Retinal Structure of Birds of Prey Revealed by Ultra-High Resolution Spectral-Domain Optical Coherence Tomography

PubMed Central

Ruggeri, Marco; Major, James C.; McKeown, Craig; Knighton, Robert W.; Puliafito, Carmen A.

2010-01-01

Purpose. To reveal three-dimensional (3-D) information about the retinal structures of birds of prey in vivo. Methods. An ultra-high resolution spectral-domain optical coherence tomography (SD-OCT) system was built for in vivo imaging of retinas of birds of prey. The calibrated imaging depth and axial resolution of the system were 3.1 mm and 2.8 μm (in tissue), respectively. 3-D segmentation was performed for calculation of the retinal nerve fiber layer (RNFL) map. Results. High-resolution OCT images were obtained of the retinas of four species of birds of prey: two diurnal hawks (Buteo platypterus and Buteo brachyurus) and two nocturnal owls (Bubo virginianus and Strix varia). These images showed the detailed retinal anatomy, including the retinal layers and the structure of the deep and shallow foveae. The calculated thickness map showed the RNFL distribution. Traumatic injury to one bird's retina was also successfully imaged. Conclusions. Ultra-high resolution SD-OCT provides unprecedented high-quality 2-D and 3-D in vivo visualization of the retinal structures of birds of prey. SD-OCT is a powerful imaging tool for vision research in birds of prey. PMID:20554605

Structural Analysis of Titan's Tholins by Ultra-High Resolution Mass Spectrometry

NASA Astrophysics Data System (ADS)

Vuitton, V.; Frisari, M.; Thissen, R.; Dutuit, O.; Bonnet, J.-Y.; Quirico, E.; Sciamma O'Brien, E.; Szopa, C.; Carrasco, N.; Somogyi, A.; Smith, M.; Hörst, S. M.; Yelle, R.

2010-04-01

We propose here a systematic ultra-high resolution mass spectrometry and MS/MS study in order to provide a more coherent and complete characterization of the structure of the molecules making up the soluble fraction of the Titan tholins.

High-Resolution Printing of 3D Structures Using an Electrohydrodynamic Inkjet with Multiple Functional Inks.

PubMed

An, Byeong Wan; Kim, Kukjoo; Lee, Heejoo; Kim, So-Yun; Shim, Yulhui; Lee, Dae-Young; Song, Jun Yeob; Park, Jang-Ung

2015-08-05

Electrohydrodynamic-inkjet-printed high-resolution complex 3D structures with multiple functional inks are demonstrated. Printed 3D structures can have a variety of fine patterns, such as vertical or helix-shaped pillars and straight or rounded walls, with high aspect ratios (greater than ≈50) and narrow diameters (≈0.7 μm). Furthermore, the formation of freestanding, bridge-like Ag wire structures on plastic substrates suggests substantial potentials as high-precision, flexible 3D interconnects. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-resolution measurements of the multilayer ultra-structure of articular cartilage and their translational potential

PubMed Central

2014-01-01

Current musculoskeletal imaging techniques usually target the macro-morphology of articular cartilage or use histological analysis. These techniques are able to reveal advanced osteoarthritic changes in articular cartilage but fail to give detailed information to distinguish early osteoarthritis from healthy cartilage, and this necessitates high-resolution imaging techniques measuring cells and the extracellular matrix within the multilayer structure of articular cartilage. This review provides a comprehensive exploration of the cellular components and extracellular matrix of articular cartilage as well as high-resolution imaging techniques, including magnetic resonance image, electron microscopy, confocal laser scanning microscopy, second harmonic generation microscopy, and laser scanning confocal arthroscopy, in the measurement of multilayer ultra-structures of articular cartilage. This review also provides an overview for micro-structural analysis of the main components of normal or osteoarthritic cartilage and discusses the potential and challenges associated with developing non-invasive high-resolution imaging techniques for both research and clinical diagnosis of early to late osteoarthritis. PMID:24946278

High-resolution structure of viruses from random diffraction snapshots

PubMed Central

Hosseinizadeh, A.; Schwander, P.; Dashti, A.; Fung, R.; D'Souza, R. M.; Ourmazd, A.

2014-01-01

The advent of the X-ray free-electron laser (XFEL) has made it possible to record diffraction snapshots of biological entities injected into the X-ray beam before the onset of radiation damage. Algorithmic means must then be used to determine the snapshot orientations and thence the three-dimensional structure of the object. Existing Bayesian approaches are limited in reconstruction resolution typically to 1/10 of the object diameter, with the computational expense increasing as the eighth power of the ratio of diameter to resolution. We present an approach capable of exploiting object symmetries to recover three-dimensional structure to high resolution, and thus reconstruct the structure of the satellite tobacco necrosis virus to atomic level. Our approach offers the highest reconstruction resolution for XFEL snapshots to date and provides a potentially powerful alternative route for analysis of data from crystalline and nano-crystalline objects. PMID:24914154

High-resolution structure of viruses from random diffraction snapshots.

PubMed

Hosseinizadeh, A; Schwander, P; Dashti, A; Fung, R; D'Souza, R M; Ourmazd, A

2014-07-17

The advent of the X-ray free-electron laser (XFEL) has made it possible to record diffraction snapshots of biological entities injected into the X-ray beam before the onset of radiation damage. Algorithmic means must then be used to determine the snapshot orientations and thence the three-dimensional structure of the object. Existing Bayesian approaches are limited in reconstruction resolution typically to 1/10 of the object diameter, with the computational expense increasing as the eighth power of the ratio of diameter to resolution. We present an approach capable of exploiting object symmetries to recover three-dimensional structure to high resolution, and thus reconstruct the structure of the satellite tobacco necrosis virus to atomic level. Our approach offers the highest reconstruction resolution for XFEL snapshots to date and provides a potentially powerful alternative route for analysis of data from crystalline and nano-crystalline objects.

Fabrication of [001]-oriented tungsten tips for high resolution scanning tunneling microscopy

PubMed Central

Chaika, A. N.; Orlova, N. N.; Semenov, V. N.; Postnova, E. Yu.; Krasnikov, S. A.; Lazarev, M. G.; Chekmazov, S. V.; Aristov, V. Yu.; Glebovsky, V. G.; Bozhko, S. I.; Shvets, I. V.

2014-01-01

The structure of the [001]-oriented single crystalline tungsten probes sharpened in ultra-high vacuum using electron beam heating and ion sputtering has been studied using scanning and transmission electron microscopy. The electron microscopy data prove reproducible fabrication of the single-apex tips with nanoscale pyramids grained by the {011} planes at the apexes. These sharp, [001]-oriented tungsten tips have been successfully utilized in high resolution scanning tunneling microscopy imaging of HOPG(0001), SiC(001) and graphene/SiC(001) surfaces. The electron microscopy characterization performed before and after the high resolution STM experiments provides direct correlation between the tip structure and picoscale spatial resolution achieved in the experiments. PMID:24434734

Pollen structure visualization using high-resolution laboratory-based hard X-ray tomography

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

Li, Qiong; Gluch, Jürgen; Krüger, Peter

A laboratory-based X-ray microscope is used to investigate the 3D structure of unstained whole pollen grains. For the first time, high-resolution laboratory-based hard X-ray microscopy is applied to study pollen grains. Based on the efficient acquisition of statistically relevant information-rich images using Zernike phase contrast, both surface- and internal structures of pine pollen - including exine, intine and cellular structures - are clearly visualized. The specific volumes of these structures are calculated from the tomographic data. The systematic three-dimensional study of pollen grains provides morphological and structural information about taxonomic characters that are essential in palynology. Such studies have amore » direct impact on disciplines such as forestry, agriculture, horticulture, plant breeding and biodiversity. - Highlights: • The unstained whole pine pollen was visualized by high-resolution laboratory-based HXRM for the first time. • The comparison study of pollen grains by LM, SEM and high-resolution laboratory-based HXRM. • Phase contrast imaging provides significantly higher contrast of the raw images compared to absorption contrast imaging. • Surface and internal structure of the pine pollen including exine, intine and cellular structures are clearly visualized. • 3D volume data of unstained whole pollen grains are acquired and the specific volumes of the different layer are calculated.« less

High Resolution Crystal Structure of Human β-Glucuronidase Reveals Structural Basis of Lysosome Targeting

PubMed Central

Hassan, Md. Imtaiyaz; Waheed, Abdul; Grubb, Jeffery H.; Klei, Herbert E.; Korolev, Sergey; Sly, William S.

2013-01-01

Human β-glucuronidase (GUS) cleaves β-D-glucuronic acid residues from the non-reducing termini of glycosaminoglycan and its deficiency leads to mucopolysaccharidosis type VII (MPSVII). Here we report a high resolution crystal structure of human GUS at 1.7 Å resolution and present an extensive analysis of the structural features, unifying recent findings in the field of lysosome targeting and glycosyl hydrolases. The structure revealed several new details including a new glycan chain at Asn272, in addition to that previously observed at Asn173, and coordination of the glycan chain at Asn173 with Lys197 of the lysosomal targeting motif which is essential for phosphotransferase recognition. Analysis of the high resolution structure not only provided new insights into the structural basis for lysosomal targeting but showed significant differences between human GUS, which is medically important in its own right, and E. coli GUS, which can be selectively inhibited in the human gut to prevent prodrug activation and is also widely used as a reporter gene by plant biologists. Despite these differences, both human and E. coli GUS share a high structure homology in all three domains with most of the glycosyl hydrolases, suggesting that they all evolved from a common ancestral gene. PMID:24260279

High Resolution Crystal Structure of the Catalytic Domain of ADAMTS-5 (Aggrecanase-2)

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

Shieh, Huey-Sheng; Mathis, Karl J.; Williams, Jennifer M.

Aggrecanase-2 (a disintegrin and metalloproteinase with thrombospondin motifs-5 (ADAMTS-5)), a member of the ADAMTS protein family, is critically involved in arthritic diseases because of its direct role in cleaving the cartilage component aggrecan. The catalytic domain of aggrecanase-2 has been refolded, purified, and crystallized, and its three-dimensional structure determined to 1.4{angstrom} resolution in the presence of an inhibitor. A high resolution structure of an ADAMTS/aggrecanase protein provides an opportunity for the development of therapeutics to treat osteoarthritis.

High resolution PFPE-based molding High resolution PFPE-based molding High resolution PFPE-based molding techniques for nanofabrication of high pattern density sub-20 nm features: A fundamental materials approach

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

Williams, Stuart S; Samulski, Edward; Lopez, Renee

2010-01-01

ABSTRACT. Described herein is the development and investigation of PFPE-based elastomers for high resolution replica molding applications. The modulus of the elastomeric materials was increased through synthetic and additive approaches while maintaining relatively low surface energies (<25 mN/m). Using practically relevant large area master templates, we show that the resolution of the molds is strongly dependant upon the elastomeric mold modulus. A composite mold approach was used to form flexible molds out of stiff, high modulus materials that allow for replication of sub-20 nm post structures. Sub-100 nm line grating master templates, formed using e-beam lithography, were used to determinemore » the experimental stability of the molding materials. It was observed that as the feature spacing decreased, high modulus composite molds were able to effectively replicate the nano-grating structures without cracking or tear-out defects that typically occur with high modulus elastomers.« less

3D printing of high-resolution PLA-based structures by hybrid electrohydrodynamic and fused deposition modeling techniques

NASA Astrophysics Data System (ADS)

Zhang, Bin; Seong, Baekhoon; Nguyen, VuDat; Byun, Doyoung

2016-02-01

Recently, the three-dimensional (3D) printing technique has received much attention for shape forming and manufacturing. The fused deposition modeling (FDM) printer is one of the various 3D printers available and has become widely used due to its simplicity, low-cost, and easy operation. However, the FDM technique has a limitation whereby its patterning resolution is too low at around 200 μm. In this paper, we first present a hybrid mechanism of electrohydrodynamic jet printing with the FDM technique, which we name E-FDM. We then develop a novel high-resolution 3D printer based on the E-FDM process. To determine the optimal condition for structuring, we also investigated the effect of several printing parameters, such as temperature, applied voltage, working height, printing speed, flow-rate, and acceleration on the patterning results. This method was capable of fabricating both high resolution 2D and 3D structures with the use of polylactic acid (PLA). PLA has been used to fabricate scaffold structures for tissue engineering, which has different hierarchical structure sizes. The fabrication speed was up to 40 mm/s and the pattern resolution could be improved to 10 μm.

Insulated Conducting Cantilevered Nanotips and Two-Chamber Recording System for High Resolution Ion Sensing AFM

PubMed Central

Meckes, Brian; Arce, Fernando Teran; Connelly, Laura S.; Lal, Ratnesh

2014-01-01

Biological membranes contain ion channels, which are nanoscale pores allowing controlled ionic transport and mediating key biological functions underlying normal/abnormal living. Synthetic membranes with defined pores are being developed to control various processes, including filtration of pollutants, charge transport for energy storage, and separation of fluids and molecules. Although ionic transport (currents) can be measured with single channel resolution, imaging their structure and ionic currents simultaneously is difficult. Atomic force microscopy enables high resolution imaging of nanoscale structures and can be modified to measure ionic currents simultaneously. Moreover, the ionic currents can also be used to image structures. A simple method for fabricating conducting AFM cantilevers to image pore structures at high resolution is reported. Tungsten microwires with nanoscale tips are insulated except at the apex. This allows simultaneous imaging via cantilever deflections in normal AFM force feedback mode as well as measuring localized ionic currents. These novel probes measure ionic currents as small as picoampere while providing nanoscale spatial resolution surface topography and is suitable for measuring ionic currents and conductance of biological ion channels. PMID:24663394

Near-Atomic Resolution Structure of a Highly Neutralizing Fab Bound to Canine Parvovirus.

PubMed

Organtini, Lindsey J; Lee, Hyunwook; Iketani, Sho; Huang, Kai; Ashley, Robert E; Makhov, Alexander M; Conway, James F; Parrish, Colin R; Hafenstein, Susan

2016-11-01

Canine parvovirus (CPV) is a highly contagious pathogen that causes severe disease in dogs and wildlife. Previously, a panel of neutralizing monoclonal antibodies (MAb) raised against CPV was characterized. An antibody fragment (Fab) of MAb E was found to neutralize the virus at low molar ratios. Using recent advances in cryo-electron microscopy (cryo-EM), we determined the structure of CPV in complex with Fab E to 4.1 Å resolution, which allowed de novo building of the Fab structure. The footprint identified was significantly different from the footprint obtained previously from models fitted into lower-resolution maps. Using single-chain variable fragments, we tested antibody residues that control capsid binding. The near-atomic structure also revealed that Fab binding had caused capsid destabilization in regions containing key residues conferring receptor binding and tropism, which suggests a mechanism for efficient virus neutralization by antibody. Furthermore, a general technical approach to solving the structures of small molecules is demonstrated, as binding the Fab to the capsid allowed us to determine the 50-kDa Fab structure by cryo-EM. Using cryo-electron microscopy and new direct electron detector technology, we have solved the 4 Å resolution structure of a Fab molecule bound to a picornavirus capsid. The Fab induced conformational changes in regions of the virus capsid that control receptor binding. The antibody footprint is markedly different from the previous one identified by using a 12 Å structure. This work emphasizes the need for a high-resolution structure to guide mutational analysis and cautions against relying on older low-resolution structures even though they were interpreted with the best methodology available at the time. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Near-Atomic Resolution Structure of a Highly Neutralizing Fab Bound to Canine Parvovirus

PubMed Central

Organtini, Lindsey J.; Lee, Hyunwook; Iketani, Sho; Huang, Kai; Ashley, Robert E.; Makhov, Alexander M.; Conway, James F.

2016-01-01

ABSTRACT Canine parvovirus (CPV) is a highly contagious pathogen that causes severe disease in dogs and wildlife. Previously, a panel of neutralizing monoclonal antibodies (MAb) raised against CPV was characterized. An antibody fragment (Fab) of MAb E was found to neutralize the virus at low molar ratios. Using recent advances in cryo-electron microscopy (cryo-EM), we determined the structure of CPV in complex with Fab E to 4.1 Å resolution, which allowed de novo building of the Fab structure. The footprint identified was significantly different from the footprint obtained previously from models fitted into lower-resolution maps. Using single-chain variable fragments, we tested antibody residues that control capsid binding. The near-atomic structure also revealed that Fab binding had caused capsid destabilization in regions containing key residues conferring receptor binding and tropism, which suggests a mechanism for efficient virus neutralization by antibody. Furthermore, a general technical approach to solving the structures of small molecules is demonstrated, as binding the Fab to the capsid allowed us to determine the 50-kDa Fab structure by cryo-EM. IMPORTANCE Using cryo-electron microscopy and new direct electron detector technology, we have solved the 4 Å resolution structure of a Fab molecule bound to a picornavirus capsid. The Fab induced conformational changes in regions of the virus capsid that control receptor binding. The antibody footprint is markedly different from the previous one identified by using a 12 Å structure. This work emphasizes the need for a high-resolution structure to guide mutational analysis and cautions against relying on older low-resolution structures even though they were interpreted with the best methodology available at the time. PMID:27535057

Deriving high-resolution protein backbone structure propensities from all crystal data using the information maximization device.

PubMed

Solis, Armando D

2014-01-01

The most informative probability distribution functions (PDFs) describing the Ramachandran phi-psi dihedral angle pair, a fundamental descriptor of backbone conformation of protein molecules, are derived from high-resolution X-ray crystal structures using an information-theoretic approach. The Information Maximization Device (IMD) is established, based on fundamental information-theoretic concepts, and then applied specifically to derive highly resolved phi-psi maps for all 20 single amino acid and all 8000 triplet sequences at an optimal resolution determined by the volume of current data. The paper shows that utilizing the latent information contained in all viable high-resolution crystal structures found in the Protein Data Bank (PDB), totaling more than 77,000 chains, permits the derivation of a large number of optimized sequence-dependent PDFs. This work demonstrates the effectiveness of the IMD and the superiority of the resulting PDFs by extensive fold recognition experiments and rigorous comparisons with previously published triplet PDFs. Because it automatically optimizes PDFs, IMD results in improved performance of knowledge-based potentials, which rely on such PDFs. Furthermore, it provides an easy computational recipe for empirically deriving other kinds of sequence-dependent structural PDFs with greater detail and precision. The high-resolution phi-psi maps derived in this work are available for download.

High-Resolution Crystal Structures of Protein Helices Reconciled with Three-Centered Hydrogen Bonds and Multipole Electrostatics

PubMed Central

Kuster, Daniel J.; Liu, Chengyu; Fang, Zheng; Ponder, Jay W.; Marshall, Garland R.

2015-01-01

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.613 α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.613/10-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding. PMID:25894612

High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.

PubMed

Kuster, Daniel J; Liu, Chengyu; Fang, Zheng; Ponder, Jay W; Marshall, Garland R

2015-01-01

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.6(13) α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.6(13/10)-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding.

High resolution Talbot self-imaging applied to structural characterization of self-assembled monolayers of microspheres.

PubMed

Garcia-Sucerquia, J; Alvarez-Palacio, D C; Kreuzer, H J

2008-09-10

We report the observation of the Talbot self-imaging effect in high resolution digital in-line holographic microscopy (DIHM) and its application to structural characterization of periodic samples. Holograms of self-assembled monolayers of micron-sized polystyrene spheres are reconstructed at different image planes. The point-source method of DIHM and the consequent high lateral resolution allows the true image (object) plane to be identified. The Talbot effect is then exploited to improve the evaluation of the pitch of the assembly and to examine defects in its periodicity.

Diagnostic and functional structure of a high-resolution thyroid nodule clinic.

PubMed

Fernández-García, José Carlos; Mancha-Doblas, Isabel; Ortega-Jiménez, María Victoria; Ruiz-Escalante, José Francisco; Castells-Fusté, Ignasi; Tofé-Povedano, Santiago; Argüelles-Jiménez, Iñaki; Tinahones, Francisco José

2014-01-01

Appearance of a thyroid nodule has become a daily occurrence in clinical practice. Adequate thyroid nodule assessment requires several diagnostic tests and multiple medical appointments, which results in a substantial delay in diagnosis. Implementation of a high-resolution thyroid nodule clinic largely avoids these drawbacks by condensing in a single appointment all tests required for adequate evaluation of thyroid nodule. This paper reviews the diagnostic and functional structure of a high-resolution thyroid nodule clinic. Copyright © 2013 SEEN. Published by Elsevier Espana. All rights reserved.

Xenia Mission: Spacecraft Design Concept

NASA Technical Reports Server (NTRS)

Hopkins, R. C.; Johnson, C. L.; Kouveliotou, C.; Jones, D.; Baysinger, M.; Bedsole, T.; Maples, C. C.; Benfield, P. J.; Turner, M.; Capizzo, P.;

High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography

PubMed Central

Boutet, Sébastien; Lomb, Lukas; Williams, Garth J.; Barends, Thomas R. M.; Aquila, Andrew; Doak, R. Bruce; Weierstall, Uwe; DePonte, Daniel P.; Steinbrener, Jan; Shoeman, Robert L.; Messerschmidt, Marc; Barty, Anton; White, Thomas A.; Kassemeyer, Stephan; Kirian, Richard A.; Seibert, M. Marvin; Montanez, Paul A.; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M.; Philipp, Hugh T.; Tate, Mark W.; Hromalik, Marianne; Koerner, Lucas J.; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J.; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y.; Hunter, Mark S.; Johansson, Linda C.; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V.; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A.; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C. H.; Chapman, Henry N.; Schlichting, Ilme

2013-01-01

Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules. PMID:22653729

Resolution of ab initio shapes determined from small-angle scattering.

PubMed

Tuukkanen, Anne T; Kleywegt, Gerard J; Svergun, Dmitri I

2016-11-01

Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models.

Resolution of ab initio shapes determined from small-angle scattering

PubMed Central

Tuukkanen, Anne T.; Kleywegt, Gerard J.; Svergun, Dmitri I.

2016-01-01

Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models. PMID:27840683

High-resolution x-ray imaging using a structured scintillator.

PubMed

Hormozan, Yashar; Sychugov, Ilya; Linnros, Jan

2016-02-01

In this study, the authors introduce a new generation of finely structured scintillators with a very high spatial resolution (a few micrometers) compared to conventional scintillators, yet maintaining a thick absorbing layer for improved detectivity. Their concept is based on a 2D array of high aspect ratio pores which are fabricated by ICP etching, with spacings (pitches) of a few micrometers, on silicon and oxidation of the pore walls. The pores were subsequently filled by melting of powdered CsI(Tl), as the scintillating agent. In order to couple the secondary emitted photons of the back of the scintillator array to a CCD device, having a larger pixel size than the pore pitch, an open optical microscope with adjustable magnification was designed and implemented. By imaging a sharp edge, the authors were able to calculate the modulation transfer function (MTF) of this finely structured scintillator. The x-ray images of individually resolved pores suggest that they have been almost uniformly filled, and the MTF measurements show the feasibility of a few microns spatial resolution imaging, as set by the scintillator pore size. Compared to existing techniques utilizing CsI needles as a structured scintillator, their results imply an almost sevenfold improvement in resolution. Finally, high resolution images, taken by their detector, are presented. The presented work successfully shows the functionality of their detector concept for high resolution imaging and further fabrication developments are most likely to result in higher quantum efficiencies.

High-resolution x-ray imaging using a structured scintillator

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

Hormozan, Yashar, E-mail: hormozan@kth.se; Sychugov, Ilya; Linnros, Jan

2016-02-15

Purpose: In this study, the authors introduce a new generation of finely structured scintillators with a very high spatial resolution (a few micrometers) compared to conventional scintillators, yet maintaining a thick absorbing layer for improved detectivity. Methods: Their concept is based on a 2D array of high aspect ratio pores which are fabricated by ICP etching, with spacings (pitches) of a few micrometers, on silicon and oxidation of the pore walls. The pores were subsequently filled by melting of powdered CsI(Tl), as the scintillating agent. In order to couple the secondary emitted photons of the back of the scintillator arraymore » to a CCD device, having a larger pixel size than the pore pitch, an open optical microscope with adjustable magnification was designed and implemented. By imaging a sharp edge, the authors were able to calculate the modulation transfer function (MTF) of this finely structured scintillator. Results: The x-ray images of individually resolved pores suggest that they have been almost uniformly filled, and the MTF measurements show the feasibility of a few microns spatial resolution imaging, as set by the scintillator pore size. Compared to existing techniques utilizing CsI needles as a structured scintillator, their results imply an almost sevenfold improvement in resolution. Finally, high resolution images, taken by their detector, are presented. Conclusions: The presented work successfully shows the functionality of their detector concept for high resolution imaging and further fabrication developments are most likely to result in higher quantum efficiencies.« less

The robustness of T2 value as a trabecular structural index at multiple spatial resolutions of 7 Tesla MRI.

PubMed

Lee, D K; Song, Y K; Park, B W; Cho, H P; Yeom, J S; Cho, G; Cho, H

2018-04-15

To evaluate the robustness of MR transverse relaxation times of trabecular bone from spin-echo and gradient-echo acquisitions at multiple spatial resolutions of 7 T. The effects of MRI resolutions to T 2 and T2* of trabecular bone were numerically evaluated by Monte Carlo simulations. T 2 , T2*, and trabecular structural indices from multislice multi-echo and UTE acquisitions were measured in defatted human distal femoral condyles on a 7 T scanner. Reference structural indices were extracted from high-resolution microcomputed tomography images. For bovine knee trabecular samples with intact bone marrow, T 2 and T2* were measured by degrading spatial resolutions on a 7 T system. In the defatted trabecular experiment, both T 2 and T2* values showed strong ( |r| > 0.80) correlations with trabecular spacing and number, at a high spatial resolution of 125 µm 3 . The correlations for MR image-segmentation-derived structural indices were significantly degraded ( |r| < 0.50) at spatial resolutions of 250 and 500 µm 3 . The correlations for T2* rapidly dropped ( |r| < 0.50) at a spatial resolution of 500 µm 3 , whereas those for T 2 remained consistently high ( |r| > 0.85). In the bovine trabecular experiments with intact marrow, low-resolution (approximately 1 mm 3 , 2 minutes) T 2 values did not shorten ( |r| > 0.95 with respect to approximately 0.4 mm 3 , 11 minutes) and maintained consistent correlations ( |r| > 0.70) with respect to trabecular spacing (turbo spin echo, 22.5 minutes). T 2 measurements of trabeculae at 7 T are robust with degrading spatial resolution and may be preferable in assessing trabecular spacing index with reduced scan time, when high-resolution 3D micro-MRI is difficult to obtain. © 2018 International Society for Magnetic Resonance in Medicine.

Lipid and glycolipid isomer analyses using ultra-high resolution ion mobility spectrometry separations

DOE PAGES

Wojcik, Roza; Webb, Ian K.; Deng, Liulin; ...

2017-01-18

Understanding the biological mechanisms related to lipids and glycolipids is challenging due to the vast number of possible isomers. Mass spectrometry (MS) measurements are currently the dominant approach for studying and providing detailed information on lipid and glycolipid structures. However, difficulties in distinguishing many structural isomers (e.g. distinct acyl chain positions, double bond locations, as well as glycan isomers) inhibit the understanding of their biological roles. Here we utilized ultra-high resolution ion mobility spectrometry (IMS) separations based upon the use of traveling waves in a serpentine long path length multi-pass Structures for Lossless Manipulations (SLIM) to enhance isomer resolution. Themore » multi-pass arrangement allowed separations ranging from ~16 m (1 pass) to ~470 m (32 passes) to be investigated for the distinction of lipids and glycolipids with extremely small structural differences. Lastly, these ultra-high resolution SLIM IMS-MS analyses provide a foundation for exploring and better understanding isomer specific biological and disease processes.« less

High-resolution solution-state NMR of unfractionated plant cell walls

Treesearch

John Ralph; Fachuang Lu; Hoon Kim; Dino Ress; Daniel J. Yelle; Kenneth E. Hammel; Sally A. Ralph; Bernadette Nanayakkara; Armin Wagner; Takuya Akiyama; Paul F. Schatz; Shawn D. Mansfield; Noritsugu Terashima; Wout Boerjan; Bjorn Sundberg; Mattias Hedenstrom

2009-01-01

Detailed structural studies on the plant cell wall have traditionally been difficult. NMR is one of the preeminent structural tools, but obtaining high-resolution solution-state spectra has typically required fractionation and isolation of components of interest. With recent methods for dissolution of, admittedly, finely divided plant cell wall material, the wall can...

The Application of High-Resolution Electron Microscopy to Problems in Solid State Chemistry: The Exploits of a Peeping TEM.

ERIC Educational Resources Information Center

Eyring, LeRoy

1980-01-01

Describes methods for using the high-resolution electron microscope in conjunction with other tools to reveal the identity and environment of atoms. Problems discussed include the ultimate structure of real crystalline solids including defect structure and the mechanisms of chemical reactions. (CS)

High axial resolution imaging system for large volume tissues using combination of inclined selective plane illumination and mechanical sectioning

PubMed Central

Zhang, Qi; Yang, Xiong; Hu, Qinglei; Bai, Ke; Yin, Fangfang; Li, Ning; Gang, Yadong; Wang, Xiaojun; Zeng, Shaoqun

2017-01-01

To resolve fine structures of biological systems like neurons, it is required to realize microscopic imaging with sufficient spatial resolution in three dimensional systems. With regular optical imaging systems, high lateral resolution is accessible while high axial resolution is hard to achieve in a large volume. We introduce an imaging system for high 3D resolution fluorescence imaging of large volume tissues. Selective plane illumination was adopted to provide high axial resolution. A scientific CMOS working in sub-array mode kept the imaging area in the sample surface, which restrained the adverse effect of aberrations caused by inclined illumination. Plastic embedding and precise mechanical sectioning extended the axial range and eliminated distortion during the whole imaging process. The combination of these techniques enabled 3D high resolution imaging of large tissues. Fluorescent bead imaging showed resolutions of 0.59 μm, 0.47μm, and 0.59 μm in the x, y, and z directions, respectively. Data acquired from the volume sample of brain tissue demonstrated the applicability of this imaging system. Imaging of different depths showed uniform performance where details could be recognized in either the near-soma area or terminal area, and fine structures of neurons could be seen in both the xy and xz sections. PMID:29296503

Numerical viscosity and resolution of high-order weighted essentially nonoscillatory schemes for compressible flows with high Reynolds numbers.

PubMed

Zhang, Yong-Tao; Shi, Jing; Shu, Chi-Wang; Zhou, Ye

2003-10-01

A quantitative study is carried out in this paper to investigate the size of numerical viscosities and the resolution power of high-order weighted essentially nonoscillatory (WENO) schemes for solving one- and two-dimensional Navier-Stokes equations for compressible gas dynamics with high Reynolds numbers. A one-dimensional shock tube problem, a one-dimensional example with parameters motivated by supernova and laser experiments, and a two-dimensional Rayleigh-Taylor instability problem are used as numerical test problems. For the two-dimensional Rayleigh-Taylor instability problem, or similar problems with small-scale structures, the details of the small structures are determined by the physical viscosity (therefore, the Reynolds number) in the Navier-Stokes equations. Thus, to obtain faithful resolution to these small-scale structures, the numerical viscosity inherent in the scheme must be small enough so that the physical viscosity dominates. A careful mesh refinement study is performed to capture the threshold mesh for full resolution, for specific Reynolds numbers, when WENO schemes of different orders of accuracy are used. It is demonstrated that high-order WENO schemes are more CPU time efficient to reach the same resolution, both for the one-dimensional and two-dimensional test problems.

Homology-based hydrogen bond information improves crystallographic structures in the PDB.

PubMed

van Beusekom, Bart; Touw, Wouter G; Tatineni, Mahidhar; Somani, Sandeep; Rajagopal, Gunaretnam; Luo, Jinquan; Gilliland, Gary L; Perrakis, Anastassis; Joosten, Robbie P

2018-03-01

The Protein Data Bank (PDB) is the global archive for structural information on macromolecules, and a popular resource for researchers, teachers, and students, amassing more than one million unique users each year. Crystallographic structure models in the PDB (more than 100,000 entries) are optimized against the crystal diffraction data and geometrical restraints. This process of crystallographic refinement typically ignored hydrogen bond (H-bond) distances as a source of information. However, H-bond restraints can improve structures at low resolution where diffraction data are limited. To improve low-resolution structure refinement, we present methods for deriving H-bond information either globally from well-refined high-resolution structures from the PDB-REDO databank, or specifically from on-the-fly constructed sets of homologous high-resolution structures. Refinement incorporating HOmology DErived Restraints (HODER), improves geometrical quality and the fit to the diffraction data for many low-resolution structures. To make these improvements readily available to the general public, we applied our new algorithms to all crystallographic structures in the PDB: using massively parallel computing, we constructed a new instance of the PDB-REDO databank (https://pdb-redo.eu). This resource is useful for researchers to gain insight on individual structures, on specific protein families (as we demonstrate with examples), and on general features of protein structure using data mining approaches on a uniformly treated dataset. © 2017 The Protein Society.

Improving the accuracy of macromolecular structure refinement at 7 Å resolution.

PubMed

Brunger, Axel T; Adams, Paul D; Fromme, Petra; Fromme, Raimund; Levitt, Michael; Schröder, Gunnar F

2012-06-06

In X-ray crystallography, molecular replacement and subsequent refinement is challenging at low resolution. We compared refinement methods using synchrotron diffraction data of photosystem I at 7.4 Å resolution, starting from different initial models with increasing deviations from the known high-resolution structure. Standard refinement spoiled the initial models, moving them further away from the true structure and leading to high R(free)-values. In contrast, DEN refinement improved even the most distant starting model as judged by R(free), atomic root-mean-square differences to the true structure, significance of features not included in the initial model, and connectivity of electron density. The best protocol was DEN refinement with initial segmented rigid-body refinement. For the most distant initial model, the fraction of atoms within 2 Å of the true structure improved from 24% to 60%. We also found a significant correlation between R(free) values and the accuracy of the model, suggesting that R(free) is useful even at low resolution. Copyright © 2012 Elsevier Ltd. All rights reserved.

Atomic-resolution 3D structure of amyloid β fibrils: The Osaka mutation

DOE PAGES

Schutz, Anne K.; Wall, Joseph; Vagt, Toni; ...

2014-11-13

Despite its central importance for understanding the molecular basis of Alzheimer's disease (AD), high-resolution structural information on amyloid β-peptide (Aβ) fibrils, which are intimately linked with AD, is scarce. We report an atomic-resolution fibril structure of the Aβ 1-40 peptide with the Osaka mutation (E22Δ), associated with early-onset AD. The structure, which differs substantially from all previously proposed models, is based on a large number of unambiguous intra- and intermolecular solid-state NMR distance restraints

Lidar Data Products and Applications Enabled by Conical Scanning

NASA Technical Reports Server (NTRS)

Schwemmer, Geary K.; Miller, David O.; Wilkerson, Thomas D.; Lee, Sang-Woo

2004-01-01

Several new data products and applications for elastic backscatter lidar are achieved using simple conical scanning. Atmospheric boundary layer spatial and temporal structure is revealed with resolution not possible with static pointing lidars. Cloud fractional coverage as a function of altitude is possible with high temporal resolution. Wind profiles are retrieved from the cloud and aerosol structure motions revealed by scanning. New holographic technology will soon allow quasi-conical scanning and push-broom lidar imaging without mechanical scanning, high resolution, on the order of seconds.

High resolution multidetector CT aided tissue analysis and quantification of lung fibrosis

NASA Astrophysics Data System (ADS)

Zavaletta, Vanessa A.; Karwoski, Ronald A.; Bartholmai, Brian; Robb, Richard A.

2006-03-01

Idiopathic pulmonary fibrosis (IPF, also known as Idiopathic Usual Interstitial Pneumontis, pathologically) is a progressive diffuse lung disease which has a median survival rate of less than four years with a prevalence of 15-20/100,000 in the United States. Global function changes are measured by pulmonary function tests and the diagnosis and extent of pulmonary structural changes are typically assessed by acquiring two-dimensional high resolution CT (HRCT) images. The acquisition and analysis of volumetric high resolution Multi-Detector CT (MDCT) images with nearly isotropic pixels offers the potential to measure both lung function and structure. This paper presents a new approach to three dimensional lung image analysis and classification of normal and abnormal structures in lungs with IPF.

Ultra-High Spectral Resolution Observations of Fragmentation in Dark Cloud Cores

NASA Technical Reports Server (NTRS)

Velusamy, T.; Langer, W.; Kuiper, T; Levin, S.; Olsen, E.

1993-01-01

This paper presents new evidence of the fragmentary structure of dense cores in dark clouds using the high resolution spectra of the carbon chain molecule CCS transition (J subscript N = 2 subscript 1 - 1 subscript o) at 22.344033 GHz with 0.008 km s superscript -1 resolution.

A high-resolution cattle CNV map by population-scale genome sequencing

USDA-ARS?s Scientific Manuscript database

Copy Number Variations (CNVs) are common genomic structural variations that have been linked to human diseases and phenotypic traits. Prior studies in cattle have produced low-resolution CNV maps. We constructed a draft, high-resolution map of cattle CNVs based on whole genome sequencing data from 7...

Improvements in High Speed, High Resolution Dynamic Digital Image Correlation for Experimental Evaluation of Composite Drive System Components

NASA Technical Reports Server (NTRS)

Kohlman, Lee W.; Ruggeri, Charles R.; Roberts, Gary D.; Handschuh, Robert Frederick

2013-01-01

Composite materials have the potential to reduce the weight of rotating drive system components. However, these components are more complex to design and evaluate than static structural components in part because of limited ability to acquire deformation and failure initiation data during dynamic tests. Digital image correlation (DIC) methods have been developed to provide precise measurements of deformation and failure initiation for material test coupons and for structures under quasi-static loading. Attempts to use the same methods for rotating components (presented at the AHS International 68th Annual Forum in 2012) are limited by high speed camera resolution, image blur, and heating of the structure by high intensity lighting. Several improvements have been made to the system resulting in higher spatial resolution, decreased image noise, and elimination of heating effects. These improvements include the use of a high intensity synchronous microsecond pulsed LED lighting system, different lenses, and changes in camera configuration. With these improvements, deformation measurements can be made during rotating component tests with resolution comparable to that which can be achieved in static tests

Improvements in High Speed, High Resolution Dynamic Digital Image Correlation for Experimental Evaluation of Composite Drive System Components

NASA Technical Reports Server (NTRS)

Kohlman, Lee; Ruggeri, Charles; Roberts, Gary; Handshuh, Robert

2013-01-01

Composite materials have the potential to reduce the weight of rotating drive system components. However, these components are more complex to design and evaluate than static structural components in part because of limited ability to acquire deformation and failure initiation data during dynamic tests. Digital image correlation (DIC) methods have been developed to provide precise measurements of deformation and failure initiation for material test coupons and for structures under quasi-static loading. Attempts to use the same methods for rotating components (presented at the AHS International 68th Annual Forum in 2012) are limited by high speed camera resolution, image blur, and heating of the structure by high intensity lighting. Several improvements have been made to the system resulting in higher spatial resolution, decreased image noise, and elimination of heating effects. These improvements include the use of a high intensity synchronous microsecond pulsed LED lighting system, different lenses, and changes in camera configuration. With these improvements, deformation measurements can be made during rotating component tests with resolution comparable to that which can be achieved in static tests.

