressive form of root resorption, leading to a loss of dental hard tissues. This is due to clastic action, activated by a damage of the covering cementum and stimulated probably by infection. Clinically, it is a challenging situation as it is characterized by a late symptomatology. This is due to the pericanalar protection from a resorption-resistant sheet, composed of pre-dentine and surrounding dentine. The clastic activity is often associated with an attempt to repair, seen by the formation of osteoid tissue. Cone beam CT is extremely useful in the diagnoses and treatment planning of ECR. SEM analyses provide a better insight into the activity of osteoclasts. The root canal is surrounded by a layer of dentine that is resistant to resorption. © 2013 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Electron Tomography Reveals Posttranscriptional Binding of Pre-Mrnps to Specific Fibers in the Nucleoplasm

PubMed Central

Miralles, Francesc; Öfverstedt, Lars-Göran; Sabri, Nafiseh; Aissouni, Youssef; Hellman, Ulf; Skoglund, Ulf; Visa, Neus

2000-01-01

Using electron tomography, we have analyzed whether the Balbiani ring (BR) pre-mRNP particles in transit from the gene to the nuclear pore complex (NPC) are bound to any structure that could impair free diffusion through the nucleoplasm. We show that one-third of the BR particles are in contact with thin connecting fibers (CFs), which in some cases merge into large fibrogranular clusters. The CFs have a specific protein composition different from that of BR particles, as shown by immuno-EM. Moreover, we have identified hrp65 as one of the protein components of the CFs. The sequencing of hrp65 cDNA reveals similarities with hnRNP proteins and splicing factors. However, hrp65 is likely to have a different function because it does not bind to nascent pre-mRNA and is not part of the pre-mRNP itself. Taken together, our observations indicate that pre-mRNPs are not always freely diffusible in the nucleoplasm but interact with fibers of specific structure and composition, which implies that some of the posttranscriptional events that the pre-mRNPs undergo before reaching the NPC occur in a bound state. PMID:10648560

Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging.

PubMed

Hagen, Wim J H; Wan, William; Briggs, John A G

2017-02-01

Cryo-electron tomography (cryoET) allows 3D structural information to be obtained from cells and other biological samples in their close-to-native state. In combination with subtomogram averaging, detailed structures of repeating features can be resolved. CryoET data is collected as a series of images of the sample from different tilt angles; this is performed by physically rotating the sample in the microscope between each image. The angles at which the images are collected, and the order in which they are collected, together are called the tilt-scheme. Here we describe a "dose-symmetric tilt-scheme" that begins at low tilt and then alternates between increasingly positive and negative tilts. This tilt-scheme maximizes the amount of high-resolution information maintained in the tomogram for subsequent subtomogram averaging, and may also be advantageous for other applications. We describe implementation of the tilt-scheme in combination with further data-collection refinements including setting thresholds on acceptable drift and improving focus accuracy. Requirements for microscope set-up are introduced, and a macro is provided which automates the application of the tilt-scheme within SerialEM. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Multi-signal FIB/SEM tomography

NASA Astrophysics Data System (ADS)

Giannuzzi, Lucille A.

2012-06-01

Focused ion beam (FIB) milling coupled with scanning electron microscopy (SEM) on the same platform enables 3D microstructural analysis of structures using FIB for serial sectioning and SEM for imaging. Since FIB milling is a destructive technique, the acquisition of multiple signals from each slice is desirable. The feasibility of collecting both an inlens backscattered electron (BSE) signal and an inlens secondary electron (SE) simultaneously from a single scan of the electron beam from each FIB slice is demonstrated. The simultaneous acquisition of two different SE signals from two different detectors (inlens vs. Everhart-Thornley (ET) detector) is also possible. Obtaining multiple signals from each FIB slice with one scan increases the acquisition throughput. In addition, optimization of microstructural and morphological information from the target is achieved using multi-signals. Examples of multi-signal FIB/SEM tomography from a dental implant will be provided where both material contrast from the bone/ceramic coating/Ti substrate phases and porosity in the ceramic coating will be characterized.

Attenuation-difference radar tomography: results of a multiple-plane experiment at the U.S. Geological Survey Fractured-Rock Research Site, Mirror Lake, New Hampshire

USGS Publications Warehouse

Lane, J.W.; Day-Lewis, F. D.; Harris, J.M.; Haeni, F.P.; Gorelick, S.M.

2000-01-01

Attenuation-difference, borehole-radar tomography was used to monitor a series of sodium chloride tracer injection tests conducted within the FSE, wellfield at the U.S. Geological Survey Fractured-Rock Hydrology Research Site in Grafton County, New Hampshire, USA. Borehole-radar tomography surveys were conducted using the sequential-scanning and injection method in three boreholes that form a triangular prism of adjoining tomographic image planes. Results indicate that time-lapse tomography methods provide high-resolution images of tracer distribution in permeable zones.

Quantitative Cryo-Scanning Transmission Electron Microscopy of Biological Materials.

PubMed

Elbaum, Michael

2018-05-11

Electron tomography provides a detailed view into the 3D structure of biological cells and tissues. Physical fixation by vitrification of the aqueous medium provides the most faithful preservation of biological specimens in the native, fully hydrated state. Cryo-microscopy is challenging, however, because of the sensitivity to electron irradiation and due to the weak electron scattering of organic material. Tomography is even more challenging because of the dependence on multiple exposures of the same area. Tomographic imaging is typically performed in wide-field transmission electron microscopy (TEM) mode with phase contrast generated by defocus. Scanning transmission electron microscopy (STEM) is an alternative mode based on detection of scattering from a focused probe beam, without imaging optics following the specimen. While careful configuration of the illumination and detectors is required to generate useful contrast, STEM circumvents the major restrictions of phase contrast TEM to very thin specimens and provides a signal that is more simply interpreted in terms of local composition and density. STEM has gained popularity in recent years for materials science. The extension of STEM to cryomicroscopy and tomography of cells and macromolecules is summarized herein. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spectral optimization for measuring electron density by the dual-energy computed tomography coupled with balanced filter method.

PubMed

Saito, Masatoshi

2009-08-01

Dual-energy computed tomography (DECT) has the potential for measuring electron density distribution in a human body to predict the range of particle beams for treatment planning in proton or heavy-ion radiotherapy. However, thus far, a practical dual-energy method that can be used to precisely determine electron density for treatment planning in particle radiotherapy has not been developed. In this article, another DECT technique involving a balanced filter method using a conventional x-ray tube is described. For the spectral optimization of DECT using balanced filters, the author calculates beam-hardening error and air kerma required to achieve a desired noise level in electron density and effective atomic number images of a cylindrical water phantom with 50 cm diameter. The calculation enables the selection of beam parameters such as tube voltage, balanced filter material, and its thickness. The optimized parameters were applied to cases with different phantom diameters ranging from 5 to 50 cm for the calculations. The author predicts that the optimal combination of tube voltages would be 80 and 140 kV with Tb/Hf and Bi/Mo filter pairs for the 50-cm-diameter water phantom. When a single phantom calibration at a diameter of 25 cm was employed to cover all phantom sizes, maximum absolute beam-hardening errors were 0.3% and 0.03% for electron density and effective atomic number, respectively, over a range of diameters of the water phantom. The beam-hardening errors were 1/10 or less as compared to those obtained by conventional DECT, although the dose was twice that of the conventional DECT case. From the viewpoint of beam hardening and the tube-loading efficiency, the present DECT using balanced filters would be significantly more effective in measuring the electron density than the conventional DECT. Nevertheless, further developments of low-exposure imaging technology should be necessary as well as x-ray tubes with higher outputs to apply DECT coupled with the

Advanced Instrumentation for Positron Emission Tomography [PET

DOE R&D Accomplishments Database

Derenzo, S. E.; Budinger, T. F.

1985-04-01

This paper summarizes the physical processes and medical science goals that underlay modern instrumentation design for Positron Emission Tomography. The paper discusses design factors such as detector material, crystalphototube coupling, shielding geometry, sampling motion, electronics design, time-of-flight, and the interrelationships with quantitative accuracy, spatial resolution, temporal resolution, maximum data rates, and cost.

Use of borehole radar tomography to monitor steam injection in fractured limestone

USGS Publications Warehouse

Gregoire, C.; Joesten, P.K.

2006-01-01

Borehole radar tomography was used as part of a pilot study to monitor steam-enhanced remediation of a fractured limestone contaminated with volatile organic compounds at the former Loring Air Force Base, Maine, USA. Radar tomography data were collected using 100-MHz electric-dipole antennae before and during steam injection to evaluate whether cross-hole radar methods could detect changes in medium properties resulting from the steam injection. Cross-hole levelrun profiles, in which transmitting and receiving antennae are positioned at a common depth, were made before and after the collection of each full tomography data set to check the stability of the radar instruments. Before tomographic inversion, the levelrun profiles were used to calibrate the radar tomography data to compensate for changes in traveltime and antenna power caused by instrument drift. Observed changes in cross-hole radar traveltime and attenuation before and during steam injection were small. Slowness- and attenuation-difference tomograms indicate small increases in radar slowness and attenuation at depths greater than about 22 m below the surface, consistent with increases in water temperature observed in the boreholes used for the tomography. Based on theoretical modelling results, increases in slowness and attenuation are interpreted as delineating zones where steam injection heating increased the electrical conductivity of the limestone matrix and fluid. The results of this study show the potential of cross-hole radar tomography methods to monitor the effects of steam-induced heating in fractured rock environments. ?? 2006 European Association of Geoscientists & Engineers.

Application of nondestructive testing methods to study the damage zone underneath impact craters of MEMIN laboratory experiments

NASA Astrophysics Data System (ADS)

Moser, Dorothee; Poelchau, Michael H.; Stark, Florian; Grosse, Christian

2013-01-01

Within the framework of the Multidisciplinary Experimental and Modeling Impact Research Network (MEMIN) research group, the damage zones underneath two experimentally produced impact craters in sandstone targets were investigated using several nondestructive testing (NDT) methods. The 20 × 20 × 20 cm sandstones were impacted by steel projectiles with a radius of 1.25 mm at approximately 5 km s-1, resulting in craters with approximately 6 cm diameter and approximately 1 cm depth. Ultrasound (US) tomography and vibrational analysis were applied before and after the impact experiments to characterize the damage zone, and micro-computer tomography (μ-CT) measurements were performed to visualize subsurface fractures. The newly obtained experimental data can help to quantify the extent of the damage zone, which extends to about 8 cm depth in the target. The impacted sandstone shows a local p-wave reduction of 18% below the crater floor, and a general reduction in elastic moduli by between approximately 9 and approximately 18%, depending on the type of elastic modulus. The results contribute to a better empirical and theoretical understanding of hypervelocity events and simulations of cratering processes.

Understanding Atom Probe Tomography of Oxide-Supported Metal Nanoparticles by Correlation with Atomic Resolution Electron Microscopy and Field Evaporation Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Devaraj, Arun; Colby, Robert J.; Vurpillot, F.

2014-03-26

Metal-dielectric composite materials, specifically metal nanoparticles supported on or embedded in metal oxides, are widely used in catalysis. The accurate optimization of such nanostructures warrants the need for detailed three-dimensional characterization. Atom probe tomography is uniquely capable of generating sub-nanometer structural and compositional data with part-per-million mass sensitivity, but there are reconstruction artifacts for composites containing materials with strongly differing fields of evaporation, as for oxide-supported metal nanoparticles. By correlating atom probe tomography with scanning transmission electron microscopy for Au nanoparticles embedded in an MgO support, deviations from an ideal topography during evaporation are demonstrated directly, and correlated with compositionalmore » errors in the reconstructed data. Finite element simulations of the field evaporation process confirm that protruding Au nanoparticles will evolve on the tip surface, and that evaporation field variations lead to an inaccurate assessment of the local composition, effectively lowering the spatial resolution of the final reconstructed dataset. Cross-correlating the experimental data with simulations results in a more detailed understanding of local evaporation aberrations during APT analysis of metal-oxide composites, paving the way towards a more accurate three-dimensional characterization of this technologically important class of materials.« less

Large volume serial section tomography by Xe Plasma FIB dual beam microscopy.

PubMed

Burnett, T L; Kelley, R; Winiarski, B; Contreras, L; Daly, M; Gholinia, A; Burke, M G; Withers, P J

2016-02-01

Ga(+) Focused Ion Beam-Scanning Electron Microscopes (FIB-SEM) have revolutionised the level of microstructural information that can be recovered in 3D by block face serial section tomography (SST), as well as enabling the site-specific removal of smaller regions for subsequent transmission electron microscope (TEM) examination. However, Ga(+) FIB material removal rates limit the volumes and depths that can be probed to dimensions in the tens of microns range. Emerging Xe(+) Plasma Focused Ion Beam-Scanning Electron Microscope (PFIB-SEM) systems promise faster removal rates. Here we examine the potential of the method for large volume serial section tomography as applied to bainitic steel and WC-Co hard metals. Our studies demonstrate that with careful control of milling parameters precise automated serial sectioning can be achieved with low levels of milling artefacts at removal rates some 60× faster. Volumes that are hundreds of microns in dimension have been collected using fully automated SST routines in feasible timescales (<24h) showing good grain orientation contrast and capturing microstructural features at the tens of nanometres to the tens of microns scale. Accompanying electron back scattered diffraction (EBSD) maps show high indexing rates suggesting low levels of surface damage. Further, under high current Ga(+) FIB milling WC-Co is prone to amorphisation of WC surface layers and phase transformation of the Co phase, neither of which have been observed at PFIB currents as high as 60nA at 30kV. Xe(+) PFIB dual beam microscopes promise to radically extend our capability for 3D tomography, 3D EDX, 3D EBSD as well as correlative tomography. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Diverse continental subduction scenarios along the Arabia-Eurasia collision zone

NASA Astrophysics Data System (ADS)

Kaban, M. K.; Petrunin, A.; El Khrepy, S.; Al-Arifi, N. S.

2017-12-01

The Arabia-Eurasia continental collision zone is one of the largest and most active on the Earth. It has been discussed already long ago that the convergence of these plates implies subduction of the lithosphere. However, scenarios of this process are still debatable. Even direction of the present-day continental subduction is not clear. Previously, principal conclusions about structure of the upper mantle in this region were chiefly based on seismic tomography results. However, seismic velocities not always provide a complete image of the deep interiors since they are chiefly affected by temperature variations and less - by composition. Here we construct a 3D model of the mantle down to 700 km, which is based on a joint inversion of seismic tomography, residual (crust free) gravity field and residual topography (Kaban et al., 2016). Several cross-sections across the collision zone demonstrate principal variations of the continental subduction scenarios from northwest to southeast. In the southeastern part we observe subduction of the Eurasian plate under the West Great Caucasus, Pontic mountains and further under the northwestern part of the Arabian plate. However, the situation is changed when we move to the East Great Caucasus and Zagros, where clear double-sided subduction is observed. The Arabian plate is subducting under the Zagros, while the Eurasian plate - under the Caucasus merging in the transition zone. This situation persists further to the southeast, where we observe the subduction of the South Caspian block under Alborz accompanied by the counteracting penetration of the Arabian plate from the south. More to the southeast, the subduction of the Arabian plate is stagnated, while the subduction of the Eurasian plate can be traced down to the bottom of the transition zone under the northeastern flank of the Arabian plate. In the southern rim of the collision zone under Makran, we don't find any evidence for the present day subduction; remnants of the

75 FR 17691 - Foreign-Trade Zone 196 - Fort Worth, Texas, Application for Manufacturing Authority, ATC...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-07

... DEPARTMENT OF COMMERCE Foreign-Trade Zones Board [Docket 19-2010] Foreign-Trade Zone 196 - Fort Worth, Texas, Application for Manufacturing Authority, ATC Logistics & Electronics (Cell Phone Kitting... Board (the Board) by ATC Logistics & Electronics (ATCLE), operator of Site 2, FTZ 196, Fort Worth, Texas...

Sonic logging for detecting the excavation disturbed and fracture zones

NASA Astrophysics Data System (ADS)

Lin, Y. C.; Chang, Y. F.; Liu, J. W.; Tseng, C. W.

2017-12-01

This study presents a new sonic logging method to detect the excavation disturbed zone (EDZ) and fracture zones in a tunnel. The EDZ is a weak rock zone where its properties and conditions have been changed by excavation, which results such as fracturing, stress redistribution and desaturation in this zone. Thus, the EDZ is considered as a physically less stable and could form a continuous and high-permeable pathway for groundwater flow. Since EDZ and fracture zone have the potential of affecting the safety of the underground openings and repository performance, many studies were conducted to characterize the EDZ and fracture zone by different methods, such as the rock mass displacements and strain measurements, seismic refraction survey, seismic tomography and hydraulic test, etc. In this study, we designed a new sonic logging method to explore the EDZ and fracture zone in a tunnel at eastern Taiwan. A high power and high frequency sonic system was set up which includes a two hydrophones pitch-catch technique with a common-offset immersed in water-filled uncased wells and producing a 20 KHz sound to scan the well rock. Four dominant sonic events were observed in the measurements, they are refracted P- and S-wave along the well rock, direct water wave and the reverberation in the well water. Thus the measured P- and S-wave velocities, the signal-to-noise ratio of the refraction and the amplitudes of reverberation along the well rock were used as indexes to determine the EDZ and fracture zone. Comparing these indexes with core samples shows that significant changes in the indexes are consistent with the EDZ and fracture zone. Thus, the EDZ and fracture zone can be detected by this new sonic method conclusively.

Natural variations in the geomagnetically trapped electron population

NASA Technical Reports Server (NTRS)

Vampola, A. L.

1972-01-01

Temporal variations in the trapped natural electron flux intensities and energy spectra are discussed and demonstrated using recent satellite data. These data are intended to acquaint the space systems engineer with the types of natural variations that may be encountered during a mission and to augment the models of the electron environment currently being used in space system design and orbit selection. An understanding of the temporal variations which may be encountered should prove helpful. Some of the variations demonstrated here which are not widely known include: (1) addition of very energetic electrons to the outer zone during moderate magnetic storms: (2) addition of energetic electrons to the inner zone during major magnetic storms; (3) inversions in the outer zone electron energy spectrum during the decay phase of a storm injection event and (4) occasional formation of multiple maxima in the flux vs altitude profile of moderately energetic electrons.

Tomography images of the Alpine roots and surrounding upper mantle

NASA Astrophysics Data System (ADS)

Plomerova, Jaroslava; Babuska, Vladislav

2017-04-01

Teleseismic body-wave tomography represents powerful tool to study regional velocity structure of the upper mantle and to image velocity anomalies, such as subducted lithosphere plates in collisional zones. In this contribution, we recapitulate 3D models of the upper mantle beneath the Alps, which developed at a collision zone of the Eurasian and African plates. Seismic tomography studies indicate a leading role of the rigid mantle lithosphere that functioned as a major stress guide during the plate collisions. Interactions of the European lithosphere with several micro-plates in the south resulted in an arcuate shape of this mountain range on the surface and in a complicated geometry of the Alpine subductions in the mantle. Early models with one bended lithosphere root have been replaced with more advanced models showing two separate lithosphere roots beneath the Western and Eastern Alps (Babuska et al., Tectonophysics 1990; Lippitsch et al., JGR 2003). The standard isotropic velocity tomography, based on pre-AlpArray data (the currently performed passive seismic experiment in the Alps and surroundings) images the south-eastward dipping curved slab of the Eurasian lithosphere in the Western Alps. On the contrary, beneath the Eastern Alps the results indicate a very steep northward dipping root that resulted from the collision of the European plate with the Adriatic microplate. Dando et al. (2011) interpret high-velocity heterogeneities at the bottom of their regional tomographic model as a graveyard of old subducted lithospheres. High density of stations, large amount of rays and dense ray-coverage of the volume studied are not the only essential pre-requisites for reliable tomography results. A compromise between the amount of pre-processed data and the high-quality of the tomography input (travel-time residuals) is of the high importance as well. For the first time, the existence of two separate roots beneath the Alps has been revealed from carefully pre

Electron tomography and fractal aspects of MoS2 and MoS2/Co spheres.