Ultra-high-resolution X-ray structure of proteins.

PubMed

Lecomte, C; Guillot, B; Muzet, N; Pichon-Pesme, V; Jelsch, C

2004-04-01

The constant advances in synchrotron radiation sources and crystallogenesis methods and the impulse of structural genomics projects have brought biocrystallography to a context favorable to subatomic resolution protein and nucleic acid structures. Thus, as soon as such precision can be frequently obtained, the amount of information available in the precise electron density should also be easily and naturally exploited, similarly to the field of small molecule charge density studies. Indeed, the use of a nonspherical model for the atomic electron density in the refinement of subatomic resolution protein structures allows the experimental description of their electrostatic properties. Some methods we have developed and implemented in our multipolar refinement program MoPro for this purpose are presented. Examples of successful applications to several subatomic resolution protein structures, including the 0.66 angstrom resolution human aldose reductase, are described.

High-Resolution of Electron Microscopy of Montmorillonite and Montmorillonite/Epoxy Nanocomposites

DTIC Science & Technology

2005-01-01

AFRL-ML-WP-TP-2006-464 HIGH-RESOLUTION OF ELECTRON MICROSCOPY OF MONTMORILLONITE AND MONTMORILLONITE /EPOXY NANOCOMPOSITES Lawrence F...HIGH-RESOLUTION OF ELECTRON MICROSCOPY OF MONTMORILLONITE AND MONTMORILLONITE /EPOXY NANOCOMPOSITES 5c. PROGRAM ELEMENT NUMBER 62102F 5d...transmission electron microscopy the structure and morphology of montmorillonite (MMT), a material of current interest for use in polymer nanocomposites, was

High-resolution imaging of craniofacial sutures: new tools for understanding the origins of craniosynostoses.

PubMed

Khonsari, R H; Di Rocco, F; Arnaud, E; Sanchez, S; Tafforeau, P

2012-09-01

The developmental genetics and the biomechanics of sutures are well-studied topics, while their microanatomy is still imperfectly known. Here, we aim to investigate the structure of skull vault sutures using a high-resolution imaging device. We used synchrotron X-ray microtomography in order to obtain high-resolution images of skull vault sutures from an extant mammal (the mouse Mus musculus) and from an extinct fish (the placoderm Compagopiscis croucheri). We used segmentation and 3D reconstruction softwares in order to reveal the microanatomy of sutures in these species. The high-resolution images allowed us to study the distribution of osteocytes, the organisation of vascular canals, the shapes of the suture borders, the insertion of Sharpey's fibres, the bone growth lines and the structure of the soft tissues surrounding the sutures. Synchrotron imaging provides new perspectives for the study of the normal microanatomy of sutures. The submicronic resolution of the synchrotron scans gives access to the 3D organisation of structures that were previously only known in 2D, even in normal sutures. The description of anatomical entities such as vascular canals and Sharpey's fibres in abnormally fused sutures would be of interest in the understanding of craniosynostoses.

Apolipoprotein AI tertiary structures determine stability and phospholipid-binding activity of discoidal high-density lipoprotein particles of different sizes

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

Chen, Bin; Ren, Xuefeng; Neville, Tracey

2009-05-18

Human high-density lipoprotein (HDL) plays a key role in the reverse cholesterol transport pathway that delivers excess cholesterol back to the liver for clearance. In vivo, HDL particles vary in size, shape and biological function. The discoidal HDL is a 140-240 kDa, disk-shaped intermediate of mature HDL. During mature spherical HDL formation, discoidal HDLs play a key role in loading cholesterol ester onto the HDL particles by activating the enzyme, lecithin:cholesterol acyltransferase (LCAT). One of the major problems for high-resolution structural studies of discoidal HDL is the difficulty in obtaining pure and, foremost, homogenous sample. We demonstrate here that themore » commonly used cholate dialysis method for discoidal HDL preparation usually contains 5-10% lipid-poor apoAI that significantly interferes with the high-resolution structural analysis of discoidal HDL using biophysical methods. Using an ultracentrifugation method, we quickly removed lipid-poor apoAI. We also purified discoidal reconstituted HDL (rHDL) into two pure discoidal HDL species of different sizes that are amendable for high-resolution structural studies. A small rHDL has a diameter of 7.6 nm, and a large rHDL has a diameter of 9.8 nm. We show that these two different sizes of discoidal HDL particles display different stability and phospholipid-binding activity. Interestingly, these property/functional differences are independent from the apoAI -helical secondary structure, but are determined by the tertiary structural difference of apoAI on different discoidal rHDL particles, as evidenced by two-dimensional NMR and negative stain electron microscopy data. Our result further provides the first high-resolution NMR data, demonstrating a promise of structural determination of discoidal HDL at atomic resolution using a combination of NMR and other biophysical techniques.« less

High-resolution anatomy of the human brain stem using 7-T MRI: improved detection of inner structures and nerves?

PubMed

Gizewski, Elke R; Maderwald, Stefan; Linn, Jennifer; Dassinger, Benjamin; Bochmann, Katja; Forsting, Michael; Ladd, Mark E

2014-03-01

The purpose of this paper is to assess the value of 7 Tesla (7 T) MRI for the depiction of brain stem and cranial nerve (CN) anatomy. Six volunteers were examined at 7 T using high-resolution SWI, MPRAGE, MP2RAGE, 3D SPACE T2, T2, and PD images to establish scanning parameters targeted at optimizing spatial resolution. Direct comparisons between 3 and 7 T were performed in two additional subjects using the finalized sequences (3 T: T2, PD, MPRAGE, SWAN; 7 T: 3D T2, MPRAGE, SWI, MP2RAGE). Artifacts and the depiction of structures were evaluated by two neuroradiologists using a standardized score sheet. Sequences could be established for high-resolution 7 T imaging even in caudal cranial areas. High in-plane resolution T2, PD, and SWI images provided depiction of inner brain stem structures such as pons fibers, raphe, reticular formation, nerve roots, and periaqueductal gray. MPRAGE and MP2RAGE provided clear depiction of the CNs. 3D T2 images improved depiction of inner brain structure in comparison to T2 images at 3 T. Although the 7-T SWI sequence provided improved contrast to some inner structures, extended areas were influenced by artifacts due to image disturbances from susceptibility differences. Seven-tesla imaging of basal brain areas is feasible and might have significant impact on detection and diagnosis in patients with specific diseases, e.g., trigeminal pain related to affection of the nerve root. Some inner brain stem structures can be depicted at 3 T, but certain sequences at 7 T, in particular 3D SPACE T2, are superior in producing anatomical in vivo images of deep brain stem structures.

Mobile and embedded fast high resolution image stitching for long length rectangular monochromatic objects with periodic structure

NASA Astrophysics Data System (ADS)

Limonova, Elena; Tropin, Daniil; Savelyev, Boris; Mamay, Igor; Nikolaev, Dmitry

2018-04-01

In this paper we describe stitching protocol, which allows to obtain high resolution images of long length monochromatic objects with periodic structure. This protocol can be used for long length documents or human-induced objects in satellite images of uninhabitable regions like Arctic regions. The length of such objects can reach notable values, while modern camera sensors have limited resolution and are not able to provide good enough image of the whole object for further processing, e.g. using in OCR system. The idea of the proposed method is to acquire a video stream containing full object in high resolution and use image stitching. We expect the scanned object to have straight boundaries and periodic structure, which allow us to introduce regularization to the stitching problem and adapt algorithm for limited computational power of mobile and embedded CPUs. With the help of detected boundaries and structure we estimate homography between frames and use this information to reduce complexity of stitching. We demonstrate our algorithm on mobile device and show image processing speed of 2 fps on Samsung Exynos 5422 processor

IMART software for correction of motion artifacts in images collected in intravital microscopy

PubMed Central

Dunn, Kenneth W; Lorenz, Kevin S; Salama, Paul; Delp, Edward J

2014-01-01

Intravital microscopy is a uniquely powerful tool, providing the ability to characterize cell and organ physiology in the natural context of the intact, living animal. With the recent development of high-resolution microscopy techniques such as confocal and multiphoton microscopy, intravital microscopy can now characterize structures at subcellular resolution and capture events at sub-second temporal resolution. However, realizing the potential for high resolution requires remarkable stability in the tissue. Whereas the rigid structure of the skull facilitates high-resolution imaging of the brain, organs of the viscera are free to move with respiration and heartbeat, requiring additional apparatus for immobilization. In our experience, these methods are variably effective, so that many studies are compromised by residual motion artifacts. Here we demonstrate the use of IMART, a software tool for removing motion artifacts from intravital microscopy images collected in time series or in three dimensions. PMID:26090271

Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling

PubMed Central

Baker, Matthew L.; Hryc, Corey F.; Zhang, Qinfen; Wu, Weimin; Jakana, Joanita; Haase-Pettingell, Cameron; Afonine, Pavel V.; Adams, Paul D.; King, Jonathan A.; Jiang, Wen; Chiu, Wah

2013-01-01

High-resolution structures of viruses have made important contributions to modern structural biology. Bacteriophages, the most diverse and abundant organisms on earth, replicate and infect all bacteria and archaea, making them excellent potential alternatives to antibiotics and therapies for multidrug-resistant bacteria. Here, we improved upon our previous electron cryomicroscopy structure of Salmonella bacteriophage epsilon15, achieving a resolution sufficient to determine the tertiary structures of both gp7 and gp10 protein subunits that form the T = 7 icosahedral lattice. This study utilizes recently established best practice for near-atomic to high-resolution (3–5 Å) electron cryomicroscopy data evaluation. The resolution and reliability of the density map were cross-validated by multiple reconstructions from truly independent data sets, whereas the models of the individual protein subunits were validated adopting the best practices from X-ray crystallography. Some sidechain densities are clearly resolved and show the subunit–subunit interactions within and across the capsomeres that are required to stabilize the virus. The presence of the canonical phage and jellyroll viral protein folds, gp7 and gp10, respectively, in the same virus suggests that epsilon15 may have emerged more recently relative to other bacteriophages. PMID:23840063

Micromirror structured illumination microscope for high-speed in vivo drosophila brain imaging.

PubMed

Masson, A; Pedrazzani, M; Benrezzak, S; Tchenio, P; Preat, T; Nutarelli, D

2014-01-27

Genetic tools and especially genetically encoded fluorescent reporters have given a special place to optical microscopy in drosophila neurobiology research. In order to monitor neural networks activity, high speed and sensitive techniques, with high spatial resolution are required. Structured illumination microscopies are wide-field approaches with optical sectioning ability. Despite the large progress made with the introduction of the HiLo principle, they did not meet the criteria of speed and/or spatial resolution for drosophila brain imaging. We report on a new implementation that took advantage of micromirror matrix technology to structure the illumination. Thus, we showed that the developed instrument exhibits a spatial resolution close to that of confocal microscopy but it can record physiological responses with a speed improved by more than an order a magnitude.

Microsphere-assisted super-resolution imaging with enlarged numerical aperture by semi-immersion

NASA Astrophysics Data System (ADS)

Wang, Fengge; Yang, Songlin; Ma, Huifeng; Shen, Ping; Wei, Nan; Wang, Meng; Xia, Yang; Deng, Yun; Ye, Yong-Hong

2018-01-01

Microsphere-assisted imaging is an extraordinary simple technology that can obtain optical super-resolution under white-light illumination. Here, we introduce a method to improve the resolution of a microsphere lens by increasing its numerical aperture. In our proposed structure, BaTiO3 glass (BTG) microsphere lenses are semi-immersed in a S1805 layer with a refractive index of 1.65, and then, the semi-immersed microspheres are fully embedded in an elastomer with an index of 1.4. We experimentally demonstrate that this structure, in combination with a conventional optical microscope, can clearly resolve a two-dimensional 200-nm-diameter hexagonally close-packed (hcp) silica microsphere array. On the contrary, the widely used structure where BTG microsphere lenses are fully immersed in a liquid or elastomer cannot even resolve a 250-nm-diameter hcp silica microsphere array. The improvement in resolution through the proposed structure is due to an increase in the effective numerical aperture by semi-immersing BTG microsphere lenses in a high-refractive-index S1805 layer. Our results will inform on the design of microsphere-based high-resolution imaging systems.

High-resolution structure of infectious prion protein: the final frontier

PubMed Central

Diaz-Espinoza, Rodrigo; Soto, Claudio

2014-01-01

Prions are the proteinaceous infectious agents responsible for the transmission of prion diseases. The main or sole component of prions is the misfolded prion protein (PrPSc), which is able to template the conversion of the host’s natively folded form of the protein (PrPC). The detailed mechanism of prion replication and the high-resolution structure of PrPSc are unknown. The currently available information on PrPSc structure comes mostly from low-resolution biophysical techniques, which have resulted in quite divergent models. Recent advances in the production of infectious prions, using very pure recombinant protein, offer new hope for PrPSc structural studies. This review highlights the importance of, challenges for and recent progress toward elucidating the elusive structure of PrPSc, arguably the major pending milestone to reach in understanding prions. PMID:22472622

A brain MRI atlas of the common squirrel monkey, Saimiri sciureus

NASA Astrophysics Data System (ADS)

Gao, Yurui; Schilling, Kurt G.; Khare, Shweta P.; Panda, Swetasudha; Choe, Ann S.; Stepniewska, Iwona; Li, Xia; Ding, Zhoahua; Anderson, Adam; Landman, Bennett A.

2014-03-01

The common squirrel monkey, Saimiri sciureus, is a New World monkey with functional and microstructural organization of central nervous system similar to that of humans. It is one of the most commonly used South American primates in biomedical research. Unlike its Old World macaque cousins, no digital atlases have described the organization of the squirrel monkey brain. Here, we present a multi-modal magnetic resonance imaging (MRI) atlas constructed from the brain of an adult female squirrel monkey. In vivo MRI acquisitions include high resolution T2 structural imaging and low resolution diffusion tensor imaging. Ex vivo MRI acquisitions include high resolution T2 structural imaging and high resolution diffusion tensor imaging. Cortical regions were manually annotated on the co-registered volumes based on published histological sections.

High-resolution resistivity imaging of marine gas hydrate structures by combined inversion of CSEM towed and ocean-bottom receiver data

NASA Astrophysics Data System (ADS)

Attias, Eric; Weitemeyer, Karen; Hölz, Sebastian; Naif, Samer; Minshull, Tim A.; Best, Angus I.; Haroon, Amir; Jegen-Kulcsar, Marion; Berndt, Christian

2018-06-01

We present high-resolution resistivity imaging of gas hydrate pipe-like structures, as derived from marine controlled-source electromagnetic (CSEM) inversions that combine towed and ocean-bottom electric field receiver data, acquired from the Nyegga region, offshore Norway. Two-dimensional CSEM inversions applied to the towed receiver data detected four new prominent vertical resistive features that are likely gas hydrate structures, located in proximity to a major gas hydrate pipe-like structure, known as the CNE03 pockmark. The resistivity model resulting from the CSEM data inversion resolved the CNE03 hydrate structure in high resolution, as inferred by comparison to seismically constrained inversions. Our results indicate that shallow gas hydrate vertical features can be delineated effectively by inverting both ocean-bottom and towed receiver CSEM data simultaneously. The approach applied here can be utilised to map and monitor seafloor mineralisation, freshwater reservoirs, CO2 sequestration sites and near-surface geothermal systems.

The hydration structure at yttria-stabilized cubic zirconia (110)-water interface with sub-Ångström resolution

DOE PAGES

Hou, Binyang; Kim, Seunghyun; Kim, Taeho; ...

2016-06-15

The interfacial hydration structure of yttria-stabilized cubic zirconia (110) surface in contact with water was determined with ~0.5 Å resolution by high-resolution X-ray reflectivity measurement. The terminal layer shows a reduced electron density compared to the following substrate lattice layers, which indicates there are additional defects generated by metal depletion as well as intrinsic oxygen vacancies, both of which are apparently filled by water species. Above this top surface layer, two additional adsorbed layers are observed forming a characteristic interfacial hydration structure. The first adsorbed layer shows abnormally high density as pure water and likely includes metal species, whereas themore » second layer consists of pure water. The observed interfacial hydration structure seems responsible for local equilibration of the defective surface in water and eventually regulating the long-term degradation processes. As a result, the multitude of water interactions with the zirconia surface results in the complex but highly ordered interfacial structure constituting the reaction front.« less

ATOMIC RESOLUTION CRYO ELECTRON MICROSCOPY OF MACROMOLECULAR COMPLEXES

PubMed Central

ZHOU, Z. HONG

2013-01-01

Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their “native,” noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines. PMID:21501817

Blind identification of full-field vibration modes of output-only structures from uniformly-sampled, possibly temporally-aliased (sub-Nyquist), video measurements

NASA Astrophysics Data System (ADS)

Yang, Yongchao; Dorn, Charles; Mancini, Tyler; Talken, Zachary; Nagarajaiah, Satish; Kenyon, Garrett; Farrar, Charles; Mascareñas, David

2017-03-01

Enhancing the spatial and temporal resolution of vibration measurements and modal analysis could significantly benefit dynamic modelling, analysis, and health monitoring of structures. For example, spatially high-density mode shapes are critical for accurate vibration-based damage localization. In experimental or operational modal analysis, higher (frequency) modes, which may be outside the frequency range of the measurement, contain local structural features that can improve damage localization as well as the construction and updating of the modal-based dynamic model of the structure. In general, the resolution of vibration measurements can be increased by enhanced hardware. Traditional vibration measurement sensors such as accelerometers have high-frequency sampling capacity; however, they are discrete point-wise sensors only providing sparse, low spatial sensing resolution measurements, while dense deployment to achieve high spatial resolution is expensive and results in the mass-loading effect and modification of structure's surface. Non-contact measurement methods such as scanning laser vibrometers provide high spatial and temporal resolution sensing capacity; however, they make measurements sequentially that requires considerable acquisition time. As an alternative non-contact method, digital video cameras are relatively low-cost, agile, and provide high spatial resolution, simultaneous, measurements. Combined with vision based algorithms (e.g., image correlation or template matching, optical flow, etc.), video camera based measurements have been successfully used for experimental and operational vibration measurement and subsequent modal analysis. However, the sampling frequency of most affordable digital cameras is limited to 30-60 Hz, while high-speed cameras for higher frequency vibration measurements are extremely costly. This work develops a computational algorithm capable of performing vibration measurement at a uniform sampling frequency lower than what is required by the Shannon-Nyquist sampling theorem for output-only modal analysis. In particular, the spatio-temporal uncoupling property of the modal expansion of structural vibration responses enables a direct modal decoupling of the temporally-aliased vibration measurements by existing output-only modal analysis methods, yielding (full-field) mode shapes estimation directly. Then the signal aliasing properties in modal analysis is exploited to estimate the modal frequencies and damping ratios. The proposed method is validated by laboratory experiments where output-only modal identification is conducted on temporally-aliased acceleration responses and particularly the temporally-aliased video measurements of bench-scale structures, including a three-story building structure and a cantilever beam.

Unraveling the martian water cycle with high-resolution global climate simulations

NASA Astrophysics Data System (ADS)

Pottier, Alizée; Forget, François; Montmessin, Franck; Navarro, Thomas; Spiga, Aymeric; Millour, Ehouarn; Szantai, André; Madeleine, Jean-Baptiste

2017-07-01

Global climate modeling of the Mars water cycle is usually performed at relatively coarse resolution (200 - 300km), which may not be sufficient to properly represent the impact of waves, fronts, topography effects on the detailed structure of clouds and surface ice deposits. Here, we present new numerical simulations of the annual water cycle performed at a resolution of 1° × 1° (∼ 60 km in latitude). The model includes the radiative effects of clouds, whose influence on the thermal structure and atmospheric dynamics is significant, thus we also examine simulations with inactive clouds to distinguish the direct impact of resolution on circulation and winds from the indirect impact of resolution via water ice clouds. To first order, we find that the high resolution does not dramatically change the behavior of the system, and that simulations performed at ∼ 200 km resolution capture well the behavior of the simulated water cycle and Mars climate. Nevertheless, a detailed comparison between high and low resolution simulations, with reference to observations, reveal several significant changes that impact our understanding of the water cycle active today on Mars. The key northern cap edge dynamics are affected by an increase in baroclinic wave strength, with a complication of northern summer dynamics. South polar frost deposition is modified, with a westward longitudinal shift, since southern dynamics are also influenced. Baroclinic wave mode transitions are observed. New transient phenomena appear, like spiral and streak clouds, already documented in the observations. Atmospheric circulation cells in the polar region exhibit a large variability and are fine structured, with slope winds. Most modeled phenomena affected by high resolution give a picture of a more turbulent planet, inducing further variability. This is challenging for long-period climate studies.

Probing the Complexities of Structural Changes in Layered Oxide Cathode Materials for Li-Ion Batteries during Fast Charge-Discharge Cycling and Heating.

PubMed

Hu, Enyuan; Wang, Xuelong; Yu, Xiqian; Yang, Xiao-Qing

2018-02-20

The rechargeable lithium-ion battery (LIB) is the most promising energy storage system to power electric vehicles with high energy density and long cycling life. However, in order to meet customers' demands for fast charging, the power performances of current LIBs need to be improved. From the cathode aspect, layer-structured cathode materials are widely used in today's market and will continue to play important roles in the near future. The high rate capability of layered cathode materials during charging and discharging is critical to the power performance of the whole cell and the thermal stability is closely related to the safety issues. Therefore, the in-depth understanding of structural changes of layered cathode materials during high rate charging/discharging and the thermal stability during heating are essential in developing new materials and improving current materials. Since structural changes take place from the atomic level to the whole electrode level, combination of characterization techniques covering multilength scales is quite important. In many cases, this means using comprehensive tools involving diffraction, spectroscopy, and imaging to differentiate the surface from the bulk and to obtain structural/chemical information with different levels of spatial resolution. For example, hard X-ray spectroscopy can yield the bulk information and soft X-ray spectroscopy can give the surface information; X-ray based imaging techniques can obtain spatial resolution of tens of nanometers, and electron-based microcopy can go to angstroms. In addition to challenges associated with different spatial resolution, the dynamic nature of structural changes during high rate cycling and heating requires characterization tools to have the capability of collecting high quality data in a time-resolved fashion. Thanks to the advancement in synchrotron based techniques and high-resolution electron microscopy, high temporal and spatial resolutions can now be achieved. In this Account, we focus on the recent works studying kinetic and thermal properties of layer-structured cathode materials, especially the structural changes during high rate cycling and the thermal stability during heating. Advanced characterization techniques relating to the rate capability and thermal stability will be introduced. The different structure evolution behavior of cathode materials cycled at high rate will be compared with that cycled at low rate. Different response of individual transition metals and the inhomogeneity in chemical distribution will be discussed. For the thermal stability, the relationship between structural changes and oxygen release will be emphatically pointed out. In all these studies being reviewed, advanced characterization techniques are critically applied to reveal complexities at multiscale in layer-structured cathode materials.

The Fundamental Structure of Coronal Loops

NASA Technical Reports Server (NTRS)

Winebarger, Amy; Warren, Harry; Cirtain, Jonathan; Kobayashi, Ken; Korreck, Kelly; Golub, Leon; Kuzin, Sergey; Walsh, Robert; DePontieu, Bart; Title, Alan;

High spatial resolution mapping of folds and fractures using Unmanned Aerial Vehicle (UAV) photogrammetry

NASA Astrophysics Data System (ADS)

Cruden, A. R.; Vollgger, S.

2016-12-01

The emerging capability of UAV photogrammetry combines a simple and cost-effective method to acquire digital aerial images with advanced computer vision algorithms that compute spatial datasets from a sequence of overlapping digital photographs from various viewpoints. Depending on flight altitude and camera setup, sub-centimeter spatial resolution orthophotographs and textured dense point clouds can be achieved. Orientation data can be collected for detailed structural analysis by digitally mapping such high-resolution spatial datasets in a fraction of time and with higher fidelity compared to traditional mapping techniques. Here we describe a photogrammetric workflow applied to a structural study of folds and fractures within alternating layers of sandstone and mudstone at a coastal outcrop in SE Australia. We surveyed this location using a downward looking digital camera mounted on commercially available multi-rotor UAV that autonomously followed waypoints at a set altitude and speed to ensure sufficient image overlap, minimum motion blur and an appropriate resolution. The use of surveyed ground control points allowed us to produce a geo-referenced 3D point cloud and an orthophotograph from hundreds of digital images at a spatial resolution < 10 mm per pixel, and cm-scale location accuracy. Orientation data of brittle and ductile structures were semi-automatically extracted from these high-resolution datasets using open-source software. This resulted in an extensive and statistically relevant orientation dataset that was used to 1) interpret the progressive development of folds and faults in the region, and 2) to generate a 3D structural model that underlines the complex internal structure of the outcrop and quantifies spatial variations in fold geometries. Overall, our work highlights how UAV photogrammetry can contribute to new insights in structural analysis.

Long Time-lapse Nanoscopy with Spontaneously Blinking Membrane Probes

PubMed Central

Takakura, Hideo; Zhang, Yongdeng; Erdmann, Roman S.; Thompson, Alexander D.; Lin, Yu; McNellis, Brian; Rivera-Molina, Felix; Uno, Shin-nosuke; Kamiya, Mako; Urano, Yasuteru; Rothman, James E.; Bewersdorf, Joerg; Schepartz, Alanna; Toomre, Derek

2017-01-01

Long time-lapse, diffraction-unlimited super-resolution imaging of cellular structures and organelles in living cells is highly challenging, as it requires dense labeling, bright, highly photostable dyes, and non-toxic conditions. We developed a set of high-density, environment-sensitive (HIDE) membrane probes based on HMSiR that assemble in situ and enable long time-lapse, live cell nanoscopy of discrete cellular structures and organelles with high spatio-temporal resolution. HIDE-enabled nanoscopy movies are up to 50x longer than movies obtained with labeled proteins, reveal the 2D dynamics of the mitochondria, plasma membrane, and filopodia, and the 2D and 3D dynamics of the endoplasmic reticulum in living cells. These new HIDE probes also facilitate the acquisition of live cell, two-color, super-resolution images, greatly expanding the utility of nanoscopy to visualize processes and structures in living cells. PMID:28671662

High resolution axicon-based endoscopic FD OCT imaging with a large depth range

NASA Astrophysics Data System (ADS)

Lee, Kye-Sung; Hurley, William; Deegan, John; Dean, Scott; Rolland, Jannick P.

2010-02-01

Endoscopic imaging in tubular structures, such as the tracheobronchial tree, could benefit from imaging optics with an extended depth of focus (DOF). This optics could accommodate for varying sizes of tubular structures across patients and along the tree within a single patient. In the paper, we demonstrate an extended DOF without sacrificing resolution showing rotational images in biological tubular samples with 2.5 μm axial resolution, 10 ìm lateral resolution, and > 4 mm depth range using a custom designed probe.

Localization microscopy of DNA in situ using Vybrant{sup ®} DyeCycle™ Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution

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

Żurek-Biesiada, Dominika; Szczurek, Aleksander T.; Prakash, Kirti

Higher order chromatin structure is not only required to compact and spatially arrange long chromatids within a nucleus, but have also important functional roles, including control of gene expression and DNA processing. However, studies of chromatin nanostructures cannot be performed using conventional widefield and confocal microscopy because of the limited optical resolution. Various methods of superresolution microscopy have been described to overcome this difficulty, like structured illumination and single molecule localization microscopy. We report here that the standard DNA dye Vybrant{sup ®} DyeCycle™ Violet can be used to provide single molecule localization microscopy (SMLM) images of DNA in nuclei ofmore » fixed mammalian cells. This SMLM method enabled optical isolation and localization of large numbers of DNA-bound molecules, usually in excess of 10{sup 6} signals in one cell nucleus. The technique yielded high-quality images of nuclear DNA density, revealing subdiffraction chromatin structures of the size in the order of 100 nm; the interchromatin compartment was visualized at unprecedented optical resolution. The approach offers several advantages over previously described high resolution DNA imaging methods, including high specificity, an ability to record images using a single wavelength excitation, and a higher density of single molecule signals than reported in previous SMLM studies. The method is compatible with DNA/multicolor SMLM imaging which employs simple staining methods suited also for conventional optical microscopy. - Highlights: • Super-resolution imaging of nuclear DNA with Vybrant Violet and blue excitation. • 90nm resolution images of DNA structures in optically thick eukaryotic nuclei. • Enhanced resolution confirms the existence of DNA-free regions inside the nucleus. • Optimized imaging conditions enable multicolor super-resolution imaging.« less

Super-resolution differential interference contrast microscopy by structured illumination.

PubMed

Chen, Jianling; Xu, Yan; Lv, Xiaohua; Lai, Xiaomin; Zeng, Shaoqun

2013-01-14

We propose a structured illumination differential interference contrast (SI-DIC) microscopy, breaking the diffraction resolution limit of differential interference contrast (DIC) microscopy. SI-DIC extends the bandwidth of coherent transfer function of the DIC imaging system, thus the resolution is improved. With 0.8 numerical aperture condenser and objective, the reconstructed SI-DIC image of 53 nm polystyrene beads reveals lateral resolution of approximately 190 nm, doubling that of the conventional DIC image. We also demonstrate biological observations of label-free cells with improved spatial resolution. The SI-DIC microscopy can provide sub-diffraction resolution and high contrast images with marker-free specimens, and has the potential for achieving sub-diffraction resolution quantitative phase imaging.

Advances in high-resolution imaging--techniques for three-dimensional imaging of cellular structures.

PubMed

Lidke, Diane S; Lidke, Keith A

2012-06-01

A fundamental goal in biology is to determine how cellular organization is coupled to function. To achieve this goal, a better understanding of organelle composition and structure is needed. Although visualization of cellular organelles using fluorescence or electron microscopy (EM) has become a common tool for the cell biologist, recent advances are providing a clearer picture of the cell than ever before. In particular, advanced light-microscopy techniques are achieving resolutions below the diffraction limit and EM tomography provides high-resolution three-dimensional (3D) images of cellular structures. The ability to perform both fluorescence and electron microscopy on the same sample (correlative light and electron microscopy, CLEM) makes it possible to identify where a fluorescently labeled protein is located with respect to organelle structures visualized by EM. Here, we review the current state of the art in 3D biological imaging techniques with a focus on recent advances in electron microscopy and fluorescence super-resolution techniques.

Realistic 3D computer model of the gerbil middle ear, featuring accurate morphology of bone and soft tissue structures.

PubMed

Buytaert, Jan A N; Salih, Wasil H M; Dierick, Manual; Jacobs, Patric; Dirckx, Joris J J

2011-12-01

In order to improve realism in middle ear (ME) finite-element modeling (FEM), comprehensive and precise morphological data are needed. To date, micro-scale X-ray computed tomography (μCT) recordings have been used as geometric input data for FEM models of the ME ossicles. Previously, attempts were made to obtain these data on ME soft tissue structures as well. However, due to low X-ray absorption of soft tissue, quality of these images is limited. Another popular approach is using histological sections as data for 3D models, delivering high in-plane resolution for the sections, but the technique is destructive in nature and registration of the sections is difficult. We combine data from high-resolution μCT recordings with data from high-resolution orthogonal-plane fluorescence optical-sectioning microscopy (OPFOS), both obtained on the same gerbil specimen. State-of-the-art μCT delivers high-resolution data on the 3D shape of ossicles and other ME bony structures, while the OPFOS setup generates data of unprecedented quality both on bone and soft tissue ME structures. Each of these techniques is tomographic and non-destructive and delivers sets of automatically aligned virtual sections. The datasets coming from different techniques need to be registered with respect to each other. By combining both datasets, we obtain a complete high-resolution morphological model of all functional components in the gerbil ME. The resulting 3D model can be readily imported in FEM software and is made freely available to the research community. In this paper, we discuss the methods used, present the resulting merged model, and discuss the morphological properties of the soft tissue structures, such as muscles and ligaments.

Evaluation of variability in high-resolution protein structures by global distance scoring.

PubMed

Anzai, Risa; Asami, Yoshiki; Inoue, Waka; Ueno, Hina; Yamada, Koya; Okada, Tetsuji

2018-01-01

Systematic analysis of the statistical and dynamical properties of proteins is critical to understanding cellular events. Extraction of biologically relevant information from a set of high-resolution structures is important because it can provide mechanistic details behind the functional properties of protein families, enabling rational comparison between families. Most of the current structural comparisons are pairwise-based, which hampers the global analysis of increasing contents in the Protein Data Bank. Additionally, pairing of protein structures introduces uncertainty with respect to reproducibility because it frequently accompanies other settings for superimposition. This study introduces intramolecular distance scoring for the global analysis of proteins, for each of which at least several high-resolution structures are available. As a pilot study, we have tested 300 human proteins and showed that the method is comprehensively used to overview advances in each protein and protein family at the atomic level. This method, together with the interpretation of the model calculations, provide new criteria for understanding specific structural variation in a protein, enabling global comparison of the variability in proteins from different species.

High-resolution dynamic 31 P-MRSI using a low-rank tensor model.

PubMed

Ma, Chao; Clifford, Bryan; Liu, Yuchi; Gu, Yuning; Lam, Fan; Yu, Xin; Liang, Zhi-Pei

2017-08-01

To develop a rapid 31 P-MRSI method with high spatiospectral resolution using low-rank tensor-based data acquisition and image reconstruction. The multidimensional image function of 31 P-MRSI is represented by a low-rank tensor to capture the spatial-spectral-temporal correlations of data. A hybrid data acquisition scheme is used for sparse sampling, which consists of a set of "training" data with limited k-space coverage to capture the subspace structure of the image function, and a set of sparsely sampled "imaging" data for high-resolution image reconstruction. An explicit subspace pursuit approach is used for image reconstruction, which estimates the bases of the subspace from the "training" data and then reconstructs a high-resolution image function from the "imaging" data. We have validated the feasibility of the proposed method using phantom and in vivo studies on a 3T whole-body scanner and a 9.4T preclinical scanner. The proposed method produced high-resolution static 31 P-MRSI images (i.e., 6.9 × 6.9 × 10 mm 3 nominal resolution in a 15-min acquisition at 3T) and high-resolution, high-frame-rate dynamic 31 P-MRSI images (i.e., 1.5 × 1.5 × 1.6 mm 3 nominal resolution, 30 s/frame at 9.4T). Dynamic spatiospectral variations of 31 P-MRSI signals can be efficiently represented by a low-rank tensor. Exploiting this mathematical structure for data acquisition and image reconstruction can lead to fast 31 P-MRSI with high resolution, frame-rate, and SNR. Magn Reson Med 78:419-428, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

AVHRR/1-FM Advanced Very High Resolution Radiometer

NASA Technical Reports Server (NTRS)

1979-01-01

The advanced very high resolution radiometer is discussed. The program covers design, construction, and test of a breadboard model, engineering model, protoflight model, mechanical/structural model, and a life test model. Special bench test and calibration equipment was developed for use on the program. The flight model program objectives were to fabricate, assemble and test four of the advanced very high resolution radiometers along with a bench cooler and collimator.

High resolution studies of the solar X-ray corona from Aerobee rockets

NASA Technical Reports Server (NTRS)

Davis, J. M.; Haggerty, R.; Krieger, A. S.; Manko, H.; Sherman, G.; Ting, J. W. S.; Vaiana, G. S.

1973-01-01

The research in high resolution solar X-ray astronomy is reported. The payload for the Aerobee 150 launch vehicle, which included a 23 cm diameter mirror whose polished surface was a nickel-phosphorus alloy is discussed along with the high resolution measurements, by Flight 13.028 CS, of the temperature and density structure of the lower corona. Flight 13.029 CS is also discussed.

Predicting nucleic acid binding interfaces from structural models of proteins

PubMed Central

Dror, Iris; Shazman, Shula; Mukherjee, Srayanta; Zhang, Yang; Glaser, Fabian; Mandel-Gutfreund, Yael

2011-01-01

The function of DNA- and RNA-binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However the main pitfall of various structure-based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high-resolution three dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I-TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches extracted from high-resolution structures. Furthermore, by testing our pipeline on a set of 55 known nucleic acid binding proteins for which I-TASSER produces high-quality models, we show that the method accurately identifies the nucleic acids binding interface on structural models of proteins. Employing a combined patch approach we show that patches extracted from an ensemble of models better predicts the real nucleic acid binding interfaces compared to patches extracted from independent models. Overall, these results suggest that combining information from a collection of low-resolution structural models could be a valuable approach for functional annotation. We suggest that our method will be further applicable for predicting other functional surfaces of proteins with unknown structure. PMID:22086767

High-resolution 3D imaging of polymerized photonic crystals by lab-based x-ray nanotomography with 50-nm resolution

NASA Astrophysics Data System (ADS)

Yin, Leilei; Chen, Ying-Chieh; Gelb, Jeff; Stevenson, Darren M.; Braun, Paul A.

2010-09-01

High resolution x-ray computed tomography is a powerful non-destructive 3-D imaging method. It can offer superior resolution on objects that are opaque or low contrast for optical microscopy. Synchrotron based x-ray computed tomography systems have been available for scientific research, but remain difficult to access for broader users. This work introduces a lab-based high-resolution x-ray nanotomography system with 50nm resolution in absorption and Zernike phase contrast modes. Using this system, we have demonstrated high quality 3-D images of polymerized photonic crystals which have been analyzed for band gap structures. The isotropic volumetric data shows excellent consistency with other characterization results.

Evaluation and development of unmanned aircraft (UAV) for UDOT needs.

DOT National Transportation Integrated Search

2012-05-01

This research involved the use of high-resolution aerial photography obtained from Unmanned Aerial Vehicles (UAV) to aid UDOT in monitoring and documenting State Roadway structures and associated issues. Using geo-referenced UAV high resolution aeria...

Localization-based super-resolution imaging of cellular structures.

PubMed

Kanchanawong, Pakorn; Waterman, Clare M

2013-01-01

Fluorescence microscopy allows direct visualization of fluorescently tagged proteins within cells. However, the spatial resolution of conventional fluorescence microscopes is limited by diffraction to ~250 nm, prompting the development of super-resolution microscopy which offers resolution approaching the scale of single proteins, i.e., ~20 nm. Here, we describe protocols for single molecule localization-based super-resolution imaging, using focal adhesion proteins as an example and employing either photoswitchable fluorophores or photoactivatable fluorescent proteins. These protocols should also be easily adaptable to imaging a broad array of macromolecular assemblies in cells whose components can be fluorescently tagged and assemble into high density structures.

How good can cryo-EM become?

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

Glaeser, Robert M.

The suddenness with which single-particle cryo-electron microscopy (cryo-EM) has emerged as a method for determining high-resolution structures of biological macromolecules invites the questions, how much better can this technology get, and how fast is that likely to happen? While we can rightly celebrate the maturation of cryo-EM as a high-resolution structure-determination tool, I believe there still are many developments to look forward to.

Automated method for relating regional pulmonary structure and function: integration of dynamic multislice CT and thin-slice high-resolution CT

NASA Astrophysics Data System (ADS)

Tajik, Jehangir K.; Kugelmass, Steven D.; Hoffman, Eric A.

1993-07-01

We have developed a method utilizing x-ray CT for relating pulmonary perfusion to global and regional anatomy, allowing for detailed study of structure to function relationships. A thick slice, high temporal resolution mode is used to follow a bolus contrast agent for blood flow evaluation and is fused with a high spatial resolution, thin slice mode to obtain structure- function detail. To aid analysis of blood flow, we have developed a software module, for our image analysis package (VIDA), to produce the combined structure-function image. Color coded images representing blood flow, mean transit time, regional tissue content, regional blood volume, regional air content, etc. are generated and imbedded in the high resolution volume image. A text file containing these values along with a voxel's 3-D coordinates is also generated. User input can be minimized to identifying the location of the pulmonary artery from which the input function to a blood flow model is derived. Any flow model utilizing one input and one output function can be easily added to a user selectable list. We present examples from our physiologic based research findings to demonstrate the strengths of combining dynamic CT and HRCT relative to other scanning modalities to uniquely characterize pulmonary normal and pathophysiology.

Noninvasive imaging analysis of biological tissue associated with laser thermal injury.

PubMed

Chang, Cheng-Jen; Yu, De-Yi; Hsiao, Yen-Chang; Ho, Kuang-Hua

2017-04-01

The purpose of our study is to use a noninvasive tomographic imaging technique with high spatial resolution to characterize and monitor biological tissue responses associated with laser thermal injury. Optical doppler tomography (ODT) combines laser doppler flowmetry (LDF) with optical coherence tomography (OCT) to obtain high resolution tomographic velocity and structural images of static and moving constituents in highly scattering biological tissues. A SurgiLase XJ150 carbon dioxide (CO 2 ) laser using a continuous mode of 3 watts (W) was used to create first, second or third degree burns on anesthetized Sprague-Dawley rats. Additional parameters for laser thermal injury were assessed as well. The rationale for using ODT in the evaluation of laser thermal injury offers a means of constructing a high resolution tomographic image of the structure and perfusion of laser damaged skin. In the velocity images, the blood flow is coded at 1300 μm/s and 0 velocity, 1000 μm/s and 0 velocity, 700 μm/s and 0 velocity adjacent to the first, second, and third degree injuries, respectively. ODT produces exceptional spatial resolution while having a non-invasive way of measurement, therefore, ODT is an accurate measuring method for high-resolution fluid flow velocity and structural images for biological tissue with laser thermal injury. Copyright © 2017 Chang Gung University. Published by Elsevier B.V. All rights reserved.

Ultra high spatial and temporal resolution breast imaging at 7T.

PubMed

van de Bank, B L; Voogt, I J; Italiaander, M; Stehouwer, B L; Boer, V O; Luijten, P R; Klomp, D W J

2013-04-01

There is a need to obtain higher specificity in the detection of breast lesions using MRI. To address this need, Dynamic Contrast-Enhanced (DCE) MRI has been combined with other structural and functional MRI techniques. Unfortunately, owing to time constraints structural images at ultra-high spatial resolution can generally not be obtained during contrast uptake, whereas the relatively low spatial resolution of functional imaging (e.g. diffusion and perfusion) limits the detection of small lesions. To be able to increase spatial as well as temporal resolution simultaneously, the sensitivity of MR detection needs to increase as well as the ability to effectively accelerate the acquisition. The required gain in signal-to-noise ratio (SNR) can be obtained at 7T, whereas acceleration can be obtained with high-density receiver coil arrays. In this case, morphological imaging can be merged with DCE-MRI, and other functional techniques can be obtained at higher spatial resolution, and with less distortion [e.g. Diffusion Weighted Imaging (DWI)]. To test the feasibility of this concept, we developed a unilateral breast coil for 7T. It comprises a volume optimized dual-channel transmit coil combined with a 30-channel receive array coil. The high density of small coil elements enabled efficient acceleration in any direction to acquire ultra high spatial resolution MRI of close to 0.6 mm isotropic detail within a temporal resolution of 69 s, high spatial resolution MRI of 1.5 mm isotropic within an ultra high temporal resolution of 6.7 s and low distortion DWI at 7T, all validated in phantoms, healthy volunteers and a patient with a lesion in the right breast classified as Breast Imaging Reporting and Data System (BI-RADS) IV. Copyright © 2012 John Wiley & Sons, Ltd.

Imaging of patients with hippocampal sclerosis at 7 Tesla: initial results.

PubMed

Breyer, Tobias; Wanke, Isabel; Maderwald, Stefan; Woermann, Friedrich G; Kraff, Oliver; Theysohn, Jens M; Ebner, Alois; Forsting, Michael; Ladd, Mark E; Schlamann, Marc

2010-04-01

Focal epilepsies potentially can be cured by neurosurgery; other treatment options usually remain symptomatic. High-resolution magnetic resonance (MR) imaging is the central imaging strategy in the evaluation of focal epilepsy. The most common substrate of temporal epilepsies is hippocampal sclerosis (HS), which cannot always be sufficiently characterized with current MR field strengths. Therefore, the purpose of our study was to demonstrate the feasibility of high-resolution MR imaging at 7 Tesla in patients with focal epilepsy resulting from a HS and to improve image resolution at 7 Tesla in patients with HS. Six patients with known HS were investigated with T1-, T2-, T2(*)-, and fluid-attenuated inversion recovery-weighted sequences at 7 Tesla with an eight-channel transmit-receive head coil. Total imaging time did not exceed 90 minutes per patient. High-resolution imaging at 7 Tesla is feasible and reveals high resolution of intrahippocampal structures in vivo. HS was confirmed in all patients. The maximum non-interpolated in-plane resolution reached 0.2 x 0.2 mm(2) in T2(*)-weighted images. The increased susceptibility effects at 7 Tesla revealed identification of intrahippocampal structures in more detail than at 1.5 Tesla, but otherwise led to stronger artifacts. Imaging revealed regional differences in hippocampal atrophy between patients. The scan volume was limited because of specific absorption rate restrictions, scanning time was reasonable. High-resolution imaging at 7 Tesla is promising in presurgical epilepsy imaging. "New" contrasts may further improve detection of even very small intrahippocampal structural changes. Therefore, further investigations will be necessary to demonstrate the potential benefit for presurgical selection of patients with various lesion patterns in mesial temporal epilepsies resulting from a unilateral HS. Copyright 2010 AUR. Published by Elsevier Inc. All rights reserved.

High-Resolution Solid-State NMR Spectroscopy: Characterization of Polymorphism in Cimetidine, a Pharmaceutical Compound

ERIC Educational Resources Information Center

Pacilio, Julia E.; Tokarski, John T.; Quiñones, Rosalynn; Iuliucci, Robbie J.

2014-01-01

High-resolution solid-state NMR (SSNMR) spectroscopy has many advantages as a tool to characterize solid-phase material that finds applications in polymer chemistry, nanotechnology, materials science, biomolecular structure determination, and others, including the pharmaceutical industry. The technology associated with achieving high resolution…

Super-resolved Mirau digital holography by structured illumination

NASA Astrophysics Data System (ADS)

Ganjkhani, Yasaman; Charsooghi, Mohammad A.; Akhlaghi, Ehsan A.; Moradi, Ali-Reza

2017-12-01

In this paper, we apply structured illumination toward super-resolved 3D imaging in a common-path digital holography arrangement. Digital holographic microscopy (DHM) provides non-invasive 3D images of transparent samples as well as 3D profiles of reflective surfaces. A compact and vibration-immune arrangement for DHM may be obtained through the use of a Mirau microscope objective. However, high-magnification Mirau objectives have a low working distance and are expensive. Low-magnification ones, on the other hand, suffer from low lateral resolution. Structured illumination has been widely used for resolution improvement of intensity images, but the technique can also be readily applied to DHM. We apply structured illumination to Mirau DHM by implementing successive sinusoidal gratings with different orientations onto a spatial light modulator (SLM) and forming its image on the specimen. Moreover, we show that, instead of different orientations of 1D gratings, alternative single 2D gratings, e.g. checkerboard or hexagonal patterns, can provide resolution enhancement in multiple directions. Our results show a 35% improvement in the resolution power of the DHM. The presented arrangement has the potential to serve as a table-top device for high resolution holographic microscopy.

Monitoring Termite-Mediated Ecosystem Processes Using Moderate and High Resolution Satellite Imagery

NASA Astrophysics Data System (ADS)

Lind, B. M.; Hanan, N. P.

2016-12-01

Termites are considered dominant decomposers and prominent ecosystem engineers in the global tropics and they build some of the largest and architecturally most complex non-human-made structures in the world. Termite mounds significantly alter soil texture, structure, and nutrients, and have major implications for local hydrological dynamics, vegetation characteristics, and biological diversity. An understanding of how these processes change across large scales has been limited by our ability to detect termite mounds at high spatial resolutions. Our research develops methods to detect large termite mounds in savannas across extensive geographic areas using moderate and high resolution satellite imagery. We also investigate the effect of termite mounds on vegetation productivity using Landsat-8 maximum composite NDVI data as a proxy for production. Large termite mounds in arid and semi-arid Senegal generate highly reflective `mound scars' with diameters ranging from 10 m at minimum to greater than 30 m. As Sentinel-2 has several bands with 10 m resolution and Landsat-8 has improved calibration, higher radiometric resolution, 15 m spatial resolution (pansharpened), and improved contrast between vegetated and bare surfaces compared to previous Landsat missions, we found that the largest and most influential mounds in the landscape can be detected. Because mounds as small as 4 m in diameter are easily detected in high resolution imagery we used these data to validate detection results and quantify omission errors for smaller mounds.

Three-dimensional nature of the band structure of ZrTe 5 measured by high-momentum-resolution photoemission spectroscopy [3D nature ZrTe 5 band structure measured by high-momentum-resolution photoemission spectroscopy

DOE PAGES

Xiong, H.; Sobota, J. A.; Yang, S. -L.; ...

2017-05-10

Here, we have performed a systematic high-momentum-resolution photoemission study on ZrTe 5 using 6-eV photon energy. We have measured the band structure near the Γ point, and quantified the gap between the conduction and valence band as 18 ≤ Δ ≤ 29 meV. We have also observed photon-energy-dependent behavior attributed to final-state effects and the three-dimensional (3D) nature of the material's band structure. Our interpretation indicates the gap is intrinsic and reconciles discrepancies on the existence of a topological surface state reported by different studies. The existence of a gap suggests that ZrTe 5 is not a 3D strong topologicalmore » insulator nor a 3D Dirac semimetal. Therefore, our experiment is consistent with ZrTe 5 being a 3D weak topological insulator.« less

Adding polarimetric imaging to depth map using improved light field camera 2.0 structure

NASA Astrophysics Data System (ADS)

Zhang, Xuanzhe; Yang, Yi; Du, Shaojun; Cao, Yu

2017-06-01

Polarization imaging plays an important role in various fields, especially for skylight navigation and target identification, whose imaging system is always required to be designed with high resolution, broad band, and single-lens structure. This paper describe such a imaging system based on light field 2.0 camera structure, which can calculate the polarization state and depth distance from reference plane for every objet point within a single shot. This structure, including a modified main lens, a multi-quadrants Polaroid, a honeycomb-liked micro lens array, and a high resolution CCD, is equal to an "eyes array", with 3 or more polarization imaging "glasses" in front of each "eye". Therefore, depth can be calculated by matching the relative offset of corresponding patch on neighboring "eyes", while polarization state by its relative intensity difference, and their resolution will be approximately equal to each other. An application on navigation under clear sky shows that this method has a high accuracy and strong robustness.

Strategies for dereplication of natural compounds using high-resolution tandem mass spectrometry.

PubMed

Kind, Tobias; Fiehn, Oliver

2017-09-01

Complete structural elucidation of natural products is commonly performed by nuclear magnetic resonance spectroscopy (NMR), but annotating compounds to most likely structures using high-resolution tandem mass spectrometry is a faster and feasible first step. The CASMI contest 2016 (Critical Assessment of Small Molecule Identification) provided spectra of eighteen compounds for the best manual structure identification in the natural products category. High resolution precursor and tandem mass spectra (MS/MS) were available to characterize the compounds. We used the Seven Golden Rules, Sirius2 and MS-FINDER software for determination of molecular formulas, and then we queried the formulas in different natural product databases including DNP, UNPD, ChemSpider and REAXYS to obtain molecular structures. We used different in-silico fragmentation tools including CFM-ID, CSI:FingerID and MS-FINDER to rank these compounds. Additional neutral losses and product ion peaks were manually investigated. This manual and time consuming approach allowed for the correct dereplication of thirteen of the eighteen natural products.

Three-dimensional nature of the band structure of ZrTe 5 measured by high-momentum-resolution photoemission spectroscopy [3D nature ZrTe 5 band structure measured by high-momentum-resolution photoemission spectroscopy

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

Xiong, H.; Sobota, J. A.; Yang, S. -L.

Here, we have performed a systematic high-momentum-resolution photoemission study on ZrTe 5 using 6-eV photon energy. We have measured the band structure near the Γ point, and quantified the gap between the conduction and valence band as 18 ≤ Δ ≤ 29 meV. We have also observed photon-energy-dependent behavior attributed to final-state effects and the three-dimensional (3D) nature of the material's band structure. Our interpretation indicates the gap is intrinsic and reconciles discrepancies on the existence of a topological surface state reported by different studies. The existence of a gap suggests that ZrTe 5 is not a 3D strong topologicalmore » insulator nor a 3D Dirac semimetal. Therefore, our experiment is consistent with ZrTe 5 being a 3D weak topological insulator.« less

High resolution structural characterization of giant magnetoresistance structures containing a nano-oxide layer

NASA Astrophysics Data System (ADS)

You, C. Y.; Cerezo, A.; Clifton, P. H.; Folks, L.; Carey, M. J.; Petford-Long, A. K.

2007-07-01

The microstructure and chemistry of a current-perpendicular-to-plane giant magnetoresistance structure containing a nano-oxide layer (NOL) have been studied using a combination of high resolution transmission electron microscopy and three-dimensional atom probe analysis. It was found that the morphology of the NOL changes from a planar layer to discrete particles on annealing, indicating the dominance of surface energy on the morphology evolution. Direct evidence was obtained for significant Mn diffusion from the IrMn antiferromagnetic layer and partitioning to the oxide region during annealing.

Speckle correlation resolution enhancement of wide-field fluorescence imaging (Conference Presentation)

NASA Astrophysics Data System (ADS)

Yilmaz, Hasan

2016-03-01

Structured illumination enables high-resolution fluorescence imaging of nanostructures [1]. We demonstrate a new high-resolution fluorescence imaging method that uses a scattering layer with a high-index substrate as a solid immersion lens [2]. Random scattering of coherent light enables a speckle pattern with a very fine structure that illuminates the fluorescent nanospheres on the back surface of the high-index substrate. The speckle pattern is raster-scanned over the fluorescent nanospheres using a speckle correlation effect known as the optical memory effect. A series of standard-resolution fluorescence images per each speckle pattern displacement are recorded by an electron-multiplying CCD camera using a commercial microscope objective. We have developed a new phase-retrieval algorithm to reconstruct a high-resolution, wide-field image from several standard-resolution wide-field images. We have introduced phase information of Fourier components of standard-resolution images as a new constraint in our algorithm which discards ambiguities therefore ensures convergence to a unique solution. We demonstrate two-dimensional fluorescence images of a collection of nanospheres with a deconvolved Abbe resolution of 116 nm and a field of view of 10 µm × 10 µm. Our method is robust against optical aberrations and stage drifts, therefore excellent for imaging nanostructures under ambient conditions. [1] M. G. L. Gustafsson, J. Microsc. 198, 82-87 (2000). [2] H. Yilmaz, E. G. van Putten, J. Bertolotti, A. Lagendijk, W. L. Vos, and A. P. Mosk, Optica 2, 424-429 (2015).

A high-resolution imaging technique using a whole-body, research photon counting detector CT system

NASA Astrophysics Data System (ADS)

Leng, S.; Yu, Z.; Halaweish, A.; Kappler, S.; Hahn, K.; Henning, A.; Li, Z.; Lane, J.; Levin, D. L.; Jorgensen, S.; Ritman, E.; McCollough, C.

2016-03-01

A high-resolution (HR) data collection mode has been introduced to a whole-body, research photon-counting-detector CT system installed in our laboratory. In this mode, 64 rows of 0.45 mm x 0.45 mm detector pixels were used, which corresponded to a pixel size of 0.25 mm x 0.25 mm at the iso-center. Spatial resolution of this HR mode was quantified by measuring the MTF from a scan of a 50 micron wire phantom. An anthropomorphic lung phantom, cadaveric swine lung, temporal bone and heart specimens were scanned using the HR mode, and image quality was subjectively assessed by two experienced radiologists. High spatial resolution of the HR mode was evidenced by the MTF measurement, with 15 lp/cm and 20 lp/cm at 10% and 2% modulation. Images from anthropomorphic phantom and cadaveric specimens showed clear delineation of small structures, such as lung vessels, lung nodules, temporal bone structures, and coronary arteries. Temporal bone images showed critical anatomy (i.e. stapes superstructure) that was clearly visible in the PCD system. These results demonstrated the potential application of this imaging mode in lung, temporal bone, and vascular imaging. Other clinical applications that require high spatial resolution, such as musculoskeletal imaging, may also benefit from this high resolution mode.

Experimental Investigation of Ultrafast Hydration Structure and Dynamics at Sub-Angstrom Lengthscales

ERIC Educational Resources Information Center

Coridan, Robert Henry

2009-01-01

This thesis outlines how meV-resolution inelastic x-ray scattering and causality-enforcing mathematics can be used to measure the dynamical density-density linear response function for liquid water with Angstrom spatial resolution and 50fs temporal resolution. The results are compared to high-resolution spectroscopic and scattering experiments and…

X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

DOE PAGES

Jackson, Ryan N.; McCoy, Airlie J.; Terwilliger, Thomas C.; ...

2015-07-30

Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging.more » Here we show a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and Xray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.« less

Sub-Millimeter Heterodyne Focal-Plane Arrays for High-Resolution Astronomical Spectroscopy

NASA Astrophysics Data System (ADS)

Goldsmith, Paul F.

2017-09-01

Spectral lines are vital tools for astronomy, particularly for studying the interstellar medium, which is widely distributed throughout the volume of our Milky Way and of other galaxies. Broadband emissions, including synchrotron, free-free, and thermal dust emissions give astronomers important information. However, they do not give information about the motions of, for example, interstellar clouds, the filamentary structures found within them, star-forming dense cores, and photon-dominated regions energized by massive young stars. For study of the interstellar medium, spectral lines at sub-millimeter wavelengths are particularly important, for two reasons. First, they offer the unique ability to observe a variety of important molecules, atoms, and ions, which are the most important gas coolants (fine-structure lines of ionized and neutral carbon, neutral oxygen), probes of physical conditions (high-J transitions of CO, HF, fine-structure lines of ionized nitrogen), and of obvious biogenic importance (H2O). In addition, high-resolution observations of spectral lines offer the unique ability to disentangle the complex motions within these regions and, in some cases, to determine their arrangement along the line of sight. To accomplish this, spectral resolution high enough to resolve the spectral lines of interest is required. We can measure the resolution of the spectrometer in terms of its resolution, R = f/δf, where f is the rest frequency of the line, and δJ is the frequency resolution of the spectrometer. More-active sources can be advantageously studied with R = 3 × 10^5, while more quiescent sources require R as high as 10^7.

Image quality improvement in cone-beam CT using the super-resolution technique.

PubMed

Oyama, Asuka; Kumagai, Shinobu; Arai, Norikazu; Takata, Takeshi; Saikawa, Yusuke; Shiraishi, Kenshiro; Kobayashi, Takenori; Kotoku, Jun'ichi

2018-04-05

This study was conducted to improve cone-beam computed tomography (CBCT) image quality using the super-resolution technique, a method of inferring a high-resolution image from a low-resolution image. This technique is used with two matrices, so-called dictionaries, constructed respectively from high-resolution and low-resolution image bases. For this study, a CBCT image, as a low-resolution image, is represented as a linear combination of atoms, the image bases in the low-resolution dictionary. The corresponding super-resolution image was inferred by multiplying the coefficients and the high-resolution dictionary atoms extracted from planning CT images. To evaluate the proposed method, we computed the root mean square error (RMSE) and structural similarity (SSIM). The resulting RMSE and SSIM between the super-resolution images and the planning CT images were, respectively, as much as 0.81 and 1.29 times better than those obtained without using the super-resolution technique. We used super-resolution technique to improve the CBCT image quality.

High Resolution Three-Dimensional MR Imaging of the Skull Base: Compartments, Boundaries, and Critical Structures.

PubMed

Blitz, Ari Meir; Aygun, Nafi; Herzka, Daniel A; Ishii, Masaru; Gallia, Gary L

2017-01-01

High-resolution 3D MRI of the skull base allows for a more detailed and accurate assessment of normal anatomic structures as well as the location and extent of skull base pathologies than has previously been possible. This article describes the techniques employed for high-resolution skull base MRI including pre- and post-contrast constructive interference in the steady state (CISS) imaging and their utility for evaluation of the many small structures of the skull base, focusing on those regions and concepts most pertinent to localization of cranial nerve palsies and in providing pre-operative guidance and post-operative assessment. The concept of skull base compartments as a means of conceptualizing the various layers of the skull base and their importance in assessment of masses of the skull base is discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

Rotavirus architecture at subnanometer resolution.

PubMed

Li, Zongli; Baker, Matthew L; Jiang, Wen; Estes, Mary K; Prasad, B V Venkataram

2009-02-01

Rotavirus, a nonturreted member of the Reoviridae, is the causative agent of severe infantile diarrhea. The double-stranded RNA genome encodes six structural proteins that make up the triple-layer particle. X-ray crystallography has elucidated the structure of one of these capsid proteins, VP6, and two domains from VP4, the spike protein. Complementing this work, electron cryomicroscopy (cryoEM) has provided relatively low-resolution structures for the triple-layer capsid in several biochemical states. However, a complete, high-resolution structural model of rotavirus remains unresolved. Combining new structural analysis techniques with the subnanometer-resolution cryoEM structure of rotavirus, we now provide a more detailed structural model for the major capsid proteins and their interactions within the triple-layer particle. Through a series of intersubunit interactions, the spike protein (VP4) adopts a dimeric appearance above the capsid surface, while forming a trimeric base anchored inside one of the three types of aqueous channels between VP7 and VP6 capsid layers. While the trimeric base suggests the presence of three VP4 molecules in one spike, only hints of the third molecule are observed above the capsid surface. Beyond their interactions with VP4, the interactions between VP6 and VP7 subunits could also be readily identified. In the innermost T=1 layer composed of VP2, visualization of the secondary structure elements allowed us to identify the polypeptide fold for VP2 and examine the complex network of interactions between this layer and the T=13 VP6 layer. This integrated structural approach has resulted in a relatively high-resolution structural model for the complete, infectious structure of rotavirus, as well as revealing the subtle nuances required for maintaining interactions in such a large macromolecular assembly.

Improving axial resolution in confocal microscopy with new high refractive index mounting media.

PubMed

Fouquet, Coralie; Gilles, Jean-François; Heck, Nicolas; Dos Santos, Marc; Schwartzmann, Richard; Cannaya, Vidjeacoumary; Morel, Marie-Pierre; Davidson, Robert Stephen; Trembleau, Alain; Bolte, Susanne

2015-01-01

Resolution, high signal intensity and elevated signal to noise ratio (SNR) are key issues for biologists who aim at studying the localisation of biological structures at the cellular and subcellular levels using confocal microscopy. The resolution required to separate sub-cellular biological structures is often near to the resolving power of the microscope. When optimally used, confocal microscopes may reach resolutions of 180 nm laterally and 500 nm axially, however, axial resolution in depth is often impaired by spherical aberration that may occur due to refractive index mismatches. Spherical aberration results in broadening of the point-spread function (PSF), a decrease in peak signal intensity when imaging in depth and a focal shift that leads to the distortion of the image along the z-axis and thus in a scaling error. In this study, we use the novel mounting medium CFM3 (Citifluor Ltd., UK) with a refractive index of 1.518 to minimize the effects of spherical aberration. This mounting medium is compatible with most common fluorochromes and fluorescent proteins. We compare its performance with established mounting media, harbouring refractive indices below 1.500, by estimating lateral and axial resolution with sub-resolution fluorescent beads. We show furthermore that the use of the high refractive index media renders the tissue transparent and improves considerably the axial resolution and imaging depth in immuno-labelled or fluorescent protein labelled fixed mouse brain tissue. We thus propose to use those novel high refractive index mounting media, whenever optimal axial resolution is required.

High-resolution three-dimensional magnetic resonance imaging of mouse lung in situ.

PubMed

Scadeng, Miriam; Rossiter, Harry B; Dubowitz, David J; Breen, Ellen C

2007-01-01

This study establishes a method for high-resolution isotropic magnetic resonance (MR) imaging of mouse lungs using tracheal liquid-instillation to remove MR susceptibility artifacts. C57BL/6J mice were instilled sequentially with perfluorocarbon and phosphate-buffered saline to an airway pressure of 10, 20, or 30 cm H2O. Imaging was performed in a 7T MR scanner using a 2.5-cm Quadrature volume coil and a 3-dimensional (3D) FLASH imaging sequence. Liquid-instillation removed magnetic susceptibility artifacts and allowed lung structure to be viewed at an isotropic resolution of 78-90 microm. Instilled liquid and modeled lung volumes were well correlated (R = 0.92; P < 0.05) and differed by a constant tissue volume (220 +/- 92 microL). 3D image renderings allowed differences in structural dimensions (volumes and areas) to be accurately measured at each inflation pressure. These data demonstrate the efficacy of pulmonary liquid instillation for in situ high-resolution MR imaging of mouse lungs for accurate measurement of pulmonary airway, parenchymal, and vascular structures.

Platinum replica electron microscopy: Imaging the cytoskeleton globally and locally.

PubMed

Svitkina, Tatyana M

2017-05-01

Structural studies reveal how smaller components of a system work together as a whole. However, combining high resolution of details with full coverage of the whole is challenging. In cell biology, light microscopy can image many cells in their entirety, but at a lower resolution, whereas electron microscopy affords very high resolution, but usually at the expense of the sample size and coverage. Structural analyses of the cytoskeleton are especially demanding, because cytoskeletal networks are unresolvable by light microscopy due to their density and intricacy, whereas their proper preservation is a challenge for electron microscopy. Platinum replica electron microscopy can uniquely bridge the gap between the "comfort zones" of light and electron microscopy by allowing high resolution imaging of the cytoskeleton throughout the entire cell and in many cells in the population. This review describes the principles and applications of platinum replica electron microscopy for studies of the cytoskeleton. Copyright © 2017 Elsevier Ltd. All rights reserved.

Platinum Replica Electron Microscopy: Imaging the Cytoskeleton Globally and Locally

PubMed Central

SVITKINA, Tatyana M.

2017-01-01

Structural studies reveal how smaller components of a system work together as a whole. However, combining high resolution of details with full coverage of the whole is challenging. In cell biology, light microscopy can image many cells in their entirety, but at a lower resolution, whereas electron microscopy affords very high resolution, but usually at the expense of the sample size and coverage. Structural analyses of the cytoskeleton are especially demanding, because cytoskeletal networks are unresolvable by light microscopy due to their density and intricacy, whereas their proper preservation is a challenge for electron microscopy. Platinum replica electron microscopy can uniquely bridge the gap between the “comfort zones” of light and electron microscopy by allowing high resolution imaging of the cytoskeleton throughout the entire cell and in many cells in the population. This review describes the principles and applications of platinum replica electron microscopy for studies of the cytoskeleton. PMID:28323208

Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation.

PubMed

Belaghzal, Houda; Dekker, Job; Gibcus, Johan H

2017-07-01

Chromosome conformation capture-based methods such as Hi-C have become mainstream techniques for the study of the 3D organization of genomes. These methods convert chromatin interactions reflecting topological chromatin structures into digital information (counts of pair-wise interactions). Here, we describe an updated protocol for Hi-C (Hi-C 2.0) that integrates recent improvements into a single protocol for efficient and high-resolution capture of chromatin interactions. This protocol combines chromatin digestion and frequently cutting enzymes to obtain kilobase (kb) resolution. It also includes steps to reduce random ligation and the generation of uninformative molecules, such as unligated ends, to improve the amount of valid intra-chromosomal read pairs. This protocol allows for obtaining information on conformational structures such as compartment and topologically associating domains, as well as high-resolution conformational features such as DNA loops. Copyright © 2017 Elsevier Inc. All rights reserved.

Mapping Cortical Laminar Structure in the 3D BigBrain.

PubMed

Wagstyl, Konrad; Lepage, Claude; Bludau, Sebastian; Zilles, Karl; Fletcher, Paul C; Amunts, Katrin; Evans, Alan C

2018-07-01

Histological sections offer high spatial resolution to examine laminar architecture of the human cerebral cortex; however, they are restricted by being 2D, hence only regions with sufficiently optimal cutting planes can be analyzed. Conversely, noninvasive neuroimaging approaches are whole brain but have relatively low resolution. Consequently, correct 3D cross-cortical patterns of laminar architecture have never been mapped in histological sections. We developed an automated technique to identify and analyze laminar structure within the high-resolution 3D histological BigBrain. We extracted white matter and pial surfaces, from which we derived histologically verified surfaces at the layer I/II boundary and within layer IV. Layer IV depth was strongly predicted by cortical curvature but varied between areas. This fully automated 3D laminar analysis is an important requirement for bridging high-resolution 2D cytoarchitecture and in vivo 3D neuroimaging. It lays the foundation for in-depth, whole-brain analyses of cortical layering.

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.

Blind identification of full-field vibration modes of output-only structures from uniformly-sampled, possibly temporally-aliased (sub-Nyquist), video measurements

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

Yang, Yongchao; Dorn, Charles; Mancini, Tyler

Enhancing the spatial and temporal resolution of vibration measurements and modal analysis could significantly benefit dynamic modelling, analysis, and health monitoring of structures. For example, spatially high-density mode shapes are critical for accurate vibration-based damage localization. In experimental or operational modal analysis, higher (frequency) modes, which may be outside the frequency range of the measurement, contain local structural features that can improve damage localization as well as the construction and updating of the modal-based dynamic model of the structure. In general, the resolution of vibration measurements can be increased by enhanced hardware. Traditional vibration measurement sensors such as accelerometers havemore » high-frequency sampling capacity; however, they are discrete point-wise sensors only providing sparse, low spatial sensing resolution measurements, while dense deployment to achieve high spatial resolution is expensive and results in the mass-loading effect and modification of structure's surface. Non-contact measurement methods such as scanning laser vibrometers provide high spatial and temporal resolution sensing capacity; however, they make measurements sequentially that requires considerable acquisition time. As an alternative non-contact method, digital video cameras are relatively low-cost, agile, and provide high spatial resolution, simultaneous, measurements. Combined with vision based algorithms (e.g., image correlation or template matching, optical flow, etc.), video camera based measurements have been successfully used for experimental and operational vibration measurement and subsequent modal analysis. However, the sampling frequency of most affordable digital cameras is limited to 30–60 Hz, while high-speed cameras for higher frequency vibration measurements are extremely costly. This work develops a computational algorithm capable of performing vibration measurement at a uniform sampling frequency lower than what is required by the Shannon-Nyquist sampling theorem for output-only modal analysis. In particular, the spatio-temporal uncoupling property of the modal expansion of structural vibration responses enables a direct modal decoupling of the temporally-aliased vibration measurements by existing output-only modal analysis methods, yielding (full-field) mode shapes estimation directly. Then the signal aliasing properties in modal analysis is exploited to estimate the modal frequencies and damping ratios. Furthermore, the proposed method is validated by laboratory experiments where output-only modal identification is conducted on temporally-aliased acceleration responses and particularly the temporally-aliased video measurements of bench-scale structures, including a three-story building structure and a cantilever beam.« less

Blind identification of full-field vibration modes of output-only structures from uniformly-sampled, possibly temporally-aliased (sub-Nyquist), video measurements

DOE PAGES

Yang, Yongchao; Dorn, Charles; Mancini, Tyler; ...

2016-12-05

Enhancing the spatial and temporal resolution of vibration measurements and modal analysis could significantly benefit dynamic modelling, analysis, and health monitoring of structures. For example, spatially high-density mode shapes are critical for accurate vibration-based damage localization. In experimental or operational modal analysis, higher (frequency) modes, which may be outside the frequency range of the measurement, contain local structural features that can improve damage localization as well as the construction and updating of the modal-based dynamic model of the structure. In general, the resolution of vibration measurements can be increased by enhanced hardware. Traditional vibration measurement sensors such as accelerometers havemore » high-frequency sampling capacity; however, they are discrete point-wise sensors only providing sparse, low spatial sensing resolution measurements, while dense deployment to achieve high spatial resolution is expensive and results in the mass-loading effect and modification of structure's surface. Non-contact measurement methods such as scanning laser vibrometers provide high spatial and temporal resolution sensing capacity; however, they make measurements sequentially that requires considerable acquisition time. As an alternative non-contact method, digital video cameras are relatively low-cost, agile, and provide high spatial resolution, simultaneous, measurements. Combined with vision based algorithms (e.g., image correlation or template matching, optical flow, etc.), video camera based measurements have been successfully used for experimental and operational vibration measurement and subsequent modal analysis. However, the sampling frequency of most affordable digital cameras is limited to 30–60 Hz, while high-speed cameras for higher frequency vibration measurements are extremely costly. This work develops a computational algorithm capable of performing vibration measurement at a uniform sampling frequency lower than what is required by the Shannon-Nyquist sampling theorem for output-only modal analysis. In particular, the spatio-temporal uncoupling property of the modal expansion of structural vibration responses enables a direct modal decoupling of the temporally-aliased vibration measurements by existing output-only modal analysis methods, yielding (full-field) mode shapes estimation directly. Then the signal aliasing properties in modal analysis is exploited to estimate the modal frequencies and damping ratios. Furthermore, the proposed method is validated by laboratory experiments where output-only modal identification is conducted on temporally-aliased acceleration responses and particularly the temporally-aliased video measurements of bench-scale structures, including a three-story building structure and a cantilever beam.« less

High-resolution imaging of silicene on an Ag(111) surface by atomic force microscopy

NASA Astrophysics Data System (ADS)

Onoda, Jo; Yabuoshi, Keisuke; Miyazaki, Hiroki; Sugimoto, Yoshiaki

2017-12-01

Silicene, a two-dimensional (2D) honeycomb arrangement of Si atoms, is expected to have better electronic properties than graphene and has been mostly synthesized on Ag surfaces. Although scanning tunneling microscopy (STM) has been used for visualizing its atomic structure in real space, the interpretation of STM contrast is not straightforward and only the topmost Si atoms were observed on the (4 ×4 ) silicene/Ag(111) surface. Here, we demonstrate that high-resolution atomic force microscopy (AFM) can resolve all constituent Si atoms in the buckled honeycomb arrangement of the (4 ×4 ) silicene. Site-specific force spectroscopy attributes the origin of the high-resolution AFM images to chemical bonds between the AFM probe apex and the individual Si atoms on the (4 ×4 ) silicene. A detailed analysis of the geometric parameters suggests that the pulling up of lower-buckled Si atoms by the AFM tip could be a key for high-resolution AFM, implying a weakening of the Si-Ag interactions at the interface. We expect that high-resolution AFM will also unveil atomic structures of edges and defects of silicene, or other emerging 2D materials.

A simulation for gravity fine structure recovery from high-low GRAVSAT SST data

NASA Technical Reports Server (NTRS)

Estes, R. H.; Lancaster, E. R.

1976-01-01

Covariance error analysis techniques were applied to investigate estimation strategies for the high-low SST mission for accurate local recovery of gravitational fine structure, considering the aliasing effects of unsolved for parameters. Surface density blocks of 5 deg x 5 deg and 2 1/2 deg x 2 1/2 deg resolution were utilized to represent the high order geopotential with the drag-free GRAVSAT configured in a nearly circular polar orbit at 250 km. altitude. GEOPAUSE and geosynchronous satellites were considered as high relay spacecraft. It is demonstrated that knowledge of gravitational fine structure can be significantly improved at 5 deg x 5 deg resolution using SST data from a high-low configuration with reasonably accurate orbits for the low GRAVSAT. The gravity fine structure recoverability of the high-low SST mission is compared with the low-low configuration and shown to be superior.

Predicting nucleic acid binding interfaces from structural models of proteins.

PubMed

Dror, Iris; Shazman, Shula; Mukherjee, Srayanta; Zhang, Yang; Glaser, Fabian; Mandel-Gutfreund, Yael

2012-02-01

The function of DNA- and RNA-binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However, the main pitfall of various structure-based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high-resolution three-dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I-TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches extracted from high-resolution structures. Furthermore, by testing our pipeline on a set of 55 known nucleic acid binding proteins for which I-TASSER produces high-quality models, we show that the method accurately identifies the nucleic acids binding interface on structural models of proteins. Employing a combined patch approach we show that patches extracted from an ensemble of models better predicts the real nucleic acid binding interfaces compared with patches extracted from independent models. Overall, these results suggest that combining information from a collection of low-resolution structural models could be a valuable approach for functional annotation. We suggest that our method will be further applicable for predicting other functional surfaces of proteins with unknown structure. Copyright © 2011 Wiley Periodicals, Inc.