PubMed

Ramos, Manuel; Galindo-Hernández, Félix; Arslan, Ilke; Sanders, Toby; Domínguez, José Manuel

2017-09-26

A study was made by a combination of 3D electron tomography reconstruction methods and N 2 adsorption for determining the fractal dimension for nanometric MoS 2 and MoS 2 /Co catalyst particles. DFT methods including Neimarke-Kiselev's method allowed to determine the particle porosity and fractal arrays at the atomic scale for the S-Mo-S(Co) 2D- layers that conform the spherically shaped catalyst particles. A structural and textural correlation was sought by further characterization performed by x-ray Rietveld refinement and Radial Distribution Function (RDF) methods, electron density maps, computational density functional theory methods and nitrogen adsorption methods altogether, for studying the structural and textural features of spherical MoS 2 and MoS 2 /Co particles. Neimark-Kiselev's equations afforded the evaluation of a pore volume variation from 10 to 110 cm 3 /g by cobalt insertion in the MoS 2 crystallographic lattice, which induces the formation of cavities and throats in between of less than 29 nm, with a curvature radius r k  < 14.4 nm; typical large needle-like arrays having 20 2D layers units correspond to a model consisting of smooth surfaces within these cavities. Decreasing D P , D B , D I and D M values occur when Co atoms are present in the MoS 2 laminates, which promote the formation of smoother edges and denser surfaces that have an influence on the catalytic properties of the S-Mo-S(Co) system.

Seismic evidence for a possible deep crustal hot zone beneath Southwest Washington.

PubMed

Flinders, Ashton F; Shen, Yang

2017-08-07

Crustal pathways connecting deep sources of melt and the active volcanoes they supply are poorly understood. Beneath Mounts St. Helens, Adams, and Rainier these pathways connect subduction-induced ascending melts to shallow magma reservoirs. Petrogenetic modeling predicts that when these melts are emplaced as a succession of sills into the lower crust they generate deep crustal hot zones. While these zones are increasingly recognized as a primary site for silicic differentiation at a range of volcanic settings globally, imaging them remains challenging. Near Mount Rainier, ascending melt has previously been imaged ~28 km northwest of the volcano, while to the south, the volcano lies on the margin of a broad conductive region in the deep crust. Using 3D full-waveform tomography, we reveal an expansive low-velocity zone, which we interpret as a possible hot zone, linking ascending melts and shallow reservoirs. This hot zone may supply evolved magmas to Mounts St. Helens and Adams, and possibly Rainier, and could contain approximately twice the melt volume as the total eruptive products of all three volcanoes combined. Hot zones like this may be the primary reservoirs for arc volcanism, influencing compositional variations and spatial-segmentation along the entire 1100 km-long Cascades Arc.

Seismic evidence for a possible deep crustal hot zone beneath Southwest Washington

USGS Publications Warehouse

Flinders, Ashton; Shen, Yang

2017-01-01

Crustal pathways connecting deep sources of melt and the active volcanoes they supply are poorly understood. Beneath Mounts St. Helens, Adams, and Rainier these pathways connect subduction-induced ascending melts to shallow magma reservoirs. Petrogenetic modeling predicts that when these melts are emplaced as a succession of sills into the lower crust they generate deep crustal hot zones. While these zones are increasingly recognized as a primary site for silicic differentiation at a range of volcanic settings globally, imaging them remains challenging. Near Mount Rainier, ascending melt has previously been imaged ~28 km northwest of the volcano, while to the south, the volcano lies on the margin of a broad conductive region in the deep crust. Using 3D full-waveform tomography, we reveal an expansive low-velocity zone, which we interpret as a possible hot zone, linking ascending melts and shallow reservoirs. This hot zone may supply evolved magmas to Mounts St. Helens and Adams, and possibly Rainier, and could contain approximately twice the melt volume as the total eruptive products of all three volcanoes combined. Hot zones like this may be the primary reservoirs for arc volcanism, influencing compositional variations and spatial-segmentation along the entire 1100 km-long Cascades Arc.

Zone plate lenses for X-ray microscopy

NASA Astrophysics Data System (ADS)

Vladimirsky, Y.; Kern, D. P.; Chang, T. H. P.; Attwood, D. T.; Iskander, N.; Rothman, S.; McQuaide, K.; Kirz, J.; Ade, H.; McNulty, I.; Rarback, H.; Shu, D.

1988-04-01

Fresnel zone plate lenses with feature sizes as small as 50 nm have been constructed and used in the Stony Brook/NSLS scanning X-ray microscope with 3.1 nm radiation from Brookhaven's X-17 mini-undulator. The zone plates were fabricated at IBM using electron beam writing techniques, moiré pattern techniques to monitor ellipticity, and a double development/double plating technique to provide additional thickness in the central region. A spatial resolution down to 75 nm was measured in the microscope. Using these zone plates, biological images were obtained of unaltered subcellular components. The images highlight protein concentration in unsectioned, unfixed, and unstained enzymatic granules in an aqueous environment.

Local-time survey of plasma at low altitudes over the auroral zones.

NASA Technical Reports Server (NTRS)

Frank, L. A.; Ackerson, K. L.

1972-01-01

Local-time survey of the low-energy proton and electron intensities precipitated into the earth's atmosphere over the auroral zones during periods of magnetic quiescence. This survey was constructed by selecting a typical individual satellite crossing of this region in each of eight local-time sectors from a large library of similar observations with the polar-orbiting satellite Injun 5. The trapping boundary for more-energetic electron intensities, E greater than 45 keV, was found to be a 'natural coordinate' for delineating the boundary between the two major types of lower-energy, 50 less than or equal to E less than or equal to 15,000 eV, electron precipitation commonly observed over the auroral zones at low altitudes. Poleward of this trapping boundary inverted 'V' electron precipitation bands are observed in all local-time sectors. These inverted 'V' electron bands in the evening and midnight sectors are typically more energetic and have greater latitudinal widths than their counterparts in the noon and morning sectors. In general, the main contributors to the electron energy influx into the earth's atmosphere over the auroral zones are the electron inverted 'V' precipitation poleward of the trapping boundary in late evening, the plasma-sheet electron intensities equatorward of this boundary in early morning, and both of these precipitation events near local midnight.

FIB-SEM tomography of human skin telocytes and their extracellular vesicles.

PubMed

Cretoiu, Dragos; Gherghiceanu, Mihaela; Hummel, Eric; Zimmermann, Hans; Simionescu, Olga; Popescu, Laurentiu M

2015-04-01

We have shown in 2012 the existence of telocytes (TCs) in human dermis. TCs were described by transmission electron microscopy (TEM) as interstitial cells located in non-epithelial spaces (stroma) of many organs (see www.telocytes.com). TCs have very long prolongations (tens to hundreds micrometers) named Telopodes (Tps). These Tps have a special conformation with dilated portions named podoms (containing mitochondria, endoplasmic reticulum and caveolae) and very thin segments (below resolving power of light microscopy), called podomers. To show the real 3D architecture of TC network, we used the most advanced available electron microscope technology: focused ion beam scanning electron microscopy (FIB-SEM) tomography. Generally, 3D reconstruction of dermal TCs by FIB-SEM tomography revealed the existence of Tps with various conformations: (i) long, flattened irregular veils (ribbon-like segments) with knobs, corresponding to podoms, and (ii) tubular structures (podomers) with uneven calibre because of irregular dilations (knobs) - the podoms. FIB-SEM tomography also showed numerous extracellular vesicles (diameter 438.6 ± 149.1 nm, n = 30) released by a human dermal TC. Our data might be useful for understanding the role(s) of TCs in intercellular signalling and communication, as well as for comprehension of pathologies like scleroderma, multiple sclerosis, psoriasis, etc. © 2015 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

Modern Focused-Ion-Beam-Based Site-Specific Specimen Preparation for Atom Probe Tomography.

PubMed

Prosa, Ty J; Larson, David J

2017-04-01

Approximately 30 years after the first use of focused ion beam (FIB) instruments to prepare atom probe tomography specimens, this technique has grown to be used by hundreds of researchers around the world. This past decade has seen tremendous advances in atom probe applications, enabled by the continued development of FIB-based specimen preparation methodologies. In this work, we provide a short review of the origin of the FIB method and the standard methods used today for lift-out and sharpening, using the annular milling method as applied to atom probe tomography specimens. Key steps for enabling correlative analysis with transmission electron-beam backscatter diffraction, transmission electron microscopy, and atom probe tomography are presented, and strategies for preparing specimens for modern microelectronic device structures are reviewed and discussed in detail. Examples are used for discussion of the steps for each of these methods. We conclude with examples of the challenges presented by complex topologies such as nanowires, nanoparticles, and organic materials.

Storage of fluids and melts at subduction zones detectable by seismic tomography

NASA Astrophysics Data System (ADS)

Luehr, B. G.; Koulakov, I.; Rabbel, W.; Brotopuspito, K. S.; Surono, S.

2015-12-01

During the last decades investigations at active continental margins discovered the link between the subduction of fluid saturated oceanic plates and the process of ascent of these fluids and partial melts forming a magmatic system that leads to volcanism at the earth surface. For this purpose the geophysical structure of the mantle and crustal range above the down going slap has been imaged. Information is required about the slap, the ascent paths, as well as the reservoires of fluids and partial melts in the mantle and the crust up to the volcanoes at the surface. Statistically the distance between the volcanoes of volcanic arcs down to their Wadati Benioff zone results of approximately 100 kilometers in mean value. Surprisingly, this depth range shows pronounced seismicity at most of all subduction zones. Additionally, mineralogical laboratory investigations have shown that dehydration of the diving plate has a maximum at temperature and pressure conditions we find at around 100 km depth. The ascent of the fluids and the appearance of partial melts as well as the distribution of these materials in the crust can be resolved by seismic tomographic methods using records of local natural seismicity. With these methods these areas are corresponding to lowered seismic velocities, high Vp/Vs ratios, as well as increased attenuation of seismic shear waves. The anomalies and their time dependence are controlled by the fluids. The seismic velocity anomalies detected so far are within a range of a few per cent to more than 30% reduction. But, to explore plate boundaries large and complex amphibious experiments are required, in which active and passive seismic investigations should be combined to achieve best results. The seismic station distribution should cover an area from before the trench up to far behind the volcanic chain, to provide under favorable conditions information down to 150 km depth. Findings of different subduction zones will be compared and discussed.

MULTIMODAL IMAGING OF ACUTE EXUDATIVE POLYMORPHOUS VITELLIFORM MACULOPATHY WITH OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY AND ADAPTIVE OPTICS SCANNING LASER OPHTHALMOSCOPY.

PubMed

Skondra, Dimitra; Nesper, Peter L; Fawzi, Amani A

2017-05-16

To report a case of acute exudative polymorphous vitelliform maculopathy including the findings of optical coherence tomography angiography and adaptive optics scanning laser ophthalmoscopy. Findings on clinical examination, color fundus photography, spectral-domain optical coherence tomography, infrared reflectance, autofluorescence, optical coherence tomography angiography, and adaptive optics scanning laser ophthalmoscopy. A 54-year-old white man with no significant medical history and history of smoking presented with bilateral multiple serous and vitelliform detachments consistent with acute exudative polymorphous vitelliform maculopathy. Extensive infectious, inflammatory, and malignancy workup was negative. Spectral-domain optical coherence tomography showed thickened, hyperreflective ellipsoid zone, subretinal fluid, and focal as well as diffuse subretinal hyperreflective material corresponding to the vitelliform lesions. Optical coherence tomography angiography showed normal retinal and choroidal vasculature, whereas adaptive optics scanning laser ophthalmoscopy showed circular focal "target" lesions at the level of the photoreceptors in the area of foveal detachment. Multimodal imaging is valuable in evaluating patients with acute exudative polymorphous vitelliform maculopathy.

Plasmon 3D Electron Tomography and Local Electric-Field Enhancement of Engineered Plasmonic Nanoantennas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Archanjo, B. S.; Vasconcelos, T. L.; Oliveira, B. S.

Plasmonic nano-antennas are pushing the limits of optical imaging resolution capabilities in near-field scanning optical microscopy (NSOM). Accordingly, these techniques are driving the basic understanding of photonic and optoelectronic nanoscale devices with applications in sensing, energy conversion, solid-state lighting and information technology. Imaging the localized surface plasmon resonance (LSPR) at the nanoscale is a key to understanding the optical responses of a given tip geometry in order to engineer better plasmonic nano-antennas for near-field experiments. In recent years the advancement of focused ion beam technology provides the ability to directly modify plasmonic structures with nanometer resolution. Also, scanning transmission electronmore » microscopy (STEM) with electron energy loss spectroscopy (EELS) is an established technique allowing imaging of LSPR. Specifically, the combination of these two techniques provides spectrally sensitive two-dimensional (2D) imaging information to better visualize and understand LSPR on the nanometer scale. This can be combined with electron tomography to provide the three-dimensional LSPR distribution. Here in this paper we demonstrate the fabrication of Au nano-pyramids using helium ion microscopy, and analyze the LSPR in 3D reconstructions produced by total variation (TV)-norm minimization of a set of 2D STEM-EELS maps. Additionally, a boundary element simulation method was used to verify the experimentally observed nanopyramid LSPR modes. Finally, we show that the point-spread-functions (PSF) of LSPR mode hot spots in nanopyramids differ to local electric-field enhancement under optical excitation making direct comparison to NSOM experimental resolution difficult. However, the STEM-EELS results show how LSPR modes are influenced by the tip characteristics, which can inform the development of new nano-antenna designs.« less

Plasmon 3D Electron Tomography and Local Electric-Field Enhancement of Engineered Plasmonic Nanoantennas

DOE PAGES

Archanjo, B. S.; Vasconcelos, T. L.; Oliveira, B. S.; ...

2018-06-01

Plasmonic nano-antennas are pushing the limits of optical imaging resolution capabilities in near-field scanning optical microscopy (NSOM). Accordingly, these techniques are driving the basic understanding of photonic and optoelectronic nanoscale devices with applications in sensing, energy conversion, solid-state lighting and information technology. Imaging the localized surface plasmon resonance (LSPR) at the nanoscale is a key to understanding the optical responses of a given tip geometry in order to engineer better plasmonic nano-antennas for near-field experiments. In recent years the advancement of focused ion beam technology provides the ability to directly modify plasmonic structures with nanometer resolution. Also, scanning transmission electronmore » microscopy (STEM) with electron energy loss spectroscopy (EELS) is an established technique allowing imaging of LSPR. Specifically, the combination of these two techniques provides spectrally sensitive two-dimensional (2D) imaging information to better visualize and understand LSPR on the nanometer scale. This can be combined with electron tomography to provide the three-dimensional LSPR distribution. Here in this paper we demonstrate the fabrication of Au nano-pyramids using helium ion microscopy, and analyze the LSPR in 3D reconstructions produced by total variation (TV)-norm minimization of a set of 2D STEM-EELS maps. Additionally, a boundary element simulation method was used to verify the experimentally observed nanopyramid LSPR modes. Finally, we show that the point-spread-functions (PSF) of LSPR mode hot spots in nanopyramids differ to local electric-field enhancement under optical excitation making direct comparison to NSOM experimental resolution difficult. However, the STEM-EELS results show how LSPR modes are influenced by the tip characteristics, which can inform the development of new nano-antenna designs.« less

75 FR 4344 - Foreign-Trade Zone 22-Chicago, IL Application for Temporary/Interim Manufacturing Authority LG...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-27

... DEPARTMENT OF COMMERCE Foreign-Trade Zones Board [Docket T-1-2010] Foreign-Trade Zone 22--Chicago, IL Application for Temporary/ Interim Manufacturing Authority LG Electronics MobileComm USA, Inc... Electronics MobileComm USA, Inc. (LGEMU) facility, located in Bolingbrook, Illinois. The application was filed...

Controlled microaspiration for high-pressure freezing: a new method for ultrastructural preservation of fragile and sparse tissues for TEM and electron tomography

PubMed Central

Triffo, W. J.; Palsdottir, H.; McDonald, K. L.; Lee, J. K.; Inman, J. L.; Bissell, M. J.; Raphael, R. M.; Auer, M.

2009-01-01

Summary High-pressure freezing is the preferred method to prepare thick biological specimens for ultrastructural studies. However, the advantages obtained by this method often prove unattainable for samples that are difficult to handle during the freezing and substitution protocols. Delicate and sparse samples are difficult to manipulate and maintain intact throughout the sequence of freezing, infiltration, embedding and final orientation for sectioning and subsequent transmission electron microscopy. An established approach to surmount these difficulties is the use of cellulose microdialysis tubing to transport the sample. With an inner diameter of 200 µm, the tubing protects small and fragile samples within the thickness constraints of high-pressure freezing, and the tube ends can be sealed to avoid loss of sample. Importantly, the transparency of the tubing allows optical study of the specimen at different steps in the process. Here, we describe the use of a micromanipulator and microinjection apparatus to handle and position delicate specimens within the tubing. We report two biologically significant examples that benefit from this approach, 3D cultures of mammary epithelial cells and cochlear outer hair cells. We illustrate the potential for correlative light and electron microscopy as well as electron tomography. PMID:18445158

Large enhancements in low latitude total electron content during 15 May 2005 geomagnetic storm in Indian zone

NASA Astrophysics Data System (ADS)

Dashora, N.; Sharma, S.; Dabas, R. S.; Alex, S.; Pandey, R.

2009-05-01

Results pertaining to the response of the equatorial and low latitude ionosphere to a major geomagnetic storm that occurred on 15 May 2005 are presented. These results are also the first from the Indian zone in terms of (i) GPS derived total electron content (TEC) variations following the storm (ii) Local low latitude electrodynamics response to penetration of high latitude convection electric field (iii) effect of storm induced traveling atmospheric disturbances (TAD's) on GPS-TEC in equatorial ionization anomaly (EIA) zone. Data set comprising of ionospheric TEC obtained from GPS measurements, ionograms from an EIA zone station, New Delhi (Geog. Lat. 28.42° N, Geog. Long. 77.21° E), ground based magnetometers in equatorial and low latitude stations and solar wind data obtained from Advanced Composition Explorer (ACE) has been used in the present study. GPS receivers located at Udaipur (Geog. Lat. 24.73° N, Geog. Long. 73.73° E) and Hyderabad (Geog. Lat. 17.33° N, Geog. Long. 78.47° E) have been used for wider spatial coverage in the Indian zone. Storm induced features in vertical TEC (VTEC) have been obtained comparing them with the mean VTEC of quiet days. Variations in solar wind parameters, as obtained from ACE and in the SYM-H index, indicate that the storm commenced on 15 May 2005 at 02:39 UT. The main phase of the storm commenced at 06:00 UT on 15 May with a sudden southward turning of the Z-component of interplanetary magnetic field (IMF-Bz) and subsequent decrease in SYM-H index. The dawn-to-dusk convection electric field of high latitude origin penetrated to low and equatorial latitudes simultaneously as corroborated by the magnetometer data from the Indian zone. Subsequent northward turning of the IMF-Bz, and the penetration of the dusk-to-dawn electric field over the dip equator is also discernible. Response of the low latitude ionosphere to this storm may be characterized in terms of (i) enhanced background level of VTEC as compared to the mean

Long Indian Slab in the Mantle Transition Zone Under Eastern Tibet: Evidence from Teleseismic Tomography

NASA Astrophysics Data System (ADS)

Lei, J.; Zhao, D.; Zha, X.

2014-12-01

We present a new 3-D P-wave velocity model of the upper mantle under eastern Tibet determined from 113,831 high-quality teleseismic arrival-time data. Our data are hand-picked from seismograms of 784 teleseismic events (30o-90o) with magnitudes of 5.2 or greater. These events were recorded by 21 portable seismic stations deployed in Yunnan during April 2010 to July 2011 and 259 permanent stations of Chinese provincial seismic networks during September 2008 to December 2011 in the study region. Our results provide new insights into the mantle structure and dynamics of eastern Tibet. High-velocity (high-V) anomalies are revealed down to 200 km depth under stable cratonic regions, such as Sichuan basin, Ordos and Alashan blocks. Prominent low-velocity (low-V) anomalies are revealed in the upper mantle under the Kunlun-Qinling fold zone, Songpan-Ganzi, Qiangtang, Lahsa, and Chuan-Dian diamond blocks, suggesting that the eastward moving low-V materials are obstructed by Sichuan basin, Ordos and Alashan blocks, and they could be extruded through the Qinling fold zone and the Chuan-Dian block to eastern China. In addition, the extent and thickness of these low-V anomalies are well correlated with the surface topography, suggesting that uplift of eastern Tibet is closely related to the low-V anomalies which may reflect hot materials and have strong buoyancy. In the mantle transition zone, broad high-V anomalies are visible from the Burma arc northward to the Kunlun fault and eastward to the Xiaojiang fault, which extend for a total of approximately 700 km. The high-V anomalies are connected upward to the Wadati-Benioff seismic zone beneath the Burma arc. These results suggest that the Indian slab has subducted horizontally for a long distance in the mantle transition zone after it descended into the mantle, and its deep dehydration has contributed to forming the low-V anomalies in the big mantle wedge above the slab. Our present results shed new light on the formation and

The crustal and mantle velocity structure in central Asia from 3D traveltime tomography

NASA Astrophysics Data System (ADS)

Sun, Y.; Martin, R. V.; Toksoz, M. N.; Pei, S.

2010-12-01

The lithospheric structure in central Asia features large blocks such as the Indian plate, the Afghan block, the Turan plate, and the Tarim block. This geologically and tectonically complicated area is also one of the most seismically active regions in the world. We developed P- and S- wave velocity structures of the central Asia in the crust using the traveltime data from Kyrgyzstan, Tajikistan, Kazakhstan, and Uzbek. We chose the events and stations between 32N65E and 45N85E and focused on the areas of Pamir and western Tianshan. In this data set, there are more than 6000 P and S arrivals received at 80 stations from about 300 events. The double difference tomography is applied to relocate events and to invert for seismic structures simultaneously. Our results provide accurate locations of earthquakes and high resolution crustal structure in this region. To extend the model deeper into the mantle through the upper mantle transition zone, ISC/EHB data for P and PP phases are combined with the ABCE data. To counteract the “smearing effect,” the crust and upper mantle velocity structure, derived from regional travel-times, is used. An adaptive grid method based on ray density is used in the inversion. A P-wave velocity model extending down to a depth of 2000 km is obtained. regional-teleseismic tomography provides a high-resolution, 3-D P-wave velocity model for the crust, upper mantle, and the transition zone. The crustal models correlate well with geologic and tectonic features. The upper mantle tomograms show the images of Tian Shan. The slab geometry is quite complex, reflecting the history of the changes in the plate motions and collision processes. Vp/Vs tomography was also determined in the study region, and an attenuation tomography was obtained as well.

Zernike phase contrast cryo-electron tomography of sodium-driven flagellar hook-basal bodies from Vibrio alginolyticus.

PubMed

Hosogi, Naoki; Shigematsu, Hideki; Terashima, Hiroyuki; Homma, Michio; Nagayama, Kuniaki

2011-01-01

Vibrio alginolyticus use flagella to swim. A flagellum consists of a filament, hook and basal body. The basal body is made up of a rod and several ring structures. This study investigates the structure of the T ring which is a unique component of the V. alginolyticus sodium ion-driven flagellar basal body. Using Zernike phase contrast (ZPC) cryo-electron tomography, we compared the 3D structures of purified hook-basal bodies (HBB) from a wild-type strain (KK148) and a deletion mutant lacking MotX and MotY (TH3), which are thought to form the T ring. ZPC images of HBBs had highly improved signal-to-noise ratio compared to conventional phase contrast images. We observed the outline of the HBBs from strains KK148 and TH3, and the TH3 mutant was missing its T ring. In the wild-type strain, the T ring was beneath the LP ring and seemed to form a ring shape with diameter of 32 nm. Copyright © 2010 Elsevier Inc. All rights reserved.

Electron tomography of early melanosomes: Implications for melanogenesis and the generation of fibrillar amyloid sheets

PubMed Central

Hurbain, Ilse; Geerts, Willie J. C.; Boudier, Thomas; Marco, Sergio; Verkleij, Arie J.; Marks, Michael S.; Raposo, Graç

2008-01-01

Melanosomes are lysosome-related organelles (LROs) in which melanins are synthesized and stored. Early stage melanosomes are characterized morphologically by intralumenal fibrils upon which melanins are deposited in later stages. The integral membrane protein Pmel17 is a component of the fibrils, can nucleate fibril formation in the absence of other pigment cell-specific proteins, and forms amyloid-like fibrils in vitro. Before fibril formation Pmel17 traffics through multivesicular endosomal compartments, but how these compartments participate in downstream events leading to fibril formation is not fully known. By using high-pressure freezing of MNT-1 melanoma cells and freeze substitution to optimize ultrastructural preservation followed by double tilt 3D electron tomography, we show that the amyloid-like fibrils begin to form in multivesicular compartments, where they radiate from the luminal side of intralumenal membrane vesicles. The fibrils in fully formed stage II premelanosomes organize into sheet-like arrays and exclude the remaining intralumenal vesicles, which are smaller and often in continuity with the limiting membrane. These observations indicate that premelanosome fibrils form in association with intralumenal endosomal membranes. We suggest that similar processes regulate amyloid formation in pathological models. PMID:19033461

Electron tomography of early melanosomes: implications for melanogenesis and the generation of fibrillar amyloid sheets.

PubMed

Hurbain, Ilse; Geerts, Willie J C; Boudier, Thomas; Marco, Sergio; Verkleij, Arie J; Marks, Michael S; Raposo, Graç

2008-12-16

Melanosomes are lysosome-related organelles (LROs) in which melanins are synthesized and stored. Early stage melanosomes are characterized morphologically by intralumenal fibrils upon which melanins are deposited in later stages. The integral membrane protein Pmel17 is a component of the fibrils, can nucleate fibril formation in the absence of other pigment cell-specific proteins, and forms amyloid-like fibrils in vitro. Before fibril formation Pmel17 traffics through multivesicular endosomal compartments, but how these compartments participate in downstream events leading to fibril formation is not fully known. By using high-pressure freezing of MNT-1 melanoma cells and freeze substitution to optimize ultrastructural preservation followed by double tilt 3D electron tomography, we show that the amyloid-like fibrils begin to form in multivesicular compartments, where they radiate from the luminal side of intralumenal membrane vesicles. The fibrils in fully formed stage II premelanosomes organize into sheet-like arrays and exclude the remaining intralumenal vesicles, which are smaller and often in continuity with the limiting membrane. These observations indicate that premelanosome fibrils form in association with intralumenal endosomal membranes. We suggest that similar processes regulate amyloid formation in pathological models.

Magnetospheric electrons

NASA Technical Reports Server (NTRS)

Coroniti, F. V.; Thorne, R. M.

1972-01-01

Coupling of source, transport, and sink processes produces a fairly accurate model for the macroscopic structure and dynamics of magnetospheric electrons. Auroral electrons are controlled by convective transport from a plasma sheet source coupled with a precipitation loss due to whistler and electrostatic plasma turbulence. Outer and inner zone electrons are governed by radial diffusion transport from convection and acceleration sources external to the plasmapause and by parasitic precipitation losses arising from cyclotron and Landau interactions with whistler and ion cyclotron turbulence.

Neutrino tomography - Tevatron mapping versus the neutrino sky. [for X-rays of earth interior

NASA Technical Reports Server (NTRS)

Wilson, T. L.

1984-01-01

The feasibility of neutrino tomography of the earth's interior is discussed, taking the 80-GeV W-boson mass determined by Arnison (1983) and Banner (1983) into account. The opacity of earth zones is calculated on the basis of the preliminary reference earth model of Dziewonski and Anderson (1981), and the results are presented in tables and graphs. Proposed tomography schemes are evaluated in terms of the well-posedness of the inverse-Radon-transform problems involved, the neutrino generators and detectors required, and practical and economic factors. The ill-posed schemes are shown to be infeasible; the well-posed schemes (using Tevatrons or the neutrino sky as sources) are considered feasible but impractical.

Zone-dependent changes in human vertebral trabecular bone: clinical implications.

PubMed

Thomsen, Jesper Skovhus; Ebbesen, E N; Mosekilde, Li

2002-05-01

We have previously shown that there are pronounced age-related changes in human vertebral cancellous bone density and microarchitecture. However, the magnitude of these changes seemed to be dependent on zone location in the vertebral body-the central third vs. the areas adjacent to the endplates. The aim of the present study was, therefore, to investigate whether such zone-specific differences could be identified by static histomorphometric measures. The material comprised 48 individuals (24 women aged 19-97 years, and 24 men aged 23-95 years). Three of the women had a known fracture of the L-2. From each L-2, thick frontal sections of half of the vertebra were embedded undecalcified in methylmethacrylate, cut into 10-microm-thick sections, and stained with aniline blue. The sections were scanned into a computer, and classic static histomorphometry was performed on the images. The histomorphometry was performed on both the whole section and on the separate zones (central and sub-endplate zone). The results showed that trabecular bone volume, trabecular number, and connectivity density decreased significantly faster with age, whereas marrow space star volume increased significantly faster with age in the zones adjacent to the endplates than in the central zone. The other histomorphometric measures showed no zone specificity in relation to aging. However, trabecular thickness and trabecular separation were both higher at all ages in the central zone than in the sub-endplate zone, although this was significant only for trabecular separation. The described differences might have significant clinical implications concerning quantitative computed tomography (QCT) scanning, X-ray analyses, and assessment of fracture liability in the human spine, but the underlying pathogenesis is still not known. This study shows that the human vertebral body can be described as two distinct zones with very specific age-related changes in density and microstructure. This zone

Experimental Characterization of Electron Beam Welded SAE 5137H Thick Steel Plate

NASA Astrophysics Data System (ADS)

Kattire, Prakash; Bhawar, Valmik; Thakare, Sandeep; Patil, Sachin; Mane, Santosh; Singh, Rajkumar, Dr.

2017-09-01

Electron beam welding is known for its narrow weld zone with high depth to width ratio, less heat affected zone, less distortion and contamination. Electron beam welding is fusion welding process, where high velocity electrons impinge on material joint to be welded and kinetic energy of this electron is transformed into heat upon impact to fuse the material. In the present work electron beam welding of 60 mm thick SAE 5137H steel is studied. Mechanical and metallurgical properties of electron beam welded joint of SAE 5137H were evaluated. Mechanical properties are analysed by tensile, impact and hardness test. Metallurgical properties are investigated through optical and scanning electron microscope. The hardness traverse across weld zone shows HV 370-380, about 18% increase in the tensile strength and very low toughness of weld joint compared to parent metal. Microstructural observation shows equiaxed dendrite in the fusion zone and partial grain refinement was found in the HAZ.

Positron emission tomography in neurological diseases.

PubMed

Kumar, Sudhir; Rajshekher, G; Prabhakar, Subhashini

2005-06-01

Positron emission tomography (PET) is the study of human physiology by electronic detection of positron-emitting radiopharmaceuticals. It is one of the noninvasive technologies that can measure the metabolic and functional activity of living tissue. Positron emission tomography finds its clinical applications in broadly three specialties--oncology, cardiology, and neurology. The current review focuses on its indications in neurological diseases. Recently published literature on the use of PET in neurology has been thoroughly analyzed. Several reports regarding the usage of PET in epilepsy, stroke, dementia, and movement disorders are available. Positron emission tomography does not appear to be useful as a primary or sole imaging technique in these conditions. On the other hand, it is useful in very specific situations, which have been elaborated in the review. It is also noteworthy that PET is complementary to the computed tomography/magnetic resonance imaging findings and data obtained from combining these modalities can be valuable in situations such as localization of the epileptogenic focus in cases of refractory epilepsy or for prediction of the outcome after thrombolysis in acute ischemic stroke. The major handicaps in widespread use of PET appear to be its lack of availability and its relatively high cost. Nevertheless, a review such as this would be helpful in judiciously selecting those patients who would benefit from undergoing a PET scan, at a time when PET imaging facility is likely to be available soon in the Indian private sector.

Microseismic Velocity Imaging of the Fracturing Zone

NASA Astrophysics Data System (ADS)

Zhang, H.; Chen, Y.

2015-12-01

Hydraulic fracturing of low permeability reservoirs can induce microseismic events during fracture development. For this reason, microseismic monitoring using sensors on surface or in borehole have been widely used to delineate fracture spatial distribution and to understand fracturing mechanisms. It is often the case that the stimulated reservoir volume (SRV) is determined solely based on microseismic locations. However, it is known that for some fracture development stage, long period long duration events, instead of microseismic events may be associated. In addition, because microseismic events are essentially weak and there exist different sources of noise during monitoring, some microseismic events could not be detected and thus located. Therefore the estimation of the SRV is biased if it is solely determined by microseismic locations. With the existence of fluids and fractures, the seismic velocity of reservoir layers will be decreased. Based on this fact, we have developed a near real time seismic velocity tomography method to characterize velocity changes associated with fracturing process. The method is based on double-difference seismic tomography algorithm to image the fracturing zone where microseismic events occur by using differential arrival times from microseismic event pairs. To take into account varying data distribution for different fracking stages, the method solves the velocity model in the wavelet domain so that different scales of model features can be obtained according to different data distribution. We have applied this real time tomography method to both acoustic emission data from lab experiment and microseismic data from a downhole microseismic monitoring project for shale gas hydraulic fracturing treatment. The tomography results from lab data clearly show the velocity changes associated with different rock fracturing stages. For the field data application, it shows that microseismic events are located in low velocity anomalies. By

Correlative Energy-Dispersive X-Ray Spectroscopic Tomography and Atom Probe Tomography of the Phase Separation in an Alnico 8 Alloy.

PubMed

Guo, Wei; Sneed, Brian T; Zhou, Lin; Tang, Wei; Kramer, Matthew J; Cullen, David A; Poplawsky, Jonathan D

2016-12-01

Alnico alloys have long been used as strong permanent magnets because of their ferromagnetism and high coercivity. Understanding their structural details allows for better prediction of the resulting magnetic properties. However, quantitative three-dimensional characterization of the phase separation in these alloys is still challenged by the spatial quantification of nanoscale phases. Herein, we apply a dual tomography approach, where correlative scanning transmission electron microscopy (STEM) energy-dispersive X-ray spectroscopic (EDS) tomography and atom probe tomography (APT) are used to investigate the initial phase separation process of an alnico 8 alloy upon non-magnetic annealing. STEM-EDS tomography provides information on the morphology and volume fractions of Fe-Co-rich and Νi-Al-rich phases after spinodal decomposition in addition to quantitative information of the composition of a nanoscale volume. Subsequent analysis of a portion of the same specimen by APT offers quantitative chemical information of each phase at the sub-nanometer scale. Furthermore, APT reveals small, 2-4 nm Fe-rich α 1 phases that are nucleated in the Ni-rich α 2 matrix. From this information, we show that phase separation of the alnico 8 alloy consists of both spinodal decomposition and nucleation and growth processes. The complementary benefits and challenges associated with correlative STEM-EDS and APT are discussed.

Automated detection of preserved photoreceptor on optical coherence tomography in choroideremia based on machine learning.

PubMed

Wang, Zhuo; Camino, Acner; Hagag, Ahmed M; Wang, Jie; Weleber, Richard G; Yang, Paul; Pennesi, Mark E; Huang, David; Li, Dengwang; Jia, Yali

2018-05-01

Optical coherence tomography (OCT) can demonstrate early deterioration of the photoreceptor integrity caused by inherited retinal degeneration diseases (IRDs). A machine learning method based on random forests was developed to automatically detect continuous areas of preserved ellipsoid zone structure (an easily recognizable part of the photoreceptors on OCT) in 16 eyes of patients with choroideremia (a type of IRD). Pseudopodial extensions protruding from the preserved ellipsoid zone areas are detected separately by a local active contour routine. The algorithm is implemented on en face images with minimum segmentation requirements, only needing delineation of the Bruch's membrane, thus evading the inaccuracies and technical challenges associated with automatic segmentation of the ellipsoid zone in eyes with severe retinal degeneration. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Anomalous mantle transition zone beneath the Yellowstone hotspot track

NASA Astrophysics Data System (ADS)

Zhou, Ying

2018-06-01

The origin of the Yellowstone and Snake River Plain volcanism has been strongly debated. The mantle plume model successfully explains the age-progressive volcanic track, but a deep plume structure has been absent in seismic imaging. Here I apply diffractional tomography to receiver functions recorded at USArray stations to map high-resolution topography of mantle transition-zone discontinuities. The images reveal a trail of anomalies that closely follow the surface hotspot track and correlate well with a seismic wave-speed gap in the subducting Farallon slab. This observation contradicts the plume model, which requires anomalies in the mid mantle to be confined in a narrow region directly beneath the present-day Yellowstone caldera. I propose an alternative interpretation of the Yellowstone volcanism. About 16 million years ago, a section of young slab that had broken off from a subducted spreading centre in the mantle first penetrated the 660 km discontinuity beneath Oregon and Idaho, and pulled down older stagnant slab. Slab tearing occurred along pre-existing fracture zones and propagated northeastward. This reversed-polarity subduction generated passive upwellings from the lower mantle, which ascended through a water-rich mantle transition zone to produce melting and age-progressive volcanism.

Multiscale microstructural characterization of Sn-rich alloys by three dimensional (3D) X-ray synchrotron tomography and focused ion beam (FIB) tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yazzie, K.E.; Williams, J.J.; Phillips, N.C.

2012-08-15

Sn-rich (Pb-free) alloys serve as electrical and mechanical interconnects in electronic packaging. It is critical to quantify the microstructures of Sn-rich alloys to obtain a fundamental understanding of their properties. In this work, the intermetallic precipitates in Sn-3.5Ag and Sn-0.7Cu, and globular lamellae in Sn-37Pb solder joints were visualized and quantified using 3D X-ray synchrotron tomography and focused ion beam (FIB) tomography. 3D reconstructions were analyzed to extract statistics on particle size and spatial distribution. In the Sn-Pb alloy the interconnectivity of Sn-rich and Pb-rich constituents was quantified. It will be shown that multiscale characterization using 3D X-ray and FIBmore » tomography enabled the characterization of the complex morphology, distribution, and statistics of precipitates and contiguous phases over a range of length scales. - Highlights: Black-Right-Pointing-Pointer Multiscale characterization by X-ray synchrotron and focused ion beam tomography. Black-Right-Pointing-Pointer Characterized microstructural features in several Sn-based alloys. Black-Right-Pointing-Pointer Quantified size, fraction, and clustering of microstructural features.« less

Glaucoma Diagnostic Capabilities of Foveal Avascular Zone Parameters Using Optical Coherence Tomography Angiography According to Visual Field Defect Location.

PubMed

Kwon, Junki; Choi, Jaewan; Shin, Joong Won; Lee, Jiyun; Kook, Michael S

2017-12-01

To assess the diagnostic ability of foveal avascular zone (FAZ) parameters to discriminate glaucomatous eyes with visual field defects (VFDs) in different locations (central vs. peripheral) from normal eyes. Totally, 125 participants were separated into 3 groups: normal (n=45), glaucoma with peripheral VFD (PVFD, n=45), and glaucoma with central VFD (CVFD, n=35). The FAZ area, perimeter, and circularity and parafoveal vessel density were calculated from optical coherence tomography angiography images. The diagnostic ability of the FAZ parameters and other structural parameters was determined according to glaucomatous VFD location. Associations between the FAZ parameters and central visual function were evaluated. A larger FAZ area and longer FAZ perimeter were observed in the CVFD group than in the PVFD and normal groups. The FAZ area, perimeter, and circularity were better in differentiating glaucomatous eyes with CVFDs from normal eyes [areas under the receiver operating characteristic curves (AUC), 0.78 to 0.88] than in differentiating PVFDs from normal eyes (AUC, 0.51 to 0.64). The FAZ perimeter had a similar AUC value to the circumpapillary retinal nerve fiber layer and macular ganglion cell-inner plexiform layer thickness for differentiating eyes with CVFDs from normal eyes (all P>0.05, the DeLong test). The FAZ area was significantly correlated with central visual function (β=-112.7, P=0.035, multivariate linear regression). The FAZ perimeter had good diagnostic capability in differentiating glaucomatous eyes with CVFDs from normal eyes, and may be a potential diagnostic biomarker for detecting glaucomatous patients with CVFDs.

Axial Length Variation Impacts on Superficial Retinal Vessel Density and Foveal Avascular Zone Area Measurements Using Optical Coherence Tomography Angiography.