Seeing tobacco mosaic virus through direct electron detectors

PubMed Central

Fromm, Simon A.; Bharat, Tanmay A.M.; Jakobi, Arjen J.; Hagen, Wim J.H.; Sachse, Carsten

2015-01-01

With the introduction of direct electron detectors (DED) to the field of electron cryo-microscopy, a wave of atomic-resolution structures has become available. As the new detectors still require comparative characterization, we have used tobacco mosaic virus (TMV) as a test specimen to study the quality of 3D image reconstructions from data recorded on the two direct electron detector cameras, K2 Summit and Falcon II. Using DED movie frames, we explored related image-processing aspects and compared the performance of micrograph-based and segment-based motion correction approaches. In addition, we investigated the effect of dose deposition on the atomic-resolution structure of TMV and show that radiation damage affects negative carboxyl chains first in a side-chain specific manner. Finally, using 450,000 asymmetric units and limiting the effects of radiation damage, we determined a high-resolution cryo-EM map at 3.35 Å resolution. Here, we provide a comparative case study of highly ordered TMV recorded on different direct electron detectors to establish recording and processing conditions that enable structure determination up to 3.2 Å in resolution using cryo-EM. PMID:25528571

Hybrid-coded 3D structured illumination imaging with Bayesian estimation (Conference Presentation)

NASA Astrophysics Data System (ADS)

Chen, Hsi-Hsun; Luo, Yuan; Singh, Vijay R.

2016-03-01

Light induced fluorescent microscopy has long been developed to observe and understand the object at microscale, such as cellular sample. However, the transfer function of lense-based imaging system limits the resolution so that the fine and detailed structure of sample cannot be identified clearly. The techniques of resolution enhancement are fascinated to break the limit of resolution for objective given. In the past decades, the resolution enhancement imaging has been investigated through variety of strategies, including photoactivated localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), stimulated emission depletion (STED), and structure illuminated microscopy (SIM). In those methods, only SIM can intrinsically improve the resolution limit for a system without taking the structure properties of object into account. In this paper, we develop a SIM associated with Bayesian estimation, furthermore, with optical sectioning capability rendered from HiLo processing, resulting the high resolution through 3D volume. This 3D SIM can provide the optical sectioning and resolution enhancement performance, and be robust to noise owing to the Data driven Bayesian estimation reconstruction proposed. For validating the 3D SIM, we show our simulation result of algorithm, and the experimental result demonstrating the 3D resolution enhancement.

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

PubMed Central

Moriya, Toshio; Saur, Michael; Stabrin, Markus; Merino, Felipe; Voicu, Horatiu; Huang, Zhong; Penczek, Pawel A.; Raunser, Stefan; Gatsogiannis, Christos

2017-01-01

SPHIRE (SPARX for High-Resolution Electron Microscopy) is a novel open-source, user-friendly software suite for the semi-automated processing of single particle electron cryo-microscopy (cryo-EM) data. The protocol presented here describes in detail how to obtain a near-atomic resolution structure starting from cryo-EM micrograph movies by guiding users through all steps of the single particle structure determination pipeline. These steps are controlled from the new SPHIRE graphical user interface and require minimum user intervention. Using this protocol, a 3.5 Å structure of TcdA1, a Tc toxin complex from Photorhabdus luminescens, was derived from only 9500 single particles. This streamlined approach will help novice users without extensive processing experience and a priori structural information, to obtain noise-free and unbiased atomic models of their purified macromolecular complexes in their native state. PMID:28570515

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

Wojcik, Roza; Webb, Ian K.; Deng, Liulin

Understanding the biological mechanisms related to lipids and glycolipids is challenging due to the vast number of possible isomers. Mass spectrometry (MS) measurements are currently the dominant approach for studying and providing detailed information on lipid and glycolipid structures. However, difficulties in distinguishing many structural isomers (e.g. distinct acyl chain positions, double bond locations, as well as glycan isomers) inhibit the understanding of their biological roles. Here we utilized ultra-high resolution ion mobility spectrometry (IMS) separations based upon the use of traveling waves in a serpentine long path length multi-pass Structures for Lossless Manipulations (SLIM) to enhance isomer resolution. Themore » multi-pass arrangement allowed separations ranging from ~16 m (1 pass) to ~470 m (32 passes) to be investigated for the distinction of lipids and glycolipids with extremely small structural differences. Lastly, these ultra-high resolution SLIM IMS-MS analyses provide a foundation for exploring and better understanding isomer specific biological and disease processes.« less

Electron crystallography of PhoE porin, an outer membrane, channel- forming protein from E. coli

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

Walian, P.J.

1989-11-01

One approach to studying the structure of membrane proteins is the use of electron crystallography. Dr. Bing Jap has crystallized PhoE pore-forming protein (porin) from the outer membrane of escherichia coli (E. coli) into monolayer crystals. The findings of this research and those of Jap (1988, 1989) have determined these crystals to be highly ordered, yielding structural information to a resolution of better than 2.8 angstroms. The task of this thesis has been to collect and process the electron diffraction patterns necessary to generate a complete three-dimensional set of high resolution structure factor amplitudes of PhoE porin. Fourier processing ofmore » these amplitudes when combined with the corresponding phase data is expected to yield the three-dimensional structure of PhoE porin at better than 3.5 angstroms resolution. 92 refs., 33 figs., 3 tabs. (CBS)« less

Structural Characterization of a Thrombin-Aptamer Complex by High Resolution Native Top-Down Mass Spectrometry

NASA Astrophysics Data System (ADS)

Zhang, Jiang; Loo, Rachel R. Ogorzalek; Loo, Joseph A.

2017-09-01

Native mass spectrometry (MS) with electrospray ionization (ESI) has evolved as an invaluable tool for the characterization of intact native proteins and non-covalently bound protein complexes. Here we report the structural characterization by high resolution native top-down MS of human thrombin and its complex with the Bock thrombin binding aptamer (TBA), a 15-nucleotide DNA with high specificity and affinity for thrombin. Accurate mass measurements revealed that the predominant form of native human α-thrombin contains a glycosylation mass of 2205 Da, corresponding to a sialylated symmetric biantennary oligosaccharide structure without fucosylation. Native MS showed that thrombin and TBA predominantly form a 1:1 complex under near physiological conditions (pH 6.8, 200 mM NH4OAc), but the binding stoichiometry is influenced by the solution ionic strength. In 20 mM ammonium acetate solution, up to two TBAs were bound to thrombin, whereas increasing the solution ionic strength destabilized the thrombin-TBA complex and 1 M NH4OAc nearly completely dissociated the complex. This observation is consistent with the mediation of thrombin-aptamer binding through electrostatic interactions and it is further consistent with the human thrombin structure that contains two anion binding sites on the surface. Electron capture dissociation (ECD) top-down MS of the thrombin-TBA complex performed with a high resolution 15 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer showed the primary binding site to be at exosite I located near the N-terminal sequence of the heavy chain, consistent with crystallographic data. High resolution native top-down MS is complementary to traditional structural biology methods for structurally characterizing native proteins and protein-DNA complexes. [Figure not available: see fulltext.

Advanced very high resolution radiometer

NASA Technical Reports Server (NTRS)

1976-01-01

The advanced very high resolution radiometer development program is considered. The program covered the design, construction, and test of a breadboard model, engineering model, protoflight model, mechanical structural model, and a life test model. Special bench test and calibration equipment was also developed for use on the program.

HIPS: A new hippocampus subfield segmentation method.

PubMed

Romero, José E; Coupé, Pierrick; Manjón, José V

2017-12-01

The importance of the hippocampus in the study of several neurodegenerative diseases such as Alzheimer's disease makes it a structure of great interest in neuroimaging. However, few segmentation methods have been proposed to measure its subfields due to its complex structure and the lack of high resolution magnetic resonance (MR) data. In this work, we present a new pipeline for automatic hippocampus subfield segmentation using two available hippocampus subfield delineation protocols that can work with both high and standard resolution data. The proposed method is based on multi-atlas label fusion technology that benefits from a novel multi-contrast patch match search process (using high resolution T1-weighted and T2-weighted images). The proposed method also includes as post-processing a new neural network-based error correction step to minimize systematic segmentation errors. The method has been evaluated on both high and standard resolution images and compared to other state-of-the-art methods showing better results in terms of accuracy and execution time. Copyright © 2017 Elsevier Inc. All rights reserved.

Microdome-gooved Gd(2)O(2)S:Tb scintillator for flexible and high resolution digital radiography.

PubMed

Jung, Phill Gu; Lee, Chi Hoon; Bae, Kong Myeong; Lee, Jae Min; Lee, Sang Min; Lim, Chang Hwy; Yun, Seungman; Kim, Ho Kyung; Ko, Jong Soo

2010-07-05

A flexible microdome-grooved Gd(2)O(2)S:Tb scintillator is simulated, fabricated, and characterized for digital radiography applications. According to Monte Carlo simulation results, the dome-grooved structure has a high spatial resolution, which is verified by X-ray image performance of the scintillator. The proposed scintillator has lower X-ray sensitivity than a nonstructured scintillator but almost two times higher spatial resolution at high spatial frequency. Through evaluation of the X-ray performance of the fabricated scintillators, we confirm that the microdome-grooved scintillator can be applied to next-generation flexible digital radiography systems requiring high spatial resolution.

Profiling of integral membrane proteins and their post translational modifications using high-resolution mass spectrometry

PubMed Central

Souda, Puneet; Ryan, Christopher M.; Cramer, William A.; Whitelegge, Julian

2011-01-01

Integral membrane proteins pose challenges to traditional proteomics approaches due to unique physicochemical properties including hydrophobic transmembrane domains that limit solubility in aqueous solvents. A well resolved intact protein molecular mass profile defines a protein’s native covalent state including post-translational modifications, and is thus a vital measurement toward full structure determination. Both soluble loop regions and transmembrane regions potentially contain post-translational modifications that must be characterized if the covalent primary structure of a membrane protein is to be defined. This goal has been achieved using electrospray-ionization mass spectrometry (ESI-MS) with low-resolution mass analyzers for intact protein profiling, and high-resolution instruments for top-down experiments, toward complete covalent primary structure information. In top-down, the intact protein profile is supplemented by gas-phase fragmentation of the intact protein, including its transmembrane regions, using collisionally activated and/or electroncapture dissociation (CAD/ECD) to yield sequence-dependent high-resolution MS information. Dedicated liquid chromatography systems with aqueous/organic solvent mixtures were developed allowing us to demonstrate that polytopic integral membrane proteins are amenable to ESI-MS analysis, including top-down measurements. Covalent post-translational modifications are localized regardless of their position in transmembrane domains. Top-down measurements provide a more detail oriented high-resolution description of post-transcriptional and post-translational diversity for enhanced understanding beyond genomic translation. PMID:21982782

Profiling of integral membrane proteins and their post translational modifications using high-resolution mass spectrometry.

PubMed

Souda, Puneet; Ryan, Christopher M; Cramer, William A; Whitelegge, Julian

2011-12-01

Integral membrane proteins pose challenges to traditional proteomics approaches due to unique physicochemical properties including hydrophobic transmembrane domains that limit solubility in aqueous solvents. A well resolved intact protein molecular mass profile defines a protein's native covalent state including post-translational modifications, and is thus a vital measurement toward full structure determination. Both soluble loop regions and transmembrane regions potentially contain post-translational modifications that must be characterized if the covalent primary structure of a membrane protein is to be defined. This goal has been achieved using electrospray-ionization mass spectrometry (ESI-MS) with low-resolution mass analyzers for intact protein profiling, and high-resolution instruments for top-down experiments, toward complete covalent primary structure information. In top-down, the intact protein profile is supplemented by gas-phase fragmentation of the intact protein, including its transmembrane regions, using collisionally activated and/or electron-capture dissociation (CAD/ECD) to yield sequence-dependent high-resolution MS information. Dedicated liquid chromatography systems with aqueous/organic solvent mixtures were developed allowing us to demonstrate that polytopic integral membrane proteins are amenable to ESI-MS analysis, including top-down measurements. Covalent post-translational modifications are localized regardless of their position in transmembrane domains. Top-down measurements provide a more detail oriented high-resolution description of post-transcriptional and post-translational diversity for enhanced understanding beyond genomic translation. Copyright © 2011 Elsevier Inc. All rights reserved.

Local atomic and electronic structure of oxide/GaAs and SiO2/Si interfaces using high-resolution XPS

NASA Technical Reports Server (NTRS)

Grunthaner, F. J.; Grunthaner, P. J.; Vasquez, R. P.; Lewis, B. F.; Maserjian, J.; Madhukar, A.

1979-01-01

The chemical structures of thin SiO2 films, thin native oxides of GaAs (20-30 A), and the respective oxide-semiconductor interfaces, have been investigated using high-resolution X-ray photoelectron spectroscopy. Depth profiles of these structures have been obtained using argon ion bombardment and wet chemical etching techniques. The chemical destruction induced by the ion profiling method is shown by direct comparison of these methods for identical samples. Fourier transform data-reduction methods based on linear prediction with maximum entropy constraints are used to analyze the discrete structure in oxides and substrates. This discrete structure is interpreted by means of a structure-induced charge-transfer model.

Determination of atmospheric moisture structure and infrared cooling rates from high resolution MAMS radiance data

NASA Technical Reports Server (NTRS)

Menzel, W. Paul; Moeller, Christopher C.; Smith, William L.

1991-01-01

This program has applied Multispectral Atmospheric Mapping Sensor (MAMS) high resolution data to the problem of monitoring atmospheric quantities of moisture and radiative flux at small spatial scales. MAMS, with 100-m horizontal resolution in its four infrared channels, was developed to study small scale atmospheric moisture and surface thermal variability, especially as related to the development of clouds, precipitation, and severe storms. High-resolution Interferometer Sounder (HIS) data has been used to develop a high spectral resolution retrieval algorithm for producing vertical profiles of atmospheric temperature and moisture. The results of this program are summarized and a list of publications resulting from this contract is presented. Selected publications are attached as an appendix.

Subatomic and atomic crystallographic studies of aldose reductase: implications for inhibitor binding.

PubMed

Podjarny, A; Cachau, R E; Schneider, T; Van Zandt, M; Joachimiak, A

2004-04-01

The determination of several of aldose reductase-inhibitor complexes at subatomic resolution has revealed new structural details, including the specific interatomic contacts involved in inhibitor binding. In this article, we review the structures of the complexes of ALR2 with IDD 594 (resolution: 0.66 angstrom, IC50 (concentration of the inhibitor that produced half-maximal effect): 30 nM, space group: P2(1)), IDD 393 (resolution: 0.90 angstrom, IC50: 6 nM, space group: P1), fidarestat (resolution: 0.92 angstrom, IC50: 9 nM, space group: P2(1)) and minalrestat (resolution: 1.10 angstrom, IC50: 73 nM, space group: P1). The structures are compared and found to be highly reproductible within the same space group (root mean square (RMS) deviations: 0.15 approximately 0.3 angstrom). The mode of binding of the carboxylate inhibitors IDD 594 and IDD 393 is analysed. The binding of the carboxylate head can be accurately determined by the subatomic resolution structures, since both the protonation states and the positions of the atoms are very precisely known. The differences appear in the binding in the specificity pocket. The high-resolution structures explain the differences in IC50, which are confirmed both experimentally by mass spectrometry measures of VC50 and theoretically by free energy perturbation calculations. The binding of the cyclic imide inhibitors fidarestat and minalrestat is also described, focusing on the observation of a Cl(-) ion which binds simultaneously with fidarestat. The presence of this anion, binding also to the active site residue His110, leads to a mechanism in which the inhibitor can bind in a neutral state and then become charged inside the active site pocket. This mechanism can explain the excellent in vivo properties of cyclic imide inhibitors. In summary, the complete and detailed information supplied by the subatomic resolution structures can explain the differences in binding energy of the different inhibitors.

Purification, characterization and crystallization of the human 80S ribosome

PubMed Central

Khatter, Heena; Myasnikov, Alexander G.; Mastio, Leslie; Billas, Isabelle M. L.; Birck, Catherine; Stella, Stefano; Klaholz, Bruno P.

2014-01-01

Ribosomes are key macromolecular protein synthesis machineries in the cell. Human ribosomes have so far not been studied to atomic resolution because of their particularly complex structure as compared with other eukaryotic or prokaryotic ribosomes, and they are difficult to prepare to high homogeneity, which is a key requisite for high-resolution structural work. We established a purification protocol for human 80S ribosomes isolated from HeLa cells that allows obtaining large quantities of homogenous samples as characterized by biophysical methods using analytical ultracentrifugation and multiangle laser light scattering. Samples prepared under different conditions were characterized by direct single particle imaging using cryo electron microscopy, which helped optimizing the preparation protocol. From a small data set, a 3D reconstruction at subnanometric resolution was obtained showing all prominent structural features of the human ribosome, and revealing a salt concentration dependence of the presence of the exit site tRNA, which we show is critical for obtaining crystals. With these well-characterized samples first human 80S ribosome crystals were obtained from several crystallization conditions in capillaries and sitting drops, which diffract to 26 Å resolution at cryo temperatures and for which the crystallographic parameters were determined, paving the way for future high-resolution work. PMID:24452798

Experimental flat-panel high-spatial-resolution volume CT of the temporal bone.

PubMed

Gupta, Rajiv; Bartling, Soenke H; Basu, Samit K; Ross, William R; Becker, Hartmut; Pfoh, Armin; Brady, Thomas; Curtin, Hugh D

2004-09-01

A CT scanner employing a digital flat-panel detector is capable of very high spatial resolution as compared with a multi-section CT (MSCT) scanner. Our purpose was to determine how well a prototypical volume CT (VCT) scanner with a flat-panel detector system defines fine structures in temporal bone. Four partially manipulated temporal-bone specimens were imaged by use of a prototypical cone-beam VCT scanner with a flat-panel detector system at an isometric resolution of 150 microm at the isocenter. These specimens were also depicted by state-of-the-art multisection CT (MSCT). Forty-two structures imaged by both scanners were qualitatively assessed and rated, and scores assigned to VCT findings were compared with those of MSCT. Qualitative assessment of anatomic structures, lesions, cochlear implants, and middle-ear hearing aids indicated that image quality was significantly better with VCT (P < .001). Structures near the spatial-resolution limit of MSCT (e.g., bony covering of the tympanic segment of the facial canal, the incudo-stapedial joint, the proximal vestibular aqueduct, the interscalar septum, and the modiolus) had higher contrast and less partial-volume effect with VCT. The flat-panel prototype provides better definition of fine osseous structures of temporal bone than that of currently available MSCT scanners. This study provides impetus for further research in increasing spatial resolution beyond that offered by the current state-of-the-art scanners.

Demonstrating the Uneven Importance of Fine-Scale Forest Structure on Snow Distributions using High Resolution Modeling

NASA Astrophysics Data System (ADS)

Broxton, P. D.; Harpold, A. A.; van Leeuwen, W.; Biederman, J. A.

2016-12-01

Quantifying the amount of snow in forested mountainous environments, as well as how it may change due to warming and forest disturbance, is critical given its importance for water supply and ecosystem health. Forest canopies affect snow accumulation and ablation in ways that are difficult to observe and model. Furthermore, fine-scale forest structure can accentuate or diminish the effects of forest-snow interactions. Despite decades of research demonstrating the importance of fine-scale forest structure (e.g. canopy edges and gaps) on snow, we still lack a comprehensive understanding of where and when forest structure has the largest impact on snowpack mass and energy budgets. Here, we use a hyper-resolution (1 meter spatial resolution) mass and energy balance snow model called the Snow Physics and Laser Mapping (SnowPALM) model along with LIDAR-derived forest structure to determine where spatial variability of fine-scale forest structure has the largest influence on large scale mass and energy budgets. SnowPALM was set up and calibrated at sites representing diverse climates in New Mexico, Arizona, and California. Then, we compared simulations at different model resolutions (i.e. 1, 10, and 100 m) to elucidate the effects of including versus not including information about fine scale canopy structure. These experiments were repeated for different prescribed topographies (i.e. flat, 30% slope north, and south-facing) at each site. Higher resolution simulations had more snow at lower canopy cover, with the opposite being true at high canopy cover. Furthermore, there is considerable scatter, indicating that different canopy arrangements can lead to different amounts of snow, even when the overall canopy coverage is the same. This modeling is contributing to the development of a high resolution machine learning algorithm called the Snow Water Artificial Network (SWANN) model to generate predictions of snow distributions over much larger domains, which has implications for improving land surface models that do not currently resolve or parameterize fine-scale canopy structure. In addition, these findings have implications for understanding the potential of different forest management strategies (i.e. thinning) based on local topography and climate to maximize the amount and retention of snow.

The future of structural fieldwork - UAV assisted aerial photogrammetry

NASA Astrophysics Data System (ADS)

Vollgger, Stefan; Cruden, Alexander

2015-04-01

Unmanned aerial vehicles (UAVs), commonly referred to as drones, are opening new and low cost possibilities to acquire high-resolution aerial images and digital surface models (DSM) for applications in structural geology. UAVs can be programmed to fly autonomously along a user defined grid to systematically capture high-resolution photographs, even in difficult to access areas. The photographs are subsequently processed using software that employ SIFT (scale invariant feature transform) and SFM (structure from motion) algorithms. These photogrammetric routines allow the extraction of spatial information (3D point clouds, digital elevation models, 3D meshes, orthophotos) from 2D images. Depending on flight altitude and camera setup, sub-centimeter spatial resolutions can be achieved. By "digitally mapping" georeferenced 3D models and images, orientation data can be extracted directly and used to analyse the structural framework of the mapped object or area. We present UAV assisted aerial mapping results from a coastal platform near Cape Liptrap (Victoria, Australia), where deformed metasediments of the Palaeozoic Lachlan Fold Belt are exposed. We also show how orientation and spatial information of brittle and ductile structures extracted from the photogrammetric model can be linked to the progressive development of folds and faults in the region. Even though there are both technical and legislative limitations, which might prohibit the use of UAVs without prior commercial licensing and training, the benefits that arise from the resulting high-resolution, photorealistic models can substantially contribute to the collection of new data and insights for applications in structural geology.

High Resolution Higher Energy X-ray Microscope for Mesoscopic Materials

NASA Astrophysics Data System (ADS)

Snigireva, I.; Snigirev, A.

2013-10-01

We developed a novel X-ray microscopy technique to study mesoscopically structured materials, employing compound refractive lenses. The easily seen advantage of lens-based methodology is the possibility to retrieve high resolution diffraction pattern and real-space images in the same experimental setup. Methodologically the proposed approach is similar to the studies of crystals by high resolution transmission electron microscopy. The proposed microscope was applied for studying of mesoscopic materials such as natural and synthetic opals, inverted photonic crystals.

Spacer layer thickness dependent structural and magnetic properties of Co/Si multilayers

NASA Astrophysics Data System (ADS)

Roy, Ranjan; Singh, Dushyant; Kumar, M. Senthil

2018-05-01

In this article, the study of high resolution x-ray diffraction and magnetization of sputter deposited Co/Si multilayer is reported. Multilayers are prepared at ambient temperature by dc magnetron sputtering. Structural properties are studied by high resolution x-ray diffraction. Magnetic properties are studied at room temperature by vibrating sample magnetometer. Structural properties show that the Co layer is polycrystalline and the Si layer is amorphous. The magnetization study indicates that the samples are soft ferromagnetic in nature. The study of magnetization also shows that the easy axis of magnetization lies in the plane of the film.

Structured Illumination Microscopy for the Investigation of Synaptic Structure and Function.

PubMed

Hong, Soyon; Wilton, Daniel K; Stevens, Beth; Richardson, Douglas S

2017-01-01

The neuronal synapse is a primary building block of the nervous system to which alterations in structure or function can result in numerous pathologies. Studying its formation and elimination is the key to understanding how brains are wired during development, maintained throughout adulthood plasticity, and disrupted during disease. However, due to its diffraction-limited size, investigations of the synaptic junction at the structural level have primarily relied on labor-intensive electron microscopy or ultra-thin section array tomography. Recent advances in the field of super-resolution light microscopy now allow researchers to image synapses and associated molecules with high-spatial resolution, while taking advantage of the key characteristics of light microscopy, such as easy sample preparation and the ability to detect multiple targets with molecular specificity. One such super-resolution technique, Structured Illumination Microscopy (SIM), has emerged as an attractive method to examine synapse structure and function. SIM requires little change in standard light microscopy sample preparation steps, but results in a twofold improvement in both lateral and axial resolutions compared to widefield microscopy. The following protocol outlines a method for imaging synaptic structures at resolutions capable of resolving the intricacies of these neuronal connections.

Angular reconstitution-based 3D reconstructions of nanomolecular structures from superresolution light-microscopy images

PubMed Central

Salas, Desirée; Le Gall, Antoine; Fiche, Jean-Bernard; Valeri, Alessandro; Ke, Yonggang; Bron, Patrick; Bellot, Gaetan

2017-01-01

Superresolution light microscopy allows the imaging of labeled supramolecular assemblies at a resolution surpassing the classical diffraction limit. A serious limitation of the superresolution approach is sample heterogeneity and the stochastic character of the labeling procedure. To increase the reproducibility and the resolution of the superresolution results, we apply multivariate statistical analysis methods and 3D reconstruction approaches originally developed for cryogenic electron microscopy of single particles. These methods allow for the reference-free 3D reconstruction of nanomolecular structures from two-dimensional superresolution projection images. Since these 2D projection images all show the structure in high-resolution directions of the optical microscope, the resulting 3D reconstructions have the best possible isotropic resolution in all directions. PMID:28811371

An automatic chip structure optical inspection system for electronic components

NASA Astrophysics Data System (ADS)

Song, Zhichao; Xue, Bindang; Liang, Jiyuan; Wang, Ke; Chen, Junzhang; Liu, Yunhe

2018-01-01

An automatic chip structure inspection system based on machine vision is presented to ensure the reliability of electronic components. It consists of four major modules, including a metallographic microscope, a Gigabit Ethernet high-resolution camera, a control system and a high performance computer. An auto-focusing technique is presented to solve the problem that the chip surface is not on the same focusing surface under the high magnification of the microscope. A panoramic high-resolution image stitching algorithm is adopted to deal with the contradiction between resolution and field of view, caused by different sizes of electronic components. In addition, we establish a database to storage and callback appropriate parameters to ensure the consistency of chip images of electronic components with the same model. We use image change detection technology to realize the detection of chip images of electronic components. The system can achieve high-resolution imaging for chips of electronic components with various sizes, and clearly imaging for the surface of chip with different horizontal and standardized imaging for ones with the same model, and can recognize chip defects.

The commensurate-to-incommensurate phase transition of an organic monolayer: A high resolution LEED analysis of the superstructures of NTCDA on Ag(1 1 1)

NASA Astrophysics Data System (ADS)

Kilian, L.; Stahl, U.; Kossev, I.; Sokolowski, M.; Fink, R.; Umbach, E.

2008-07-01

The structural order of 1,4,9,10-naphthalene-tetracarboxylicacid-dianhydride (NTCDA) monolayers on Ag(1 1 1) has been investigated by spot profile analysis low energy electron diffraction (SPA-LEED). For increasing coverage, we find a sequence of three highly ordered structures: a commensurate structure (α), a uniaxially incommensurate structure (α 2), and an incommensurate structure (β) with coverages of 0.9 ML, 0.95 ML, and 1 (saturated) monolayer (ML), respectively. In the high coverage regime, the structures coexist and a coverage increase causes a change of their relative fractions. The α and β structures were known before [U. Stahl, D. Gador, A. Soukopp, R. Fink, E. Umbach, Surf. Sci. 414 (1998) 423], but the β structure was proposed as commensurate, since its very small misfit with respect to a commensurate structure could not be resolved. This misfit leads to a periodic modulation, causing additional Moiré satellites in the diffraction pattern. This finding demonstrates the importance of high resolution methods for the geometry determination of large organic adsorbates.

Patch-Based Super-Resolution of MR Spectroscopic Images: Application to Multiple Sclerosis

PubMed Central

Jain, Saurabh; Sima, Diana M.; Sanaei Nezhad, Faezeh; Hangel, Gilbert; Bogner, Wolfgang; Williams, Stephen; Van Huffel, Sabine; Maes, Frederik; Smeets, Dirk

2017-01-01

Purpose: Magnetic resonance spectroscopic imaging (MRSI) provides complementary information to conventional magnetic resonance imaging. Acquiring high resolution MRSI is time consuming and requires complex reconstruction techniques. Methods: In this paper, a patch-based super-resolution method is presented to increase the spatial resolution of metabolite maps computed from MRSI. The proposed method uses high resolution anatomical MR images (T1-weighted and Fluid-attenuated inversion recovery) to regularize the super-resolution process. The accuracy of the method is validated against conventional interpolation techniques using a phantom, as well as simulated and in vivo acquired human brain images of multiple sclerosis subjects. Results: The method preserves tissue contrast and structural information, and matches well with the trend of acquired high resolution MRSI. Conclusions: These results suggest that the method has potential for clinically relevant neuroimaging applications. PMID:28197066

Light-sheet Bayesian microscopy enables deep-cell super-resolution imaging of heterochromatin in live human embryonic stem cells.

PubMed

Hu, Ying S; Zhu, Quan; Elkins, Keri; Tse, Kevin; Li, Yu; Fitzpatrick, James A J; Verma, Inder M; Cang, Hu

2013-01-01

Heterochromatin in the nucleus of human embryonic cells plays an important role in the epigenetic regulation of gene expression. The architecture of heterochromatin and its dynamic organization remain elusive because of the lack of fast and high-resolution deep-cell imaging tools. We enable this task by advancing instrumental and algorithmic implementation of the localization-based super-resolution technique. We present light-sheet Bayesian super-resolution microscopy (LSBM). We adapt light-sheet illumination for super-resolution imaging by using a novel prism-coupled condenser design to illuminate a thin slice of the nucleus with high signal-to-noise ratio. Coupled with a Bayesian algorithm that resolves overlapping fluorophores from high-density areas, we show, for the first time, nanoscopic features of the heterochromatin structure in both fixed and live human embryonic stem cells. The enhanced temporal resolution allows capturing the dynamic change of heterochromatin with a lateral resolution of 50-60 nm on a time scale of 2.3 s. Light-sheet Bayesian microscopy opens up broad new possibilities of probing nanometer-scale nuclear structures and real-time sub-cellular processes and other previously difficult-to-access intracellular regions of living cells at the single-molecule, and single cell level.

Light-sheet Bayesian microscopy enables deep-cell super-resolution imaging of heterochromatin in live human embryonic stem cells

PubMed Central

Hu, Ying S; Zhu, Quan; Elkins, Keri; Tse, Kevin; Li, Yu; Fitzpatrick, James A J; Verma, Inder M; Cang, Hu

2016-01-01

Background Heterochromatin in the nucleus of human embryonic cells plays an important role in the epigenetic regulation of gene expression. The architecture of heterochromatin and its dynamic organization remain elusive because of the lack of fast and high-resolution deep-cell imaging tools. We enable this task by advancing instrumental and algorithmic implementation of the localization-based super-resolution technique. Results We present light-sheet Bayesian super-resolution microscopy (LSBM). We adapt light-sheet illumination for super-resolution imaging by using a novel prism-coupled condenser design to illuminate a thin slice of the nucleus with high signal-to-noise ratio. Coupled with a Bayesian algorithm that resolves overlapping fluorophores from high-density areas, we show, for the first time, nanoscopic features of the heterochromatin structure in both fixed and live human embryonic stem cells. The enhanced temporal resolution allows capturing the dynamic change of heterochromatin with a lateral resolution of 50–60 nm on a time scale of 2.3 s. Conclusion Light-sheet Bayesian microscopy opens up broad new possibilities of probing nanometer-scale nuclear structures and real-time sub-cellular processes and other previously difficult-to-access intracellular regions of living cells at the single-molecule, and single cell level. PMID:27795878

Nano-Computed Tomography: Technique and Applications.

PubMed

Kampschulte, M; Langheinirch, A C; Sender, J; Litzlbauer, H D; Althöhn, U; Schwab, J D; Alejandre-Lafont, E; Martels, G; Krombach, G A

2016-02-01

Nano-computed tomography (nano-CT) is an emerging, high-resolution cross-sectional imaging technique and represents a technical advancement of the established micro-CT technology. Based on the application of a transmission target X-ray tube, the focal spot size can be decreased down to diameters less than 400 nanometers (nm). Together with specific detectors and examination protocols, a superior spatial resolution up to 400 nm (10 % MTF) can be achieved, thereby exceeding the resolution capacity of typical micro-CT systems. The technical concept of nano-CT imaging as well as the basics of specimen preparation are demonstrated exemplarily. Characteristics of atherosclerotic plaques (intraplaque hemorrhage and calcifications) in a murine model of atherosclerosis (ApoE (-/-)/LDLR(-/-) double knockout mouse) are demonstrated in the context of superior spatial resolution in comparison to micro-CT. Furthermore, this article presents the application of nano-CT for imaging cerebral microcirculation (murine), lung structures (porcine), and trabecular microstructure (ovine) in contrast to micro-CT imaging. This review shows the potential of nano-CT as a radiological method in biomedical basic research and discusses the application of experimental, high resolution CT techniques in consideration of other high resolution cross-sectional imaging techniques. Nano-computed tomography is a high resolution CT-technology for 3D imaging at sub-micrometer resolution. The technical concept bases on a further development of the established ex-vivo-micro-CT technology. By improvement of the spatial resolution, structures at a cellular level become visible (e.g. osteocyte lacunae). © Georg Thieme Verlag KG Stuttgart · New York.

Improving Axial Resolution in Confocal Microscopy with New High Refractive Index Mounting Media

PubMed Central

Fouquet, Coralie; Gilles, Jean-François; Heck, Nicolas; Dos Santos, Marc; Schwartzmann, Richard; Cannaya, Vidjeacoumary; Morel, Marie-Pierre; Davidson, Robert Stephen; Trembleau, Alain; Bolte, Susanne

2015-01-01

Resolution, high signal intensity and elevated signal to noise ratio (SNR) are key issues for biologists who aim at studying the localisation of biological structures at the cellular and subcellular levels using confocal microscopy. The resolution required to separate sub-cellular biological structures is often near to the resolving power of the microscope. When optimally used, confocal microscopes may reach resolutions of 180 nm laterally and 500 nm axially, however, axial resolution in depth is often impaired by spherical aberration that may occur due to refractive index mismatches. Spherical aberration results in broadening of the point-spread function (PSF), a decrease in peak signal intensity when imaging in depth and a focal shift that leads to the distortion of the image along the z-axis and thus in a scaling error. In this study, we use the novel mounting medium CFM3 (Citifluor Ltd., UK) with a refractive index of 1.518 to minimize the effects of spherical aberration. This mounting medium is compatible with most common fluorochromes and fluorescent proteins. We compare its performance with established mounting media, harbouring refractive indices below 1.500, by estimating lateral and axial resolution with sub-resolution fluorescent beads. We show furthermore that the use of the high refractive index media renders the tissue transparent and improves considerably the axial resolution and imaging depth in immuno-labelled or fluorescent protein labelled fixed mouse brain tissue. We thus propose to use those novel high refractive index mounting media, whenever optimal axial resolution is required. PMID:25822785

High resolution atomic force microscopy of double-stranded RNA.

PubMed

Ares, Pablo; Fuentes-Perez, Maria Eugenia; Herrero-Galán, Elías; Valpuesta, José M; Gil, Adriana; Gomez-Herrero, Julio; Moreno-Herrero, Fernando

2016-06-09

Double-stranded (ds) RNA mediates the suppression of specific gene expression, it is the genetic material of a number of viruses, and a key activator of the innate immune response against viral infections. The ever increasing list of roles played by dsRNA in the cell and its potential biotechnological applications over the last decade has raised an interest for the characterization of its mechanical properties and structure, and that includes approaches using Atomic Force Microscopy (AFM) and other single-molecule techniques. Recent reports have resolved the structure of dsDNA with AFM at unprecedented resolution. However, an equivalent study with dsRNA is still lacking. Here, we have visualized the double helix of dsRNA under near-physiological conditions and at sufficient resolution to resolve the A-form sub-helical pitch periodicity. We have employed different high-sensitive force-detection methods and obtained images with similar spatial resolution. Therefore, we show here that the limiting factors for high-resolution AFM imaging of soft materials in liquid medium are, rather than the imaging mode, the force between the tip and the sample and the sharpness of the tip apex.

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography.

PubMed

Bhardwaj, Anshul; Casjens, Sherwood R; Cingolani, Gino

2014-02-01

Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20-35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.

New features in Saturn's atmosphere revealed by high-resolution thermal infrared images

NASA Technical Reports Server (NTRS)

Gezari, D. Y.; Mumma, M. J.; Espenak, F.; Deming, D.; Bjoraker, G.; Woods, L.; Folz, W.

1989-01-01

Observations of the stratospheric IR emission structure on Saturn are presented. The high-spatial-resolution global images show a variety of new features, including a narrow equatorial belt of enhanced emission at 7.8 micron, a prominent symmetrical north polar hotspot at all three wavelengths, and a midlatitude structure which is asymmetrically brightened at the east limb. The results confirm the polar brightening and reversal in position predicted by recent models for seasonal thermal variations of Saturn's stratosphere.

High resolution X-ray diffraction imaging of lead tin telluride

NASA Technical Reports Server (NTRS)

Steiner, Bruce; Dobbyn, Ronald C.; Black, David; Burdette, Harold; Kuriyama, Masao; Spal, Richard; Simchick, Richard; Fripp, Archibald

1991-01-01

High resolution X-ray diffraction images of two directly comparable crystals of lead tin telluride, one Bridgman-grown on Space Shuttle STS 61A and the other terrestrially Bridgman-grown under similar conditions from identical material, present different subgrain structure. In the terrestrial, sample 1 the appearance of an elaborate array of subgrains is closely associated with the intrusion of regions that are out of diffraction in all of the various images. The formation of this elaborate subgrain structure is inhibited by growth in microgravity.

Time stamping of single optical photons with 10 ns resolution

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

Chakaberia, Irakli; Cotlet, Mircea; Fisher-Levine, Merlin

High spatial and temporal resolution are key features for many modern applications, e.g. mass spectrometry, probing the structure of materials via neutron scattering, studying molecular structure, etc. Fast imaging also provides the capability of coincidence detection, and the further addition of sensitivity to single optical photons with the capability of timestamping them further broadens the field of potential applications. Here, photon counting is already widely used in X-ray imaging, where the high energy of the photons makes their detection easier.