PubMed

Sampson, Danuta M; Gong, Peijun; An, Di; Menghini, Moreno; Hansen, Alex; Mackey, David A; Sampson, David D; Chen, Fred K

2017-06-01

To evaluate the impact of image magnification correction on superficial retinal vessel density (SRVD) and foveal avascular zone area (FAZA) measurements using optical coherence tomography angiography (OCTA). Participants with healthy retinas were recruited for ocular biometry, refraction, and RTVue XR Avanti OCTA imaging with the 3 × 3-mm protocol. The foveal and parafoveal SRVD and FAZA were quantified with custom software before and after correction for magnification error using the Littman and the modified Bennett formulae. Relative changes between corrected and uncorrected SRVD and FAZA were calculated. Forty subjects were enrolled and the median (range) age of the participants was 30 (18-74) years. The mean (range) spherical equivalent refractive error was -1.65 (-8.00 to +4.88) diopters and mean (range) axial length was 24.42 mm (21.27-28.85). Images from 13 eyes were excluded due to poor image quality leaving 67 for analysis. Relative changes in foveal and parafoveal SRVD and FAZA after correction ranged from -20% to +10%, -3% to +2%, and -20% to +51%, respectively. Image size correction in measurements of foveal SRVD and FAZA was greater than 5% in 51% and 74% of eyes, respectively. In contrast, 100% of eyes had less than 5% correction in measurements of parafoveal SRVD. Ocular biometry should be performed with OCTA to correct image magnification error induced by axial length variation. We advise caution when interpreting interocular and interindividual comparisons of SRVD and FAZA derived from OCTA without image size correction.

X-ray analysis of electron Bernstein wave heating in MST

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seltzman, A. H., E-mail: seltzman@wisc.edu; Anderson, J. K.; DuBois, A. M.

2016-11-15

A pulse height analyzing x-ray tomography system has been developed to detect x-rays from electron Bernstein wave heated electrons in the Madison symmetric torus reversed field pinch (RFP). Cadmium zinc telluride detectors are arranged in a parallel beam array with two orthogonal multi-chord detectors that may be used for tomography. In addition a repositionable 16 channel fan beam camera with a 55° field of view is used to augment data collected with the Hard X-ray array. The chord integrated signals identify target emission from RF heated electrons striking a limiter located 12° toroidally away from the RF injection port. Thismore » provides information on heated electron spectrum, transport, and diffusion. RF induced x-ray emission from absorption on harmonic electron cyclotron resonances in low current (<250 kA) RFP discharges has been observed.« less

Electron beam diagnostic system using computed tomography and an annular sensor

DOEpatents

Elmer, John W.; Teruya, Alan T.

2014-07-29

A system for analyzing an electron beam including a circular electron beam diagnostic sensor adapted to receive the electron beam, the circular electron beam diagnostic sensor having a central axis; an annular sensor structure operatively connected to the circular electron beam diagnostic sensor, wherein the sensor structure receives the electron beam; a system for sweeping the electron beam radially outward from the central axis of the circular electron beam diagnostic sensor to the annular sensor structure wherein the electron beam is intercepted by the annular sensor structure; and a device for measuring the electron beam that is intercepted by the annular sensor structure.

Structural dissection of Ebola virus and its assembly determinants using cryo-electron tomography.

PubMed

Bharat, Tanmay A M; Noda, Takeshi; Riches, James D; Kraehling, Verena; Kolesnikova, Larissa; Becker, Stephan; Kawaoka, Yoshihiro; Briggs, John A G

2012-03-13

Ebola virus is a highly pathogenic filovirus causing severe hemorrhagic fever with high mortality rates. It assembles heterogenous, filamentous, enveloped virus particles containing a negative-sense, single-stranded RNA genome packaged within a helical nucleocapsid (NC). We have used cryo-electron microscopy and tomography to visualize Ebola virus particles, as well as Ebola virus-like particles, in three dimensions in a near-native state. The NC within the virion forms a left-handed helix with an inner nucleoprotein layer decorated with protruding arms composed of VP24 and VP35. A comparison with the closely related Marburg virus shows that the N-terminal region of nucleoprotein defines the inner diameter of the Ebola virus NC, whereas the RNA genome defines its length. Binding of the nucleoprotein to RNA can assemble a loosely coiled NC-like structure; the loose coil can be condensed by binding of the viral matrix protein VP40 to the C terminus of the nucleoprotein, and rigidified by binding of VP24 and VP35 to alternate copies of the nucleoprotein. Four proteins (NP, VP24, VP35, and VP40) are necessary and sufficient to mediate assembly of an NC with structure, symmetry, variability, and flexibility indistinguishable from that in Ebola virus particles released from infected cells. Together these data provide a structural and architectural description of Ebola virus and define the roles of viral proteins in its structure and assembly.

Effect of electron beam on the properties of electron-acoustic rogue waves

NASA Astrophysics Data System (ADS)

El-Shewy, E. K.; Elwakil, S. A.; El-Hanbaly, A. M.; Kassem, A. I.

2015-04-01

The properties of nonlinear electron-acoustic rogue waves have been investigated in an unmagnetized collisionless four-component plasma system consisting of a cold electron fluid, Maxwellian hot electrons, an electron beam and stationary ions. It is found that the basic set of fluid equations is reduced to a nonlinear Schrodinger equation. The dependence of rogue wave profiles and the associated electric field on the carrier wave number, normalized density of hot electron and electron beam, relative cold electron temperature and relative beam temperature are discussed. The results of the present investigation may be applicable in auroral zone plasma.

Electron beam diagnostic system using computed tomography and an annular sensor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elmer, John W.; Teruya, Alan T.

2015-08-11

A system for analyzing an electron beam including a circular electron beam diagnostic sensor adapted to receive the electron beam, the circular electron beam diagnostic sensor having a central axis; an annular sensor structure operatively connected to the circular electron beam diagnostic sensor, wherein the sensor structure receives the electron beam; a system for sweeping the electron beam radially outward from the central axis of the circular electron beam diagnostic sensor to the annular sensor structure wherein the electron beam is intercepted by the annular sensor structure; and a device for measuring the electron beam that is intercepted by themore » annular sensor structure.« less

Tomography & Geochemistry: Precision, Repeatability, Accuracy and Joint Interpretations

NASA Astrophysics Data System (ADS)

Foulger, G. R.; Panza, G. F.; Artemieva, I. M.; Bastow, I. D.; Cammarano, F.; Doglioni, C.; Evans, J. R.; Hamilton, W. B.; Julian, B. R.; Lustrino, M.; Thybo, H.; Yanovskaya, T. B.

2015-12-01

Seismic tomography can reveal the spatial seismic structure of the mantle, but has little ability to constrain composition, phase or temperature. In contrast, petrology and geochemistry can give insights into mantle composition, but have severely limited spatial control on magma sources. For these reasons, results from these three disciplines are often interpreted jointly. Nevertheless, the limitations of each method are often underestimated, and underlying assumptions de-emphasized. Examples of the limitations of seismic tomography include its ability to image in detail the three-dimensional structure of the mantle or to determine with certainty the strengths of anomalies. Despite this, published seismic anomaly strengths are often unjustifiably translated directly into physical parameters. Tomography yields seismological parameters such as wave speed and attenuation, not geological or thermal parameters. Much of the mantle is poorly sampled by seismic waves, and resolution- and error-assessment methods do not express the true uncertainties. These and other problems have become highlighted in recent years as a result of multiple tomography experiments performed by different research groups, in areas of particular interest e.g., Yellowstone. The repeatability of the results is often poorer than the calculated resolutions. The ability of geochemistry and petrology to identify magma sources and locations is typically overestimated. These methods have little ability to determine source depths. Models that assign geochemical signatures to specific layers in the mantle, including the transition zone, the lower mantle, and the core-mantle boundary, are based on speculative models that cannot be verified and for which viable, less-astonishing alternatives are available. Our knowledge is poor of the size, distribution and location of protoliths, and of metasomatism of magma sources, the nature of the partial-melting and melt-extraction process, the mixing of disparate

Electron Tomography of Cryo-Immobilized Plant Tissue: A Novel Approach to Studying 3D Macromolecular Architecture of Mature Plant Cell Walls In Situ

PubMed Central

Sarkar, Purbasha; Bosneaga, Elena; Yap, Edgar G.; Das, Jyotirmoy; Tsai, Wen-Ting; Cabal, Angelo; Neuhaus, Erica; Maji, Dolonchampa; Kumar, Shailabh; Joo, Michael; Yakovlev, Sergey; Csencsits, Roseann; Yu, Zeyun; Bajaj, Chandrajit; Downing, Kenneth H.; Auer, Manfred

2014-01-01

Cost-effective production of lignocellulosic biofuel requires efficient breakdown of cell walls present in plant biomass to retrieve the wall polysaccharides for fermentation. In-depth knowledge of plant cell wall composition is therefore essential for improving the fuel production process. The precise spatial three-dimensional (3D) organization of cellulose, hemicellulose, pectin and lignin within plant cell walls remains unclear to date since the microscopy techniques used so far have been limited to two-dimensional, topographic or low-resolution imaging, or required isolation or chemical extraction of the cell walls. In this paper we demonstrate that by cryo-immobilizing fresh tissue, then either cryo-sectioning or freeze-substituting and resin embedding, followed by cryo- or room temperature (RT) electron tomography, respectively, we can visualize previously unseen details of plant cell wall architecture in 3D, at macromolecular resolution (∼2 nm), and in near-native state. Qualitative and quantitative analyses showed that wall organization of cryo-immobilized samples were preserved remarkably better than conventionally prepared samples that suffer substantial extraction. Lignin-less primary cell walls were well preserved in both self-pressurized rapidly frozen (SPRF), cryo-sectioned samples as well as high-pressure frozen, freeze-substituted and resin embedded (HPF-FS-resin) samples. Lignin-rich secondary cell walls appeared featureless in HPF-FS-resin sections presumably due to poor stain penetration, but their macromolecular features could be visualized in unprecedented details in our cryo-sections. While cryo-tomography of vitreous tissue sections is currently proving to be instrumental in developing 3D models of lignin-rich secondary cell walls, here we confirm that the technically easier method of RT-tomography of HPF-FS-resin sections could be used immediately for routine study of low-lignin cell walls. As a proof of principle, we characterized the

Deep structure of Llaima Volcano from seismic ambient noise tomography: Preliminary results

NASA Astrophysics Data System (ADS)

Franco, L.; Mikesell, T. D.; Rodd, R.; Lees, J. M.; Johnson, J. B.; Ronan, T.

2015-12-01

The ambient seismic noise tomography (ANT) method has become an important tool to image crustal structures and magmatic bodies at volcanoes. The frequency band of ambient noise provides complimentary data and added resolution to the deeper volcanic structures when compared to traditional tomography based on local earthquakes. The Llaima Volcano (38° 41.9' S and 71° 43.8' W) is a stratovolcano of basaltic-andesitic composition. Llaima is located in the South Volcanic Zone (ZVS) of the Andes and is listed as one of the most active volcanoes in South America, with a long documented historical record dating back to 1640. Llaima experienced violent eruptions in 1927 and 1957 (Naranjo and Moreno, 1991), and its last eruptive cycle (2008-2010) is considered the most important after the 1957 eruption. Lacking seismic constraints on the deep structure under Llaima, petrologic data have suggested the presence of magmatic bodies (dikes). These bodies likely play an important role in the eruptive dynamics of Llaima (Bouvet de Maisonneuve, C., et al 2012). Analysis of the 2008-2010 seismicity shows a southern zone (approx. 15 km from the Llaima summit) where there were many Very Long Period events occurring prior to the eruptions. This is in agreement with a deformation zone determined by InSAR analysis (Fournier et al, 2010 and Bathke, 2011), but no geologic model based on geophysical imaging has been created yet. Beginning in 2009, staff from the Chilean Geological Survey (SERNAGEOMIN) started to install a permanent seismic network consisting of nine stations. These nine stations have allowed Chilean seismologists to closely monitor the activity at Llaima, but prevented a high-resolution tomographic imaging study. During the summer of 2015, a temporary seismic network consisting of 26 stations was installed around Llaima. In the work presented here, we analyze continuous waveforms recorded between January and April 2015 from a total of 35 broadband stations (permanent and

Definition and automatic anatomy recognition of lymph node zones in the pelvis on CT images

NASA Astrophysics Data System (ADS)

Liu, Yu; Udupa, Jayaram K.; Odhner, Dewey; Tong, Yubing; Guo, Shuxu; Attor, Rosemary; Reinicke, Danica; Torigian, Drew A.

2016-03-01

Currently, unlike IALSC-defined thoracic lymph node zones, no explicitly provided definitions for lymph nodes in other body regions are available. Yet, definitions are critical for standardizing the recognition, delineation, quantification, and reporting of lymphadenopathy in other body regions. Continuing from our previous work in the thorax, this paper proposes a standardized definition of the grouping of pelvic lymph nodes into 10 zones. We subsequently employ our earlier Automatic Anatomy Recognition (AAR) framework designed for body-wide organ modeling, recognition, and delineation to actually implement these zonal definitions where the zones are treated as anatomic objects. First, all 10 zones and key anatomic organs used as anchors are manually delineated under expert supervision for constructing fuzzy anatomy models of the assembly of organs together with the zones. Then, optimal hierarchical arrangement of these objects is constructed for the purpose of achieving the best zonal recognition. For actual localization of the objects, two strategies are used -- optimal thresholded search for organs and one-shot method for the zones where the known relationship of the zones to key organs is exploited. Based on 50 computed tomography (CT) image data sets for the pelvic body region and an equal division into training and test subsets, automatic zonal localization within 1-3 voxels is achieved.

Computed Tomography

NASA Astrophysics Data System (ADS)

Castellano, Isabel; Geleijns, Jacob

After its clinical introduction in 1973, computed tomography developed from an x-ray modality for axial imaging in neuroradiology into a versatile three dimensional imaging modality for a wide range of applications in for example oncology, vascular radiology, cardiology, traumatology and even in interventional radiology. Computed tomography is applied for diagnosis, follow-up studies and screening of healthy subpopulations with specific risk factors. This chapter provides a general introduction in computed tomography, covering a short history of computed tomography, technology, image quality, dosimetry, room shielding, quality control and quality criteria.

Analysis of compositional uniformity in Al{sub x}Ga{sub 1−x}N thin films using atom probe tomography and electron microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Fang; Huang, Li; Porter, Lisa M.

2016-07-15

Calculated frequency distributions of atom probe tomography reconstructions (∼80 nm field of view) of very thin Al{sub x}Ga{sub 1−x}N (0.18 ≤ x ≤ 0.51) films grown via metalorganic vapor phase epitaxy on both (0001) GaN/AlN/SiC and (0001) GaN/sapphire heterostructures revealed homogeneous concentrations of Al and chemically abrupt Al{sub x}Ga{sub 1−x}N/GaN interfaces. The results of scanning transmission electron microscopy and selected area diffraction corroborated these results and revealed that neither superlattice ordering nor phase separation was present at nanometer length scales.

FIB Plan View Preparation and Electron Tomography of Ga-Containing Droplets Induced by Melt-Back Etching in Si.

PubMed

Gries, Katharina I; Werner, Katharina; Beyer, Andreas; Stolz, Wolfgang; Volz, Kerstin

2016-02-01

Melt-back etching is an effect that can occur for gallium (Ga) containing III/V semiconductors grown on Si. Since this effect influences interfaces between the two compounds and therefore the physical characteristics of the material composition, it is desirable to understand its driving forces. Therefore, we investigated Ga grown on Si (001) via metal organic chemical vapor deposition using trimethyl Ga as a precursor. As a result of the melt-back etching, Ga-containing droplets formed on the Si surface which reach into the Si wafer. The shape of these structures was analyzed by plan view investigation and cross sectional tomography in a (scanning) transmission electron microscope. For plan view preparation a focused ion beam was used to avoid damage to the Ga-containing structures, which are sensitive to the chemicals normally used during conventional plan view preparation. Combining the results of both investigation methods confirms that the Ga-containing structure within the Si exhibits a pyramid shape with facets along the Si {111} lattice planes.

3D tomography of midlatitude sporadic-E in Japan from GNSS-TEC data

NASA Astrophysics Data System (ADS)

Muafiry, Ihsan Naufal; Heki, Kosuke; Maeda, Jun

2018-03-01

We studied ionospheric irregularities caused by midlatitude sporadic-E ( Es) in Japan using ionospheric total electron content (TEC) data from a dense GNSS array, GEONET, with a 3D (three-dimensional) tomography technique. Es is a thin layer of unusually high ionization that appears at altitudes of 100 km. Here, we studied five cases of Es irregularities in 2010 and 2012, also reported in previous studies, over the Kanto and Kyushu Districts. We used slant TEC residuals as the input and estimated the number of electron density anomalies of more than 2000 small blocks with dimensions of 20-30 km covering a horizontal region of 300 × 500 km. We applied a continuity constraint to stabilize the solution and performed several different resolution tests with synthetic data to assess the accuracy of the results. The tomography results showed that positive electron density anomalies occurred at the E region height, and the morphology and dynamics were consistent with those reported by earlier studies.

Electron tomography of the microtubule cytoskeleton in multinucleated hyphae of Ashbya gossypii.

PubMed

Gibeaux, Romain; Lang, Claudia; Politi, Antonio Z; Jaspersen, Sue L; Philippsen, Peter; Antony, Claude

2012-12-01

We report the mechanistic basis guiding the migration pattern of multiple nuclei in hyphae of Ashbya gossypii. Using electron tomography, we reconstructed the cytoplasmic microtubule (cMT) cytoskeleton in three tip regions with a total of 13 nuclei and also the spindle microtubules of four mitotic nuclei. Each spindle pole body (SPB) nucleates three cMTs and most cMTs above a certain length grow according to their plus-end structure. Long cMTs closely align for several microns along the cortex, presumably marking regions where dynein generates pulling forces on nuclei. Close proximity between cMTs emanating from adjacent nuclei was not observed. The majority of nuclei carry duplicated side-by-side SPBs, which together emanate an average of six cMTs, in most cases in opposite orientation with respect to the hyphal growth axis. Such cMT arrays explain why many nuclei undergo short-range back and forth movements. Only occasionally do all six cMTs orient in one direction, a precondition for long-range nuclear bypassing. Following mitosis, daughter nuclei carry a single SPB with three cMTs. The increased probability that all three cMTs orient in one direction explains the high rate of nuclear bypassing observed in these nuclei. The A. gossypii mitotic spindle was found to be structurally similar to that of Saccharomyces cerevisiae in terms of nuclear microtubule (nMT) number, length distribution and three-dimensional organization even though the two organisms differ significantly in chromosome number. Our results suggest that two nMTs attach to each kinetochore in A. gossypii and not only one nMT like in S. cerevisiae.

Concordance of coronary artery calcium estimates between MDCT and electron beam tomography.

PubMed

Daniell, Anthony L; Wong, Nathan D; Friedman, John D; Ben-Yosef, Nachum; Miranda-Peats, Romalisa; Hayes, Sean W; Kang, Xingping; Sciammarella, Maria G; de Yang, Ling; Germano, Guido; Berman, Daniel S

2005-12-01

The objective of our study was to compare MDCT with electron beam tomography (EBT) for the quantification of coronary artery calcification (CAC). Sixty-eight patients underwent both MDCT and EBT within 2 months for the quantification of CAC. The images were scored in a blinded fashion and independently by two observers with a minimum of 7 days between the interpretations of images obtained from one scanner type to the other. Presence versus absence of CAC was discordant by EBT versus MDCT in 6% (n = 4) of the cases by observer 1, with one of these cases also discordant by observer 2. All cases except one (aortic calcium misidentified as CAC) were among those with a mean Agatston score of less than 5 present on EBT but absent on MDCT. EBT and MDCT scores correlated well (r = 0.98-0.99). The relative median variability between EBT and MDCT for the Agatston score was 24% for observer 1 and 27% for observer 2 and was 18% and 14%, respectively, for volume score (average for both observers: 27% for Agatston score and 16% for volume score). Scores were higher for EBT than MDCT in approximately half of the cases, with little systematic difference between the two (median EBT-MDCT difference: Agatston score, -0.55; volume score, 3.4 mm3). The absolute median difference averaged for the two observers was 28.75 for the Agatston score and 15.4 mm3 for the volume score. Differences in CAC measurements using EBT and MDCT are similar to interscan differences in CAC measurements previously reported for EBT or for other MDCT scanners individually.

Solid-state nanopores of controlled geometry fabricated in a transmission electron microscope

NASA Astrophysics Data System (ADS)

Qian, Hui; Egerton, Ray F.

2017-11-01

Energy-filtered transmission electron microscopy and electron tomography were applied to in situ studies of the formation, shape, and diameter of nanopores formed in a silicon nitride membrane in a transmission electron microscope. The nanopore geometry was observed in three dimensions by electron tomography. Drilling conditions, such as probe current, beam convergence angle, and probe position, affect the formation rate and the geometry of the pores. With a beam convergence semi-angle of α = 22 mrad, a conical shaped nanopore is formed but at α = 45 mrad, double-cone (hourglass-shaped) nanopores were produced. Nanopores with an effective diameter between 10 nm and 1.8 nm were fabricated by controlling the drilling time.

Medical Electronics and Physiological Measurement.

ERIC Educational Resources Information Center

Cochrane, T.

1989-01-01

Described are developments in medical electronics and physiological measurement. Discussed are electrocardiology, audiology, and urology as mature applications; applied potential tomography, magnetic stimulation of nerves, and laser Doppler flowmetry as new techniques; and optical sensors, ambulatory monitoring, and biosensors as future…

Complete Tem-Tomography: 3D Structure of Gems Cluster

NASA Technical Reports Server (NTRS)

Matsuno, J.; Miyake, A.; Tsuchiyama, A.; Messenger, S.; Nakamura-Messenger, K.

2015-01-01

GEMS (glass with embedded metal and sulfide) grains in interplanetary dust particles (IDPs) are considered to be one of the ubiquitous and fundamental building blocks of solids in the Solar System. They have been considered to be interstellar silicate dust that survived various metamorphism or alteration processes in the protoplanetary disk but the elemental and isotopic composition measurements suggest that most of them have been formed in the protoplanetary disk as condensates from high temperature gas. This formation model is also supported by the formation of GEMS-like grains with respect to the size, mineral assemblage, texture and infrared spectrum by condensation experiments from mean GEMS composition materials. Previous GEMS studies were performed only with 2D observation by transmission electron microscopy (TEM) or scanning TEM (STEM). However, the 3D shape and structure of GEMS grains and the spatial distribution of Fe/FeS's has critical information about their formation and origin. Recently, the 3D structure of GEMS grains in ultrathin sections of cluster IDPs was revealed by electron tomography using a TEM/STEM (JEM-2100F, JEOL). However, CT images of thin sections mounted on Cu grids acquired by conventional TEM-tomography are limited to low tilt angles (e. g., less than absolute value of 75 deg. In fact, previous 3D TEM observations of GEMS were affected by some artifacts related to the limited tilt range in the TEM used. Complete tomographic images should be acquired by rotating the sample tilt angle over a range of more than absolute value of 80 deg otherwise the CT images lose their correct structures. In order to constrain the origin and formation process of GEMS grains more clearly, we performed complete electron tomography for GEMS grains. Here we report the sample preparation method we have developed for this study, and the preliminary results.

2-D Electrical Resistivity Tomography (ERT) Assessment of Ground Failure in Urban Area

NASA Astrophysics Data System (ADS)

Nordiana, M. M.; Bery, A. A.; Taqiuddin, Z. M.; Jinmin, M.; Abir, I. A.

2018-04-01

This study was carried out to assess the foundation defects around an urban area in Selangor, Malaysia using 2-D electrical resistivity tomography (ERT). The affected structure is a three storey houses and having severe foundation-based cracks. Six 2-D ERT survey lines with 5 m minimum electrode spacing using Pole-dipole array were executed parallel to building’s wall. Four boreholes were conducted to identify the depth to competent layer to verify the 2-D ERT results. Inversion model of 2-D resistivity show that the study area consists of two main zones. The first zone is a low resistivity value (<100 Ωm), which appears to be a zone that is fully saturated with sandy silt and this could be an influence factor the increasing water level because sandy silt is highly permeable in nature and alluvium (silt, sand and clay), boulder (1200-3500 Ωm) or highly weathered with the resistivity values of 100-1000 Ωm at 20-70 m depth. The second zone is the granite bedrock of more than 3500 Ωm with depth greater than 70 m. These results were complimented and confirmed by borehole records. The ERT and borehole record suggest that the clay, sand, saturated zone, highly weathered zone and boulders at foundation depths may lead to ground movements which affected the stability of the building.

Seismic evidence for water transport out of the mantle transition zone beneath the European Alps

NASA Astrophysics Data System (ADS)

Liu, Zhen; Park, Jeffrey; Karato, Shun-ichiro

2018-01-01

The mantle transition zone has been considered a major water reservoir in the deep Earth. Mass transfer across the transition-zone boundaries may transport water-rich minerals from the transition zone into the water-poor upper or lower mantle. Water release in the mantle surrounding the transition zone could cause dehydration melting and produce seismic low-velocity anomalies if some conditions are met. Therefore, seismic observations of low-velocity layers surrounding the transition zone could provide clues of water circulation at mid-mantle depths. Below the Alpine orogen, a depressed 660-km discontinuity has been imaged clearly using seismic tomography and receiver functions, suggesting downwellings of materials from the transition zone. Multitaper-correlation receiver functions show prominent ∼0.5-1.5% velocity reductions at ∼750-800-km depths, possibly caused by partial melting in the upper part of lower mantle. The gap between the depressed 660-km discontinuity and the low-velocity layers is consistent with metallic iron as a minor phase in the topmost lower mantle reported by laboratory studies. Velocity drops atop the 410-km discontinuity are observed surrounding the Alpine orogeny, suggesting upwelling of water-rich rock from the transition zone in response to the downwelled materials below the orogeny. Our results provide evidence that convective penetration of the mantle transition zone pushes hydrated minerals both upward and downward to add hydrogen to the surrounding mantle.

Mantle transition zone thinning beneath eastern Africa: Evidence for a whole-mantle superplume structure

NASA Astrophysics Data System (ADS)

Mulibo, Gabriel D.; Nyblade, Andrew A.

2013-07-01

to S conversions from the 410 and 660 km discontinuities observed in receiver function stacks reveal a mantle transition zone that is ~30-40 km thinner than the global average in a region ~200-400 km wide extending in a SW-NE direction from central Zambia, across Tanzania and into Kenya. The thinning of the transition zone indicates a ~190-300 K thermal anomaly in the same location where seismic tomography models suggest that the lower mantle African superplume structure connects to thermally perturbed upper mantle beneath eastern Africa. This finding provides compelling evidence for the existence of a continuous thermal structure extending from the core-mantle boundary to the surface associated with the African superplume.

Correlative Energy-Dispersive X-Ray Spectroscopic Tomography and Atom Probe Tomography of the Phase Separation in an Alnico 8 Alloy

DOE PAGES

Guo, Wei; Sneed, Brian T.; Zhou, Lin; ...

2016-12-21

Alnico alloys have long been used as strong permanent magnets because of their ferromagnetism and high coercivity. Understanding their structural details allows for better prediction of the resulting magnetic properties. However, quantitative three-dimensional characterization of the phase separation in these alloys is still challenged by the spatial quantification of nanoscale phases. Herein, we apply a dual tomography approach, where correlative scanning transmission electron microscopy (STEM) energy-dispersive X-ray spectroscopic (EDS) tomography and atom probe tomography (APT) are used to investigate the initial phase separation process of an alnico 8 alloy upon non-magnetic annealing. STEM-EDS tomography provides information on the morphology andmore » volume fractions of Fe–Co-rich and Νi–Al-rich phases after spinodal decomposition in addition to quantitative information of the composition of a nanoscale volume. Subsequent analysis of a portion of the same specimen by APT offers quantitative chemical information of each phase at the sub-nanometer scale. Furthermore, APT reveals small, 2–4 nm Fe-rich α 1 phases that are nucleated in the Ni-rich α 2 matrix. From this information, we show that phase separation of the alnico 8 alloy consists of both spinodal decomposition and nucleation and growth processes. Lastly, we discuss the complementary benefits and challenges associated with correlative STEM-EDS and APT.« less

Relativistic Electron Precipitation in the Auroral Zone. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Simons, D. J.

1975-01-01

The energy spectra and pitch angle distributions of electrons in the energy range from 50 keV to 2 MeV were determined by a solid state electron energy spectrometer during the Relativistic Electron Precipitation (REP) event of 31 May 1972. The pitch angle distributions were determined from a knowledge of the rocket aspect and the direction in space of the earth's magnetic field. The rocket aspect determination was therefore treated in depth and a method was developed to compensate for the malfunctioning of the aspect magnetometer. The electron fluxes during the REP event were highly variable demonstrating correlated energy, flux, and pitch angle pulsations with time periods of less than one second. A theoretical model for the production of relativistic electrons was proposed. It follows from this model that, at comparatively low background electron densities, the anomalous Doppler resonance leads to the acceleration of near relativistic particles.

Mantle shear-wave tomography and the fate of subducted slabs.

PubMed

Grand, Steven P

2002-11-15

A new seismic model of the three-dimensional variation in shear velocity throughout the Earth's mantle is presented. The model is derived entirely from shear bodywave travel times. Multibounce shear waves, core-reflected waves and SKS and SKKS waves that travel through the core are used in the analysis. A unique aspect of the dataset used in this study is the use of bodywaves that turn at shallow depths in the mantle, some of which are triplicated. The new model is compared with other global shear models. Although competing models show significant variations, several large-scale structures are common to most of the models. The high-velocity anomalies are mostly associated with subduction zones. In some regions the anomalies only extend into the shallow lower mantle, whereas in other regions tabular high-velocity structures seem to extend to the deepest mantle. The base of the mantle shows long-wavelength high-velocity zones also associated with subduction zones. The heterogeneity seen in global tomography models is difficult to interpret in terms of mantle flow due to variations in structure from one subduction zone to another. The simplest interpretation of the seismic images is that slabs in general penetrate to the deepest mantle, although the flow is likely to be sporadic. The interruption in slab sinking is likely to be associated with the 660 km discontinuity.

Extracellular vesicles of calcifying turkey leg tendon characterized by immunocytochemistry and high voltage electron microscopic tomography and 3-D graphic image reconstruction

NASA Technical Reports Server (NTRS)

Landis, W. J.; Hodgens, K. J.; McKee, M. D.; Nanci, A.; Song, M. J.; Kiyonaga, S.; Arena, J.; McEwen, B.

1992-01-01

To gain insight into the structure and possible function of extracellular vesicles in certain calcifying vertebrate tissues, normally mineralizing leg tendons from the domestic turkey, Meleagris gallopavo, have been studied in two separate investigations, one concerning the electron microscopic immunolocalization of the 66 kDa phosphoprotein, osteopontin, and the other detailing the organization and distribution of mineral crystals associated with the vesicles as determined by high voltage microscopic tomography and 3-D graphic image reconstruction. Immunolabeling shows that osteopontin is related to extracellular vesicles of the tendon in the sense that its initial presence appears coincident with the development of mineral associated with the vesicle loci. By high voltage electron microscopy and 3-D imaging techniques, mineral crystals are found to consist of small irregularly shaped particles somewhat randomly oriented throughout individual vesicles sites. Their appearance is different from that found for the mineral observed within calcifying tendon collagen, and their 3-D disposition is not regularly ordered. Possible spatial and temporal relationships of vesicles, osteopontin, mineral, and collagen are being examined further by these approaches.

Evaluation of Automatically Quantified Foveal Avascular Zone Metrics for Diagnosis of Diabetic Retinopathy Using Optical Coherence Tomography Angiography.

PubMed

Lu, Yansha; Simonett, Joseph M; Wang, Jie; Zhang, Miao; Hwang, Thomas; Hagag, Ahmed M; Huang, David; Li, Dengwang; Jia, Yali

2018-05-01

To describe an automated algorithm to quantify the foveal avascular zone (FAZ), using optical coherence tomography angiography (OCTA), and to compare its performance for diagnosis of diabetic retinopathy (DR) and association with best-corrected visual acuity (BCVA) to that of extrafoveal avascular area (EAA). We obtained 3 × 3-mm macular OCTA scans in diabetic patients with various levels of DR and healthy controls. An algorithm based on a generalized gradient vector flow (GGVF) snake model detected the FAZ, and metrics assessing FAZ size and irregularity were calculated. We compared the automated FAZ segmentation to manual delineation and tested the within-visit repeatability of FAZ metrics. The correlations of two conventional FAZ metrics, two novel FAZ metrics, and EAA with DR severity and BCVA, as determined by Early Treatment Diabetic Retinopathy Study (ETDRS) charts, were assessed. Sixty-six eyes from 66 diabetic patients and 19 control eyes from 19 healthy participants were included. The agreement between manual and automated FAZ delineation had a Jaccard index > 0.82, and the repeatability of automated FAZ detection was excellent in eyes at all levels of DR severity. FAZ metrics that incorporated both FAZ size and shape irregularity had the strongest correlation with clinical DR grade and BCVA. Of all the tested OCTA metrics, EAA had the greatest sensitivity in differentiating diabetic eyes without clinical evidence of retinopathy, mild to moderate nonproliferative DR (NPDR), and severe NPDR to proliferative DR from healthy controls. The GGVF snake algorithm tested in this study can accurately and reliably detect the FAZ, using OCTA data at all DR severity grades, and may be used to obtain clinically useful information from OCTA data regarding macular ischemia in patients with diabetes. While FAZ metrics can provide clinically useful information regarding macular ischemia, and possibly visual acuity potential, EAA measurements may be a better biomarker for

Small scale characterization of vine plant root zone via 3D electrical resistivity tomography and Mise-à-la-Masse method: a case study in a Bordeaux Vineyard

NASA Astrophysics Data System (ADS)

Mary, Benjamin; Peruzzo, Luca; Boaga, Jacopo; Schmutz, Myriam; Wu, Yuxin; Hubbard, Susan S.; Cassiani, Giorgio

2017-04-01

Nowadays, best viticulture practices require the joint interpretation of climate and soils data. However, information about the soil structure and subsoil processes is often lacking, as point measurements, albeit precise, cannot ensure sufficient spatial coverage and resolution. Non-invasive methods can provide spatially extensive, high resolution information that, supported by traditional point-like data, help complete the complex picture of subsoil static and dynamic reality. So far very little emphasis has been given to investigating the role of soil properties and even less of roots activity on winegrapes. Vine plant's root systems play an important role in providing the minerals to the plants, but also control the water uptake and thus the water state of the vines, which is a key factor determining the grape quality potential. In this contribution we report about the measurements conducted since June 2016 in a vineyard near Bordeaux (France, Pessac Leognan Chateau). Two neighbor plants of different sizes have been selected. In order to spot small scale soil variations and root zone physical structure at the vicinity of the vine plants, we applied a methodology using longitudinal 2D tomography, 3D borehole-based electrical resistivity tomography and a variation of the mise-à-la-masse method (MALM) to assess the effect of plant roots on the current injection in the ground. Time-lapse measurements are particularly informative about the plant dynamics, and the focus is particularly applied on this approach. The time-lapse 3D ERT and MALM results are presented, and the potential to assimilate these data into a hydrological model that can account for the root water uptake as a function of atmospheric conditions is discussed.

Simulation and experimental study of aspect ratio limitation in Fresnel zone plates for hard-x-ray optics.

PubMed

Liu, Jianpeng; Shao, Jinhai; Zhang, Sichao; Ma, Yaqi; Taksatorn, Nit; Mao, Chengwen; Chen, Yifang; Deng, Biao; Xiao, Tiqiao

2015-11-10

For acquiring high-contrast and high-brightness images in hard-x-ray optics, Fresnel zone plates with high aspect ratios (zone height/zone width) have been constantly pursued. However, knowledge of aspect ratio limits remains limited. This work explores the achievable aspect ratio limit in polymethyl methacrylate (PMMA) by electron-beam lithography (EBL) under 100 keV, and investigates the lithographic factors for this limitation. Both Monte Carlo simulation and EBL on thick PMMA are applied to investigate the profile evolution with exposure doses over 100 nm wide dense zones. A high-resolution scanning electron microscope at low acceleration mode for charging free is applied to characterize the resultant zone profiles. It was discovered for what we believe is the first time that the primary electron-beam spreading in PMMA and the proximity effect due to extra exposure from neighboring areas could be the major causes of limiting the aspect ratio. Using the optimized lithography condition, a 100 nm zone plate with aspect ratio of 15/1 was fabricated and its focusing property was characterized at the Shanghai Synchrotron Radiation Facility. The aspect ratio limit found in this work should be extremely useful for guiding further technical development in nanofabrication of high-quality Fresnel zone plates.

Stability of Y–Ti–O precipitates in friction stir welded nanostructured ferritic alloys

DOE PAGES

Yu, Xinghua; Mazumder, B.; Miller, M. K.; ...

2015-01-19

Nanostructured ferritic alloys, which have complex microstructures which consist of ultrafine ferritic grains with a dispersion of stable oxide particles and nanoclusters, are promising materials for fuel cladding and structural applications in the next generation nuclear reactor. This paper evaluates microstructure of friction stir welded nanostructured ferritic alloys using electron microscopy and atom probe tomography techniques. Atom probe tomography results revealed that nanoclusters are coarsened and inhomogeneously distributed in the stir zone and thermomechanically affected zone. Three hypotheses on coarsening of nanoclusters are presented. Finally, the hardness difference in different regions of friction stir weld has been explained.

Rocket measurements of energetic particles in the midlatitude precipitation zone

NASA Technical Reports Server (NTRS)

Voss, H. D.; Smith, L. G.; Braswell, F. M.

1980-01-01

Measurements of energetic ion and electron properties as a function of altitude in the midlatitude zone of nighttime energetic particle precipitation are reported. The measurements of particle fluxes, energy spectra and pitch angle distributions were obtained by a Langmuir probe, six energetic particle spectrometers and an electrostatic analyzer on board a Nike Apache rocket launched near the center of the midlatitude zone during disturbed conditions. It is found that the incident flux was primarily absorbed rather than backscattered, and consists of mainly energetic hydrogen together with some helium and a small energetic electron component. Observed differential energy spectra of protons having an exponential energy spectrum, and pitch angle distributions at various altitudes indicate that the energetic particle flux decreases rapidly for pitch angles less than 70 deg. An energetic particle energy flux of 0.002 ergs/sq cm per sec is calculated which indicates the significance of energetic particles as a primary nighttime ionization source for altitudes between 120 and 200 km in the midlatitude precipitation zone.

On a gas electron multiplier based synthetic diagnostic for soft x-ray tomography on WEST with focus on impurity transport studies

NASA Astrophysics Data System (ADS)

Jardin, A.; Mazon, D.; Malard, P.; O'Mullane, M.; Chernyshova, M.; Czarski, T.; Malinowski, K.; Kasprowicz, G.; Wojenski, A.; Pozniak, K.

2017-08-01

The tokamak WEST aims at testing ITER divertor high heat flux component technology in long pulse operation. Unfortunately, heavy impurities like tungsten (W) sputtered from the plasma facing components can pollute the plasma core by radiation cooling in the soft x-ray (SXR) range, which is detrimental for the energy confinement and plasma stability. SXR diagnostics give valuable information to monitor impurities and study their transport. The WEST SXR diagnostic is composed of two new cameras based on the Gas Electron Multiplier (GEM) technology. The WEST GEM cameras will be used for impurity transport studies by performing 2D tomographic reconstructions with spectral resolution in tunable energy bands. In this paper, we characterize the GEM spectral response and investigate W density reconstruction thanks to a synthetic diagnostic recently developed and coupled with a tomography algorithm based on the minimum Fisher information (MFI) inversion method. The synthetic diagnostic includes the SXR source from a given plasma scenario, the photoionization, electron cloud transport and avalanche in the detection volume using Magboltz, and tomographic reconstruction of the radiation from the GEM signal. Preliminary studies of the effect of transport on the W ionization equilibrium and on the reconstruction capabilities are also presented.

Tomography-based mantle flow beneath Mongolia-Baikal area

NASA Astrophysics Data System (ADS)

Zhu, Tao

2014-12-01

Recent progress in seismic tomography of Asia allows us to explore and understand more clearly the mantle flow below the Mongolia-Baikal area. We present a tomography-based model of mantle convection that provides a good match to the residual topography. The model provides predictions on the present-day mantle flow and flow-induced asthenospheric deformation which give us new insights on the mantle dynamics in the Mongolia-Baikal area. The predicted mantle flow takes on a very similar pattern at the depths shallower or deeper than 400 km and almost opposite flow directions between the upper (shallower than 400 km) and lower (deeper than 400 km) parts. The flow pattern could be divided into the 'simple' eastern region and the 'complex' western region in the Mongolia. The upwelling originating from about 350 km depth beneath Baikal rift zone is an important possible drive force to the rifting. The seismic anisotropy cannot be simply related with asthenospheric flow and flow-induced deformation in the entire Mongolia-Baikal area, but they could be considered as an important contributor to the seismic anisotropy in the eastern region of Mongolia and around and in Sayan-Baikal orogenic belt.