Time stamping of single optical photons with 10 ns resolution

DOE PAGES

Chakaberia, Irakli; Cotlet, Mircea; Fisher-Levine, Merlin; ...

2017-05-08

High spatial and temporal resolution are key features for many modern applications, e.g. mass spectrometry, probing the structure of materials via neutron scattering, studying molecular structure, etc. Fast imaging also provides the capability of coincidence detection, and the further addition of sensitivity to single optical photons with the capability of timestamping them further broadens the field of potential applications. Here, photon counting is already widely used in X-ray imaging, where the high energy of the photons makes their detection easier.

Precision mechanical structure of an ultra-high-resolution spectrometer for inelastic X-ray scattering instrument

DOEpatents

Shu, Deming; Shvydko, Yuri; Stoupin, Stanislav A.; Khachatryan, Ruben; Goetze, Kurt A.; Roberts, Timothy

2015-04-14

A method and an ultrahigh-resolution spectrometer including a precision mechanical structure for positioning inelastic X-ray scattering optics are provided. The spectrometer includes an X-ray monochromator and an X-ray analyzer, each including X-ray optics of a collimating (C) crystal, a pair of dispersing (D) element crystals, anomalous transmission filter (F) and a wavelength (W) selector crystal. A respective precision mechanical structure is provided with the X-ray monochromator and the X-ray analyzer. The precision mechanical structure includes a base plate, such as an aluminum base plate; positioning stages for D-crystal alignment; positioning stages with an incline sensor for C/F/W-crystal alignment, and the positioning stages including flexure-based high-stiffness structure.

Analysis of very-high-resolution Galileo images of Europa: Implications for small-scale structure and surface evolution

NASA Astrophysics Data System (ADS)

Leonard, E. J.; Pappalardo, R. T.; Yin, A.; Prockter, L. M.; Patthoff, D. A.

2014-12-01

The Galileo Solid State Imager (SSI) recorded nine very high-resolution frames (8 at 12 m/pixel and 1 at 6 m/pixel) during the E12 flyby of Europa in Dec. 1997. To understand the implications for the small-scale structure and evolution of Europa, we mosaicked these frames (observations 12ESMOTTLE01 and 02, incidence ≈18°, emission ≈77°) into their regional context (part of observation 11ESREGMAP01, 220 m/pixel, incidence ≈74°, emission ≈23°), despite their very different viewing and lighting conditions. We created a map of geological units based on morphology, structure, and albedo along with stereoscopic images where the frames overlapped. The highly diverse units range from: high albedo sub-parallel ridge and grooved terrain; to variegated-albedo hummocky terrain; to low albedo and relatively smooth terrain. We classified and analyzed the diverse units solely based on the high-resolution image mosaic, prior to comparison to the context image, to obtain an in-depth look at possible surface evolution and underlying formational processes. We infer that some of these units represent different stages and forms of resurfacing, including cryovolcanic and tectonic resurfacing. However, significant morphological variation among units in the region indicates that there are different degrees of resurfacing at work. We have created candidate morphological sequences that provide insight into the conversion of ridged plains to chaotic terrain—generally, a process of subduing formerly sharp features through tectonic modification and/or cryovolcanism. When the map of the high-resolution area is compared to the regional context, features that appear to be one unit at regional resolution are comprised of several distinct units at high resolution, and features that appear to be smooth in the context image are found to show distinct textures. Moreover, in the context image, transitions from ridged units to disrupted units appear to be gradual; however the high-resolution image reveals them to be abrupt, suggesting tectonic control of these boundaries. These discrepancies could have important implications for a future landed exploration.

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

Zhu, Fan, E-mail: zf5016@126.com; Center of Ultra-precision Optoelectronic Instrument Engineering, Harbin Institute of Technology, Harbin 150080; Tan, Xinran

An autocollimation (AC) setup with ultra-high resolution and stability for micro-angle measurement is presented. The telephoto objective, which is characterized in long focal length at a compact structure size, and the optical enlargement unit, which can magnify the image displacement to improve its measurement resolution and accuracy, are used to obtain an ultra-high measurement resolution of the AC. The common-path beam drift compensation is used to suppress the drift of measurement results, which is evident in the high-resolution AC, thus to obtain a high measurement stability. Experimental results indicate that an effective resolution of better than 0.0005 arc sec (2.42more » nrad) over a measurement range of ±30 arc sec and a 2-h stability of 0.0061 arc sec (29.57 nrad) can be achieved.« less

Pollen structure visualization using high-resolution laboratory-based hard X-ray tomography.

PubMed

Li, Qiong; Gluch, Jürgen; Krüger, Peter; Gall, Martin; Neinhuis, Christoph; Zschech, Ehrenfried

2016-10-14

A laboratory-based X-ray microscope is used to investigate the 3D structure of unstained whole pollen grains. For the first time, high-resolution laboratory-based hard X-ray microscopy is applied to study pollen grains. Based on the efficient acquisition of statistically relevant information-rich images using Zernike phase contrast, both surface- and internal structures of pine pollen - including exine, intine and cellular structures - are clearly visualized. The specific volumes of these structures are calculated from the tomographic data. The systematic three-dimensional study of pollen grains provides morphological and structural information about taxonomic characters that are essential in palynology. Such studies have a direct impact on disciplines such as forestry, agriculture, horticulture, plant breeding and biodiversity. Copyright © 2016 Elsevier Inc. All rights reserved.

Towards a minimally invasive sampling tool for high resolution tissue analytical mapping

NASA Astrophysics Data System (ADS)

Gottardi, R.

2015-09-01

Multiple spatial mapping techniques of biological tissues have been proposed over the years, but all present limitations either in terms of resolution, analytical capacity or invasiveness. Ren et al (2015 Nanotechnology 26 284001) propose in their most recent work the use of a picosecond infrared laser (PIRL) under conditions of ultrafast desorption by impulsive vibrational excitation (DIVE) to extract small amounts of cellular and molecular components, conserving their viability, structure and activity. The PIRL DIVE technique would then work as a nanobiopsy with minimal damage to the surrounding tissues, which could potentially be applied for high resolution local structural characterization of tissues in health and disease with the spatial limit determined by the laser focus.

Ultra-high resolution, polarization sensitive transversal optical coherence tomography for structural analysis and strain mapping

NASA Astrophysics Data System (ADS)

Wiesauer, Karin; Pircher, Michael; Goetzinger, Erich; Hitzenberger, Christoph K.; Engelke, Rainer; Ahrens, Gisela; Pfeiffer, Karl; Ostrzinski, Ute; Gruetzner, Gabi; Oster, Reinhold; Stifter, David

2006-02-01

Optical coherence tomography (OCT) is a contactless and non-invasive technique nearly exclusively applied for bio-medical imaging of tissues. Besides the internal structure, additionally strains within the sample can be mapped when OCT is performed in a polarization sensitive (PS) way. In this work, we demonstrate the benefits of PS-OCT imaging for non-biological applications. We have developed the OCT technique beyond the state-of-the-art: based on transversal ultra-high resolution (UHR-)OCT, where an axial resolution below 2 μm within materials is obtained using a femtosecond laser as light source, we have modified the setup for polarization sensitive measurements (transversal UHR-PS-OCT). We perform structural analysis and strain mapping for different types of samples: for a highly strained elastomer specimen we demonstrate the necessity of UHR-imaging. Furthermore, we investigate epoxy waveguide structures, photoresist moulds for the fabrication of micro-electromechanical parts (MEMS), and the glass-fibre composite outer shell of helicopter rotor blades where cracks are present. For these examples, transversal scanning UHR-PS-OCT is shown to provide important information about the structural properties and the strain distribution within the samples.

Compton imaging tomography technique for NDE of large nonuniform structures

NASA Astrophysics Data System (ADS)

Grubsky, Victor; Romanov, Volodymyr; Patton, Ned; Jannson, Tomasz

2011-09-01

In this paper we describe a new nondestructive evaluation (NDE) technique called Compton Imaging Tomography (CIT) for reconstructing the complete three-dimensional internal structure of an object, based on the registration of multiple two-dimensional Compton-scattered x-ray images of the object. CIT provides high resolution and sensitivity with virtually any material, including lightweight structures and organics, which normally pose problems in conventional x-ray computed tomography because of low contrast. The CIT technique requires only one-sided access to the object, has no limitation on the object's size, and can be applied to high-resolution real-time in situ NDE of large aircraft/spacecraft structures and components. Theoretical and experimental results will be presented.

Automatic optimization high-speed high-resolution OCT retinal imaging at 1μm

NASA Astrophysics Data System (ADS)

Cua, Michelle; Liu, Xiyun; Miao, Dongkai; Lee, Sujin; Lee, Sieun; Bonora, Stefano; Zawadzki, Robert J.; Mackenzie, Paul J.; Jian, Yifan; Sarunic, Marinko V.

2015-03-01

High-resolution OCT retinal imaging is important in providing visualization of various retinal structures to aid researchers in better understanding the pathogenesis of vision-robbing diseases. However, conventional optical coherence tomography (OCT) systems have a trade-off between lateral resolution and depth-of-focus. In this report, we present the development of a focus-stacking optical coherence tomography (OCT) system with automatic optimization for high-resolution, extended-focal-range clinical retinal imaging. A variable-focus liquid lens was added to correct for de-focus in real-time. A GPU-accelerated segmentation and optimization was used to provide real-time layer-specific enface visualization as well as depth-specific focus adjustment. After optimization, multiple volumes focused at different depths were acquired, registered, and stitched together to yield a single, high-resolution focus-stacked dataset. Using this system, we show high-resolution images of the ONH, from which we extracted clinically-relevant parameters such as the nerve fiber layer thickness and lamina cribrosa microarchitecture.

High-resolution seismic-reflection images across the ICDP-USGS Eyreville deep drilling site, Chesapeake Bay impact structure

USGS Publications Warehouse

Powars, David S.; Catchings, Rufus D.; Goldman, Mark R.; Gohn, Gregory S.; Horton, J. Wright; Edwards, Lucy E.; Rymer, Michael J.; Gandhok, Gini

2009-01-01

The U.S. Geological Survey (USGS) acquired two 1.4-km-long, high-resolution (~5 m vertical resolution) seismic-reflection lines in 2006 that cross near the International Continental Scientific Drilling Program (ICDP)-USGS Eyreville deep drilling site located above the late Eocene Chesapeake Bay impact structure in Virginia, USA. Five-meter spacing of seismic sources and geophones produced high-resolution images of the subsurface adjacent to the 1766-m-depth Eyreville core holes. Analysis of these lines, in the context of the core hole stratigraphy, shows that moderate-amplitude, discontinuous, dipping reflections below ~527 m correlate with a variety of Chesapeake Bay impact structure sediment and rock breccias recovered in the cores. High-amplitude, continuous, subhorizontal reflections above ~527 m depth correlate with the uppermost part of the Chesapeake Bay impact structure crater-fill sediments and postimpact Eocene to Pleistocene sediments. Reflections with ~20-30 m of relief in the uppermost part of the crater-fill and lowermost part of the postimpact section suggest differential compaction of the crater-fill materials during early postimpact time. The top of the crater-fill section also shows ~20 m of relief that appears to represent an original synimpact surface. Truncation surfaces, locally dipping reflections, and depth variations in reflection amplitudes generally correlate with the lithostrati-graphic and sequence-stratigraphic units and contacts in the core. Seismic images show apparent postimpact paleochannels that include the first possible Miocene paleochannels in the Mid-Atlantic Coastal Plain. Broad downwarping in the postim-pact section unrelated to structures in the crater fill indicates postimpact sediment compaction.

Photoionization Rate of Atomic Oxygen

NASA Astrophysics Data System (ADS)

Meier, R. R.; McLaughlin, B. M.; Warren, H. P.; Bishop, J.

2006-05-01

Accurate knowledge of the photoionization rate of atomic oxygen is important for the study and understanding of the ionospheres and emission processes of terrestrial, planetary, and cometary atmospheres. Past calculations of the photoionization rate have been carried out at various spectral resolutions, but none were at sufficiently high resolution to accommodate accidental resonances between solar emission lines and highly structured auto-ionization features in the photoionization cross section. A new version of the NRLEUV solar spectral irradiance model (at solar minimum) and a new model of the O photoionization cross section enable calculations at very high spectral resolution. We find unattenuated photoionization rates computed at 0.001 nm resolution are larger than those at moderate resolution (0.1 nm) by amounts approaching 20%. Allowing for attenuation in the terrestrial atmosphere, we find differences in photoionization rates computed at high and moderate resolution to vary with altitude, especially below 200 km where deviations of plus or minus 20% occur between the two cases.

FOLD-EM: automated fold recognition in medium- and low-resolution (4-15 Å) electron density maps.

PubMed

Saha, Mitul; Morais, Marc C

2012-12-15

Owing to the size and complexity of large multi-component biological assemblies, the most tractable approach to determining their atomic structure is often to fit high-resolution radiographic or nuclear magnetic resonance structures of isolated components into lower resolution electron density maps of the larger assembly obtained using cryo-electron microscopy (cryo-EM). This hybrid approach to structure determination requires that an atomic resolution structure of each component, or a suitable homolog, is available. If neither is available, then the amount of structural information regarding that component is limited by the resolution of the cryo-EM map. However, even if a suitable homolog cannot be identified using sequence analysis, a search for structural homologs should still be performed because structural homology often persists throughout evolution even when sequence homology is undetectable, As macromolecules can often be described as a collection of independently folded domains, one way of searching for structural homologs would be to systematically fit representative domain structures from a protein domain database into the medium/low resolution cryo-EM map and return the best fits. Taken together, the best fitting non-overlapping structures would constitute a 'mosaic' backbone model of the assembly that could aid map interpretation and illuminate biological function. Using the computational principles of the Scale-Invariant Feature Transform (SIFT), we have developed FOLD-EM-a computational tool that can identify folded macromolecular domains in medium to low resolution (4-15 Å) electron density maps and return a model of the constituent polypeptides in a fully automated fashion. As a by-product, FOLD-EM can also do flexible multi-domain fitting that may provide insight into conformational changes that occur in macromolecular assemblies.

Noninvasive assessment of the developing Xenopus cardiovascular system using optical coherence tomography

PubMed Central

Boppart, Stephen A.; Tearney, Gary J.; Bouma, Brett E.; Southern, James F.; Brezinski, Mark E.; Fujimoto, James G.

1997-01-01

Studies investigating normal and abnormal cardiac development are frequently limited by an inability to assess cardiovascular function within the intact organism. In this work, optical coherence tomography (OCT), a new method of micron-scale, noninvasive imaging based on the measurement of backscattered infrared light, was introduced for the high resolution assessment of structure and function in the developing Xenopus laevis cardiovascular system. Microstructural details, such as ventricular size and wall positions, were delineated with OCT at 16-μm resolution and correlated with histology. Three-dimensional representation of the cardiovascular system also was achieved by repeated cross-sectional imaging at intervals of 25 μm. In addition to structural information, OCT provides high speed in vivo axial ranging and imaging, allowing quantitative dynamic activity, such as ventricular ejection fraction, to be assessed. The sensitivity of OCT for dynamic assessment was demonstrated with an inotropic agent that altered cardiac function and dimensions. Optical coherence tomography is an attractive new technology for assessing cardiovascular development because of its high resolution, its ability to image through nontransparent structures, and its inexpensive portable design. In vivo and in vitro imaging are performed at a resolution approaching that of histopathology without the need for animal killing. PMID:9113976

Resolving anatomical and functional structure in human brain organization: identifying mesoscale organization in weighted network representations.

PubMed

Lohse, Christian; Bassett, Danielle S; Lim, Kelvin O; Carlson, Jean M

2014-10-01

Human brain anatomy and function display a combination of modular and hierarchical organization, suggesting the importance of both cohesive structures and variable resolutions in the facilitation of healthy cognitive processes. However, tools to simultaneously probe these features of brain architecture require further development. We propose and apply a set of methods to extract cohesive structures in network representations of brain connectivity using multi-resolution techniques. We employ a combination of soft thresholding, windowed thresholding, and resolution in community detection, that enable us to identify and isolate structures associated with different weights. One such mesoscale structure is bipartivity, which quantifies the extent to which the brain is divided into two partitions with high connectivity between partitions and low connectivity within partitions. A second, complementary mesoscale structure is modularity, which quantifies the extent to which the brain is divided into multiple communities with strong connectivity within each community and weak connectivity between communities. Our methods lead to multi-resolution curves of these network diagnostics over a range of spatial, geometric, and structural scales. For statistical comparison, we contrast our results with those obtained for several benchmark null models. Our work demonstrates that multi-resolution diagnostic curves capture complex organizational profiles in weighted graphs. We apply these methods to the identification of resolution-specific characteristics of healthy weighted graph architecture and altered connectivity profiles in psychiatric disease.

Three-dimensional super-resolved live cell imaging through polarized multi-angle TIRF.

PubMed

Zheng, Cheng; Zhao, Guangyuan; Liu, Wenjie; Chen, Youhua; Zhang, Zhimin; Jin, Luhong; Xu, Yingke; Kuang, Cuifang; Liu, Xu

2018-04-01

Measuring three-dimensional nanoscale cellular structures is challenging, especially when the structure is dynamic. Owing to the informative total internal reflection fluorescence (TIRF) imaging under varied illumination angles, multi-angle (MA) TIRF has been examined to offer a nanoscale axial and a subsecond temporal resolution. However, conventional MA-TIRF still performs badly in lateral resolution and fails to characterize the depth image in densely distributed regions. Here, we emphasize the lateral super-resolution in the MA-TIRF, exampled by simply introducing polarization modulation into the illumination procedure. Equipped with a sparsity and accelerated proximal algorithm, we examine a more precise 3D sample structure compared with previous methods, enabling live cell imaging with a temporal resolution of 2 s and recovering high-resolution mitochondria fission and fusion processes. We also shared the recovery program, which is the first open-source recovery code for MA-TIRF, to the best of our knowledge.

2.2 Å resolution cryo-EM structure of β-galactosidase in complex with a cell-permeant inhibitor.

PubMed

Bartesaghi, Alberto; Merk, Alan; Banerjee, Soojay; Matthies, Doreen; Wu, Xiongwu; Milne, Jacqueline L S; Subramaniam, Sriram

2015-06-05

Cryo-electron microscopy (cryo-EM) is rapidly emerging as a powerful tool for protein structure determination at high resolution. Here we report the structure of a complex between Escherichia coli β-galactosidase and the cell-permeant inhibitor phenylethyl β-D-thiogalactopyranoside (PETG), determined by cryo-EM at an average resolution of ~2.2 angstroms (Å). Besides the PETG ligand, we identified densities in the map for ~800 water molecules and for magnesium and sodium ions. Although it is likely that continued advances in detector technology may further enhance resolution, our findings demonstrate that preparation of specimens of adequate quality and intrinsic protein flexibility, rather than imaging or image-processing technologies, now represent the major bottlenecks to routinely achieving resolutions close to 2 Å using single-particle cryo-EM. Copyright © 2015, American Association for the Advancement of Science.

Laser scanning saturated structured illumination microscopy based on phase modulation

NASA Astrophysics Data System (ADS)

Huang, Yujia; Zhu, Dazhao; Jin, Luhong; Kuang, Cuifang; Xu, Yingke; Liu, Xu

2017-08-01

Wide-field saturated structured illumination microscopy has not been widely used due to the requirement of high laser power. We propose a novel method called laser scanning saturated structured illumination microscopy (LS-SSIM), which introduces high order of harmonics frequency and greatly reduces the required laser power for SSIM imaging. To accomplish that, an excitation PSF with two peaks is generated and scanned along different directions on the sample. Raw images are recorded cumulatively by a CCD detector and then reconstructed to form a high-resolution image with extended optical transfer function (OTF). Our theoretical analysis and simulation results show that LS-SSIM method reaches a resolution of 0.16 λ, equivalent to 2.7-fold resolution than conventional wide-field microscopy. In addition, LS-SSIM greatly improves the optical sectioning capability of conventional wide-field illumination system by diminishing our-of-focus light. Furthermore, this modality has the advantage of implementation in multi-photon microscopy with point scanning excitation to image samples in greater depths.

Direct observation of charged domain walls in hybrid improper ferroelectric (Ca,Sr)3Ti2O7

NASA Astrophysics Data System (ADS)

Kurushima, Kousuke; Yoshimoto, Wataru; Ishii, Yui; Cheong, Sang-Wook; Mori, Shigeo

2017-10-01

We investigated ferroelectric (FE) domain wall structures including “charged domain walls” of hybrid improper FE (Ca,Sr)3Ti2O7 at the subatomic resolution by dark-field transmission electron microscopy (TEM) and high-resolution state-of-the-art aberration-corrected high-angle annular-dark-field (HAADF) scanning transmission electron microscopy (STEM). Dark-field TEM and high-resolution HAADF-STEM images obtained in the FE phase of single crystals of Ca2.46Sr0.54Ti2O7 revealed the formation of abundant charged domain walls with the head-to-head and tail-to-tail configurations in the FE domain structure, in addition to the FE 180° domain structure. The charged domain walls with the head-to-head and tail-to-tail FE polarizations exist stably and can be characterized as the unique double arc-type displacement of Ca/Sr ions in a unit cell without charge accumulation.

Formation routes and structural details of the CaF1 layer on Si(111) from high-resolution noncontact atomic force microscopy data

NASA Astrophysics Data System (ADS)

Rahe, Philipp; Smith, Emily F.; Wollschläger, Joachim; Moriarty, Philip J.

2018-03-01

We investigate the CaF1/Si (111 ) interface using a combination of high-resolution scanning tunneling and noncontact atomic force microscopy operated at cryogenic temperature as well as x-ray photoelectron spectroscopy. Submonolayer CaF1 films grown at substrate temperatures between 550 and 600 ∘C on Si (111 ) surfaces reveal the existence of two island types that are distinguished by their edge topology, nucleation position, measured height, and inner defect structure. Our data suggest a growth model where the two island types are the result of two reaction pathways during CaF1 interface formation. A key difference between these two pathways is identified to arise from the excess species during the growth process, which can be either fluorine or silicon. Structural details as a result of this difference are identified by means of high-resolution noncontact atomic force microscopy and add insights into the growth mode of this heteroepitaxial insulator-on-semiconductor system.

A two-ply polymer-based flexible tactile sensor sheet using electric capacitance.

PubMed

Guo, Shijie; Shiraoka, Takahisa; Inada, Seisho; Mukai, Toshiharu

2014-01-29

Traditional capacitive tactile sensor sheets usually have a three-layered structure, with a dielectric layer sandwiched by two electrode layers. Each electrode layer has a number of parallel ribbon-like electrodes. The electrodes on the two electrode layers are oriented orthogonally and each crossing point of the two perpendicular electrode arrays makes up a capacitive sensor cell on the sheet. It is well known that compatibility between measuring precision and resolution is difficult, since decreasing the width of the electrodes is required to obtain a high resolution, however, this may lead to reduction of the area of the sensor cells, and as a result, lead to a low Signal/Noise (S/N) ratio. To overcome this problem, a new multilayered structure and related calculation procedure are proposed. This new structure stacks two or more sensor sheets with shifts in position. Both a high precision and a high resolution can be obtained by combining the signals of the stacked sensor sheets. Trial production was made and the effect was confirmed.

Resolution requirements for aero-optical simulations

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

Mani, Ali; Wang Meng; Moin, Parviz

2008-11-10

Analytical criteria are developed to estimate the error of aero-optical computations due to inadequate spatial resolution of refractive index fields in high Reynolds number flow simulations. The unresolved turbulence structures are assumed to be locally isotropic and at low turbulent Mach number. Based on the Kolmogorov spectrum for the unresolved structures, the computational error of the optical path length is estimated and linked to the resulting error in the computed far-field optical irradiance. It is shown that in the high Reynolds number limit, for a given geometry and Mach number, the spatial resolution required to capture aero-optics within a pre-specifiedmore » error margin does not scale with Reynolds number. In typical aero-optical applications this resolution requirement is much lower than the resolution required for direct numerical simulation, and therefore, a typical large-eddy simulation can capture the aero-optical effects. The analysis is extended to complex turbulent flow simulations in which non-uniform grid spacings are used to better resolve the local turbulence structures. As a demonstration, the analysis is used to estimate the error of aero-optical computation for an optical beam passing through turbulent wake of flow over a cylinder.« less

Graphene-enabled electron microscopy and correlated super-resolution microscopy of wet cells.

PubMed

Wojcik, Michal; Hauser, Margaret; Li, Wan; Moon, Seonah; Xu, Ke

2015-06-11

The application of electron microscopy to hydrated biological samples has been limited by high-vacuum operating conditions. Traditional methods utilize harsh and laborious sample dehydration procedures, often leading to structural artefacts and creating difficulties for correlating results with high-resolution fluorescence microscopy. Here, we utilize graphene, a single-atom-thick carbon meshwork, as the thinnest possible impermeable and conductive membrane to protect animal cells from vacuum, thus enabling high-resolution electron microscopy of wet and untreated whole cells with exceptional ease. Our approach further allows for facile correlative super-resolution and electron microscopy of wet cells directly on the culturing substrate. In particular, individual cytoskeletal actin filaments are resolved in hydrated samples through electron microscopy and well correlated with super-resolution results.

Plasmon waveguide resonance sensor using an Au-MgF2 structure.

PubMed

Zhou, Yanfei; Zhang, Pengfei; He, Yonghong; Xu, Zihao; Liu, Le; Ji, Yanhong; Ma, Hui

2014-10-01

We report an Au − MgF(2) plasmon waveguide resonance (PWR) sensor in this work. The characteristics of this sensing structure are compared with a surface plasmon resonance (SPR) structure theoretically and experimentally. The transverse-magnetic-polarized PWR sensor has a refractive index resolution of 9.3 × 10(-7) RIU, which is 6 times smaller than that of SPR at the incident light wavelength of 633 nm, and the transverse-electric-polarized PWR sensor has a refractive index resolution of 3.0 × 10(-6) RIU. This high-resolution sensor is easy to build and is less sensitive to film coating deviations.

Selenium Derivatization of Nucleic Acids for Crystallography

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

Jiang,J.; Sheng, J.; Carrasco, N.

2007-01-01

The high-resolution structure of the DNA (5'-GTGTACA-C-3') with the selenium derivatization at the 2'-position of T2 was determined via MAD and SAD phasing. The selenium-derivatized structure (1.28 {angstrom} resolution) with the 2'-Se modification in the minor groove is isomorphorous to the native structure (2.0 {angstrom}). To directly compare with the conventional bromine derivatization, we incorporated bromine into the 5-postion of T4, determined the bromine-derivatized DNA structure at 1.5 {angstrom} resolution, and found that the local backbone torsion angles and solvent hydration patterns were altered in the structure with the Br incorporation in the major groove. Furthermore, while the native andmore » Br-derivatized DNAs needed over a week to form reasonable-size crystals, we observed that the Se-derivatized DNAs grew crystals overnight with high-diffraction quality, suggesting that the Se derivatization facilitated the crystal formation. In addition, the Se-derivatized DNA sequences crystallized under a broader range of buffer conditions, and generally had a faster crystal growth rate. Our experimental results indicate that the selenium derivatization of DNAs may facilitate the determination of nucleic acid X-ray crystal structures in phasing and high-quality crystal growth. In addition, our results suggest that the Se derivatization can be an alternative to the conventional Br derivatization.« less

The 1.3 A resolution structure of the RNA tridecamer r(GCGUUUGAAACGC): metal ion binding correlates with base unstacking and groove contraction.

PubMed

Timsit, Youri; Bombard, Sophie

2007-12-01

Metal ions play a key role in RNA folding and activity. Elucidating the rules that govern the binding of metal ions is therefore an essential step for better understanding the RNA functions. High-resolution data are a prerequisite for a detailed structural analysis of ion binding on RNA and, in particular, the observation of monovalent cations. Here, the high-resolution crystal structures of the tridecamer duplex r(GCGUUUGAAACGC) crystallized under different conditions provides new structural insights on ion binding on GAAA/UUU sequences that exhibit both unusual structural and functional properties in RNA. The present study extends the repertory of RNA ion binding sites in showing that the two first bases of UUU triplets constitute a specific site for sodium ions. A striking asymmetric pattern of metal ion binding in the two equivalent halves of the palindromic sequence demonstrates that sequence and its environment act together to bind metal ions. A highly ionophilic half that binds six metal ions allows, for the first time, the observation of a disodium cluster in RNA. The comparison of the equivalent halves of the duplex provides experimental evidences that ion binding correlates with structural alterations and groove contraction.

High-resolution angle-resolved photoemission study of electronic structure and charge-density wave formation in HoTe3

NASA Astrophysics Data System (ADS)

Liu, Guodong; Wang, Chenlu; Zhang, Yan; Hu, Bingfeng; Mou, Daixiang; Yu, Li; Zhao, Lin; Zhou, Xingjiang; Wang, Nanlin; Chen, Chuangtian; Xu, Zuyan

We performed high-resolution angle-resolved photoemission spectroscopy (ARPES) measurement on high quality crystal of HoTe3, an intriguing quasi-two-dimensional rare-earth-element tritelluride charge-density-wave (CDW) compound. The main features of the electronic structure in this compound are established by employing a quasi-CW laser (7eV) and a helium discharging lamp (21.22 eV) as excitation light sources. It reveals many bands back folded according to the CDW periodicity and two incommensurate CDW gaps created by perpendicular Fermi surface (FS) nesting vectors. A large gap is found to open in well nested regions of the Fermi surface sheets, whereas other Fermi surface sections with poor nesting remain ungapped. In particular, some peculiar features are identified by using our ultra-high resolution and bulk sensitive laser-ARPES.

Column ratio mapping: a processing technique for atomic resolution high-angle annular dark-field (HAADF) images.

PubMed

Robb, Paul D; Craven, Alan J

2008-12-01

An image processing technique is presented for atomic resolution high-angle annular dark-field (HAADF) images that have been acquired using scanning transmission electron microscopy (STEM). This technique is termed column ratio mapping and involves the automated process of measuring atomic column intensity ratios in high-resolution HAADF images. This technique was developed to provide a fuller analysis of HAADF images than the usual method of drawing single intensity line profiles across a few areas of interest. For instance, column ratio mapping reveals the compositional distribution across the whole HAADF image and allows a statistical analysis and an estimation of errors. This has proven to be a very valuable technique as it can provide a more detailed assessment of the sharpness of interfacial structures from HAADF images. The technique of column ratio mapping is described in terms of a [110]-oriented zinc-blende structured AlAs/GaAs superlattice using the 1 angstroms-scale resolution capability of the aberration-corrected SuperSTEM 1 instrument.

REFMAC5 for the refinement of macromolecular crystal structures

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

Murshudov, Garib N., E-mail: garib@ysbl.york.ac.uk; Skubák, Pavol; Lebedev, Andrey A.

The general principles behind the macromolecular crystal structure refinement program REFMAC5 are described. This paper describes various components of the macromolecular crystallographic refinement program REFMAC5, which is distributed as part of the CCP4 suite. REFMAC5 utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of SAD/SIRAS experimental diffraction data. To ensure chemical and structural integrity of the refined model, REFMAC5 offers several classes of restraints and choices of model parameterization. Reliable models at resolutions at least as low as 4 Å can be achieved thanks to low-resolution refinement toolsmore » such as secondary-structure restraints, restraints to known homologous structures, automatic global and local NCS restraints, ‘jelly-body’ restraints and the use of novel long-range restraints on atomic displacement parameters (ADPs) based on the Kullback–Leibler divergence. REFMAC5 additionally offers TLS parameterization and, when high-resolution data are available, fast refinement of anisotropic ADPs. Refinement in the presence of twinning is performed in a fully automated fashion. REFMAC5 is a flexible and highly optimized refinement package that is ideally suited for refinement across the entire resolution spectrum encountered in macromolecular crystallography.« less

Molecular understanding of mutagenicity using potential energy methods. Progress report, July 1, 1992--September 30, 1993

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

Broyde, S.; Shapiro, R.

1993-09-01

Our objective has been to elucidate on a molecular level, at atomic resolution, the structures of DNAs modified by highly mutagenic aromatic amines and hydrocarbons. The underlying hypothesis is that DNA replicates with reduced fidelity when its normal right-handed B-structure is altered, and one result is a higher mutation rate. This change in structure may occur normally at a low incidence but it may be enhanced greatly after covalent modification by a mutagenic substance. The methods that we use to elucidate structures are computational, but we keep in close contact with experimental developments, and we incorporate data from NMR studiesmore » in our calculations when they are available. X-ray and low resolution spectroscopic studies have not succeeded in producing atomic resolution views of mutagen and carcinogen-oligonucleotide adducts. Even the high resolution NMR method cannot alone yield molecular views, though it does so in combination with our computations. The specific methods that we employ are minimized potential energy calculations using the torsion angle space molecular mechanics program DUPLEX to yield static views. Molecular dynamics simulations of static structures with solvent and salt can be carried out with the program AMBER; this yields mobile views in a medium that mimics aspects of the natural aqueous environment of the cell.« less

Beyond Population Distribution: Enhancing Sociocultural Resolution from Remote Sensing

NASA Astrophysics Data System (ADS)

Bhaduri, B. L.; Rose, A.

2017-12-01

At Oak Ridge National Laboratory, since late 1990s, we have focused on developing high resolution population distribution and dynamics data from local to global scales. Increasing resolutions of geographic data has been mirrored by population data sets developed across the community. However, attempts to increase temporal and sociocultural resolutions have been limited given the lack of high resolution data on human settlements and activities. While recent advancements in moderate to high resolution earth observation have led to better physiographic data, the approach of exploiting very high resolution (sub-meter resolution) imagery has also proven useful for generating accurate human settlement maps. It allows potential (social and vulnerability) characterization of population from settlement structures by exploiting image texture and spectral features. Our recent research utilizing machine learning and geocomputation has not only validated "poverty mapping from imagery" hypothesis, but has delineated a new paradigm of rapid analysis of high resolution imagery to enhance such "neighborhood" mapping techniques. Such progress in GIScience is allowing us to move towards the goal of creating a global foundation level database for impervious surfaces and "neighborhoods," and holds tremendous promise for key applications focusing on sustainable development including many social science applications.

High spatial resolution three-dimensional mapping of vegetation spectral dynamics using computer vision

Treesearch

Jonathan P. Dandois; Erle C. Ellis

2013-01-01

High spatial resolution three-dimensional (3D) measurements of vegetation by remote sensing are advancing ecological research and environmental management. However, substantial economic and logistical costs limit this application, especially for observing phenological dynamics in ecosystem structure and spectral traits. Here we demonstrate a new aerial remote sensing...

High-resolution NMR study of light and heavy crude oils: “structure-property” analysis

NASA Astrophysics Data System (ADS)

Rakhmatullin, I.; Efimov, S.; Varfolomeev, M.; Klochkov, V.

2018-05-01

Measurements of three light and one heavy crude oil samples were carried out by high-resolution nuclear magnetic resonance (NMR) spectroscopy methods. Quantitative fractions of aromatic molecules and functional groups constituting oil hydrocarbons were determined, and comparative analysis of the oil samples of different viscosity and origin was done.

Elevated-temperature luminescence measurements to improve spatial resolution

NASA Astrophysics Data System (ADS)

Pluska, Mariusz; Czerwinski, Andrzej

2018-01-01

Various branches of applied physics use luminescence based methods to investigate light-emitting specimens with high spatial resolution. A key problem is that luminescence signals lack all the advantages of high locality (i.e. of high spatial resolution) when structures with strong built-in electric field are measured. Such fields exist intentionally in most photonic structures, and occur unintentionally in many other materials. In this case, as a result of beam-induced current generation and its outflow, information that indicates irregularities, nonuniformities and inhomogeneities, such as defects, is lost. We show that to avoid nonlocality and enable truly local luminescence measurements, an elevated measurement temperature as high as 350 K (or even higher) is, perhaps surprisingly, advantageous. This is in contrast to a widely used approach, where cryogenic temperatures, or at least room temperature, are recommended. The elevated temperature of a specimen, together with the current outflow being limited by focused ion beam (FIB) milling, is shown to improve the spatial resolution of luminescence measurements greatly. All conclusions drawn using the example of cathodoluminescence are useful for other luminescence techniques.

Radial super-resolution in digital holographic microscopy using structured illumination with circular symmetry

NASA Astrophysics Data System (ADS)

Yin, Yujian; Su, Ping; Ma, Jianshe

2018-01-01

A method to improve the radial resolution using special structured light is proposed in the field of digital holographic microscopy (DHM). A specimen is illuminated with circular symmetrical structured light that makes the spectrum have radial movement, so that high frequency components of the specimen are moved into the passband of the receiver to overcome the diffraction limit. In the DHM imaging system, Computer Generated Hologram (CGH) technology is used to generate the required structured light grating. Then the grating is loaded into a spatial light modulator (SLM) to obtain specific structured illumination. After recording the hologram, digital reconstruction, for the microstructure of a binary optical element that needs to observe radial distribution, the radial resolution of the specimen is improved experimentally compare it with the result of one-dimensional sinusoidal structured light imaging. And a method of designing structured light is presented.

SPED light sheet microscopy: fast mapping of biological system structure and function

PubMed Central

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

2016-01-01

The goal of understanding living nervous systems has driven interest in high-speed and large field-of-view volumetric imaging at cellular resolution. Light-sheet microscopy approaches have emerged for cellular-resolution functional brain imaging in small organisms such as larval zebrafish, but remain fundamentally limited in speed. Here we have developed SPED light sheet microscopy, which combines large volumetric field-of-view via an extended depth of field with the optical sectioning of light sheet microscopy, thereby eliminating the need to physically scan detection objectives for volumetric imaging. SPED enables scanning of thousands of volumes-per-second, limited only by camera acquisition rate, through the harnessing of optical mechanisms that normally result in unwanted spherical aberrations. We demonstrate capabilities of SPED microscopy by performing fast sub-cellular resolution imaging of CLARITY mouse brains and cellular-resolution volumetric Ca2+ imaging of entire zebrafish nervous systems. Together, SPED light sheet methods enable high-speed cellular-resolution volumetric mapping of biological system structure and function. PMID:26687363

Low-cost, high-resolution scanning laser ophthalmoscope for the clinical environment

NASA Astrophysics Data System (ADS)

Soliz, P.; Larichev, A.; Zamora, G.; Murillo, S.; Barriga, E. S.