Slab seismicity in the Western Hellenic Subduction Zone: Constraints from tomography and double-difference relocation

NASA Astrophysics Data System (ADS)

Halpaap, Felix; Rondenay, Stéphane; Ottemöller, Lars

2016-04-01

The Western Hellenic subduction zone is characterized by a transition from oceanic to continental subduction. In the southern oceanic portion of the system, abundant seismicity reaches intermediate depths of 100-120 km, while the northern continental portion rarely exhibits deep earthquakes. Our study aims to investigate how this oceanic-continental transition affects fluid release and related seismicity along strike, by focusing on the distribution of intermediate depth earthquakes. To obtain a detailed image of the seismicity, we carry out a tomographic inversion for P- and S-velocities and double-difference earthquake relocation using a dataset of unprecedented spatial coverage in this area. Here we present results of these analyses in conjunction with high-resolution profiles from migrated receiver function images obtained from the MEDUSA experiment. We generate tomographic models by inverting data from 237 manually picked, well locatable events recorded at up to 130 stations. Stations from the permanent Greek network and the EGELADOS experiment supplement the 3-D coverage of the modeled domain, which covers a large part of mainland Greece and surrounding offshore areas. Corrections for the sphericity of the Earth and our update to the SIMULR16 package, which now allows S-inversion, help improve our previous models. Flexible gridding focusses the inversion on the domains of highest gradient around the slab, and we evaluate the resolution with checker board tests. We use the resulting velocity model to relocate earthquakes via the Double-Difference method, using a large dataset of differential traveltimes obtained by crosscorrelation of seismograms. Tens of earthquakes align along two planes forming a double seismic zone in the southern, oceanic portion of the subduction zone. With increasing subduction depth, the earthquakes appear closer to the center of the slab, outlining probable deserpentinization of the slab and concomitant eclogitization of dry crustal

New diagnostic pathways urgently needed. Protocol of PET Guidance I pilot study: positron emission tomography in suspected cardiac implantable electronic device-related infection.

PubMed

Marciniak-Emmons, Marta Barbara; Sterliński, Maciej; Syska, Paweł; Maciąg, Aleksander; Farkowski, Michał Mirosław; Firek, Bohdan; Dziuk, Mirosław; Zając, Dariusz; Pytkowski, Mariusz; Szwed, Hanna

2016-01-01

Cardiovascular implantable electronic device (CIED) infection is a complication of increasing incidence. We present a protocol of an observational case control clinical trial "Positron Emission Tomography Combined With Computed Tomography (PET CT) in Suspected Cardiac Implantable Electronic Device Infection, a Pilot Study - PET Guidance I" (NCT02196753). The aim of this observational clinical trial is to assess and standardise diagnostic algorithms for CIED infections (lead-dependent infective endocarditis, generator pocket infection, fever of unknown origin) with PET CT in Poland. Study group will consist of 20 patients with initial diagnosis of CIED-related infection paired with a control group of 20 patients with implanted CIEDs, who underwent PET CT due to other non-infectious indications and have no data for infectious process in follow-up. All patients included in the study will undergo standard diagnostic pro-cess. Conventional/standard diagnostic and therapeutic process will consist of: medical interview, physical examination, laboratory tests, blood cultures; imaging studies: echocardiography: transthoracic (TTE), and, if there are no contraindications transoesophageal, computed tomography scan for pulmonary embolism if indicated; if there are abnormalities in other systems, decisions concerning further diagnostics will be made at the physician's discretion. As well as standard diagnostic procedures, patients will undergo whole body PET CT scan to localise infection or inflammation. Diagnosis and therapeutic decision will be obtained from the Study Committee. Follow-up will be held within six months with control visits at three and six months. During each follow-up visit, all patients will undergo laboratory tests, two blood cultures collected 1 h apart, and TTE. In case of actual clinical suspicion of infective endocarditis or local generator pocket infection, patients will be referred for further diagnostics. Endpoints for the results assessment

Backarc spreading and mantle wedge flow beneath the Japan Sea: insight from Rayleigh-wave anisotropic tomography

NASA Astrophysics Data System (ADS)

Liu, Xin; Zhao, Dapeng

2016-10-01

We present the first high-resolution Rayleigh-wave phase-velocity azimuthal anisotropy tomography of the Japan subduction zone at periods of 20-150 s, which is determined using a large number of high-quality amplitude and phase data of teleseismic fundamental-mode Rayleigh waves. The obtained 2-D anisotropic phase-velocity models are then inverted for a 3-D shear-wave velocity azimuthal anisotropy tomography down to a depth of ˜300 km beneath Japan. The subducting Pacific slab is imaged as a dipping high-velocity zone with trench-parallel fast-velocity directions (FVDs) which may indicate the anisotropy arising from the normal faults produced at the outer-rise area near the Japan trench axis, overprinting the slab fossil fabric, whereas the mantle wedge generally exhibits lower velocities with trench-normal FVDs which reflect subduction-driven corner flow and anisotropy. Depth variations of azimuthal anisotropy are revealed in the big mantle wedge beneath the Japan Sea, which may reflect past deformations in the Eurasian lithosphere related to backarc spreading during 21 to 15 Ma and complex current convection in the asthenosphere induced by active subductions of both the Pacific and Philippine Sea plates.

Teleseismic tomography for imaging Earth's upper mantle

NASA Astrophysics Data System (ADS)

Aktas, Kadircan

Teleseismic tomography is an important imaging tool in earthquake seismology, used to characterize lithospheric structure beneath a region of interest. In this study I investigate three different tomographic techniques applied to real and synthetic teleseismic data, with the aim of imaging the velocity structure of the upper mantle. First, by applying well established traveltime tomographic techniques to teleseismic data from southern Ontario, I obtained high-resolution images of the upper mantle beneath the lower Great Lakes. Two salient features of the 3D models are: (1) a patchy, NNW-trending low-velocity region, and (2) a linear, NE-striking high-velocity anomaly. I interpret the high-velocity anomaly as a possible relict slab associated with ca. 1.25 Ga subduction, whereas the low-velocity anomaly is interpreted as a zone of alteration and metasomatism associated with the ascent of magmas that produced the Late Cretaceous Monteregian plutons. The next part of the thesis is concerned with adaptation of existing full-waveform tomographic techniques for application to teleseismic body-wave observations. The method used here is intended to be complementary to traveltime tomography, and to take advantage of efficient frequency-domain methodologies that have been developed for inverting large controlled-source datasets. Existing full-waveform acoustic modelling and inversion codes have been modified to handle plane waves impinging from the base of the lithospheric model at a known incidence angle. A processing protocol has been developed to prepare teleseismic observations for the inversion algorithm. To assess the validity of the acoustic approximation, the processing procedure and modelling-inversion algorithm were tested using synthetic seismograms computed using an elastic Kirchhoff integral method. These tests were performed to evaluate the ability of the frequency-domain full-waveform inversion algorithm to recover topographic variations of the Moho under a

Routine single particle CryoEM sample and grid characterization by tomography

PubMed Central

Noble, Alex J; Brasch, Julia; Chase, Jillian; Acharya, Priyamvada; Tan, Yong Zi; Zhang, Zhening; Kim, Laura Y; Scapin, Giovanna; Rapp, Micah; Eng, Edward T; Rice, William J; Cheng, Anchi; Negro, Carl J; Shapiro, Lawrence; Kwong, Peter D; Jeruzalmi, David; des Georges, Amedee; Potter, Clinton S

2018-01-01

Single particle cryo-electron microscopy (cryoEM) is often performed under the assumption that particles are not adsorbed to the air-water interfaces and in thin, vitreous ice. In this study, we performed fiducial-less tomography on over 50 different cryoEM grid/sample preparations to determine the particle distribution within the ice and the overall geometry of the ice in grid holes. Surprisingly, by studying particles in holes in 3D from over 1000 tomograms, we have determined that the vast majority of particles (approximately 90%) are adsorbed to an air-water interface. The implications of this observation are wide-ranging, with potential ramifications regarding protein denaturation, conformational change, and preferred orientation. We also show that fiducial-less cryo-electron tomography on single particle grids may be used to determine ice thickness, optimal single particle collection areas and strategies, particle heterogeneity, and de novo models for template picking and single particle alignment. PMID:29809143

High-resolution short-exposure small-animal laboratory x-ray phase-contrast tomography

NASA Astrophysics Data System (ADS)

Larsson, Daniel H.; Vågberg, William; Yaroshenko, Andre; Yildirim, Ali Önder; Hertz, Hans M.

2016-12-01

X-ray computed tomography of small animals and their organs is an essential tool in basic and preclinical biomedical research. In both phase-contrast and absorption tomography high spatial resolution and short exposure times are of key importance. However, the observable spatial resolutions and achievable exposure times are presently limited by system parameters rather than more fundamental constraints like, e.g., dose. Here we demonstrate laboratory tomography with few-ten μm spatial resolution and few-minute exposure time at an acceptable dose for small-animal imaging, both with absorption contrast and phase contrast. The method relies on a magnifying imaging scheme in combination with a high-power small-spot liquid-metal-jet electron-impact source. The tomographic imaging is demonstrated on intact mouse, phantoms and excised lungs, both healthy and with pulmonary emphysema.

Electron Microscopy Characterizations and Atom Probe Tomography of Intergranular Attack in Alloy 600 Exposed to PWR Primary Water

NASA Astrophysics Data System (ADS)

Olszta, Matthew J.; Schreiber, Daniel K.; Thomas, Larry E.; Bruemmer, Stephen M.

Detailed examinations of intergranular attack (IGA) in alloy 600 were performed after exposure to simulated PWR primary water at 325°C for 500 h. High-resolution analyses of IGA characteristics were conducted on specimens with either a 1 µm diamond or 1200-grit SiC surface finish using scanning electron microscopy, transmission electron microscopy and atom probe tomography techniques. The diamond-polish finish with very little preexisting subsurface damage revealed attack of high-energy grain boundaries that intersected the exposed surface to depths approaching 2 µm. In all cases, IGA from the surface is localized oxidation consisting of porous, nanocrystalline MO-structure and spinel particles along with regions of faceted wall oxidation. Surprisingly, this continuous IG oxidation transitions to discontinuous, discrete Cr-rich sulfide particles up to 50 nm in diameter. In the vicinity of the sulfides, the grain boundaries were severely Cr depleted (to <1 at%) and enriched in S. The 1200 grit SiC finish surface exhibited a preexisting highly strained recrystallized layer of elongated nanocrystalline matrix grains. Similar IG oxidation and leading sulfide particles were found, but the IGA depth was typically confined to the near-surface ( 400 nm) recrystallized region. Difference in IGA for the two surface finishes indicates that the formation of grain boundary sulfides occurs during the exposure to PWR primary water. The source of S remains unclear, however it is not present as sulfides in the bulk alloy nor is it segregated to bulk grain boundaries.

Seismic tomography shows that upwelling beneath Iceland is confined to the upper mantle

USGS Publications Warehouse

Foulger, G.R.; Pritchard, M.J.; Julian, B.R.; Evans, J.R.; Allen, R.M.; Nolet, G.; Morgan, W.J.; Bergsson, B.H.; Erlendsson, P.; Jakobsdottir, S.; Ragnarsson, S.; Stefansson, R.; Vogfjord, K.

2001-01-01

We report the results of the highest-resolution teleseismic tomography study yet performed of the upper mantle beneath Iceland. The experiment used data gathered by the Iceland Hotspot Project, which operated a 35-station network of continuously recording, digital, broad-band seismometers over all of Iceland 1996-1998. The structure of the upper mantle was determined using the ACH damped least-squares method and involved 42 stations, 3159 P-wave, and 1338 S-wave arrival times, including the phases P, pP, sP, PP, SP, PcP, PKIKP, pPKIKP, S, sS, SS, SKS and Sdiff. Artefacts, both perceptual and parametric, were minimized by well-tested smoothing techniques involving layer thinning and offset-and-averaging. Resolution is good beneath most of Iceland from ??? 60 km depth to a maximum of ??? 450 km depth and beneath the Tjornes Fracture Zone and near-shore parts of the Reykjanes ridge. The results reveal a coherent, negative wave-speed anomaly with a diameter of 200-250 km and anomalies in P-wave speed, Vp, as strong as -2.7 per cent and in S-wave speed, Vs, as strong as -4.9 per cent. The anomaly extends from the surface to the limit of good resolution at ??? 450 km depth. In the upper ??? 250 km it is centred beneath the eastern part of the Middle Volcanic Zone, coincident with the centre of the ??? 100 mGal Bouguer gravity low over Iceland, and a lower crustal low-velocity zone identified by receiver functions. This is probably the true centre of the Iceland hotspot. In the upper ??? 200 km, the low-wave-speed body extends along the Reykjanes ridge but is sharply truncated beneath the Tjornes Fracture Zone. This suggests that material may flow unimpeded along the Reykjanes ridge from beneath Iceland but is blocked beneath the Tjornes Fracture Zone. The magnitudes of the Vp, Vs and Vp/Vs anomalies cannot be explained by elevated temperature alone, but favour a model of maximum temperature anomalies <200 K, along with up to ??? 2 per cent of partial melt in the depth

Fusion of Tomography Tests for DNAPL Source Zone Characterization: Technology Development and Validation

DTIC Science & Technology

2011-07-01

alternative to the REV and fracture network concepts, pp. 533-561, Rock Mechanics : Proceedings of the 28th U.S. Symposium, Tucson, Arizona, edited by I.W...spatially integrated measure of residual DNAPL volume in the flow without causing disturbances to the source zone domain [ Jin et al., 1995; Nelson and...step. 6 Hydrological inversion has been a major focus of groundwater hydrology during the last three decades [see Yeh, 1986; Sun , 1994 and

Quantifying the Variation in Shear Zone Character with Depth: a Case Study from the Simplon Shear Zone, Central Alps

NASA Astrophysics Data System (ADS)

Cawood, T. K.; Platt, J. P.

2017-12-01

A widely-accepted model for the rheology of crustal-scale shear zones states that they comprise distributed strain at depth, in wide, high-temperature shear zones, which narrow to more localized, high-strain zones at lower temperature and shallower crustal levels. We test and quantify this model by investigating how the width, stress, temperature and deformation mechanisms change with depth in the Simplon Shear Zone (SSZ). The SSZ marks a major tectonic boundary in the central Alps, where normal-sense motion and rapid exhumation of the footwall have preserved evidence of older, deeper deformation in rocks progressively further into the currently-exposed footwall. As such, microstructures further from the brittle fault (which represents the most localized, most recently-active part of the SSZ) represent earlier, higher- temperature deformation from deeper crustal levels, while rocks closer to the fault have been overprinted by successively later, cooler deformation at shallower depths. This study uses field mapping and microstructural studies to identify zones representing deformation at various crustal levels, and characterize each in terms of zone width (representing width of the shear zone at that time and depth) and dominant deformation mechanism. In addition, quartz- (by Electron Backscatter Diffraction, EBSD) and feldspar grain size (measured optically) piezometry are used to calculate the flow stress for each zone, while the Ti-in-quartz thermometer (TitaniQ) is used to calculate the corresponding temperature of deformation. We document the presence of a broad zone in which quartz is recrystallized by the Grain Boundary Migration (GBM) mechanism and feldspar by Subgrain Rotation (SGR), which represents the broad, deep zone of deformation occurring at relatively high temperatures and low stresses. In map view, this transitions to successively narrower zones, respectively characterized by quartz SGR and feldspar Bulge Nucleation (BLG); quartz BLG and brittle

77 FR 43167 - Safety Zone; Electric Zoo Fireworks, East River, Randall's Island, NY

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-24

... DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 165 [Docket Number USCG-2012-0588] RIN 1625-AA00 Safety Zone; Electric Zoo Fireworks, East River, Randall's Island, NY AGENCY: Coast Guard... Zone; Electronic Zoo Fireworks, East River, Randall's Island, NY. (a) Regulated Area. The following...

Scanning transmission ion micro-tomography (STIM-T) of biological specimens.

PubMed

Schwertner, Micheal; Sakellariou, Arthur; Reinert, Tilo; Butz, Tilman

2006-05-01

Computed tomography (CT) was applied to sets of Scanning Transmission Ion Microscopy (STIM) projections recorded at the LIPSION ion beam laboratory (Leipzig) in order to visualize the 3D-mass distribution in several specimens. Examples for a test structure (copper grid) and for biological specimens (cartilage cells, cygospore) are shown. Scanning Transmission Micro-Tomography (STIM-T) at a resolution of 260 nm was demonstrated for the first time. Sub-micron features of the Cu-grid specimen were verified by scanning electron microscopy. The ion energy loss measured during a STIM-T experiment is related to the mass density of the specimen. Typically, biological specimens can be analysed without staining. Only shock freezing and freeze-drying is required to preserve the ultra-structure of the specimen. The radiation damage to the specimen during the experiment can be neglected. This is an advantage compared to other techniques like X-ray micro-tomography. At present, the spatial resolution is limited by beam position fluctuations and specimen vibrations.

Local electron tomography using angular variations of surface tangents: Stomo version 2

NASA Astrophysics Data System (ADS)

Petersen, T. C.; Ringer, S. P.

2012-03-01

In a recent publication, we investigated the prospect of measuring the outer three-dimensional (3D) shapes of nano-scale atom probe specimens from tilt-series of images collected in the transmission electron microscope. For this purpose alone, an algorithm and simplified reconstruction theory were developed to circumvent issues that arise in commercial "back-projection" computations in this context. In our approach, we give up the difficult task of computing the complete 3D continuum structure and instead seek only the 3D morphology of internal and external scattering interfaces. These interfaces can be described as embedded 2D surfaces projected onto each image in a tilt series. Curves and other features in the images are interpreted as inscribed sets of tangent lines, which intersect the scattering interfaces at unknown locations along the direction of the incident electron beam. Smooth angular variations of the tangent line abscissa are used to compute the surface tangent intersections and hence the 3D morphology as a "point cloud". We have published the explicit details of our alternative algorithm along with the source code entitled "stomo_version_1". For this work, we have further modified the code to efficiently handle rectangular image sets, perform much faster tangent-line "edge detection" and smoother tilt-axis image alignment using simple bi-linear interpolation. We have also adapted the algorithm to detect tangent lines as "ridges", based upon 2nd order partial derivatives of the image intensity; the magnitude and orientation of which is described by a Hessian matrix. Ridges are more appropriate descriptors for tangent-line curves in phase contrast images outlined by Fresnel fringes or absorption contrast data from fine-scale objects. Improved accuracy, efficiency and speed for "stomo_version_2" is demonstrated in this paper using both high resolution electron tomography data of a nano-sized atom probe tip and simulated absorption-contrast images

Asymmetric molecular-orbital tomography by manipulating electron trajectories

NASA Astrophysics Data System (ADS)

Wang, Bincheng; Zhang, Qingbin; Zhu, Xiaosong; Lan, Pengfei; Rezvani, Seyed Ali; Lu, Peixiang

2017-11-01

We present a scheme for tomographic imaging of asymmetric molecular orbital based on high-order harmonic generation with a two-color orthogonally polarized multicycle laser field. With the two-dimensional manipulation of the electron trajectories, the electrons can recollide with the target molecule from two noncollinear directions, and then the dipole moment generated from the single direction can be obtained to reconstructed the asymmetric molecular orbital. The recollision is independent from the molecular structure and the angular dependence of the ionization rate in the external field. For this reason, this scheme can avoid the negative effects arising from the modification of the angle-dependent ionization rate induced by Stark shift and be applied to various molecules.

Dopant Distribution in Atomic Layer Deposited ZnO:Al Films Visualized by Transmission Electron Microscopy and Atom Probe Tomography.

PubMed

Wu, Yizhi; Giddings, A Devin; Verheijen, Marcel A; Macco, Bart; Prosa, Ty J; Larson, David J; Roozeboom, Fred; Kessels, Wilhelmus M M

2018-02-27

The maximum conductivity achievable in Al-doped ZnO thin films prepared by atomic layer deposition (ALD) is limited by the low doping efficiency of Al. To better understand the limiting factors for the doping efficiency, the three-dimensional distribution of Al atoms in the ZnO host material matrix has been examined on the atomic scale using a combination of high-resolution transmission electron microscopy (TEM) and atom probe tomography (APT). Although the Al distribution in ZnO films prepared by so-called "ALD supercycles" is often presented as atomically flat δ-doped layers, in reality a broadening of the Al-dopant layers is observed with a full-width-half-maximum of ∼2 nm. In addition, an enrichment of the Al at grain boundaries is observed. The low doping efficiency for local Al densities > ∼1 nm -3 can be ascribed to the Al solubility limit in ZnO and to the suppression of the ionization of Al dopants from adjacent Al donors.

Dose fractionation theorem in 3-D reconstruction (tomography)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glaeser, R.M.

It is commonly assumed that the large number of projections for single-axis tomography precludes its application to most beam-labile specimens. However, Hegerl and Hoppe have pointed out that the total dose required to achieve statistical significance for each voxel of a computed 3-D reconstruction is the same as that required to obtain a single 2-D image of that isolated voxel, at the same level of statistical significance. Thus a statistically significant 3-D image can be computed from statistically insignificant projections, as along as the total dosage that is distributed among these projections is high enough that it would have resultedmore » in a statistically significant projection, if applied to only one image. We have tested this critical theorem by simulating the tomographic reconstruction of a realistic 3-D model created from an electron micrograph. The simulations verify the basic conclusions of high absorption, signal-dependent noise, varying specimen contrast and missing angular range. Furthermore, the simulations demonstrate that individual projections in the series of fractionated-dose images can be aligned by cross-correlation because they contain significant information derived from the summation of features from different depths in the structure. This latter information is generally not useful for structural interpretation prior to 3-D reconstruction, owing to the complexity of most specimens investigated by single-axis tomography. These results, in combination with dose estimates for imaging single voxels and measurements of radiation damage in the electron microscope, demonstrate that it is feasible to use single-axis tomography with soft X-ray microscopy of frozen-hydrated specimens.« less

Evaluation of noise and blur effects with SIRT-FISTA-TV reconstruction algorithm: Application to fast environmental transmission electron tomography.

PubMed

Banjak, Hussein; Grenier, Thomas; Epicier, Thierry; Koneti, Siddardha; Roiban, Lucian; Gay, Anne-Sophie; Magnin, Isabelle; Peyrin, Françoise; Maxim, Voichita

2018-06-01

Fast tomography in Environmental Transmission Electron Microscopy (ETEM) is of a great interest for in situ experiments where it allows to observe 3D real-time evolution of nanomaterials under operating conditions. In this context, we are working on speeding up the acquisition step to a few seconds mainly with applications on nanocatalysts. In order to accomplish such rapid acquisitions of the required tilt series of projections, a modern 4K high-speed camera is used, that can capture up to 100 images per second in a 2K binning mode. However, due to the fast rotation of the sample during the tilt procedure, noise and blur effects may occur in many projections which in turn would lead to poor quality reconstructions. Blurred projections make classical reconstruction algorithms inappropriate and require the use of prior information. In this work, a regularized algebraic reconstruction algorithm named SIRT-FISTA-TV is proposed. The performance of this algorithm using blurred data is studied by means of a numerical blur introduced into simulated images series to mimic possible mechanical instabilities/drifts during fast acquisitions. We also present reconstruction results from noisy data to show the robustness of the algorithm to noise. Finally, we show reconstructions with experimental datasets and we demonstrate the interest of fast tomography with an ultra-fast acquisition performed under environmental conditions, i.e. gas and temperature, in the ETEM. Compared to classically used SIRT and SART approaches, our proposed SIRT-FISTA-TV reconstruction algorithm provides higher quality tomograms allowing easier segmentation of the reconstructed volume for a better final processing and analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

Ambient noise tomography reveals upper crustal structure of Icelandic rifts

NASA Astrophysics Data System (ADS)

Green, Robert G.; Priestley, Keith F.; White, Robert S.

2017-05-01

The structure of oceanic spreading centres and subsurface melt distribution within newly formed crust is largely understood from marine seismic experiments. In Iceland, however, sub-aerial rift elevation allows both accurate surface mapping and the installation of large broadband seismic arrays. We present a study using ambient noise Rayleigh wave tomography to image the volcanic spreading centres across Iceland. Our high resolution model images a continuous band of low seismic velocities, parallelling all three segments of the branched rift in Iceland. The upper 10 km contains strong velocity variations, with shear wave velocities 0.5 km s-1 faster in the older non-volcanically active regions compared to the active rifts. Slow velocities correlate very closely with geological surface mapping, with contours of the anomalies parallelling the edges of the neo-volcanic zones. The low-velocity band extends to the full 50 km width of the neo-volcanic zones, demonstrating a significant contrast with the narrow (8 km wide) magmatic zone seen at fast spreading ridges, where the rate of melt supply is similarly high. Within the seismically slow rift band, the lowest velocity cores of the anomalies occur above the centre of the mantle plume under the Vatnajökull icecap, and in the Eastern Volcanic Zone under the central volcano Katla. This suggests localisation of melt accumulation at these specific volcanic centres, demonstrating variability in melt supply into the shallow crust along the rift axis. Shear velocity inversions with depth show that the strongest velocity contrasts are found in the upper 8 km, and show a slight depression in the shear velocity through the mid crust (10-20 km) in the rifts. Our model also shows less intensity to the slow rift anomaly in the Western Volcanic Zone, supporting the notion that rift activity here is decreasing as the ridge jumps to the Eastern Volcanic Zone.

Atomic scale chemical tomography of human bone

NASA Astrophysics Data System (ADS)

Langelier, Brian; Wang, Xiaoyue; Grandfield, Kathryn

2017-01-01

Human bone is a complex hierarchical material. Understanding bone structure and its corresponding composition at the nanometer scale is critical for elucidating mechanisms of biomineralization under healthy and pathological states. However, the three-dimensional structure and chemical nature of bone remains largely unexplored at the nanometer scale due to the challenges associated with characterizing both the structural and chemical integrity of bone simultaneously. Here, we use correlative transmission electron microscopy and atom probe tomography for the first time, to our knowledge, to reveal structures in human bone at the atomic level. This approach provides an overlaying chemical map of the organic and inorganic constituents of bone on its structure. This first use of atom probe tomography on human bone reveals local gradients, trace element detection of Mg, and the co-localization of Na with the inorganic-organic interface of bone mineral and collagen fibrils, suggesting the important role of Na-rich organics in the structural connection between mineral and collagen. Our findings provide the first insights into the hierarchical organization and chemical heterogeneity in human bone in three-dimensions at its smallest length scale - the atomic level. We demonstrate that atom probe tomography shows potential for new insights in biomineralization research on bone.

Complementary Characterization of Cu(In,Ga)Se₂ Thin-Film Photovoltaic Cells Using Secondary Ion Mass Spectrometry, Auger Electron Spectroscopy, and Atom Probe Tomography.

PubMed

Jang, Yun Jung; Lee, Jihye; Jeong, Jeung-Hyun; Lee, Kang-Bong; Kim, Donghwan; Lee, Yeonhee

2018-05-01

To enhance the conversion performance of solar cells, a quantitative and depth-resolved elemental analysis of photovoltaic thin films is required. In this study, we determined the average concentration of the major elements (Cu, In, Ga, and Se) in fabricated Cu(In,Ga)Se2 (CIGS) thin films, using inductively coupled plasma atomic emission spectroscopy, X-ray fluorescence, and wavelengthdispersive electron probe microanalysis. Depth profiling results for CIGS thin films with different cell efficiencies were obtained using secondary ion mass spectrometry and Auger electron spectroscopy to compare the atomic concentrations. Atom probe tomography, a characterization technique with sub-nanometer resolution, was used to obtain three-dimensional elemental mapping and the compositional distribution at the grain boundaries (GBs). GBs are identified by Na increment accompanied by Cu depletion and In enrichment. Segregation of Na atoms along the GB had a beneficial effect on cell performance. Comparative analyses of different CIGS absorber layers using various analytical techniques provide us with understanding of the compositional distributions and structures of high efficiency CIGS thin films in solar cells.

Tropospheric wet refractivity tomography using multiplicative algebraic reconstruction technique

NASA Astrophysics Data System (ADS)

Xiaoying, Wang; Ziqiang, Dai; Enhong, Zhang; Fuyang, K. E.; Yunchang, Cao; Lianchun, Song

2014-01-01

Algebraic reconstruction techniques (ART) have been successfully used to reconstruct the total electron content (TEC) of the ionosphere and in recent years be tentatively used in tropospheric wet refractivity and water vapor tomography in the ground-based GNSS technology. The previous research on ART used in tropospheric water vapor tomography focused on the convergence and relaxation parameters for various algebraic reconstruction techniques and rarely discussed the impact of Gaussian constraints and initial field on the iteration results. The existing accuracy evaluation parameters calculated from slant wet delay can only evaluate the resultant precision of the voxels penetrated by slant paths and cannot evaluate that of the voxels not penetrated by any slant path. The paper proposes two new statistical parameters Bias and RMS, calculated from wet refractivity of the total voxels, to improve the deficiencies of existing evaluation parameters and then discusses the effect of the Gaussian constraints and initial field on the convergence and tomography results in multiplicative algebraic reconstruction technique (MART) to reconstruct the 4D tropospheric wet refractivity field using simulation method.

Role of H2O in Generating Subduction Zone Earthquakes

NASA Astrophysics Data System (ADS)

Hasegawa, A.

2017-03-01

A dense nationwide seismic network and high seismic activity in Japan have provided a large volume of high-quality data, enabling high-resolution imaging of the seismic structures defining the Japanese subduction zones. Here, the role of H2O in generating earthquakes in subduction zones is discussed based mainly on recent seismic studies in Japan using these high-quality data. Locations of intermediate-depth intraslab earthquakes and seismic velocity and attenuation structures within the subducted slab provide evidence that strongly supports intermediate-depth intraslab earthquakes, although the details leading to the earthquake rupture are still poorly understood. Coseismic rotations of the principal stress axes observed after great megathrust earthquakes demonstrate that the plate interface is very weak, which is probably caused by overpressured fluids. Detailed tomographic imaging of the seismic velocity structure in and around plate boundary zones suggests that interplate coupling is affected by local fluid overpressure. Seismic tomography studies also show the presence of inclined sheet-like seismic low-velocity, high-attenuation zones in the mantle wedge. These may correspond to the upwelling flow portion of subduction-induced secondary convection in the mantle wedge. The upwelling flows reach the arc Moho directly beneath the volcanic areas, suggesting a direct relationship. H2O originally liberated from the subducted slab is transported by this upwelling flow to the arc crust. The H2O that reaches the crust is overpressured above hydrostatic values, weakening the surrounding crustal rocks and decreasing the shear strength of faults, thereby inducing shallow inland earthquakes. These observations suggest that H2O expelled from the subducting slab plays an important role in generating subduction zone earthquakes both within the subduction zone itself and within the magmatic arc occupying its hanging wall.

Long-term hydrocephalus alters the cytoarchitecture of the adult subventricular zone

PubMed Central

Campos-Ordoñez, Tania; Herranz-Pérez, Vicente; Chaichana, Kaisorn L.; Rincon-Torroella, Jordina; Rigamonti, Daniele; García-Verdugo, Jose M.; Quiñones-Hinojosa, Alfredo; Gonzalez-Perez, Oscar

2014-01-01

Hydrocephalus can develop secondarily to a disturbance in production, flow and/or absorption of cerebrospinal fluid. Experimental models of hydrocephalus, especially subacute and chronic hydrocephalus, are few and limited, and the effects of hydrocephalus on the subventricular zone are unclear. The aim of this study was to analyze the effects of long-term obstructive hydrocephalus on the subventricular zone, which is the neurogenic niche lining the lateral ventricles. We developed a new method to induce hydrocephalus by obstructing the aqueduct of Sylvius in the mouse brain, thus simulating aqueductal stenosis in humans. In 120-day-old rodents (n = 18 per group), the degree of ventricular dilatation and cellular composition of the subventricular zone were studied by immunofluorescence and transmission electron microscopy. In adult patients (age > 18 years), the sizes of the subventricular zone, corpus callosum, and internal capsule were analyzed by magnetic resonance images obtained from patients with and without aqueductal stenosis (n=25 per group). Mice with 60-day hydrocephalus had a reduced number of Ki67+ and doublecortin+ cells on immunofluorescence, as well as decreased number of neural progenitors and neuroblasts in the subventricular zone on electron microscopy analysis as compared to non-hydrocephalic mice. Remarkably, a number of extracellular matrix structures (fractones) contacting the ventricular lumen and blood vessels were also observed around the subventricular zone in mice with hydrocephalus. In humans, the widths of the subventricular zone, corpus callosum, and internal capsule in patients with aqueductal stenosis were significantly smaller than age and gender-matched patients without aqueductal stenosis. In summary, supratentorial hydrocephalus reduces the proliferation rate of neural progenitors and modifies the cytoarchitecture and extracellular matrix compounds of the subventricular zone. In humans, this similar process reduces the

Long-term hydrocephalus alters the cytoarchitecture of the adult subventricular zone.

PubMed

Campos-Ordoñez, Tania; Herranz-Pérez, Vicente; Chaichana, Kaisorn L; Rincon-Torroella, Jordina; Rigamonti, Daniele; García-Verdugo, Jose M; Quiñones-Hinojosa, Alfredo; Gonzalez-Perez, Oscar

2014-11-01

Hydrocephalus can develop secondarily to a disturbance in production, flow and/or absorption of cerebrospinal fluid. Experimental models of hydrocephalus, especially subacute and chronic hydrocephalus, are few and limited, and the effects of hydrocephalus on the subventricular zone are unclear. The aim of this study was to analyze the effects of long-term obstructive hydrocephalus on the subventricular zone, which is the neurogenic niche lining the lateral ventricles. We developed a new method to induce hydrocephalus by obstructing the aqueduct of Sylvius in the mouse brain, thus simulating aqueductal stenosis in humans. In 120-day-old rodents (n=18 per group), the degree of ventricular dilatation and cellular composition of the subventricular zone were studied by immunofluorescence and transmission electron microscopy. In adult patients (age>18years), the sizes of the subventricular zone, corpus callosum, and internal capsule were analyzed by magnetic resonance images obtained from patients with and without aqueductal stenosis (n=25 per group). Mice with 60-day hydrocephalus had a reduced number of Ki67+ and doublecortin+cells on immunofluorescence, as well as decreased number of neural progenitors and neuroblasts in the subventricular zone on electron microscopy analysis as compared to non-hydrocephalic mice. Remarkably, a number of extracellular matrix structures (fractones) contacting the ventricular lumen and blood vessels were also observed around the subventricular zone in mice with hydrocephalus. In humans, the widths of the subventricular zone, corpus callosum, and internal capsule in patients with aqueductal stenosis were significantly smaller than age and gender-matched patients without aqueductal stenosis. In summary, supratentorial hydrocephalus reduces the proliferation rate of neural progenitors and modifies the cytoarchitecture and extracellular matrix compounds of the subventricular zone. In humans, this similar process reduces the subventricular

Production and aging of paramagnetic point defects in P-doped floating zone silicon irradiated with high fluence 27 MeV electrons

NASA Astrophysics Data System (ADS)

Joita, A. C.; Nistor, S. V.

2018-04-01

Enhancing the long term stable performance of silicon detectors used for monitoring the position and flux of the particle beams in high energy physics experiments requires a better knowledge of the nature, stability, and transformation properties of the radiation defects created over the operation time. We report the results of an electron spin resonance investigation in the nature, transformation, and long term stability of the irradiation paramagnetic point defects (IPPDs) produced by high fluence (2 × 1016 cm-2), high energy (27 MeV) electrons in n-type, P-doped standard floating zone silicon. We found out that both freshly irradiated and aged (i.e., stored after irradiation for 3.5 years at 250 K) samples mainly contain negatively charged tetravacancy and pentavacancy defects in the first case and tetravacancy defects in the second one. The fact that such small cluster vacancy defects have not been observed by irradiation with low energy (below 5 MeV) electrons, but were abundantly produced by irradiation with neutrons, strongly suggests the presence of the same mechanism of direct formation of small vacancy clusters by irradiation with neutrons and high energy, high fluence electrons, in agreement with theoretical predictions. Differences in the nature and annealing properties of the IPPDs observed between the 27 MeV electrons freshly irradiated, and irradiated and aged samples were attributed to the presence of a high concentration of divacancies in the freshly irradiated samples, defects which transform during storage at 250 K through diffusion and recombination processes.

SWEPT-SOURCE OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY REVEALS INTERNAL LIMITING MEMBRANE PEELING ALTERS DEEP RETINAL VASCULATURE.

PubMed

Michalewska, Zofia; Nawrocki, Jerzy

2018-04-30

To describe morphology of retinal and choroidal vessels in swept-source optical coherence tomography angiography before and after vitrectomy with the temporal inverted internal limiting membrane (ILM) flap technique for full-thickness macular holes. Prospective, observational study of 36 eyes of 33 patients with full-thickness macular holes swept-source optical coherence tomography angiography was performed in patients before and 1 month after vitrectomy. Vitrectomy with the temporal inverted ILM flap technique was performed. In this method, ILM is peeled only at one side of the fovea. An ILM flap is created to cover the macular hole. Comparison of retina vasculature in the areas of ILM peeling vs. no ILM peeling at 1 and 3 months after successful vitrectomy was performed. The study demonstrated lower density of vessels in the deep retinal plexus in the area where ILM was peeled as compared to the rest of the fovea. Visual acuity and central retinal thickness 1 month after surgery correlates with fovea avascular zone diameter in deep retinal layers at the same time point (P = 0.001). This study confirmed that ILM peeling might alter blood flow in deep retinal vessels below the peeling area in the early postoperative period. The area of the fovea avascular zone corresponds to functional results at the same time point.

Characterization of calcium and zinc spatial distributions at the fibrocartilage zone of bone-tendon junction by synchrotron radiation-based micro X-ray fluorescence analysis combined with backscattered electron imaging

NASA Astrophysics Data System (ADS)

Lu, Hongbin; Chen, Can; Wang, Zhanwen; Qu, Jin; Xu, Daqi; Wu, Tianding; Cao, Yong; Zhou, Jingyong; Zheng, Cheng; Hu, Jianzhong

2015-09-01

Tendon attaches to bone through a functionally graded fibrocartilage zone, including uncalcified fibrocartilage (UF), tidemark (TM) and calcified fibrocartilage (CF). This transition zone plays a pivotal role in relaxing load transfer between tendon and bone, and serves as a boundary between otherwise structurally and functionally distinct tissue types. Calcium and zinc are believed to play important roles in the normal growth, mineralization, and repair of the fibrocartilage zone of bone-tendon junction (BTJ). However, spatial distributions of calcium and zinc at the fibrocartilage zone of BTJ and their distribution-function relationship are not totally understood. Thus, synchrotron radiation-based micro X-ray fluorescence analysis (SR-μXRF) in combination with backscattered electron imaging (BEI) was employed to characterize the distributions of calcium and zinc at the fibrocartilage zone of rabbit patella-patellar tendon complex (PPTC). For the first time, the unique distributions of calcium and zinc at the fibrocartilage zone of the PPTC were clearly mapped by this method. The distributions of calcium and zinc at the fibrocartilage zone of the PPTC were inhomogeneous. A significant accumulation of zinc was exhibited in the transition region between UF and CF. The highest zinc content (3.17 times of that of patellar tendon) was found in the TM of fibrocartilage zone. The calcium content began to increase near the TM and increased exponentially across the calcified fibrocartilage region towards the patella. The highest calcium content (43.14 times of that of patellar tendon) was in the transitional zone of calcified fibrocartilage region and the patella, approximately 69 μm from the location with the highest zinc content. This study indicated, for the first time, that there is a differential distribution of calcium and zinc at the fibrocartilage zone of PPTC. These observations reveal new insights into region-dependent changes across the fibrocartilage zone of

78 FR 28801 - Foreign-Trade Zone 22-Chicago, Illinois; Authorization of Production Activity Panasonic...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-16

... DEPARTMENT OF COMMERCE Foreign-Trade Zones Board [B-6-2013] Foreign-Trade Zone 22--Chicago, Illinois; Authorization of Production Activity Panasonic Corporation of North America (Kitting of Consumer Electronics) Aurora, Illinois On January 11, 2013, the Illinois International Port District, grantee of FTZ 22...