2010-02-01

Researchers have sought to gain greater insight into the mechanisms of the retina and the optic disc at high spatial resolutions that would enable the visualization of small structures such as photoreceptors and nerve fiber bundles. The sources of retinal image quality degradation are aberrations within the human eye, which limit the achievable resolution and the contrast of small image details. To overcome these fundamental limitations, researchers have been applying adaptive optics (AO) techniques to correct for the aberrations. Today, deformable mirror based adaptive optics devices have been developed to overcome the limitations of standard fundus cameras, but at prices that are typically unaffordable for most clinics. In this paper we demonstrate a clinically viable fundus camera with auto-focus and astigmatism correction that is easy to use and has improved resolution. We have shown that removal of low-order aberrations results in significantly better resolution and quality images. Additionally, through the application of image restoration and super-resolution techniques, the images present considerably improved quality. The improvements lead to enhanced visualization of retinal structures associated with pathology.

Super-resolution reconstruction for 4D computed tomography of the lung via the projections onto convex sets approach

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

Zhang, Yu, E-mail: yuzhang@smu.edu.cn, E-mail: qianjinfeng08@gmail.com; Wu, Xiuxiu; Yang, Wei

2014-11-01

Purpose: The use of 4D computed tomography (4D-CT) of the lung is important in lung cancer radiotherapy for tumor localization and treatment planning. Sometimes, dense sampling is not acquired along the superior–inferior direction. This disadvantage results in an interslice thickness that is much greater than in-plane voxel resolutions. Isotropic resolution is necessary for multiplanar display, but the commonly used interpolation operation blurs images. This paper presents a super-resolution (SR) reconstruction method to enhance 4D-CT resolution. Methods: The authors assume that the low-resolution images of different phases at the same position can be regarded as input “frames” to reconstruct high-resolution images.more » The SR technique is used to recover high-resolution images. Specifically, the Demons deformable registration algorithm is used to estimate the motion field between different “frames.” Then, the projection onto convex sets approach is implemented to reconstruct high-resolution lung images. Results: The performance of the SR algorithm is evaluated using both simulated and real datasets. Their method can generate clearer lung images and enhance image structure compared with cubic spline interpolation and back projection (BP) method. Quantitative analysis shows that the proposed algorithm decreases the root mean square error by 40.8% relative to cubic spline interpolation and 10.2% versus BP. Conclusions: A new algorithm has been developed to improve the resolution of 4D-CT. The algorithm outperforms the cubic spline interpolation and BP approaches by producing images with markedly improved structural clarity and greatly reduced artifacts.« less

High-Resolution Surface Reconstruction from Imagery for Close Range Cultural Heritage Applications

NASA Astrophysics Data System (ADS)

Wenzel, K.; Abdel-Wahab, M.; Cefalu, A.; Fritsch, D.

2012-07-01

The recording of high resolution point clouds with sub-mm resolution is a demanding and cost intensive task, especially with current equipment like handheld laser scanners. We present an image based approached, where techniques of image matching and dense surface reconstruction are combined with a compact and affordable rig of off-the-shelf industry cameras. Such cameras provide high spatial resolution with low radiometric noise, which enables a one-shot solution and thus an efficient data acquisition while satisfying high accuracy requirements. However, the largest drawback of image based solutions is often the acquisition of surfaces with low texture where the image matching process might fail. Thus, an additional structured light projector is employed, represented here by the pseudo-random pattern projector of the Microsoft Kinect. Its strong infrared-laser projects speckles of different sizes. By using dense image matching techniques on the acquired images, a 3D point can be derived for almost each pixel. The use of multiple cameras enables the acquisition of a high resolution point cloud with high accuracy for each shot. For the proposed system up to 3.5 Mio. 3D points with sub-mm accuracy can be derived per shot. The registration of multiple shots is performed by Structure and Motion reconstruction techniques, where feature points are used to derive the camera positions and rotations automatically without initial information.

Deep skin structural and microcirculation imaging with extended-focus OCT

NASA Astrophysics Data System (ADS)

Blatter, Cedric; Grajciar, Branislav; Huber, Robert; Leitgeb, Rainer A.

2012-02-01

We present an extended focus OCT system for dermatologic applications that maintains high lateral resolution over a large depth range by using Bessel beam illumination. More, Bessel beams exhibit a self-reconstruction property that is particularly useful to avoid shadowing from surface structures such as hairs. High lateral resolution and high-speed measurement, thanks to a rapidly tuning swept source, allows not only for imaging of small skin structures in depth but also for comprehensive visualization of the small capillary network within the human skin in-vivo. We use this information for studying temporal vaso-responses to hypothermia. In contrast to other perfusion imaging methods such as laser Doppler imaging (LDI), OCT gives specific access to vascular responses in different vascular beds in depth.

Fast, long-term, super-resolution imaging with Hessian structured illumination microscopy.

PubMed

Huang, Xiaoshuai; Fan, Junchao; Li, Liuju; Liu, Haosen; Wu, Runlong; Wu, Yi; Wei, Lisi; Mao, Heng; Lal, Amit; Xi, Peng; Tang, Liqiang; Zhang, Yunfeng; Liu, Yanmei; Tan, Shan; Chen, Liangyi

2018-06-01

To increase the temporal resolution and maximal imaging time of super-resolution (SR) microscopy, we have developed a deconvolution algorithm for structured illumination microscopy based on Hessian matrixes (Hessian-SIM). It uses the continuity of biological structures in multiple dimensions as a priori knowledge to guide image reconstruction and attains artifact-minimized SR images with less than 10% of the photon dose used by conventional SIM while substantially outperforming current algorithms at low signal intensities. Hessian-SIM enables rapid imaging of moving vesicles or loops in the endoplasmic reticulum without motion artifacts and with a spatiotemporal resolution of 88 nm and 188 Hz. Its high sensitivity allows the use of sub-millisecond excitation pulses followed by dark recovery times to reduce photobleaching of fluorescent proteins, enabling hour-long time-lapse SR imaging of actin filaments in live cells. Finally, we observed the structural dynamics of mitochondrial cristae and structures that, to our knowledge, have not been observed previously, such as enlarged fusion pores during vesicle exocytosis.

Atomic resolution structure of cucurmosin, a novel type 1 ribosome-inactivating protein from the sarcocarp of Cucurbita moschata

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

Hou, Xiaomin; Meehan, Edward J.; Xie, Jieming

2008-10-27

A novel type 1 ribosome-inactivating protein (RIP) designated cucurmosin was isolated from the sarcocarp of Cucurbita moschata (pumpkin). Besides rRNA N-glycosidase activity, cucurmosin exhibits strong cytotoxicities to three cancer cell lines of both human and murine origins, but low toxicity to normal cells. Plant genomic DNA extracted from the tender leaves was amplified by PCR between primers based on the N-terminal sequence and X-ray sequence of the C-terminal. The complete mature protein sequence was obtained from N-terminal protein sequencing and partial DNA sequencing, confirmed by high resolution crystal structure analysis. The crystal structure of cucurmosin has been determined at 1.04more » {angstrom}, a resolution that has never been achieved before for any RIP. The structure contains two domains: a large N-terminal domain composed of seven {alpha}-helices and eight {beta}-strands, and a smaller C-terminal domain consisting of three {alpha}-helices and two {beta}-strands. The high resolution structure established a glycosylation pattern of GlcNAc{sub 2}Man3Xyl. Asn225 was identified as a glycosylation site. Residues Tyr70, Tyr109, Glu158 and Arg161 define the active site of cucurmosin as an RNA N-glycosidase. The structural basis of cytotoxicity difference between cucurmosin and trichosanthin is discussed.« less

Evaluating the quality of NMR structures by local density of protons.

PubMed

Ban, Yih-En Andrew; Rudolph, Johannes; Zhou, Pei; Edelsbrunner, Herbert

2006-03-01

Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures. 2005 Wiley-Liss, Inc.

High resolution iridocorneal angle imaging system by axicon lens assisted gonioscopy.

PubMed

Perinchery, Sandeep Menon; Shinde, Anant; Fu, Chan Yiu; Jeesmond Hong, Xun Jie; Baskaran, Mani; Aung, Tin; Murukeshan, Vadakke Matham

2016-07-29

Direct visualization and assessment of the iridocorneal angle (ICA) region with high resolution is important for the clinical evaluation of glaucoma. However, the current clinical imaging systems for ICA do not provide sufficient structural details due to their poor resolution. The key challenges in achieving high quality ICA imaging are its location in the anterior region of the eye and the occurrence of total internal reflection due to refractive index difference between cornea and air. Here, we report an indirect axicon assisted gonioscopy imaging probe with white light illumination. The illustrated results with this probe shows significantly improved visualization of structures in the ICA including TM region, compared to the current available tools. It could reveal critical details of ICA and expected to aid management by providing information that is complementary to angle photography and gonioscopy.

High resolution iridocorneal angle imaging system by axicon lens assisted gonioscopy

PubMed Central

Perinchery, Sandeep Menon; Shinde, Anant; Fu, Chan Yiu; Jeesmond Hong, Xun Jie; Baskaran, Mani; Aung, Tin; Murukeshan, Vadakke Matham

2016-01-01

Direct visualization and assessment of the iridocorneal angle (ICA) region with high resolution is important for the clinical evaluation of glaucoma. However, the current clinical imaging systems for ICA do not provide sufficient structural details due to their poor resolution. The key challenges in achieving high quality ICA imaging are its location in the anterior region of the eye and the occurrence of total internal reflection due to refractive index difference between cornea and air. Here, we report an indirect axicon assisted gonioscopy imaging probe with white light illumination. The illustrated results with this probe shows significantly improved visualization of structures in the ICA including TM region, compared to the current available tools. It could reveal critical details of ICA and expected to aid management by providing information that is complementary to angle photography and gonioscopy. PMID:27471000

High resolution iridocorneal angle imaging system by axicon lens assisted gonioscopy

NASA Astrophysics Data System (ADS)

Perinchery, Sandeep Menon; Shinde, Anant; Fu, Chan Yiu; Jeesmond Hong, Xun Jie; Baskaran, Mani; Aung, Tin; Murukeshan, Vadakke Matham

2016-07-01

Direct visualization and assessment of the iridocorneal angle (ICA) region with high resolution is important for the clinical evaluation of glaucoma. However, the current clinical imaging systems for ICA do not provide sufficient structural details due to their poor resolution. The key challenges in achieving high quality ICA imaging are its location in the anterior region of the eye and the occurrence of total internal reflection due to refractive index difference between cornea and air. Here, we report an indirect axicon assisted gonioscopy imaging probe with white light illumination. The illustrated results with this probe shows significantly improved visualization of structures in the ICA including TM region, compared to the current available tools. It could reveal critical details of ICA and expected to aid management by providing information that is complementary to angle photography and gonioscopy.

Cryo-EM structure of the large subunit of the spinach chloroplast ribosome

PubMed Central

Ahmed, Tofayel; Yin, Zhan; Bhushan, Shashi

2016-01-01

Protein synthesis in the chloroplast is mediated by the chloroplast ribosome (chloro-ribosome). Overall architecture of the chloro-ribosome is considerably similar to the Escherichia coli (E. coli) ribosome but certain differences are evident. The chloro-ribosome proteins are generally larger because of the presence of chloroplast-specific extensions in their N- and C-termini. The chloro-ribosome harbours six plastid-specific ribosomal proteins (PSRPs); four in the small subunit and two in the large subunit. Deletions and insertions occur throughout the rRNA sequence of the chloro-ribosome (except for the conserved peptidyl transferase center region) but the overall length of the rRNAs do not change significantly, compared to the E. coli. Although, recent advancements in cryo-electron microscopy (cryo-EM) have provided detailed high-resolution structures of ribosomes from many different sources, a high-resolution structure of the chloro-ribosome is still lacking. Here, we present a cryo-EM structure of the large subunit of the chloro-ribosome from spinach (Spinacia oleracea) at an average resolution of 3.5 Å. High-resolution map enabled us to localize and model chloro-ribosome proteins, chloroplast-specific protein extensions, two PSRPs (PSRP5 and 6) and three rRNA molecules present in the chloro-ribosome. Although comparable to E. coli, the polypeptide tunnel and the tunnel exit site show chloroplast-specific features. PMID:27762343

High-resolution NMR structures of the domains of Saccharomyces cerevisiae Tho1

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

Jacobsen, Julian O. B.; Allen, Mark D.; Freund, Stefan M. V.

2016-05-23

In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and the C-terminal RNA-binding domain of S. cerevisiae Tho1 have been determined. THO is a multi-protein complex involved in the formation of messenger ribonuclear particles (mRNPs) by coupling transcription with mRNA processing and export. THO is thought to be formed from five subunits, Tho2p, Hpr1p, Tex1p, Mft1p and Thp2p, and recent work has determined a low-resolution structure of the complex [Poulsen et al. (2014 ▸), PLoS One, 9, e103470]. A number of additional proteins are thought to be involved in the formation of mRNP in yeast, including Tho1,more » which has been shown to bind RNA in vitro and is recruited to actively transcribed chromatin in vivo in a THO-complex and RNA-dependent manner. Tho1 is known to contain a SAP domain at the N-terminus, but the ability to suppress the expression defects of the hpr1Δ mutant of THO was shown to reside in the RNA-binding C-terminal region. In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and C-terminal RNA-binding domain have been determined.« less

The High Resolution Powder Diffraction Beam Line at ESRF.

PubMed

Fitch, A N

2004-01-01

The optical design and performance of the high-resolution powder diffraction beam line BM16 at ESRF are discussed and illustrated. Some recent studies carried out on BM16 are described, including crystal structure solution and refinement, anomalous scattering, in situ measurements, residual strain in engineering components, investigation of microstructure, and grazing-incidence diffraction from surface layers. The beam line is built on a bending magnet, and operates in the energy range from 5 keV to 40 keV. After the move to an undulator source in 2002, it will benefit from an extented energy range up to 60 keV and increased flux and resolution. It is anticipated that enhancements to the data quality will be achieved, leading to the solution of larger crystal structures, and improvements in the accuracy of refined structures. The systematic exploitation of anisotropic thermal expansion will help reduce the effects of peak overlap in the analysis of powder diffraction data.

Unravel the submesoscale dynamics of the phytoplanktonic community in the NW Mediterranean Sea by in situ observations: the 2015 OSCAHR cruise

NASA Astrophysics Data System (ADS)

Marrec, Pierre; Doglioli, Andrea M.; Grégori, Gérald; Della Penna, Alice; Wagener, Thibaut; Rougier, Gille; Bhairy, Nagib; Dugenne, Mathilde; Lahbib, Soumaya; Thyssen, Melilotus

2017-04-01

Submesoscale phenomena have been recently recognized as a key factor in physical-biological-biogeochemical interactions, even if it remains unclear how these processes affect the global state of the ocean. Significant large-scale impacts of submesoscale structures on primary production and influence on the phytoplankton community structure and diversity have also been reported. In the past decade submesoscale dynamics have been predominately studied through the analysis of numerical simulations. Observing the coupled physical and biogeochemical variability at this scale remains challenging due to the ephemeral nature of submesoscale structures. The in-situ study of such structures necessitates multidisciplinary approaches involving in situ observations, remote sensing and modeling. Last progresses in biogeochemical sensor development and advanced methodology including Lagrangian real-time adaptative strategies represent outstanding opportunities. The OSCAHR (Observing Submesoscale Coupling At High Resolution) campaign has been conducted thanks to a multidisciplinary approach in order to improve the understanding of submesoscale processes. An ephemeral submesoscale structure was first identified in the Ligurian Sea in fall 2015 using both satellite and numerical modeling data before the campaign. Afterwards, advanced observing systems for the physical, biological and biogeochemical characterization of the sea surface layer at a high spatial and temporal frequency were deployed during a 10-days cruise. A MVP (Moving Vessel Profiler) was used to obtain high resolution CTD profiles associated to a new pumping system with 1-m vertical resolution. Moreover, along the ship track, in addition to the standard measurements of seawater surface samples (Chl-a, nutrients, O2, SST, SSS …), we deployed an automated flow cytometer for near real-time characterization of phytoplankton functional groups (from micro-phytoplankton down to cyanobacteria). The observed submesoscale feature presented a cyclonic structure with a relatively cold core surrounded by warmer waters. Six phytoplankton groups were identified across the structure with an unprecedented spatial and temporal resolution. According to our observations, we could quantify the influence of the fast established physical structure on the spatial distribution of the phytoplankton functional groups, giving coherence to the observed community structuration. Moreover, the high resolution of our observations allows us to estimate the growth rate of the main phytoplankton groups. Our innovative adaptative strategy with a multidisciplinary and transversal approach provides a deeper understanding of the marine biogeochemical dynamics through the first trophic levels.

Arctic storms simulated in atmospheric general circulation models under uniform high, uniform low, and variable resolutions

NASA Astrophysics Data System (ADS)

Roesler, E. L.; Bosler, P. A.; Taylor, M.

2016-12-01

The impact of strong extratropical storms on coastal communities is large, and the extent to which storms will change with a warming Arctic is unknown. Understanding storms in reanalysis and in climate models is important for future predictions. We know that the number of detected Arctic storms in reanalysis is sensitive to grid resolution. To understand Arctic storm sensitivity to resolution in climate models, we describe simulations designed to identify and compare Arctic storms at uniform low resolution (1 degree), at uniform high resolution (1/8 degree), and at variable resolution (1 degree to 1/8 degree). High-resolution simulations resolve more fine-scale structure and extremes, such as storms, in the atmosphere than a uniform low-resolution simulation. However, the computational cost of running a globally uniform high-resolution simulation is often prohibitive. The variable resolution tool in atmospheric general circulation models permits regional high-resolution solutions at a fraction of the computational cost. The storms are identified using the open-source search algorithm, Stride Search. The uniform high-resolution simulation has over 50% more storms than the uniform low-resolution and over 25% more storms than the variable resolution simulations. Storm statistics from each of the simulations is presented and compared with reanalysis. We propose variable resolution as a cost-effective means of investigating physics/dynamics coupling in the Arctic environment. Future work will include comparisons with observed storms to investigate tuning parameters for high resolution models. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. SAND2016-7402 A

Feasibility of creating a high-resolution 3D diffusion tensor imaging based atlas of the human brainstem: A case study at 11.7T

PubMed Central

Aggarwal, Manisha; Zhang, Jiangyang; Pletnikova, Olga; Crain, Barbara; Troncoso, Juan; Mori, Susumu

2013-01-01

A three-dimensional stereotaxic atlas of the human brainstem based on high resolution ex vivo diffusion tensor imaging (DTI) is introduced. The atlas consists of high resolution (125–255 μm isotropic) three-dimensional DT images of the formalin-fixed brainstem acquired at 11.7T. The DTI data revealed microscopic neuroanatomical details, allowing three-dimensional visualization and reconstruction of fiber pathways including the decussation of the pyramidal tract fibers, and interdigitating fascicles of the corticospinal and transverse pontine fibers. Additionally, strong grey-white matter contrasts in the apparent diffusion coefficient (ADC) maps enabled precise delineation of grey matter nuclei in the brainstem, including the cranial nerve and the inferior olivary nuclei. Comparison with myelin-stained histology shows that at the level of resolution achieved in this study, the structural details resolved with DTI contrasts in the brainstem were comparable to anatomical delineation obtained with histological sectioning. Major neural structures delineated from DTI contrasts in the brainstem are segmented and three-dimensionally reconstructed. Further, the ex vivo DTI data are nonlinearly mapped to a widely-used in vivo human brain atlas, to construct a high-resolution atlas of the brainstem in the Montreal Neurological Institute (MNI) stereotaxic coordinate space. The results demonstrate the feasibility of developing a 3D DTI based atlas for detailed characterization of brainstem neuroanatomy with high resolution and contrasts, which will be a useful resource for research and clinical applications. PMID:23384518

Time stamping of single optical photons with 10 ns resolution

NASA Astrophysics Data System (ADS)

Chakaberia, Irakli; Cotlet, Mircea; Fisher-Levine, Merlin; Hodges, Diedra R.; Nguyen, Jayke; Nomerotski, Andrei

2017-05-01

High spatial and temporal resolution are key features for many modern applications, e.g. mass spectrometry, probing the structure of materials via neutron scattering, studying molecular structure, etc.1-5 Fast imaging also provides the capability of coincidence detection, and the further addition of sensitivity to single optical photons with the capability of timestamping them further broadens the field of potential applications. Photon counting is already widely used in X-ray imaging,6 where the high energy of the photons makes their detection easier. TimepixCam is a novel optical imager,7 which achieves high spatial resolution using an array of 256×256 55 μm × 55μm pixels which have individually controlled functionality. It is based on a thin-entrance-window silicon sensor, bump-bonded to a Timepix ASIC.8 TimepixCam provides high quantum efficiency in the optical wavelength range (400-1000 nm). We perform the timestamping of single photons with a time resolution of 20 ns, by coupling TimepixCam to a fast image-intensifier with a P47 phosphor screen. The fast emission time of the P479 allows us to preserve good time resolution while maintaining the capability to focus the optical output of the intensifier onto the 256×256 pixel Timepix sensor area. We demonstrate the capability of the (TimepixCam + image intensifier) setup to provide high-resolution single-photon timestamping, with an effective frame rate of 50 MHz.

Enzyme Active Site Interactions by Raman/FTIR, NMR, and Ab Initio Calculations

PubMed Central

Deng, Hua

2017-01-01

Characterization of enzyme active site structure and interactions at high resolution is important for the understanding of the enzyme catalysis. Vibrational frequency and NMR chemical shift measurements of enzyme-bound ligands are often used for such purpose when X-ray structures are not available or when higher resolution active site structures are desired. This review is focused on how ab initio calculations may be integrated with vibrational and NMR chemical shift measurements to quantitatively determine high-resolution ligand structures (up to 0.001 Å for bond length and 0.01 Å for hydrogen bonding distance) and how interaction energies between bound ligand and its surroundings at the active site may be determined. Quantitative characterization of substrate ionic states, bond polarizations, tautomeric forms, conformational changes and its interactions with surroundings in enzyme complexes that mimic ground state or transition state can provide snapshots for visualizing the substrate structural evolution along enzyme-catalyzed reaction pathway. Our results have shown that the integration of spectroscopic studies with theoretical computation greatly enhances our ability to interpret experimental data and significantly increases the reliability of the theoretical analysis. PMID:24018325

Toward correlating structure and mechanics of platelets.

PubMed

Sorrentino, Simona; Studt, Jan-Dirk; Horev, Melanie Bokstad; Medalia, Ohad; Sapra, K Tanuj

2016-09-02

The primary physiological function of blood platelets is to seal vascular lesions after injury and form hemostatic thrombi in order to prevent blood loss. This task relies on the formation of strong cellular-extracellular matrix interactions in the subendothelial lesions. The cytoskeleton of a platelet is key to all of its functions: its ability to spread, adhere and contract. Despite the medical significance of platelets, there is still no high-resolution structural information of their cytoskeleton. Here, we discuss and present 3-dimensional (3D) structural analysis of intact platelets by using cryo-electron tomography (cryo-ET) and atomic force microscopy (AFM). Cryo-ET provides in situ structural analysis and AFM gives stiffness maps of the platelets. In the future, combining high-resolution structural and mechanical techniques will bring new understanding of how structural changes modulate platelet stiffness during activation and adhesion.

GRID: a high-resolution protein structure refinement algorithm.

PubMed

Chitsaz, Mohsen; Mayo, Stephen L

2013-03-05

The energy-based refinement of protein structures generated by fold prediction algorithms to atomic-level accuracy remains a major challenge in structural biology. Energy-based refinement is mainly dependent on two components: (1) sufficiently accurate force fields, and (2) efficient conformational space search algorithms. Focusing on the latter, we developed a high-resolution refinement algorithm called GRID. It takes a three-dimensional protein structure as input and, using an all-atom force field, attempts to improve the energy of the structure by systematically perturbing backbone dihedrals and side-chain rotamer conformations. We compare GRID to Backrub, a stochastic algorithm that has been shown to predict a significant fraction of the conformational changes that occur with point mutations. We applied GRID and Backrub to 10 high-resolution (≤ 2.8 Å) crystal structures from the Protein Data Bank and measured the energy improvements obtained and the computation times required to achieve them. GRID resulted in energy improvements that were significantly better than those attained by Backrub while expending about the same amount of computational resources. GRID resulted in relaxed structures that had slightly higher backbone RMSDs compared to Backrub relative to the starting crystal structures. The average RMSD was 0.25 ± 0.02 Å for GRID versus 0.14 ± 0.04 Å for Backrub. These relatively minor deviations indicate that both algorithms generate structures that retain their original topologies, as expected given the nature of the algorithms. Copyright © 2012 Wiley Periodicals, Inc.

Investigation of solar active regions at high resolution by balloon flights of the solar optical universal polarimeter, extended definition phase

NASA Technical Reports Server (NTRS)

Tarbell, Theodore D.

1993-01-01

Technical studies of the feasibility of balloon flights of the former Spacelab instrument, the Solar Optical Universal Polarimeter, with a modern charge-coupled device (CCD) camera, to study the structure and evolution of solar active regions at high resolution, are reviewed. In particular, different CCD cameras were used at ground-based solar observatories with the SOUP filter, to evaluate their performance and collect high resolution images. High resolution movies of the photosphere and chromosphere were successfully obtained using four different CCD cameras. Some of this data was collected in coordinated observations with the Yohkoh satellite during May-July, 1992, and they are being analyzed scientifically along with simultaneous X-ray observations.

Signatures of Penumbral Magnetic Fields at Very High Spatial Resolution

NASA Astrophysics Data System (ADS)

Langhans, K.

2006-12-01

Full Stokes spectro-polarimetry, together with refined techniques to interpret the measurements and continual modeling efforts, have improved our understanding of sunspot penumbrae in the last years. In spite of this progress, an improvement in the spatial resolution of the observations is clearly needed to establish in a more direct way the fine structure of the penumbra. The discovery of dark penumbral cores by tet{l3 Sc02} suggests that we are starting to resolve the fundamental scales of the penumbra. Spectro-polarimetric measurements that are sensitive to the magnetic field in both the photosphere and higher layers, and obtained at a spatial resolution approaching 0.1 arcsec, may therefore allow us to draw firm conclusions about the fine scale organization of penumbral magnetic fields. In this paper I will discuss recent polarization measurements at very high spatial resolution, trying to reconcile the different scenarios put forward to explain the structure of the penumbra.

Fast high resolution reconstruction in multi-slice and multi-view cMRI

NASA Astrophysics Data System (ADS)

Velasco Toledo, Nelson; Romero Castro, Eduardo

2015-01-01

Cardiac magnetic resonance imaging (cMRI) is an useful tool in diagnosis, prognosis and research since it functionally tracks the heart structure. Although useful, this imaging technique is limited in spatial resolution because heart is a constant moving organ, also there are other non controled conditions such as patient movements and volumetric changes during apnea periods when data is acquired, those conditions limit the time to capture high quality information. This paper presents a very fast and simple strategy to reconstruct high resolution 3D images from a set of low resolution series of 2D images. The strategy is based on an information reallocation algorithm which uses the DICOM header to relocate voxel intensities in a regular grid. An interpolation method is applied to fill empty places with estimated data, the interpolation resamples the low resolution information to estimate the missing information. As a final step a gaussian filter that denoises the final result. A reconstructed image evaluation is performed using as a reference a super-resolution reconstructed image. The evaluation reveals that the method maintains the general heart structure with a small loss in detailed information (edge sharpening and blurring), some artifacts related with input information quality are detected. The proposed method requires low time and computational resources.

Controlling Shear Stress in 3D Bioprinting is a Key Factor to Balance Printing Resolution and Stem Cell Integrity.

PubMed

Blaeser, Andreas; Duarte Campos, Daniela Filipa; Puster, Uta; Richtering, Walter; Stevens, Molly M; Fischer, Horst

2016-02-04

A microvalve-based bioprinting system for the manufacturing of high-resolution, multimaterial 3D-structures is reported. Applying a straightforward fluid-dynamics model, the shear stress at the nozzle site can precisely be controlled. Using this system, a broad study on how cell viability and proliferation potential are affected by different levels of shear stress is conducted. Complex, multimaterial 3D structures are printed with high resolution. This work pioneers the investigation of shear stress-induced cell damage in 3D bioprinting and might help to comprehend and improve the outcome of cell-printing studies in the future. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High Resolution Orientation Imaging Microscopy

DTIC Science & Technology

2012-05-02

Structure of In-Situ Deformations of Steel , TMS, San Diego, 2011 13. Jay Basinger, David Fullwood, Brent Adams, EBSD Detail Extraction for Greater Spatial...Its use has contributed to the development of new steels , aluminum alloys, high TC superconductors, electronic materials, lead-free solders, optical...Resolution The simulated pattern method has been used to recover lattice tetragonality in high-strength low- alloy steels . Since the level of

Micro-computed tomography: Applications for high-resolution skeletal density determinations: An example using annually banded crustose coralline algae

NASA Astrophysics Data System (ADS)

Chan, P.; Halfar, J.; Norley, C. J. D.; Pollmann, S. I.; Adey, W.; Holdsworth, D. W.

2017-09-01

Warming and acidification of the world's oceans are expected to have widespread consequences for marine biodiversity and ecosystem functioning. However, due to the relatively short record of instrumental observations, one has to rely upon geochemical and physical proxy information stored in biomineralized shells and skeletons of calcareous marine organisms as in situ recorders of past environments. Of particular interest is the response of marine calcifiers to ocean acidification through the examination of structural growth characteristics. Here we demonstrate the application of micro-computed tomography (micro-CT) for three-dimensional visualization and analysis of growth, skeletal density, and calcification in a slow-growing, annually banded crustose coralline alga Clathromorphum nereostratum (increment width ˜380 µm). X-ray images and time series of skeletal density were generated at 20 µm resolution and rebinned to 40, 60, 80, and 100 µm for comparison in a sensitivity analysis. Calcification rates were subsequently calculated as the product of density and growth (linear extension). While both skeletal density and calcification rates do not significantly differ at varying spatial resolutions (the latter being strongly influenced by growth rates), clear visualization of micron-scale growth features and the quantification of structural changes on subannual time scales requires higher scanning resolutions. In the present study, imaging at 20 µm resolution reveals seasonal cycles in density that correspond to summer/winter variations in skeletal structure observed using scanning electron microscopy (SEM). Micro-CT is a fast, nondestructive, and high-resolution technique for structural and morphometric analyses of temporally banded paleoclimate archives, particularly those that exhibit slow or compressed growth or micron-scale structures.

Enhancing SMAP Soil Moisture Retrievals via Superresolution Techniques

NASA Astrophysics Data System (ADS)

Beale, K. D.; Ebtehaj, A. M.; Romberg, J. K.; Bras, R. L.

2017-12-01

Soil moisture is a key state variable that modulates land-atmosphere interactions and its high-resolution global scale estimates are essential for improved weather forecasting, drought prediction, crop management, and the safety of troop mobility. Currently, NASA's Soil Moisture Active/Passive (SMAP) satellite provides a global picture of soil moisture variability at a resolution of 36 km, which is prohibitive for some hydrologic applications. The goal of this research is to enhance the resolution of SMAP passive microwave retrievals by a factor of 2 to 4 using modern superresolution techniques that rely on the knowledge of high-resolution land surface models. In this work, we explore several super-resolution techniques including an empirical dictionary method, a learned dictionary method, and a three-layer convolutional neural network. Using a year of global high-resolution land surface model simulations as training set, we found that we are able to produce high-resolution soil moisture maps that outperform the original low-resolution observations both qualitatively and quantitatively. In particular, on a patch-by-patch basis we are able to produce estimates of high-resolution soil moisture maps that improve on the original low-resolution patches by on average 6% in terms of mean-squared error, and 14% in terms of the structural similarity index.

Ultra-high resolution crystal structure of recombinant caprine β-lactoglobulin.

PubMed

Crowther, Jennifer M; Lassé, Moritz; Suzuki, Hironori; Kessans, Sarah A; Loo, Trevor S; Norris, Gillian E; Hodgkinson, Alison J; Jameson, Geoffrey B; Dobson, Renwick C J

2014-11-03

β-Lactoglobulin (βlg) is the most abundant whey protein in the milks of ruminant animals. While bovine βlg has been subjected to a vast array of studies, little is known about the caprine ortholog. We present an ultra-high resolution crystal structure of caprine βlg complemented by analytical ultracentrifugation and small-angle X-ray scattering data. In both solution and crystalline states caprine βlg is dimeric (K(D)<5 μM); however, our data suggest a flexible quaternary arrangement of subunits within the dimer. These structural findings will provide insight into relationships among structural, processing, nutritional and immunological characteristics that distinguish cow's and goat's milk. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Structures observed on the spot radiance fields during the FIRE experiment

NASA Technical Reports Server (NTRS)

Seze, Genevieve; Smith, Leonard; Desbois, Michel

1990-01-01

Three Spot images taken during the FIRE experiment on stratocumulus are analyzed. From this high resolution data detailed observations of the true cloud radiance field may be made. The structure and inhomogeneity of these radiance fields hold important implications for the radiation budget, while the fine scale structure in radiance field provides information on cloud dynamics. Wieliki and Welsh, and Parker et al., have quantified the inhomogeneities of the cumulus clouds through a careful examination of the distribution of cloud (and hole) size as functions of an effective cloud diameter and radiance threshold. Cahalan (1988) has compared for different cloud types of (stratocumulus, fair weather cumulus, convective clouds in the ITCZ) the distributions of clouds (and holes) sizes, the relation between the size and the perimeter of these clouds (and holes), and examining the possibility of scale invariance. These results are extended from LANDSAT resolution (57 m and 30 m) to the Spot resolution (10 m) resolution in the case of boundary layer clouds. Particular emphasis is placed on the statistics of zones of high and low reflectivity as a function of a threshold reflectivity.

Structural analysis of β-glucosidase mutants derived from a hyperthermophilic tetrameric structure

PubMed Central

Nakabayashi, Makoto; Kataoka, Misumi; Mishima, Yumiko; Maeno, Yuka; Ishikawa, Kazuhiko

2014-01-01

β-Glucosidase from Pyrococcus furiosus (BGLPf) is a hyperthermophilic tetrameric enzyme which can degrade cellooligosaccharides to glucose under hyperthermophilic conditions and thus holds promise for the saccharification of lignocellulosic biomass at high temperature. Prior to the production of large amounts of this enzyme, detailed information regarding the oligomeric structure of the enzyme is required. Several crystals of BGLPf have been prepared over the past ten years, but its crystal structure had not been solved until recently. In 2011, the first crystal structure of BGLPf was solved and a model was constructed at somewhat low resolution (2.35 Å). In order to obtain more detailed structural data on BGLPf, the relationship between its tetrameric structure and the quality of the crystal was re-examined. A dimeric form of BGLPf was constructed and its crystal structure was solved at a resolution of 1.70 Å using protein-engineering methods. Furthermore, using the high-resolution crystal structural data for the dimeric form, a monomeric form of BGLPf was constructed which retained the intrinsic activity of the tetrameric form. The thermostability of BGLPf is affected by its oligomeric structure. Here, the biophysical and biochemical properties of engineered dimeric and monomeric BGLPfs are reported, which are promising prototype models to apply to the saccharification reaction. Furthermore, details regarding the oligomeric structures of BGLPf and the reasons why the mutations yielded improved crystal structures are discussed. PMID:24598756

Combined multi-plane phase retrieval and super-resolution optical fluctuation imaging for 4D cell microscopy

NASA Astrophysics Data System (ADS)

Descloux, A.; Grußmayer, K. S.; Bostan, E.; Lukes, T.; Bouwens, A.; Sharipov, A.; Geissbuehler, S.; Mahul-Mellier, A.-L.; Lashuel, H. A.; Leutenegger, M.; Lasser, T.

2018-03-01

Super-resolution fluorescence microscopy provides unprecedented insight into cellular and subcellular structures. However, going `beyond the diffraction barrier' comes at a price, since most far-field super-resolution imaging techniques trade temporal for spatial super-resolution. We propose the combination of a novel label-free white light quantitative phase imaging with fluorescence to provide high-speed imaging and spatial super-resolution. The non-iterative phase retrieval relies on the acquisition of single images at each z-location and thus enables straightforward 3D phase imaging using a classical microscope. We realized multi-plane imaging using a customized prism for the simultaneous acquisition of eight planes. This allowed us to not only image live cells in 3D at up to 200 Hz, but also to integrate fluorescence super-resolution optical fluctuation imaging within the same optical instrument. The 4D microscope platform unifies the sensitivity and high temporal resolution of phase imaging with the specificity and high spatial resolution of fluorescence microscopy.

Chemical and morphological characterization of III-V strained layered heterostructures

NASA Astrophysics Data System (ADS)

Gray, Allen Lindsay

This dissertation describes investigations into the chemical and morphological characterization of III-V strained layered heterostructures by high-resolution x-ray diffraction. The purpose of this work is two-fold. The first was to use high-resolution x-ray diffraction coupled with transmission electron microscopy to characterize structurally a quaternary AlGaAsSb/InGaAsSb multiple quantum well heterostructure laser device. A method for uniquely determining the chemical composition of the strain quaternary quantum well, information previously thought to be unattainable using high resolution x-ray diffraction is thoroughly described. The misconception that high-resolution x-ray diffraction can separately find the well and barrier thickness of a multi-quantum well from the pendellosung fringe spacing is corrected, and thus the need for transmission electron microscopy is motivated. Computer simulations show that the key in finding the well composition is the intensity of the -3rd order satellite peaks in the diffraction pattern. The second part of this work addresses the evolution of strain relief in metastable multi-period InGaAs/GaAs multi-layered structures by high-resolution x-ray reciprocal space maps. Results are accompanied by transmission electron and differential contrast microscopy. The evolution of strain relief is tracked from a coherent "pseudomorphic" growth to a dislocated state as a function of period number by examining the x-ray diffuse scatter emanating from the average composition (zeroth-order) of the multi-layer. Relaxation is determined from the relative positions of the substrate with respect to the zeroth-order peak. For the low period number, the diffuse scatter from the multi-layer structure region arises from periodic, coherent crystallites. For the intermediate period number, the displacement fields around the multi-layer structure region transition to random coherent crystallites. At the higher period number, displacement fields of overlapping dislocations from relaxation of the random crystallites cause the initial stages of relaxation of the multi-layer structure. At the highest period number studied, relaxation of the multi-layer structure becomes bi-modal characterized by overlapping dislocations caused by mosaic block relaxation and periodically spaced misfit dislocations formed by 60°-type dislocations. The relaxation of the multi-layer structure has an exponential dependence on the diffuse scatter length-scale, which is shown to be a sensitive measure of the onset of relaxation.