Ion energies in high power impulse magnetron sputtering with and without localized ionization zones

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Yuchen; Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720; Tanaka, Koichi

2015-03-23

High speed imaging of high power impulse magnetron sputtering discharges has revealed that ionization is localized in moving ionization zones but localization disappears at high currents for high yield targets. This offers an opportunity to study the effect ionization zones have on ion energies. We measure that ions have generally higher energies when ionization zones are present, supporting the concept that these zones are associated with moving potential humps. We propose that the disappearance of ionization zones is caused by an increased supply of atoms from the target which cools electrons and reduces depletion of atoms to be ionized.

Crustal tomography of the 2016 Kumamoto earthquake area in West Japan using P and PmP data

NASA Astrophysics Data System (ADS)

Wang, Haibo; Zhao, Dapeng; Huang, Zhouchuan; Xu, Mingjie; Wang, Liangshu; Nishizono, Yukihisa; Inakura, Hirohito

2018-05-01

A high-resolution model of three-dimensional (3-D) P-wave velocity (Vp) tomography of the crust in the source area of the 2016 Kumamoto earthquake (M 7.3) in West Japan is determined using a large number of arrival times of first P-waves and reflected P-waves from the Moho discontinuity (PmP). The PmP data are collected from original seismograms of the Kumamoto aftershocks and other local crustal events in Kyushu. Detailed resolution tests show that the addition of the PmP data can significantly improve the resolution of the crustal tomography, especially that of the lower crust. Our results show that significant low-velocity (low-V) anomalies exist in the entire crust beneath the active arc volcanoes, which may reflect the pathway of arc magmas. The 2016 Kumamoto earthquake occurred at the edge of a small low-V zone in the upper crust. A significant low-V anomaly is revealed in the lower crust beneath the source zone, which may reflect the arc magma and fluids ascending from the mantle wedge. These results suggest that the rupture nucleation of the 2016 Kumamoto earthquake was affected by fluids and arc magma.

Optical Coherence Tomography of Retinal Degeneration in Royal College of Surgeons Rats and Its Correlation with Morphology and Electroretinography

PubMed Central

Yamauchi, Kodai; Mounai, Natsuki; Tanabu, Reiko; Nakazawa, Mitsuru

2016-01-01

Purpose To evaluate the correlation between optical coherence tomography (OCT) and the histological, ultrastructural and electroretinography (ERG) findings of retinal degeneration in Royal College of Surgeons (RCS-/-) rats. Materials and Methods Using OCT, we qualitatively and quantitatively observed the continual retinal degeneration in RCS-/- rats, from postnatal (PN) day 17 until PN day 111. These findings were compared with the corresponding histological, electron microscopic, and ERG findings. We also compared them to OCT findings in wild type RCS+/+ rats, which were used as controls. Results After PN day 17, the hyperreflective band at the apical side of the photoreceptor layer became blurred. The inner segment (IS) ellipsoid zone then became obscured, and the photoreceptor IS and outer segment (OS) layers became diffusely hyperreflective after PN day 21. These changes correlated with histological and electron microscopic findings showing extracellular lamellar material that accumulated in the photoreceptor OS layer. After PN day 26, the outer nuclear layer became significantly thinner (P < 0.01) and hyperreflective compared with that in the controls; conversely, the photoreceptor IS and OS layers, as well as the inner retinal layers, became significantly thicker (P < 0.001 and P = 0.05, respectively). The apical hyperreflective band, as well as the IS ellipsoid zone, gradually disappeared between PN day 20 and PN day 30; concurrently, the ERG a- and b-wave amplitudes deteriorated. In contrast, the thicknesses of the combined retinal pigment epithelium and choroid did not differ significantly between RCS-/- and RCS+/+ rats. Conclusion Our results suggest that OCT demonstrates histologically validated photoreceptor degeneration in RCS rats, and that OCT findings partly correlate with ERG findings. We propose that OCT is a less invasive and useful method for evaluating photoreceptor degeneration in animal models of retinitis pigmentosa. PMID:27644042

Seismic probing of continental subduction zones

NASA Astrophysics Data System (ADS)

Zhao, Liang; Xu, Xiaobing; Malusà, Marco G.

2017-09-01

High-resolution images of Earth's interior provide pivotal information for the understanding of a range of geodynamic processes, including continental subduction and exhumation of ultrahigh-pressure (UHP) metamorphic rocks. Here we present a synthesis of available global seismic observations on continental subduction zones, and selected examples of seismic probing from the European Alps, the Himalaya-Tibet and the Qinling-Dabie orogenic belts. Our synthesis and examples show that slabs recognized beneath exhumed continental UHP terranes generally have shallow dip angles (<45°) at depths <100 km, to become much steeper at depths >100 km. Slabs underlined by a clear high velocity anomaly from Earth's surface to the mantle are generally Cenozoic in age. Some of these slabs are continuous, whereas other continental subduction zones are located above discontinuous high velocity anomalies possibly suggesting slab breakoff. The density of seismic stations and the quality of recordings are of primary importance to get high-resolution images of the upper mantle to be used as a starting point to provide reliable geodynamic interpretations. In some cases, areas previously indicated as possible site of slab breakoff, such as the European Alps, have been later proven to be located above a continuous slab by using higher quality travel time data from denser seismic arrays. Discriminating between oceanic and continental slabs can be challenging, but valuable information can be provided by combining teleseismic tomography and receiver function analysis. The upper mantle beneath most continental UHP terranes generally shows complex seismic anisotropy patterns that are potentially preserved even in pre-Cenozoic subduction zones. These patterns can be used to provide information on continental slabs that are no longer highlighted by a clear high-velocity anomaly.

High-resolution short-exposure small-animal laboratory x-ray phase-contrast tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larsson, Daniel H.; Vågberg, William; Yaroshenko, Andre

X-ray computed tomography of small animals and their organs is an essential tool in basic and preclinical biomedical research. In both phase-contrast and absorption tomography high spatial resolution and short exposure times are of key importance. However, the observable spatial resolutions and achievable exposure times are presently limited by system parameters rather than more fundamental constraints like, e.g., dose. Here we demonstrate laboratory tomography with few-ten μm spatial resolution and few-minute exposure time at an acceptable dose for small-animal imaging, both with absorption contrast and phase contrast. The method relies on a magnifying imaging scheme in combination with a high-powermore » small-spot liquid-metal-jet electron-impact source. Lastly, the tomographic imaging is demonstrated on intact mouse, phantoms and excised lungs, both healthy and with pulmonary emphysema.« less

High-resolution short-exposure small-animal laboratory x-ray phase-contrast tomography

DOE PAGES

Larsson, Daniel H.; Vågberg, William; Yaroshenko, Andre; ...

2016-12-13

X-ray computed tomography of small animals and their organs is an essential tool in basic and preclinical biomedical research. In both phase-contrast and absorption tomography high spatial resolution and short exposure times are of key importance. However, the observable spatial resolutions and achievable exposure times are presently limited by system parameters rather than more fundamental constraints like, e.g., dose. Here we demonstrate laboratory tomography with few-ten μm spatial resolution and few-minute exposure time at an acceptable dose for small-animal imaging, both with absorption contrast and phase contrast. The method relies on a magnifying imaging scheme in combination with a high-powermore » small-spot liquid-metal-jet electron-impact source. Lastly, the tomographic imaging is demonstrated on intact mouse, phantoms and excised lungs, both healthy and with pulmonary emphysema.« less

Visualization of the herpes simplex virus portal in situ by cryo-electron tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cardone, Giovanni; Winkler, Dennis C.; Trus, Benes L.

2007-05-10

Herpes simplex virus type 1 (HSV-1), the prototypical herpesvirus, has an icosahedral nucleocapsid surrounded by a proteinaceous tegument and a lipoprotein envelope. As in tailed bacteriophages, the icosahedral symmetry of the capsid is broken at one of the 12 vertices, which is occupied by a dodecameric ring of portal protein, UL6, instead of a pentamer of the capsid protein, UL19. The portal ring serves as a conduit for DNA entering and exiting the capsid. From a cryo-EM reconstruction of capsids immuno-gold-labeled with anti-UL6 antibodies, we confirmed that UL6 resides at a vertex. To visualize the portal in the context ofmore » the assembled capsid, we used cryo-electron tomography to determine the three-dimensional structures of individual A-capsids (empty, mature capsids). The similarity in size and overall shape of the portal and a UL19 pentamer - both are cylinders of {approx} 800 kDa - combined with residual noise in the tomograms, prevented us from identifying the portal vertices directly; however, this was accomplished by a computational classification procedure. Averaging the portal-containing subtomograms produced a structure that tallies with the isolated portal, as previously reconstructed by cryo-EM. The portal is mounted on the outer surface of the capsid floor layer, with its narrow end pointing outwards. This disposition differs from that of known phage portals in that the bulk of its mass lies outside, not inside, the floor. This distinction may be indicative of divergence at the level of portal-related functions other than its role as a DNA channel.« less

75 FR 4344 - Foreign-Trade Zone 50-Long Beach, California Application for Subzone Allegro Mfg. Inc. (Cosmetic...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-27

... DEPARTMENT OF COMMERCE Foreign-Trade Zones Board [Docket 6-2010] Foreign-Trade Zone 50--Long Beach, California Application for Subzone Allegro Mfg. Inc. (Cosmetic, Organizer and Electronic Bags and Accessories) Commerce, CA An application has been submitted to the Foreign-Trade Zones Board (the Board) by the Port of...

Ionospheric Tomography Using Faraday Rotation of Automatic Dependant Surveillance Broadcast UHF Signals

NASA Astrophysics Data System (ADS)

Cushley, A. C.

2013-12-01

The proposed launch of a satellite carrying the first space-borne ADS-B receiver by the Royal Military College of Canada (RMCC) will create a unique opportunity to study the modification of the 1090 MHz radio waves following propagation through the ionosphere from the transmitting aircraft to the passive satellite receiver(s). Experimental work successfully demonstrated that ADS-B data can be used to reconstruct two dimensional (2D) electron density maps of the ionosphere using computerized tomography (CT). The goal of this work is to evaluate the feasibility of CT reconstruction. The data is modelled using Ray-tracing techniques. This allows us to determine the characteristics of individual waves, including the wave path and the state of polarization at the satellite receiver. The modelled Faraday rotation (FR) is determined and converted to total electron content (TEC) along the ray-paths. The resulting TEC is used as input for computerized ionospheric tomography (CIT) using algebraic reconstruction technique (ART). This study concentrated on meso-scale structures 100-1000 km in horizontal extent. The primary scientific interest of this thesis was to show the feasibility of a new method to image the ionosphere and obtain a better understanding of magneto-ionic wave propagation. Multiple feature input electron density profile to ray-tracing program. Top: reconstructed relative electron density map of ray-trace input (Fig. 1) using TEC measurements and line-of-sight path. Bottom: reconstructed electron density map of ray-trace input using quiet background a priori estimate.

Electrical capacitance volume tomography of high contrast dielectrics using a cuboid geometry

NASA Astrophysics Data System (ADS)

Nurge, Mark A.

An Electrical Capacitance Volume Tomography system has been created for use with a new image reconstruction algorithm capable of imaging high contrast dielectric distributions. The electrode geometry consists of two 4 x 4 parallel planes of copper conductors connected through custom built switch electronics to a commercially available capacitance to digital converter. Typical electrical capacitance tomography (ECT) systems rely solely on mutual capacitance readings to reconstruct images of dielectric distributions. This dissertation presents a method of reconstructing images of high contrast dielectric materials using only the self capacitance measurements. By constraining the unknown dielectric material to one of two values, the inverse problem is no longer ill-determined. Resolution becomes limited only by the accuracy and resolution of the measurement circuitry. Images were reconstructed using this method with both synthetic and real data acquired using an aluminum structure inserted at different positions within the sensing region. Comparisons with standard two dimensional ECT systems highlight the capabilities and limitations of the electronics and reconstruction algorithm.

Mapping seismic azimuthal anisotropy of the Japan subduction zone

NASA Astrophysics Data System (ADS)

Zhao, D.; Liu, X.

2016-12-01

We present 3-D images of azimuthal anisotropy tomography of the crust and upper mantle of the Japan subduction zone, which are determined using a large number of high-quality P- and S-wave arrival-time data of local earthquakes and teleseismic events recorded by the dense seismic networks on the Japan Islands. A tomographic method for P-wave velocity azimuthal anisotropy is modified and extended to invert S-wave travel times for 3-D S-wave velocity azimuthal anisotropy. A joint inversion of the P and S wave data is conducted to constrain the 3-D azimuthal anisotropy of the Japan subduction zone. Main findings of this work are summarized as follows. (1) The high-velocity subducting Pacific and Philippine Sea (PHS) slabs exhibit trench-parallel fast-velocity directions (FVDs), which may reflect frozen-in lattice-preferred orientation of aligned anisotropic minerals formed at the mid-ocean ridge as well as shape-preferred orientation such as normal faults produced at the outer-rise area near the trench axis. (2) Significant trench-normal FVDs are revealed in the mantle wedge, which reflects corner flow in the mantle wedge due to the active subduction and dehydration of the oceanic plates. (3) Obvious toroidal FVDs and low-velocity anomalies exist in and around a window (hole) in the aseismic PHS slab beneath Southwest Japan, which may reflect a toroidal mantle flow pattern resulting from hot and wet mantle upwelling caused by the joint effects of deep dehydration of the Pacific slab and the convective circulation process in the mantle wedge above the Pacific slab. (4) Significant low-velocity anomalies with trench-normal FVDs exist in the mantle below the Pacific slab beneath Northeast Japan, which may reflect a subducting oceanic asthenosphere affected by hot mantle upwelling from the deeper mantle. ReferencesLiu, X., D. Zhao (2016) Seismic velocity azimuthal anisotropy of the Japan subduction zone: Constraints from P and S wave traveltimes. J. Geophys. Res. 121, doi

Zoned chondrules in Semarkona: Evidence for high-and low-temperature processing

USGS Publications Warehouse

Grossman, J.N.; Alexander, C.M. O'D.; Wang, Jingyuan; Brearley, A.J.

2002-01-01

At least 15% of the low-FeO chondrules in Semarkona (LL3.0) have mesostases that are concentrically zoned in Na, with enrichments near the outer margins. We have studied zoned chondrules using electron microprobe methods (x-ray mapping plus quantitative analysis), ion micropobe analysis for trace elements and hydrogen isotopes, cathodoluminescence imaging, and transmission electron microscopy in order to determine what these objects can tell us about the environment in which chondrules formed and evolved. Mesostases in these chondrules are strongly zoned in all moderately volatile elements and H (interpreted as water). Calcium is depleted in areas of volatile enrichment. Titanium and Cr generally decrease toward the chondrule surfaces, whereas Al and Si may either increase or decrease, generally in opposite directions to one another; Mn follows Na in some chondrules but not in others; Fe and Mg are unzoned. D/H ratios increase in the water-rich areas of zoned chondrules. Mesostasis shows cathodoluminescence zoning in most zoned chondrules, with the brightest yellow color near the outside. Mesostasis in zoned chondrules appears to be glassy, with no evidence for devitrification. Systematic variations in zoning patterns among pyroxene- and olivine-rich chondrules may indicate that fractionation of low- and high-Ca pyroxene played some role in Ti, Cr, Mn, Si, Al, and some Ca zoning. But direct condensation of elements into hot chondrules, secondary melting of late condensates into the outer portions of chondrules, and subsolidus diffusion of elements into warm chondrules cannot account for the sub-parallel zoning profiles of many elements, the presence of H2O, or elemental abundance patterns. Zoning of moderately volatile elements and Ca may have been produced by hydration of chondrule glass without devitrification during aqueous alteration on the parent asteroid. This could have induced structural changes in the glass allowing rapid diffusion and exchange of elements

An Application of Hydraulic Tomography to a Large-Scale Fractured Granite Site, Mizunami, Japan.

PubMed

Zha, Yuanyuan; Yeh, Tian-Chyi J; Illman, Walter A; Tanaka, Tatsuya; Bruines, Patrick; Onoe, Hironori; Saegusa, Hiromitsu; Mao, Deqiang; Takeuchi, Shinji; Wen, Jet-Chau

2016-11-01

While hydraulic tomography (HT) is a mature aquifer characterization technology, its applications to characterize hydrogeology of kilometer-scale fault and fracture zones are rare. This paper sequentially analyzes datasets from two new pumping tests as well as those from two previous pumping tests analyzed by Illman et al. (2009) at a fractured granite site in Mizunami, Japan. Results of this analysis show that datasets from two previous pumping tests at one side of a fault zone as used in the previous study led to inaccurate mapping of fracture and fault zones. Inclusion of the datasets from the two new pumping tests (one of which was conducted on the other side of the fault) yields locations of the fault zone consistent with those based on geological mapping. The new datasets also produce a detailed image of the irregular fault zone, which is not available from geological investigation alone and the previous study. As a result, we conclude that if prior knowledge about geological structures at a field site is considered during the design of HT surveys, valuable non-redundant datasets about the fracture and fault zones can be collected. Only with these non-redundant data sets, can HT then be a viable and robust tool for delineating fracture and fault distributions over kilometer scales, even when only a limited number of boreholes are available. In essence, this paper proves that HT is a new tool for geologists, geophysicists, and engineers for mapping large-scale fracture and fault zone distributions. © 2016, National Ground Water Association.

Retrospective evaluation of thoracic computed tomography findings in dogs naturally infected by Angiostrongylus vasorum.

PubMed

Coia, Mark E; Hammond, Gawain; Chan, Daniel; Drees, Randi; Walker, David; Murtagh, Kevin; Stone, Janine; Bexfield, Nicholas; Reeve, Lizzie; Helm, Jenny

2017-09-01

Angiostrongylus vasorum (A. vasorum) is an important emerging disease of canidae. Cardiorespiratory signs are common in affected dogs, therefore thoracic imaging is critical for diagnosing and monitoring disease. Descriptions of thoracic computed tomography (CT) findings in dogs naturally infected with A. vasorum are currently lacking. Aims of this multicenter, retrospective study were to describe thoracic CT findings in a group of dogs with confirmed disease, determine whether any changes were consistent among dogs, and propose standardized terms for describing thoracic CT findings. Nine UK-based referral centers' clinical and imaging databases were searched for dogs that had a confirmed diagnosis of A. vasorum, and had undergone thoracic CT examination. Eighteen dogs, from seven of the centers, fulfilled the inclusion criteria. The lung lobes were divided into the following three zones and the CT changes described in each: pleural (zone 1), subpleural (zone 2), and peribronchovascular (zone 3). The predominent abnormality was increased lung attenuation due to poorly defined ground-glass opacity or consolidation. There were regions of mosaic attenuation due to peripheral bronchiectasis. Nine/18 (50%) dogs showed hyperattenuating nodules of varying sizes with ill-defined margins. The distribution always affected zones 1 and 2 with varied involvement of zone 3; this resulted in clear delineation between zones 2 and 3. Tracheobronchial lymphadenomegaly was frequently noted. Findings were nonspecific and there was considerable overlap with other pulmonary conditions. However, authors recommend that A. vasorum be considered a likely differential diagnosis for dogs with a predominantly peripheral distribution of lung changes. © 2017 American College of Veterinary Radiology.

Time Dependent Tomography of the Solar Corona in Three Spatial Dimensions

NASA Astrophysics Data System (ADS)

Butala, M. D.; Frazin, R. A.; Kamalabadi, F.

2006-12-01

The combination of the soon to be launched STEREO mission with SOHO will provide scientists with three simultaneous space-borne views of the Sun. The increase in available measurements will reduce the data acquisition time necessary to obtain 3D coronal electron density (N_e) estimates from coronagraph images using a technique called solar rotational tomography (SRT). However, the data acquisition period will still be long enough for the corona to dynamically evolve, requiring time dependent solar tomography. The Kalman filter (KF) would seem to be an ideal computational method for time dependent SRT. Unfortunately, the KF scales poorly with problem size and is, as a result, inapplicable. A Monte Carlo approximation to the KF called the localized ensemble Kalman filter was developed for massive applications and has the promise of making the time dependent estimation of the 3D coronal N_e possible. We present simulations showing that this method will make time dependent tomography in three spatial dimensions computationally feasible.