High-resolution high-sensitivity and truly distributed optical frequency domain reflectometry for structural crack detection

NASA Astrophysics Data System (ADS)

Li, Wenhai; Bao, Xiaoyi; Chen, Liang

2014-05-01

Optical Frequency Domain Reflectometry (OFDR) with the use of polarization maintaining fiber (PMF) is capable of distinguishing strain and temperature, which is critical for successful field applications such as structural health monitoring (SHM) and smart material. Location-dependent measurement sensitivities along PMF are compensated by cross- and auto-correlations measurements of the spectra form a distributed parameter matrix. Simultaneous temperature and strain measurement accuracy of 1μstrain and 0.1°C is achieved with 2.5mm spatial resolution in over 180m range.

Can the black box be cracked? The augmentation of microbial ecology by high-resolution, automated sensing technologies.

PubMed

Shade, Ashley; Carey, Cayelan C; Kara, Emily; Bertilsson, Stefan; McMahon, Katherine D; Smith, Matthew C

2009-08-01

Automated sensing technologies, 'ASTs,' are tools that can monitor environmental or microbial-related variables at increasingly high temporal resolution. Microbial ecologists are poised to use AST data to couple microbial structure, function and associated environmental observations on temporal scales pertinent to microbial processes. In the context of aquatic microbiology, we discuss three applications of ASTs: windows on the microbial world, adaptive sampling and adaptive management. We challenge microbial ecologists to push AST potential in helping to reveal relationships between microbial structure and function.

The Astro-E/XRS Blocking Filter Calibration

NASA Technical Reports Server (NTRS)

Audley, Michael D.; Arnaud, Keith A.; Gendreau, Keith C.; Boyce, Kevin R.; Fleetwood, Charles M.; Kelley, Richard L.; Keski-Kuha, Ritva A.; Porter, F. Scott; Stahle, Caroline K.; Szymkowiak, Andrew E.

1999-01-01

We describe the transmission calibration of the Astro-E XRS blocking filters. The XRS instrument has five aluminized polyimide blocking filters. These filters are located at thermal stages ranging from 200 K to 60 mK. They are each about 1000 A thick. XRS will have high energy resolution which will enable it to see some of the extended fine structure around the oxygen and aluminum K edges of these filters. Thus, we are conducting a high spectral resolution calibration of the filters near these energies to resolve out extended flue structure and absorption lines.

LTE modeling of inhomogeneous chromospheric structure using high-resolution limb observations

NASA Technical Reports Server (NTRS)

Lindsey, C.

1987-01-01

The paper discusses considerations relevant to LTE modeling of rough atmospheres. Particular attention is given to the application of recent high-resolution observations of the solar limb in the far-infrared and radio continuum to the modeling of chromospheric spicules. It is explained how the continuum limb observations can be combined with morphological knowledge of spicule structure to model the physical conditions in chromospheric spicules. This discussion forms the basis for a chromospheric model presented in a parallel publication based on observations ranging from 100 microns to 2.6 mm.

The ultra high resolution XUV spectroheliograph: An attached payload for the Space Station Freedom

NASA Technical Reports Server (NTRS)

Walker, Arthur B. C., Jr.; Hoover, Richard B.; Barbee, Troy W., Jr.; Tandberg-Hanssen, Einar; Timothy, J. Gethyn; Lindblom, Joakim F.

1990-01-01

The principle goal of the ultra high resolution XUV spectroheliograph (UHRXS) is to improve the ability to identify and understand the fundamental physical processes that shape the structure and dynamics of the solar chromosphere and corona. The ability of the UHRXS imaging telescope and spectrographs to resolve fine scale structures over a broad wavelength (and hence temperature) range is critical to this mission. The scientific objectives and instrumental capabilities of the UHRXS investigation are reviewed before proceeding to a discussion of the expected performance of the UHRXS observatory.

Single image super-resolution using self-optimizing mask via fractional-order gradient interpolation and reconstruction.

PubMed

Yang, Qi; Zhang, Yanzhu; Zhao, Tiebiao; Chen, YangQuan

2017-04-04

Image super-resolution using self-optimizing mask via fractional-order gradient interpolation and reconstruction aims to recover detailed information from low-resolution images and reconstruct them into high-resolution images. Due to the limited amount of data and information retrieved from low-resolution images, it is difficult to restore clear, artifact-free images, while still preserving enough structure of the image such as the texture. This paper presents a new single image super-resolution method which is based on adaptive fractional-order gradient interpolation and reconstruction. The interpolated image gradient via optimal fractional-order gradient is first constructed according to the image similarity and afterwards the minimum energy function is employed to reconstruct the final high-resolution image. Fractional-order gradient based interpolation methods provide an additional degree of freedom which helps optimize the implementation quality due to the fact that an extra free parameter α-order is being used. The proposed method is able to produce a rich texture detail while still being able to maintain structural similarity even under large zoom conditions. Experimental results show that the proposed method performs better than current single image super-resolution techniques. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

High-energy-resolution monochromator for nuclear resonant scattering of synchrotron radiation by Te-125 at 35.49 keV

NASA Astrophysics Data System (ADS)

Imai, Yasuhiko; Yoda, Yoshitaka; Kitao, Shinji; Masuda, Ryo; Higashitaniguchi, Satoshi; Inaba, Chika; Seto, Makoto

2007-09-01

We have developed a high-resolution monochromator (HRM) for the measurement of nuclear resonant scattering (NRS) of synchrotron radiation by Te-125 at 35.49 keV using the backscattering of sapphire (9 1 -10 68). HRMs for nuclei with excitation energies less than 30 keV have been successfully developed using high angle diffractions by silicon crystals. Nearly perfect silicon crystal, however, is not suitable for high efficient HRMs at higher energy regions because the symmetry of the crystal structure is high and the Debye-temperature is low. Therefore, we used high quality synthetic sapphire crystal, which has low symmetry of crystal structure and high Debye-temperature. The temperature of the crystal was precisely controlled around 218 K to diffract synchrotron radiation with a Bragg angle of π/2 - 0.52 mrad. Energy was tuned by changing the crystal temperature under the condition of constant diffraction angle. Energy resolution was measured by detecting nuclear forward scattering by Te-125 in enriched TeO II. The relative energy resolution of 2.1×10 -7 is achieved, that is 7.5 meV in energy bandwidth. This HRM opens studies on element-specific dynamics and electronic state of substances containing Te-125.

Recent advances in electron tomography: TEM and HAADF-STEM tomography for materials science and semiconductor applications.

PubMed

Kübel, Christian; Voigt, Andreas; Schoenmakers, Remco; Otten, Max; Su, David; Lee, Tan-Chen; Carlsson, Anna; Bradley, John

2005-10-01

Electron tomography is a well-established technique for three-dimensional structure determination of (almost) amorphous specimens in life sciences applications. With the recent advances in nanotechnology and the semiconductor industry, there is also an increasing need for high-resolution three-dimensional (3D) structural information in physical sciences. In this article, we evaluate the capabilities and limitations of transmission electron microscopy (TEM) and high-angle-annular-dark-field scanning transmission electron microscopy (HAADF-STEM) tomography for the 3D structural characterization of partially crystalline to highly crystalline materials. Our analysis of catalysts, a hydrogen storage material, and different semiconductor devices shows that features with a diameter as small as 1-2 nm can be resolved in three dimensions by electron tomography. For partially crystalline materials with small single crystalline domains, bright-field TEM tomography provides reliable 3D structural information. HAADF-STEM tomography is more versatile and can also be used for high-resolution 3D imaging of highly crystalline materials such as semiconductor devices.

The structure of the ISM in the Zone of Avoidance by high-resolution multi-wavelength observations

NASA Astrophysics Data System (ADS)

Tóth, L. V.; Doi, Y.; Pinter, S.; Kovács, T.; Zahorecz, S.; Bagoly, Z.; Balázs, L. G.; Horvath, I.; Racz, I. I.; Onishi, T.

2018-05-01

We estimate the column density of the Galactic foreground interstellar medium (GFISM) in the direction of extragalactic sources. All-sky AKARI FIS infrared sky survey data might be used to trace the GFISM with a resolution of 2 arcminutes. The AKARI based GFISM hydrogen column density estimates are compared with similar quantities based on HI 21cm measurements of various resolution and of Planck results. High spatial resolution observations of the GFISM may be important recalculating the physical parameters of gamma-ray burst (GRB) host galaxies using the updated foreground parameters.

Developmental and morphological studies in Japanese medaka with ultra-high resolution optical coherence tomography.

PubMed

Gladys, Fanny Moses; Matsuda, Masaru; Lim, Yiheng; Jackin, Boaz Jessie; Imai, Takuto; Otani, Yukitoshi; Yatagai, Toyohiko; Cense, Barry

2015-02-01

We propose ultra-high resolution optical coherence tomography to study the morphological development of internal organs in medaka fish in the post-embryonic stages at micrometer resolution. Different stages of Japanese medaka were imaged after hatching in vivo with an axial resolution of 2.8 µm in tissue. Various morphological structures and organs identified in the OCT images were then compared with the histology. Due to the medaka's close resemblance to vertebrates, including humans, these morphological features play an important role in morphogenesis and can be used to study diseases that also occur in humans.

Ultrasound biomicroscopy. High-frequency ultrasound imaging of the eye at microscopic resolution.

PubMed

Pavlin, C J; Foster, F S

1998-11-01

UBM presents us with a new method of imaging the anterior segment of the eye at high resolution. Its strengths lie in its ability to produce cross-sections of the living eye at microscopic resolution without violating the integrity of the globe. UBM, although lacking the resolution of optical microscopy, gives us images in living eyes without affecting the internal relationships of the structures imaged. There are many other applications of this new imaging method. Examples of other uses include imaging adnexal pathology, assessing corneal changes with refractive surgery, the assessment of trauma, and determination of intraocular lens position.

Structured illumination 3D microscopy using adaptive lenses and multimode fibers

NASA Astrophysics Data System (ADS)

Czarske, Jürgen; Philipp, Katrin; Koukourakis, Nektarios

2017-06-01

Microscopic techniques with high spatial and temporal resolution are required for in vivo studying biological cells and tissues. Adaptive lenses exhibit strong potential for fast motion-free axial scanning. However, they also lead to a degradation of the achievable resolution because of aberrations. This hurdle can be overcome by digital optical technologies. We present a novel High-and-Low-frequency (HiLo) 3D-microscope using structured illumination and an adaptive lens. Uniform illumination is used to obtain optical sectioning for the high-frequency (Hi) components of the image, and nonuniform illumination is needed to obtain optical sectioning for the low-frequency (Lo) components of the image. Nonuniform illumination is provided by a multimode fiber. It ensures robustness against optical aberrations of the adaptive lens. The depth-of-field of our microscope can be adjusted a-posteriori by computational optics. It enables to create flexible scans, which compensate for irregular axial measurement positions. The adaptive HiLo 3D-microscope provides an axial scanning range of 1 mm with an axial resolution of about 4 microns and sub-micron lateral resolution over the full scanning range. In result, volumetric measurements with high temporal and spatial resolution are provided. Demonstration measurements of zebrafish embryos with reporter gene-driven fluorescence in the thyroid gland are presented.

Detailed Investigation of Core-Shell Precipitates in a Cu-Containing High Entropy Alloy

NASA Astrophysics Data System (ADS)

Alam, T.; Gwalani, B.; Viswanathan, G.; Fraser, H.; Banerjee, R.

2018-05-01

Due to the competing influences of configurational entropy and enthalpy of mixing, in recent years, secondary (including intermetallic) phases have been reported in many high entropy alloy (HEA) systems. These secondary phases offer great potential in terms of strengthening the HEA beyond the solid solution strengthening effects, and as such are of great interest in regards to alloy design for engineering applications. The present research investigates novel nano-scale core-shell precipitates forming within the disordered bcc matrix phase of an Al2CrCuFeNi2 HEA, utilizing complementary high-resolution microscopy techniques of atom probe tomography (APT) and transmission electron microscopy (TEM). The size, morphology, and local chemistry of these core-shell precipitates was measured by APT, and the composition was further corroborated by high-resolution scanning transmission electron microscopy-energy dispersive spectroscopy in an aberration-corrected TEM. Furthermore, high-resolution TEM imaging of the core-shell structure indicates that the Cu-rich core exhibits a bcc crystal structure.

High resolution spectroscopy in the microwave and far infrared

NASA Technical Reports Server (NTRS)

Pickett, Herbert M.

1990-01-01

High resolution rotational spectroscopy has long been central to remote sensing techniques in atmospheric sciences and astronomy. As such, laboratory measurements must supply the required data to make direct interpretation of data for instruments which sense atmospheres using rotational spectra. Spectral measurements in the microwave and far infrared regions are also very powerful tools when combined with infrared measurements for characterizing the rotational structure of vibrational spectra. In the past decade new techniques were developed which have pushed high resolution spectroscopy into the wavelength region between 25 micrometers and 2 mm. Techniques to be described include: (1) harmonic generation of microwave sources, (2) infrared laser difference frequency generation, (3) laser sideband generation, and (4) ultrahigh resolution interferometers.

Linking rainforest ecophysiology and microclimate through fusion of airborne LiDAR and hyperspectral imagery

Treesearch

Eben N. Broadbent; Angélica M. Almeyda Zambrano; Gregory P. Asner; Christopher B. Field; Brad E. Rosenheim; Ty Kennedy-Bowdoin; David E. Knapp; David Burke; Christian Giardina; Susan Cordell

2014-01-01

We develop and validate a high-resolution three-dimensional model of light and air temperature for a tropical forest interior in Hawaii along an elevation gradient varying greatly in structure but maintaining a consistent species composition. Our microclimate models integrate high-resolution airborne waveform light detection and ranging data (LiDAR) and hyperspectral...

High-resolution numerical models for smoke transport in plumes from wildland fires

Treesearch

Philip Cunningham; Scott Goodrick

2013-01-01

A high-resolution large-eddy simulation (LES) model is employed to examine the fundamental structure and dynamics of buoyant plumes arising from heat sources representative of wildland fires. Herein we describe several aspects of the mean properties of the simulated plumes. Mean plume trajectories are apparently well described by the traditional two-thirds law for...

High-resolution seismic-reflection images across the ICDP-USGS Eyreville deep drilling site, Chesapeake Bay impact structure

USGS Publications Warehouse

Powars, D.S.; Catchings, R.D.; Goldman, M.R.; Gohn, G.S.; Horton, J. Wright; Edwards, L.E.; Rymer, M.J.; Gandhok, G.

2009-01-01

The U.S. Geological Survey (USGS) acquired two 1.4-km-long, high-resolution (??5 m vertical resolution) seismic-reflection lines in 2006 that cross near the International Continental Scientifi c Drilling Program (ICDP)-USGS Eyreville deep drilling site located above the late Eocene Chesapeake Bay impact structure in Virginia, USA. Five-meter spacing of seismic sources and geophones produced high-resolution images of the subsurface adjacent to the 1766-m-depth Eyreville core holes. Analysis of these lines, in the context of the core hole stratigraphy, shows that moderateamplitude, discontinuous, dipping reflections below ??527 m correlate with a variety of Chesapeake Bay impact structure sediment and rock breccias recovered in the cores. High-amplitude, continuous, subhorizontal reflections above ??527 m depth correlate with the uppermost part of the Chesapeake Bay impact structure crater-fi ll sediments and postimpact Eocene to Pleistocene sediments. Refl ections with ??20-30 m of relief in the uppermost part of the crater-fi ll and lowermost part of the postimpact section suggest differential compaction of the crater-fi ll materials during early postimpact time. The top of the crater-fi ll section also shows ??20 m of relief that appears to represent an original synimpact surface. Truncation surfaces, locally dipping reflections, and depth variations in reflection amplitudes generally correlate with the lithostratigraphic and sequence-stratigraphic units and contacts in the core. Seismic images show apparent postimpact paleochannels that include the fi rst possible Miocene paleochannels in the Mid-Atlantic Coastal Plain. Broad downwarping in the postimpact section unrelated to structures in the crater fi ll indicates postimpact sediment compaction. ?? 2009 The Geological Society of America.

Terahertz-wave near-field imaging with subwavelength resolution using surface-wave-assisted bow-tie aperture

NASA Astrophysics Data System (ADS)

Ishihara, Kunihiko; Ohashi, Keishi; Ikari, Tomofumi; Minamide, Hiroaki; Yokoyama, Hiroyuki; Shikata, Jun-ichi; Ito, Hiromasa

2006-11-01

We demonstrate the terahertz-wave near-field imaging with subwavelength resolution using a bow-tie shaped aperture surrounded by concentric periodic structures in a metal film. A subwavelength aperture with concentric periodic grooves, which are known as a bull's eye structure, shows extremely large enhanced transmission beyond the diffraction limit caused by the resonant excitation of surface waves. Additionally, a bow-tie aperture exhibits extraordinary field enhancement at the sharp tips of the metal, which enhances the transmission and the subwavelength spatial resolution. We introduced a bow-tie aperture to the bull's eye structure and achieved high spatial resolution (˜λ/17) in the near-field region. The terahertz-wave near-field image of the subwavelength metal pattern (pattern width=20μm) was obtained for the wavelength of 207μm.

Nonlinear structured-illumination enhanced temporal focusing multiphoton excitation microscopy with a digital micromirror device.

PubMed

Cheng, Li-Chung; Lien, Chi-Hsiang; Da Sie, Yong; Hu, Yvonne Yuling; Lin, Chun-Yu; Chien, Fan-Ching; Xu, Chris; Dong, Chen Yuan; Chen, Shean-Jen

2014-08-01

In this study, the light diffraction of temporal focusing multiphoton excitation microscopy (TFMPEM) and the excitation patterning of nonlinear structured-illumination microscopy (NSIM) can be simultaneously and accurately implemented via a single high-resolution digital micromirror device. The lateral and axial spatial resolutions of the TFMPEM are remarkably improved through the second-order NSIM and projected structured light, respectively. The experimental results demonstrate that the lateral and axial resolutions are enhanced from 397 nm to 168 nm (2.4-fold) and from 2.33 μm to 1.22 μm (1.9-fold), respectively, in full width at the half maximum. Furthermore, a three-dimensionally rendered image of a cytoskeleton cell featuring ~25 nm microtubules is improved, with other microtubules at a distance near the lateral resolution of 168 nm also able to be distinguished.

Brillouin Optical Correlation Domain Analysis in Composite Material Beams

PubMed Central

Stern, Yonatan; London, Yosef; Preter, Eyal; Antman, Yair; Diamandi, Hilel Hagai; Silbiger, Maayan; Adler, Gadi; Shalev, Doron; Zadok, Avi

2017-01-01

Structural health monitoring is a critical requirement in many composites. Numerous monitoring strategies rely on measurements of temperature or strain (or both), however these are often restricted to point-sensing or to the coverage of small areas. Spatially-continuous data can be obtained with optical fiber sensors. In this work, we report high-resolution distributed Brillouin sensing over standard fibers that are embedded in composite structures. A phase-coded, Brillouin optical correlation domain analysis (B-OCDA) protocol was employed, with spatial resolution of 2 cm and sensitivity of 1 °K or 20 micro-strain. A portable measurement setup was designed and assembled on the premises of a composite structures manufacturer. The setup was successfully utilized in several structural health monitoring scenarios: (a) monitoring the production and curing of a composite beam over 60 h; (b) estimating the stiffness and Young’s modulus of a composite beam; and (c) distributed strain measurements across the surfaces of a model wing of an unmanned aerial vehicle. The measurements are supported by the predictions of structural analysis calculations. The results illustrate the potential added values of high-resolution, distributed Brillouin sensing in the structural health monitoring of composites. PMID:28974041

Brillouin Optical Correlation Domain Analysis in Composite Material Beams.

PubMed

Stern, Yonatan; London, Yosef; Preter, Eyal; Antman, Yair; Diamandi, Hilel Hagai; Silbiger, Maayan; Adler, Gadi; Levenberg, Eyal; Shalev, Doron; Zadok, Avi

2017-10-02

Structural health monitoring is a critical requirement in many composites. Numerous monitoring strategies rely on measurements of temperature or strain (or both), however these are often restricted to point-sensing or to the coverage of small areas. Spatially-continuous data can be obtained with optical fiber sensors. In this work, we report high-resolution distributed Brillouin sensing over standard fibers that are embedded in composite structures. A phase-coded, Brillouin optical correlation domain analysis (B-OCDA) protocol was employed, with spatial resolution of 2 cm and sensitivity of 1 °K or 20 micro-strain. A portable measurement setup was designed and assembled on the premises of a composite structures manufacturer. The setup was successfully utilized in several structural health monitoring scenarios: (a) monitoring the production and curing of a composite beam over 60 h; (b) estimating the stiffness and Young's modulus of a composite beam; and (c) distributed strain measurements across the surfaces of a model wing of an unmanned aerial vehicle. The measurements are supported by the predictions of structural analysis calculations. The results illustrate the potential added values of high-resolution, distributed Brillouin sensing in the structural health monitoring of composites.

Increasing the electron-transfer ability of Cyanidioschyzon merolae ferredoxin by a one-point mutation – A high resolution and Fe-SAD phasing crystal structure analysis of the Asp58Asn mutant

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

Ueno, Yuko; Matsumoto, Takashi; Yamano, Akihito

2013-07-12

Highlights: •A single amino acid change on the ferredoxin surface affects electron transfer. •Precise positions of amide atoms were located utilizing no prior structural data. •Ultra high resolution and SAD phasing may be used for bias-free model building. -- Abstract: Cyanidioschyzon merolae (Cm) is a single cell red algae that grows in rather thermophilic (40–50 °C) and acidic (pH 1–3) conditions. Ferredoxin (Fd) was purified from this algae and characterized as a plant-type [2Fe–2S] Fd by physicochemical techniques. A high resolution (0.97 Å) three-dimensional structure of the CmFd D58N mutant molecule has been determined using the Fe-SAD phasing method tomore » clarify the precise position of the Asn58 amide, as this substitution increases the electron-transfer ability relative to wild-type CmFd by a factor of 1.5. The crystal structure reveals an electro-positive surface surrounding Asn58 that may interact with ferredoxin NADP{sup +} reductase or cytochrome c.« less

Structure of Ce2RhIn8: an example of complementary use of high-resolution neutron powder diffraction and reciprocal-space mapping to study complex materials.

PubMed

Moshopoulou, E G; Ibberson, R M; Sarrao, J L; Thompson, J D; Fisk, Z

2006-04-01

The room-temperature crystal structure of the heavy fermion antiferromagnet Ce2RhIn8, dicerium rhodium octaindide, has been studied by a combination of high-resolution synchrotron X-ray reciprocal-space mapping of single crystals and high-resolution time-of-flight neutron powder diffraction. The structure is disordered, exhibiting a complex interplay of non-periodic, partially correlated planar defects, coexistence and segregation of polytypic phases (induced by periodic planar ;defects'), mosaicity (i.e. domain misalignment) and non-uniform strain. These effects evolve as a function of temperature in a complicated way, but they remain down to low temperatures. The room-temperature diffraction data are best represented by a complex mixture of two polytypic phases, which are affected by non-periodic, partially correlated planar defects, differ slightly in their tetragonal structures, and exhibit different mosaicities and strain values. Therefore, Ce2RhIn8 approaches the paracrystalline state, rather than the classic crystalline state and thus several of the concepts of conventional single-crystal crystallography are inapplicable. The structural results are discussed in the context of the role of disorder in the heavy-fermion state and in the interplay between superconductivity and magnetism.

Highly Coarse-Grained Representations of Transmembrane Proteins

PubMed Central

2017-01-01

Numerous biomolecules and biomolecular complexes, including transmembrane proteins (TMPs), are symmetric or at least have approximate symmetries. Highly coarse-grained models of such biomolecules, aiming at capturing the essential structural and dynamical properties on resolution levels coarser than the residue scale, must preserve the underlying symmetry. However, making these models obey the correct physics is in general not straightforward, especially at the highly coarse-grained resolution where multiple (∼3–30 in the current study) amino acid residues are represented by a single coarse-grained site. In this paper, we propose a simple and fast method of coarse-graining TMPs obeying this condition. The procedure involves partitioning transmembrane domains into contiguous segments of equal length along the primary sequence. For the coarsest (lowest-resolution) mappings, it turns out to be most important to satisfy the symmetry in a coarse-grained model. As the resolution is increased to capture more detail, however, it becomes gradually more important to match modular repeats in the secondary structure (such as helix-loop repeats) instead. A set of eight TMPs of various complexity, functionality, structural topology, and internal symmetry, representing different classes of TMPs (ion channels, transporters, receptors, adhesion, and invasion proteins), has been examined. The present approach can be generalized to other systems possessing exact or approximate symmetry, allowing for reliable and fast creation of multiscale, highly coarse-grained mappings of large biomolecular assemblies. PMID:28043122

Mesosacle eddies in a high resolution OGCM and coupled ocean-atmosphere GCM

NASA Astrophysics Data System (ADS)

Yu, Y.; Liu, H.; Lin, P.

2017-12-01

The present study described high-resolution climate modeling efforts including oceanic, atmospheric and coupled general circulation model (GCM) at the state key laboratory of numerical modeling for atmospheric sciences and geophysical fluid dynamics (LASG), Institute of Atmospheric Physics (IAP). The high-resolution OGCM is established based on the latest version of the LASG/IAP Climate system Ocean Model (LICOM2.1), but its horizontal resolution and vertical resolution are increased to 1/10° and 55 layers, respectively. Forced by the surface fluxes from the reanalysis and observed data, the model has been integrated for approximately more than 80 model years. Compared with the simulation of the coarse-resolution OGCM, the eddy-resolving OGCM not only better simulates the spatial-temporal features of mesoscale eddies and the paths and positions of western boundary currents but also reproduces the large meander of the Kuroshio Current and its interannual variability. Another aspect, namely, the complex structures of equatorial Pacific currents and currents in the coastal ocean of China, are better captured due to the increased horizontal and vertical resolution. Then we coupled the high resolution OGCM to NCAR CAM4 with 25km resolution, in which the mesoscale air-sea interaction processes are better captured.

Human brain diffusion tensor imaging at submillimeter isotropic resolution on a 3 Tesla clinical MRI scanner

PubMed Central

Chang, Hing-Chiu; Sundman, Mark; Petit, Laurent; Guhaniyogi, Shayan; Chu, Mei-Lan; Petty, Christopher; Song, Allen W.; Chen, Nan-kuei

2015-01-01

The advantages of high-resolution diffusion tensor imaging (DTI) have been demonstrated in a recent post-mortem human brain study (Miller et al., NeuroImage 2011;57(1):167–181), showing that white matter fiber tracts can be much more accurately detected in data at submillimeter isotropic resolution. To our knowledge, in vivo human brain DTI at submillimeter isotropic resolution has not been routinely achieved yet because of the difficulty in simultaneously achieving high resolution and high signal-to-noise ratio (SNR) in DTI scans. Here we report a 3D multi-slab interleaved EPI acquisition integrated with multiplexed sensitivity encoded (MUSE) reconstruction, to achieve high-quality, high-SNR and submillimeter isotropic resolution (0.85 × 0.85 × 0.85 mm3) in vivo human brain DTI on a 3 Tesla clinical MRI scanner. In agreement with the previously reported post-mortem human brain DTI study, our in vivo data show that the structural connectivity networks of human brains can be mapped more accurately and completely with high-resolution DTI as compared with conventional DTI (e.g., 2 × 2 × 2 mm3). PMID:26072250

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography

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

Bhardwaj, Anshul; Casjens, Sherwood R.; Cingolani, Gino, E-mail: gino.cingolani@jefferson.edu

2014-02-01

This study presents the crystal structure of a ∼320 Å long protein fiber generated by in-frame extension of its repeated helical coiled-coil core. Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identifiedmore » in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20–35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.« less

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

Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam ismore » often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Furthermore, our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.« less

Reflective type objective based spectral-domain phase-sensitive optical coherence tomography for high-sensitive structural and functional imaging of cochlear microstructures through intact bone of an excised guinea pig cochlea

NASA Astrophysics Data System (ADS)

Subhash, Hrebesh M.; Wang, Ruikang K.; Chen, Fangyi; Nuttall, Alfred L.

2013-03-01

Most of the optical coherence tomographic (OCT) systems for high resolution imaging of biological specimens are based on refractive type microscope objectives, which are optimized for specific wave length of the optical source. In this study, we present the feasibility of using commercially available reflective type objective for high sensitive and high resolution structural and functional imaging of cochlear microstructures of an excised guinea pig through intact temporal bone. Unlike conventional refractive type microscopic objective, reflective objective are free from chromatic aberrations due to their all-reflecting nature and can support a broadband of spectrum with very high light collection efficiency.

Resolution of anisotropic and shielded highly conductive layers using 2-D electromagnetic modelling in the Rhine Graben and Black Forest

NASA Astrophysics Data System (ADS)

Tezkan, Bülent; Červ, Václav; Pek, Josef

1992-12-01

Anisotropy in magnetotelluric (MT) data has been found very often and has been explained as the result of local structures of different conductivities. In this paper, an observed anisotropy in MT data is not interpreted qualitatively in terms of local structures but is modelled quantitatively by a quasi-anisotropic layer. Besides the MT transfer functions, measurements of the vertical magnetic component are required. The second goal of this paper is to describe a method which permits the resolution of mid-crustal conductive layers in the presence of an additional high-conductivity layer at the surface. This method is possible in a two-dimensional (2-D) situation that limits the spatial extension of the surface structure. Again, vertical magnetic field recordings are necessary, but the phase of the E-polarization with respect to the 2-D structure is the most sensitive parameter. Using two field sites in Southern Germany, it has been possible to give a quantitative explanation of anisotropy and an improved depth resolution, and to derive an integrated conductivity of the highly conductive mid-crustal layers using MT and geomagnetic depth sounding data. The anisotropic highly conductive layer is located 12 km beneath the poorly conductive Black Forest crystalline rocks, whereas it is at a depth of 6 km beneath the highly conductive Rhine Graben sediments.

In vivo high-resolution cortical imaging with extended-focus optical coherence microscopy in the visible-NIR wavelength range

NASA Astrophysics Data System (ADS)

Marchand, Paul J.; Szlag, Daniel; Bouwens, Arno; Lasser, Theo

2018-03-01

Visible light optical coherence tomography has shown great interest in recent years for spectroscopic and high-resolution retinal and cerebral imaging. Here, we present an extended-focus optical coherence microscopy system operating from the visible to the near-infrared wavelength range for high axial and lateral resolution imaging of cortical structures in vivo. The system exploits an ultrabroad illumination spectrum centered in the visible wavelength range (λc = 650 nm, Δλ ˜ 250 nm) offering a submicron axial resolution (˜0.85 μm in water) and an extended-focus configuration providing a high lateral resolution of ˜1.4 μm maintained over ˜150 μm in depth in water. The system's axial and lateral resolution are first characterized using phantoms, and its imaging performance is then demonstrated by imaging the vasculature, myelinated axons, and neuronal cells in the first layers of the somatosensory cortex of mice in vivo.

Shape Complementarity of Protein-Protein Complexes at Multiple Resolutions

PubMed Central

Zhang, Qing; Sanner, Michel; Olson, Arthur J.

2010-01-01

Biological complexes typically exhibit intermolecular interfaces of high shape complementarity. Many computational docking approaches use this surface complementarity as a guide in the search for predicting the structures of protein-protein complexes. Proteins often undergo conformational changes in order to create a highly complementary interface when associating. These conformational changes are a major cause of failure for automated docking procedures when predicting binding modes between proteins using their unbound conformations. Low resolution surfaces in which high frequency geometric details are omitted have been used to address this problem. These smoothed, or blurred, surfaces are expected to minimize the differences between free and bound structures, especially those that are due to side chain conformations or small backbone deviations. In spite of the fact that this approach has been used in many docking protocols, there has yet to be a systematic study of the effects of such surface smoothing on the shape complementarity of the resulting interfaces. Here we investigate this question by computing shape complementarity of a set of 66 protein-protein complexes represented by multi-resolution blurred surfaces. Complexed and unbound structures are available for these protein-protein complexes. They are a subset of complexes from a non-redundant docking benchmark selected for rigidity (i.e. the proteins undergo limited conformational changes between their bound and unbound states). In this work we construct the surfaces by isocontouring a density map obtained by accumulating the densities of Gaussian functions placed at all atom centers of the molecule. The smoothness or resolution is specified by a Gaussian fall-off coefficient, termed “blobbyness”. Shape complementarity is quantified using a histogram of the shortest distances between two proteins' surface mesh vertices for both the crystallographic complexes and the complexes built using the protein structures in their unbound conformation. The histograms calculated for the bound complex structures demonstrate that medium resolution smoothing (blobbyness=−0.9) can reproduce about 88% of the shape complementarity of atomic resolution surfaces. Complexes formed from the free component structures show a partial loss of shape complementarity (more overlaps and gaps) with the atomic resolution surfaces. For surfaces smoothed to low resolution (blobbyness=−0.3), we find more consistency of shape complementarity between the complexed and free cases. To further reduce bad contacts without significantly impacting the good contacts we introduce another blurred surface, in which the Gaussian densities of flexible atoms are reduced. From these results we discuss the use of shape complementarity in protein-protein docking. PMID:18837463

High-resolution matrix-assisted laser desorption ionization–imaging mass spectrometry of lipids in rodent optic nerve tissue

PubMed Central

Anderson, David M. G.; Mills, Daniel; Spraggins, Jeffrey; Lambert, Wendi S.; Calkins, David J.

2013-01-01

Purpose To develop a method for generating high spatial resolution (10 µm) matrix-assisted laser desorption ionization (MALDI) images of lipids in rodent optic nerve tissue. Methods Ice-embedded optic nerve tissue from rats and mice were cryosectioned across the coronal and sagittal axes of the nerve fiber. Sections were thaw mounted on gold-coated MALDI plates and were washed with ammonium acetate to remove biologic salts before being coated in 2,5-dihydroxybenzoic acid by sublimation. MALDI images were generated in positive and negative ion modes at 10 µm spatial resolution. Lipid identification was performed with a high mass resolution Fourier transform ion cyclotron resonance mass spectrometer. Results Several lipid species were observed with high signal intensity in MALDI images of optic nerve tissue. Several lipids were localized to specific structures including in the meninges surrounding the optic nerve and in the central neuronal tissue. Specifically, phosphatidylcholine species were observed throughout the nerve tissue in positive ion mode while sulfatide species were observed in high abundance in the meninges surrounding the optic nerve in negative ion mode. Accurate mass measurements and fragmentation using sustained off-resonance irradiation with a high mass resolution Fourier transform ion cyclotron resonance mass spectrometer instrument allowed for identification of lipid species present in the small structure of the optic nerve directly from tissue sections. Conclusions An optimized sample preparation method provides excellent sensitivity for lipid species present within optic nerve tissue. This allowed the laser spot size and fluence to be reduced to obtain a high spatial resolution of 10 µm. This new imaging modality can now be applied to determine spatial and molecular changes in optic nerve tissue with disease. PMID:23559852

Small-Scale Tropopause Dynamics and TOMS Total Ozone

NASA Technical Reports Server (NTRS)

Stanford, John L.

2002-01-01

This project used Earth Probe Total Ozone Mapping Spectrometer (EP TOMS) along-track ozone retrievals, in conjunction with ancillary meteorological fields and modeling studies, for high resolution investigations of upper troposphere and lower stratosphere dynamics. Specifically, high resolution along-track (Level 2) EP TOMS data were used to investigate the beautiful fine-scale structure in constituent and meteorological fields prominent in the evolution of highly non-linear baroclinic storm systems. Comparison was made with high resolution meteorological models. The analyses provide internal consistency checks and validation of the EP TOMS data which are vital for monitoring ozone depletion in both polar and midlatitude regions.

Helium ion microscopy and ultra-high-resolution scanning electron microscopy analysis of membrane-extracted cells reveals novel characteristics of the cytoskeleton of Giardia intestinalis.

PubMed

Gadelha, Ana Paula Rocha; Benchimol, Marlene; de Souza, Wanderley

2015-06-01

Giardia intestinalis presents a complex microtubular cytoskeleton formed by specialized structures, such as the adhesive disk, four pairs of flagella, the funis and the median body. The ultrastructural organization of the Giardia cytoskeleton has been analyzed using different microscopic techniques, including high-resolution scanning electron microscopy. Recent advances in scanning microscopy technology have opened a new venue for the characterization of cellular structures and include scanning probe microscopy techniques such as ultra-high-resolution scanning electron microscopy (UHRSEM) and helium ion microscopy (HIM). Here, we studied the organization of the cytoskeleton of G. intestinalis trophozoites using UHRSEM and HIM in membrane-extracted cells. The results revealed a number of new cytoskeletal elements associated with the lateral crest and the dorsal surface of the parasite. The fine structure of the banded collar was also observed. The marginal plates were seen linked to a network of filaments, which were continuous with filaments parallel to the main cell axis. Cytoplasmic filaments that supported the internal structures were seen by the first time. Using anti-actin antibody, we observed a labeling in these filamentous structures. Taken together, these data revealed new surface characteristics of the cytoskeleton of G. intestinalis and may contribute to an improved understanding of the structural organization of trophozoites. Copyright © 2015 Elsevier Inc. All rights reserved.

Determination of atomic-scale chemical composition at semiconductor heteroepitaxial interfaces by high-resolution transmission electron microscopy.

PubMed

Wen, C; Ma, Y J

2018-03-01

The determination of atomic structures and further quantitative information such as chemical compositions at atomic scale for semiconductor defects or heteroepitaxial interfaces can provide direct evidence to understand their formation, modification, and/or effects on the properties of semiconductor films. The commonly used method, high-resolution transmission electron microscopy (HRTEM), suffers from difficulty in acquiring images that correctly show the crystal structure at atomic resolution, because of the limitation in microscope resolution or deviation from the Scherzer-defocus conditions. In this study, an image processing method, image deconvolution, was used to achieve atomic-resolution (∼1.0 Å) structure images of small lattice-mismatch (∼1.0%) AlN/6H-SiC (0001) and large lattice-mismatch (∼8.5%) AlSb/GaAs (001) heteroepitaxial interfaces using simulated HRTEM images of a conventional 300-kV field-emission-gun transmission electron microscope under non-Scherzer-defocus conditions. Then, atomic-scale chemical compositions at the interface were determined for the atomic intermixing and Lomer dislocation with an atomic step by analyzing the deconvoluted image contrast. Furthermore, the effect of dynamical scattering on contrast analysis was also evaluated for differently weighted atomic columns in the compositions. Copyright © 2018 Elsevier Ltd. All rights reserved.

Structural and physical properties of InAlAs quantum dots grown on GaAs

NASA Astrophysics Data System (ADS)

Vasile, B. S.; Daly, A. Ben; Craciun, D.; Alexandrou, I.; Lazar, S.; Lemaître, A.; Maaref, M. A.; Iacomi, F.; Craciun, V.

2018-04-01

Quantum dots (QDs), which have particular physical properties due to the three dimensions confinement effect, could be used in many advanced optoelectronic applications. We investigated the properties of InAlAs/AlGaAs QDs grown by molecular beam epitaxy on GaAs/Al0.5Ga0.5As layers. The optical properties of QDs were studied by low-temperature photoluminescence (PL). Two bandgap transitions corresponding to the X-Sh and X-Ph energy structure were observed. The QDs structure was investigated using high-resolution X-ray diffraction (HRXRD) and high-resolution transmission electron microscopy (HRTEM). HRXRD investigations showed that the layers grew epitaxially on the substrate, with no relaxation. HRTEM investigations confirmed the epitaxial nature of the grown structures. In addition, it was revealed that the In atoms aggregated in some prismatic regions, forming areas of high In concentration, that were still in perfect registry with the substrate.

High-resolution of particle contacts via fluorophore exclusion in deep-imaging of jammed colloidal packings

NASA Astrophysics Data System (ADS)

Kyeyune-Nyombi, Eru; Morone, Flaviano; Liu, Wenwei; Li, Shuiqing; Gilchrist, M. Lane; Makse, Hernán A.

2018-01-01

Understanding the structural properties of random packings of jammed colloids requires an unprecedented high-resolution determination of the contact network providing mechanical stability to the packing. Here, we address the determination of the contact network by a novel strategy based on fluorophore signal exclusion of quantum dot nanoparticles from the contact points. We use fluorescence labeling schemes on particles inspired by biology and biointerface science in conjunction with fluorophore exclusion at the contact region. The method provides high-resolution contact network data that allows us to measure structural properties of the colloidal packing near marginal stability. We determine scaling laws of force distributions, soft modes, correlation functions, coordination number and free volume that define the universality class of jammed colloidal packings and can be compared with theoretical predictions. The contact detection method opens up further experimental testing at the interface of jamming and glass physics.

Rapid structural analysis of nanomaterials in aqueous solutions

NASA Astrophysics Data System (ADS)

Ryuzaki, Sou; Tsutsui, Makusu; He, Yuhui; Yokota, Kazumichi; Arima, Akihide; Morikawa, Takanori; Taniguchi, Masateru; Kawai, Tomoji

2017-04-01

Rapid structural analysis of nanoscale matter in a liquid environment represents innovative technologies that reveal the identities and functions of biologically important molecules. However, there is currently no method with high spatio-temporal resolution that can scan individual particles in solutions to gain structural information. Here we report the development of a nanopore platform realizing quantitative structural analysis for suspended nanomaterials in solutions with a high z-axis and xy-plane spatial resolution of 35.8 ± 1.1 and 12 nm, respectively. We used a low thickness-to-diameter aspect ratio pore architecture for achieving cross sectional areas of analyte (i.e. tomograms). Combining this with multiphysics simulation methods to translate ionic current data into tomograms, we demonstrated rapid structural analysis of single polystyrene (Pst) beads and single dumbbell-like Pst beads in aqueous solutions.

High-resolution structure of the Escherichia coli ribosome

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

Noeske, Jonas; Wasserman, Michael R.; Terry, Daniel S.

Protein synthesis by the ribosome is highly dependent on the ionic conditions in the cellular environment, but the roles of ribosome solvation remain poorly understood. Moreover, the function of modifications to ribosomal RNA and ribosomal proteins are unclear. Here we present the structure of the Escherichia coli 70S ribosome to 2.4 Å resolution. The structure reveals details of the ribosomal subunit interface that are conserved in all domains of life, and suggest how solvation contributes to ribosome integrity and function. The structure also suggests how the conformation of ribosomal protein uS12 likely impacts its contribution to messenger RNA decoding. Inmore » conclusion, this structure helps to explain the phylogenetic conservation of key elements of the ribosome, including posttranscriptional and posttranslational modifications and should serve as a basis for future antibiotic development.« less

High-resolution structure of the Escherichia coli ribosome

DOE PAGES

Noeske, Jonas; Wasserman, Michael R.; Terry, Daniel S.; ...

2015-03-16

Protein synthesis by the ribosome is highly dependent on the ionic conditions in the cellular environment, but the roles of ribosome solvation remain poorly understood. Moreover, the function of modifications to ribosomal RNA and ribosomal proteins are unclear. Here we present the structure of the Escherichia coli 70S ribosome to 2.4 Å resolution. The structure reveals details of the ribosomal subunit interface that are conserved in all domains of life, and suggest how solvation contributes to ribosome integrity and function. The structure also suggests how the conformation of ribosomal protein uS12 likely impacts its contribution to messenger RNA decoding. Inmore » conclusion, this structure helps to explain the phylogenetic conservation of key elements of the ribosome, including posttranscriptional and posttranslational modifications and should serve as a basis for future antibiotic development.« less

Hydrogens detected by subatomic resolution protein crystallography in a [NiFe] hydrogenase.

PubMed

Ogata, Hideaki; Nishikawa, Koji; Lubitz, Wolfgang

2015-04-23

The enzyme hydrogenase reversibly converts dihydrogen to protons and electrons at a metal catalyst. The location of the abundant hydrogens is of key importance for understanding structure and function of the protein. However, in protein X-ray crystallography the detection of hydrogen atoms is one of the major problems, since they display only weak contributions to diffraction and the quality of the single crystals is often insufficient to obtain sub-ångström resolution. Here we report the crystal structure of a standard [NiFe] hydrogenase (∼91.3 kDa molecular mass) at 0.89 Å resolution. The strictly anoxically isolated hydrogenase has been obtained in a specific spectroscopic state, the active reduced Ni-R (subform Ni-R1) state. The high resolution, proper refinement strategy and careful modelling allow the positioning of a large part of the hydrogen atoms in the structure. This has led to the direct detection of the products of the heterolytic splitting of dihydrogen into a hydride (H(-)) bridging the Ni and Fe and a proton (H(+)) attached to the sulphur of a cysteine ligand. The Ni-H(-) and Fe-H(-) bond lengths are 1.58 Å and 1.78Å, respectively. Furthermore, we can assign the Fe-CO and Fe-CN(-) ligands at the active site, and can obtain the hydrogen-bond networks and the preferred proton transfer pathway in the hydrogenase. Our results demonstrate the precise comprehensive information available from ultra-high-resolution structures of proteins as an alternative to neutron diffraction and other methods such as NMR structural analysis.

Crystal structure of the Msx-1 homeodomain/DNA complex.

PubMed

Hovde, S; Abate-Shen, C; Geiger, J H

2001-10-09

The Msx-1 homeodomain protein plays a crucial role in craniofacial, limb, and nervous system development. Homeodomain DNA-binding domains are comprised of 60 amino acids that show a high degree of evolutionary conservation. We have determined the structure of the Msx-1 homeodomain complexed to DNA at 2.2 A resolution. The structure has an unusually well-ordered N-terminal arm with a unique trajectory across the minor groove of the DNA. DNA specificity conferred by bases flanking the core TAAT sequence is explained by well ordered water-mediated interactions at Q50. Most interactions seen at the TAAT sequence are typical of the interactions seen in other homeodomain structures. Comparison of the Msx-1-HD structure to all other high resolution HD-DNA complex structures indicate a remarkably well-conserved sphere of hydration between the DNA and protein in these complexes.

An Investigation of G-Quadruplex Structural Polymorphism in the Human Telomere Using a Combined Approach of Hydrodynamic Bead Modeling and Molecular Dynamics Simulation

PubMed Central

2015-01-01

Guanine-rich oligonucleotides can adopt noncanonical tertiary structures known as G-quadruplexes, which can exist in different forms depending on experimental conditions. High-resolution structural methods, such as X-ray crystallography and NMR spectroscopy, have been of limited usefulness in resolving the inherent structural polymorphism associated with G-quadruplex formation. The lack of, or the ambiguous nature of, currently available high-resolution structural data, in turn, has severely hindered investigations into the nature of these structures and their interactions with small-molecule inhibitors. We have used molecular dynamics in conjunction with hydrodynamic bead modeling to study the structures of the human telomeric G-quadruplex-forming sequences at the atomic level. We demonstrated that molecular dynamics can reproduce experimental hydrodynamic measurements and thus can be a powerful tool in the structural study of existing G-quadruplex sequences or in the prediction of new G-quadruplex structures. PMID:24779348

Recent applications of gas chromatography with high-resolution mass spectrometry.

PubMed

Špánik, Ivan; Machyňáková, Andrea

2018-01-01

Gas chromatography coupled to high-resolution mass spectrometry is a powerful analytical method that combines excellent separation power of gas chromatography with improved identification based on an accurate mass measurement. These features designate gas chromatography with high-resolution mass spectrometry as the first choice for identification and structure elucidation of unknown volatile and semi-volatile organic compounds. Gas chromatography with high-resolution mass spectrometry quantitative analyses was previously focused on the determination of dioxins and related compounds using magnetic sector type analyzers, a standing requirement of many international standards. The introduction of a quadrupole high-resolution time-of-flight mass analyzer broadened interest in this method and novel applications were developed, especially for multi-target screening purposes. This review is focused on the development and the most interesting applications of gas chromatography coupled to high-resolution mass spectrometry towards analysis of environmental matrices, biological fluids, and food safety since 2010. The main attention is paid to various approaches and applications of gas chromatography coupled to high-resolution mass spectrometry for non-target screening to identify contaminants and to characterize the chemical composition of environmental, food, and biological samples. The most interesting quantitative applications, where a significant contribution of gas chromatography with high-resolution mass spectrometry over the currently used methods is expected, will be discussed as well. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Computational high-resolution optical imaging of the living human retina

NASA Astrophysics Data System (ADS)

Shemonski, Nathan D.; South, Fredrick A.; Liu, Yuan-Zhi; Adie, Steven G.; Scott Carney, P.; Boppart, Stephen A.

2015-07-01

High-resolution in vivo imaging is of great importance for the fields of biology and medicine. The introduction of hardware-based adaptive optics (HAO) has pushed the limits of optical imaging, enabling high-resolution near diffraction-limited imaging of previously unresolvable structures. In ophthalmology, when combined with optical coherence tomography, HAO has enabled a detailed three-dimensional visualization of photoreceptor distributions and individual nerve fibre bundles in the living human retina. However, the introduction of HAO hardware and supporting software adds considerable complexity and cost to an imaging system, limiting the number of researchers and medical professionals who could benefit from the technology. Here we demonstrate a fully automated computational approach that enables high-resolution in vivo ophthalmic imaging without the need for HAO. The results demonstrate that computational methods in coherent microscopy are applicable in highly dynamic living systems.

Spatial variability of the Black Sea surface temperature from high resolution modeling and satellite measurements

NASA Astrophysics Data System (ADS)

Mizyuk, Artem; Senderov, Maxim; Korotaev, Gennady

2016-04-01

Large number of numerical ocean models were implemented for the Black Sea basin during last two decades. They reproduce rather similar structure of synoptical variability of the circulation. Since 00-s numerical studies of the mesoscale structure are carried out using high performance computing (HPC). With the growing capacity of computing resources it is now possible to reconstruct the Black Sea currents with spatial resolution of several hundreds meters. However, how realistic these results can be? In the proposed study an attempt is made to understand which spatial scales are reproduced by ocean model in the Black Sea. Simulations are made using parallel version of NEMO (Nucleus for European Modelling of the Ocean). A two regional configurations with spatial resolutions 5 km and 2.5 km are described. Comparison of the SST from simulations with two spatial resolutions shows rather qualitative difference of the spatial structures. Results of high resolution simulation are compared also with satellite observations and observation-based products from Copernicus using spatial correlation and spectral analysis. Spatial scales of correlations functions for simulated and observed SST are rather close and differs much from satellite SST reanalysis. Evolution of spectral density for modelled SST and reanalysis showed agreed time periods of small scales intensification. Using of the spectral analysis for satellite measurements is complicated due to gaps. The research leading to this results has received funding from Russian Science Foundation (project № 15-17-20020)

Functional cardiac magnetic resonance microscopy

NASA Astrophysics Data System (ADS)

Brau, Anja Christina Sophie

2003-07-01

The study of small animal models of human cardiovascular disease is critical to our understanding of the origin, progression, and treatment of this pervasive disease. Complete analysis of disease pathophysiology in these animal models requires measuring structural and functional changes at the level of the whole heart---a task for which an appropriate non-invasive imaging method is needed. The purpose of this work was thus to develop an imaging technique to support in vivo characterization of cardiac structure and function in rat and mouse models of cardiovascular disease. Whereas clinical cardiac magnetic resonance imaging (MRI) provides accurate assessment of the human heart, the extension of cardiac MRI from humans to rodents presents several formidable scaling challenges. Acquiring images of the mouse heart with organ definition and fluidity of contraction comparable to that achieved in humans requires an increase in spatial resolution by a factor of 3000 and an increase in temporal resolution by a factor of ten. No single technical innovation can meet the demanding imaging requirements imposed by the small animal. A functional cardiac magnetic resonance microscopy technique was developed by integrating improvements in physiological control, imaging hardware, biological synchronization of imaging, and pulse sequence design to achieve high-quality images of the murine heart with high spatial and temporal resolution. The specific methods and results from three different sets of imaging experiments are presented: (1) 2D functional imaging in the rat with spatial resolution of 175 mum2 x 1 mm and temporal resolution of 10 ms; (2) 3D functional imaging in the rat with spatial resolution of 100 mum 2 x 500 mum and temporal resolution of 30 ms; and (3) 2D functional imaging in the mouse with spatial resolution down to 100 mum2 x 1 mm and temporal resolution of 10 ms. The cardiac microscopy technique presented here represents a novel collection of technologies capable of acquiring routine high-quality images of murine cardiac structure and function with minimal artifacts and markedly higher spatial resolution compared to conventional techniques. This work is poised to serve a valuable role in the evaluation of cardiovascular disease and should find broad application in studies ranging from basic pathophysiology to drug discovery.

High-resolution structure, interactions, and dynamics of self-assembled virus-like partilces

NASA Astrophysics Data System (ADS)

Raviv, Uri; Asor, R.; Ben-Shaul, O.; Oppenheim, A.; Schlicksup, L. C.; Seltzer, L.; Jarrold, M. F.; Zlotnick, A.

Using SAXS, in combination with Monte Carlo simulations, and our unique solution x-ray scattering data analysis program, we resolved at high spatial resolution, the manner by which wtSV40 packages its 5.2kb circular DNA about 20 histone octamers in the virus capsid (Figure 1). This structure, known as a mini-chromosome, is highly dynamic and could not be resolved by microscopy methods. Using time-resolved solution SAXS, stopped-flow, and flow-through setups the assembly process of VP1, the major caspid protein of the SV40 virus, with RNA or DNA to form virus-like particles (VLPs) was studied in msec temporal resolution. By mixing the nucleotides and the capsid protein, virus-like particles formed within 35 msec, in the case of RNA that formed T =1 particles, and within 15 seconds in the case of DNA that formed T =7 particles, similar to wt SV40. The structural changes leading to the particle formation were followed in detail. More recently, we have extended this work to study the assembly of HBV virus-like particles.

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

PubMed Central

Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike; Shilova, Anastasya; Weinhausen, Britta; Burghammer, Manfred; Colletier, Jacques-Philippe

2015-01-01

High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering. PMID:25945583

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

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

Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike

High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Åmore » resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.« less

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams.

PubMed

Coquelle, Nicolas; Brewster, Aaron S; Kapp, Ulrike; Shilova, Anastasya; Weinhausen, Britta; Burghammer, Manfred; Colletier, Jacques Philippe

2015-05-01

High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

DOE PAGES

Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike; ...

2015-04-25

High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Åmore » resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.« less

Filling the gap: adding super-resolution to array tomography for correlated ultrastructural and molecular identification of electrical synapses at the C. elegans connectome.

PubMed

Markert, Sebastian Matthias; Britz, Sebastian; Proppert, Sven; Lang, Marietta; Witvliet, Daniel; Mulcahy, Ben; Sauer, Markus; Zhen, Mei; Bessereau, Jean-Louis; Stigloher, Christian

2016-10-01

Correlating molecular labeling at the ultrastructural level with high confidence remains challenging. Array tomography (AT) allows for a combination of fluorescence and electron microscopy (EM) to visualize subcellular protein localization on serial EM sections. Here, we describe an application for AT that combines near-native tissue preservation via high-pressure freezing and freeze substitution with super-resolution light microscopy and high-resolution scanning electron microscopy (SEM) analysis on the same section. We established protocols that combine SEM with structured illumination microscopy (SIM) and direct stochastic optical reconstruction microscopy (dSTORM). We devised a method for easy, precise, and unbiased correlation of EM images and super-resolution imaging data using endogenous cellular landmarks and freely available image processing software. We demonstrate that these methods allow us to identify and label gap junctions in Caenorhabditis elegans with precision and confidence, and imaging of even smaller structures is feasible. With the emergence of connectomics, these methods will allow us to fill in the gap-acquiring the correlated ultrastructural and molecular identity of electrical synapses.

Coupling physics and biogeochemistry thanks to high-resolution observations of the phytoplankton community structure in the northwestern Mediterranean Sea

NASA Astrophysics Data System (ADS)

Marrec, Pierre; Grégori, Gérald; Doglioli, Andrea M.; Dugenne, Mathilde; Della Penna, Alice; Bhairy, Nagib; Cariou, Thierry; Hélias Nunige, Sandra; Lahbib, Soumaya; Rougier, Gilles; Wagener, Thibaut; Thyssen, Melilotus

2018-03-01

Fine-scale physical structures and ocean dynamics strongly influence and regulate biogeochemical and ecological processes. These processes are particularly challenging to describe and understand because of their ephemeral nature. The OSCAHR (Observing Submesoscale Coupling At High Resolution) campaign was conducted in fall 2015 in which a fine-scale structure (1-10 km/1-10 days) in the northwestern Mediterranean Ligurian subbasin was pre-identified using both satellite and numerical modeling data. Along the ship track, various variables were measured at the surface (temperature, salinity, chlorophyll a and nutrient concentrations) with ADCP current velocity. We also deployed a new model of the CytoSense automated flow cytometer (AFCM) optimized for small and dim cells, for near real-time characterization of the surface phytoplankton community structure of surface waters with a spatial resolution of a few kilometers and an hourly temporal resolution. For the first time with this optimized version of the AFCM, we were able to fully resolve Prochlorococcus picocyanobacteria in addition to the easily distinguishable Synechococcus. The vertical physical dynamics and biogeochemical properties of the studied area were investigated by continuous high-resolution CTD profiles thanks to a moving vessel profiler (MVP) during the vessel underway associated with a high-resolution pumping system deployed during fixed stations allowing sampling of the water column at a fine resolution (below 1 m). The observed fine-scale feature presented a cyclonic structure with a relatively cold core surrounded by warmer waters. Surface waters were totally depleted in nitrate and phosphate. In addition to the doming of the isopycnals by the cyclonic circulation, an intense wind event induced Ekman pumping. The upwelled subsurface cold nutrient-rich water fertilized surface waters and was marked by an increase in Chl a concentration. Prochlorococcus and pico- and nano-eukaryotes were more abundant in cold core waters, while Synechococcus dominated in warm boundary waters. Nanoeukaryotes were the main contributors ( > 50 %) in terms of pigment content (red fluorescence) and biomass. Biological observations based on the mean cell's red fluorescence recorded by AFCM combined with physical properties of surface waters suggest a distinct origin for two warm boundary waters. Finally, the application of a matrix growth population model based on high-frequency AFCM measurements in warm boundary surface waters provides estimates of in situ growth rate and apparent net primary production for Prochlorococcus (μ = 0.21 d-1, NPP = 0.11 mg C m-3 d-1) and Synechococcus (μ = 0.72 d-1, NPP = 2.68 mg C m-3 d-1), which corroborate their opposite surface distribution pattern. The innovative adaptive strategy applied during OSCAHR with a combination of several multidisciplinary and complementary approaches involving high-resolution in situ observations and sampling, remote-sensing and model simulations provided a deeper understanding of the marine biogeochemical dynamics through the first trophic levels.

New Insights into Ribosome Structure and Function.

PubMed

Jobe, Amy; Liu, Zheng; Gutierrez-Vargas, Cristina; Frank, Joachim

2018-06-14

In the past 4 years, because of the advent of new cameras, many ribosome structures have been solved by cryoelectron microscopy (cryo-EM) at high, often near-atomic resolution, bringing new mechanistic insights into the processes of translation initiation, peptide elongation, termination, and recycling. Thus, cryo-EM has joined X-ray crystallography as a powerful technique in structural studies of translation. The significance of this new development is that structures of ribosomes in complex with their functional binding partners can now be determined to high resolution in multiple states as they perform their work. The aim of this article is to provide an overview of these new studies and assess the contributions they have made toward an understanding of translation and translational control. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Internally bridging water molecule in transmembrane alpha-helical kink.

PubMed

Miyano, Masashi; Ago, Hideo; Saino, Hiromichi; Hori, Tetsuya; Ida, Koh

2010-08-01

There are hundreds of membrane protein atomic coordinates in the Protein Data Bank (PDB), and high-resolution structures of better than 2.5 A enable the visualization of a sizable number of amphiphiles (lipid and/or detergent) and bound water molecules as essential parts of the structure. Upon scrutinizing these high-resolution structures, water molecules were found to 'wedge' and stabilize large kink angle (30-40 degrees) in a simple cylindrical model at the transmembrane helical kinks so as to form an inter-helical cavity to accommodate a ligand binding or active site as a crucial structural feature in alpha-helical integral membrane proteins. Furthermore, some of these water molecules are proposed to play a pivotal role of their conformational change to exert their functional regulation. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

A theoretical and experimental benchmark study of core-excited states in nitrogen

NASA Astrophysics Data System (ADS)

Myhre, Rolf H.; Wolf, Thomas J. A.; Cheng, Lan; Nandi, Saikat; Coriani, Sonia; Gühr, Markus; Koch, Henrik

2018-02-01

The high resolution near edge X-ray absorption fine structure spectrum of nitrogen displays the vibrational structure of the core-excited states. This makes nitrogen well suited for assessing the accuracy of different electronic structure methods for core excitations. We report high resolution experimental measurements performed at the SOLEIL synchrotron facility. These are compared with theoretical spectra calculated using coupled cluster theory and algebraic diagrammatic construction theory. The coupled cluster singles and doubles with perturbative triples model known as CC3 is shown to accurately reproduce the experimental excitation energies as well as the spacing of the vibrational transitions. The computational results are also shown to be systematically improved within the coupled cluster hierarchy, with the coupled cluster singles, doubles, triples, and quadruples method faithfully reproducing the experimental vibrational structure.

Synthesis, high-resolution NMR spectroscopic analysis, and single-crystal X-ray diffraction of isoxazoline tetracycles.

PubMed

Fascio, Mirta L; Alvarez-Larena, Angel; D'Accorso, Norma B

2002-11-29

Three isoxazoline tetracycles were obtained enantiomerically pure by intramolecular 1,3-dipolar cycloaddition. The characterization of the new compounds was performed by high-resolution 1H and 13C NMR spectroscopy. The relative configuration of the new chiral centers was determined by NOESY experiments and confirmed by single-crystal X-ray structural analysis.

High current table-top setup for femtosecond gas electron diffraction.

PubMed

Zandi, Omid; Wilkin, Kyle J; Xiong, Yanwei; Centurion, Martin

2017-07-01

We have constructed an experimental setup for gas phase electron diffraction with femtosecond resolution and a high average beam current. While gas electron diffraction has been successful at determining molecular structures, it has been a challenge to reach femtosecond resolution while maintaining sufficient beam current to retrieve structures with high spatial resolution. The main challenges are the Coulomb force that leads to broadening of the electron pulses and the temporal blurring that results from the velocity mismatch between the laser and electron pulses as they traverse the sample. We present here a device that uses pulse compression to overcome the Coulomb broadening and deliver femtosecond electron pulses on a gas target. The velocity mismatch can be compensated using laser pulses with a tilted intensity front to excite the sample. The temporal resolution of the setup was determined with a streak camera to be better than 400 fs for pulses with up to half a million electrons and a kinetic energy of 90 keV. The high charge per pulse, combined with a repetition rate of 5 kHz, results in an average beam current that is between one and two orders of magnitude higher than previously demonstrated.

Zebrafish skeleton development: High resolution micro-CT and FIB-SEM block surface serial imaging for phenotype identification

PubMed Central

Silvent, Jeremie; Akiva, Anat; Brumfeld, Vlad; Reznikov, Natalie; Rechav, Katya; Yaniv, Karina; Addadi, Lia; Weiner, Steve

2017-01-01

Although bone is one of the most studied living materials, many questions about the manner in which bones form remain unresolved, including fine details of the skeletal structure during development. In this study, we monitored skeleton development of zebrafish larvae, using calcein fluorescence, high-resolution micro-CT 3D images and FIB-SEM in the block surface serial imaging mode. We compared calcein staining of the skeletons of the wild type and nacre mutants, which are transparent zebrafish, with micro-CT for the first 30 days post fertilization embryos, and identified significant differences. We quantified the bone volumes and mineral contents of bones, including otoliths, during development, and showed that such developmental differences, including otolith development, could be helpful in identifying phenotypes. In addition, high-resolution imaging revealed the presence of mineralized aggregates in the notochord, before the formation of the first bone in the axial skeleton. These structures might play a role in the storage of the mineral. Our results highlight the potential of these high-resolution 3D approaches to characterize the zebrafish skeleton, which in turn could prove invaluable information for better understanding the development and the characterization of skeletal phenotypes. PMID:29220379

Direct trabecular meshwork imaging in porcine eyes through multiphoton gonioscopy

PubMed Central

Masihzadeh, Omid; Ammar, David A.; Kahook, Malik Y.; Gibson, Emily A.; Lei, Tim C.

2013-01-01

Abstract. The development of technologies to characterize the ocular aqueous outflow system (AOS) is important for the understanding of the pathophysiology of glaucoma. Multiphoton microscopy (MPM) offers the advantage of high-resolution, label-free imaging with intrinsic image contrast because the emitted signals result from the specific biomolecular content of the tissue. Previous attempts to use MPM to image the murine irido-corneal region directly through the sclera have suffered from degradation in image resolution due to scattering of the focused laser light. As a result, transscleral MPM has limited ability to observe fine structures in the AOS. In this work, the porcine irido-corneal angle was successfully imaged through the transparent cornea using a gonioscopic lens to circumvent the highly scattering scleral tissue. The resulting high-resolution images allowed the detailed structures in the trabecular meshwork (TM) to be observed. Multimodal imaging by two-photon autofluorescence and second harmonic generation allowed visualization of different features in the TM without labels and without disruption of the TM or surrounding tissues. MPM gonioscopy is a promising noninvasive imaging tool for high-resolution studies of the AOS, and research continues to explore the potential for future clinical applications in humans. PMID:23515864

Direct trabecular meshwork imaging in porcine eyes through multiphoton gonioscopy.

PubMed

Masihzadeh, Omid; Ammar, David A; Kahook, Malik Y; Gibson, Emily A; Lei, Tim C

2013-03-01

The development of technologies to characterize the ocular aqueous outflow system (AOS) is important for the understanding of the pathophysiology of glaucoma. Multiphoton microscopy (MPM) offers the advantage of high-resolution, label-free imaging with intrinsic image contrast because the emitted signals result from the specific biomolecular content of the tissue. Previous attempts to use MPM to image the murine irido-corneal region directly through the sclera have suffered from degradation in image resolution due to scattering of the focused laser light. As a result, transscleral MPM has limited ability to observe fine structures in the AOS. In this work, the porcine irido-corneal angle was successfully imaged through the transparent cornea using a gonioscopic lens to circumvent the highly scattering scleral tissue. The resulting high-resolution images allowed the detailed structures in the trabecular meshwork (TM) to be observed. Multimodal imaging by two-photon autofluorescence and second harmonic generation allowed visualization of different features in the TM without labels and without disruption of the TM or surrounding tissues. MPM gonioscopy is a promising noninvasive imaging tool for high-resolution studies of the AOS, and research continues to explore the potential for future clinical applications in humans.

Direct trabecular meshwork imaging in porcine eyes through multiphoton gonioscopy

NASA Astrophysics Data System (ADS)

Masihzadeh, Omid; Ammar, David A.; Kahook, Malik Y.; Gibson, Emily A.; Lei, Tim C.

2013-03-01

The development of technologies to characterize the ocular aqueous outflow system (AOS) is important for the understanding of the pathophysiology of glaucoma. Multiphoton microscopy (MPM) offers the advantage of high-resolution, label-free imaging with intrinsic image contrast because the emitted signals result from the specific biomolecular content of the tissue. Previous attempts to use MPM to image the murine irido-corneal region directly through the sclera have suffered from degradation in image resolution due to scattering of the focused laser light. As a result, transscleral MPM has limited ability to observe fine structures in the AOS. In this work, the porcine irido-corneal angle was successfully imaged through the transparent cornea using a gonioscopic lens to circumvent the highly scattering scleral tissue. The resulting high-resolution images allowed the detailed structures in the trabecular meshwork (TM) to be observed. Multimodal imaging by two-photon autofluorescence and second harmonic generation allowed visualization of different features in the TM without labels and without disruption of the TM or surrounding tissues. MPM gonioscopy is a promising noninvasive imaging tool for high-resolution studies of the AOS, and research continues to explore the potential for future clinical applications in humans.

High current table-top setup for femtosecond gas electron diffraction

DOE PAGES

Zandi, Omid; Wilkin, Kyle J.; Xiong, Yanwei; ...

2017-05-08

Here, we have constructed an experimental setup for gas phase electron diffraction with femtosecond resolution and a high average beam current. While gas electron diffraction has been successful at determining molecular structures, it has been a challenge to reach femtosecond resolution while maintaining sufficient beam current to retrieve structures with high spatial resolution. The main challenges are the Coulomb force that leads to broadening of the electron pulses and the temporal blurring that results from the velocity mismatch between the laser and electron pulses as they traverse the sample. We also present here a device that uses pulse compression tomore » overcome the Coulomb broadening and deliver femtosecond electron pulses on a gas target. The velocity mismatch can be compensated using laser pulses with a tilted intensity front to excite the sample. The temporal resolution of the setup was determined with a streak camera to be better than 400 fs for pulses with up to half a million electrons and a kinetic energy of 90 keV. Finally, the high charge per pulse, combined with a repetition rate of 5 kHz, results in an average beam current that is between one and two orders of magnitude higher than previously demonstrated.« less

Flexible filamentous virus structure from fiber diffraction

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

Stubbs, Gerald; Kendall, Amy; McDonald, Michele

2008-10-24

Fiber diffraction data have been obtained from Narcissus mosaic virus, a potexvirus from the family Flexiviridae, and soybean mosaic virus (SMV), a potyvirus from the family Potyviridae. Analysis of the data in conjunction with cryo-electron microscopy data allowed us to determine the symmetry of the viruses and to make reconstructions of SMV at 19 {angstrom} resolution and of another potexvirus, papaya mosaic virus, at 18 {angstrom} resolution. These data include the first well-ordered data ever obtained for the potyviruses and the best-ordered data from the potexviruses, and offer the promise of eventual high resolution structure determinations.

Comment on: Polar Plumes and Fine-scale Coronal Structures - On the Interpretation of Coronal Radio Sounding Data by Patzold and Bird

NASA Technical Reports Server (NTRS)

Woo, R.; Habbal, S. R.

1998-01-01

Radio occultation measurements, which probe electron density over a wide dynamic range with high sensitivity and high spatial and temporal resolution reveal a solar corona permeated by a hierarchy of filamentary structures.

Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud.

PubMed

Cianfrocco, Michael A; Leschziner, Andres E

2015-05-08

The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. Calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available 'off-the-shelf' computing environment on Amazon's elastic cloud computing infrastructure. This environment provides users with single particle cryo-EM software packages and the ability to create computing clusters with 16-480+ CPUs. We tested our computing environment using a publicly available 80S yeast ribosome dataset and estimate that laboratories could determine high-resolution cryo-EM structures for $50 to $1500 per structure within a timeframe comparable to local clusters. Our analysis shows that Amazon's cloud computing environment may offer a viable computing environment for cryo-EM.

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

PubMed Central

Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr; Stellato, Francesco; Chiu, Elaine; Yeh, Shin-Mei; Aquila, Andrew; Basu, Shibom; Bean, Richard; Beyerlein, Kenneth R.; Botha, Sabine; Boutet, Sébastien; DePonte, Daniel P.; Doak, R. Bruce; Fromme, Raimund; Galli, Lorenzo; Grotjohann, Ingo; James, Daniel R.; Kupitz, Christopher; Lomb, Lukas; Messerschmidt, Marc; Nass, Karol; Rendek, Kimberly; Shoeman, Robert L.; Wang, Dingjie; Weierstall, Uwe; White, Thomas A.; Williams, Garth J.; Zatsepin, Nadia A.; Fromme, Petra; Spence, John C. H.; Goldie, Kenneth N.; Jehle, Johannes A.; Metcalf, Peter; Barty, Anton

2017-01-01

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach. PMID:28202732

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

DOE PAGES

Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr; ...

2017-02-15

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam ismore » often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Furthermore, our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.« less

Method and apparatus for optical Doppler tomographic imaging of fluid flow velocity in highly scattering media

DOEpatents

Nelson, John Stuart; Milner, Thomas Edward; Chen, Zhongping

1999-01-01

Optical Doppler tomography permits imaging of fluid flow velocity in highly scattering media. The tomography system combines Doppler velocimetry with high spatial resolution of partially coherent optical interferometry to measure fluid flow velocity at discrete spatial locations. Noninvasive in vivo imaging of blood flow dynamics and tissue structures with high spatial resolutions of the order of 2 to 10 microns is achieved in biological systems. The backscattered interference signals derived from the interferometer may be analyzed either through power spectrum determination to obtain the position and velocity of each particle in the fluid flow sample at each pixel, or the interference spectral density may be analyzed at each frequency in the spectrum to obtain the positions and velocities of the particles in a cross-section to which the interference spectral density corresponds. The realized resolutions of optical Doppler tomography allows noninvasive in vivo imaging of both blood microcirculation and tissue structure surrounding the vessel which has significance for biomedical research and clinical applications.

Theoretical Models of Protostellar Binary and Multiple Systems with AMR Simulations

NASA Astrophysics Data System (ADS)

Matsumoto, Tomoaki; Tokuda, Kazuki; Onishi, Toshikazu; Inutsuka, Shu-ichiro; Saigo, Kazuya; Takakuwa, Shigehisa

2017-05-01

We present theoretical models for protostellar binary and multiple systems based on the high-resolution numerical simulation with an adaptive mesh refinement (AMR) code, SFUMATO. The recent ALMA observations have revealed early phases of the binary and multiple star formation with high spatial resolutions. These observations should be compared with theoretical models with high spatial resolutions. We present two theoretical models for (1) a high density molecular cloud core, MC27/L1521F, and (2) a protobinary system, L1551 NE. For the model for MC27, we performed numerical simulations for gravitational collapse of a turbulent cloud core. The cloud core exhibits fragmentation during the collapse, and dynamical interaction between the fragments produces an arc-like structure, which is one of the prominent structures observed by ALMA. For the model for L1551 NE, we performed numerical simulations of gas accretion onto protobinary. The simulations exhibit asymmetry of a circumbinary disk. Such asymmetry has been also observed by ALMA in the circumbinary disk of L1551 NE.

The architecture of amyloid-like peptide fibrils revealed by X-ray scattering, diffraction and electron microscopy

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

Langkilde, Annette E., E-mail: annette.langkilde@sund.ku.dk; Morris, Kyle L.; Serpell, Louise C.

The aggregation process and the fibril state of an amyloidogenic peptide suggest monomer addition to be the prevailing mechanism of elongation and a model of the peptide packing in the fibrils has been obtained. Structural analysis of protein fibrillation is inherently challenging. Given the crucial role of fibrils in amyloid diseases, method advancement is urgently needed. A hybrid modelling approach is presented enabling detailed analysis of a highly ordered and hierarchically organized fibril of the GNNQQNY peptide fragment of a yeast prion protein. Data from small-angle X-ray solution scattering, fibre diffraction and electron microscopy are combined with existing high-resolution X-raymore » crystallographic structures to investigate the fibrillation process and the hierarchical fibril structure of the peptide fragment. The elongation of these fibrils proceeds without the accumulation of any detectable amount of intermediate oligomeric species, as is otherwise reported for, for example, glucagon, insulin and α-synuclein. Ribbons constituted of linearly arranged protofilaments are formed. An additional hierarchical layer is generated via the pairing of ribbons during fibril maturation. Based on the complementary data, a quasi-atomic resolution model of the protofilament peptide arrangement is suggested. The peptide structure appears in a β-sheet arrangement reminiscent of the β-zipper structures evident from high-resolution crystal structures, with specific differences in the relative peptide orientation. The complexity of protein fibrillation and structure emphasizes the need to use multiple complementary methods.« less

Multimodality hard-x-ray imaging of a chromosome with nanoscale spatial resolution

DOE PAGES

Yan, Hanfei; Nazaretski, Evgeny; Lauer, Kenneth R.; ...

2016-02-05

Here, we developed a scanning hard x-ray microscope using a new class of x-ray nano-focusing optic called a multilayer Laue lens and imaged a chromosome with nanoscale spatial resolution. The combination of the hard x-ray's superior penetration power, high sensitivity to elemental composition, high spatial-resolution and quantitative analysis creates a unique tool with capabilities that other microscopy techniques cannot provide. Using this microscope, we simultaneously obtained absorption-, phase-, and fluorescence-contrast images of Pt-stained human chromosome samples. The high spatial-resolution of the microscope and its multi-modality imaging capabilities enabled us to observe the internal ultra-structures of a thick chromosome without sectioningmore » it.« less

Multimodality hard-x-ray imaging of a chromosome with nanoscale spatial resolution

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

Yan, Hanfei; Nazaretski, Evgeny; Lauer, Kenneth R.

Here, we developed a scanning hard x-ray microscope using a new class of x-ray nano-focusing optic called a multilayer Laue lens and imaged a chromosome with nanoscale spatial resolution. The combination of the hard x-ray's superior penetration power, high sensitivity to elemental composition, high spatial-resolution and quantitative analysis creates a unique tool with capabilities that other microscopy techniques cannot provide. Using this microscope, we simultaneously obtained absorption-, phase-, and fluorescence-contrast images of Pt-stained human chromosome samples. The high spatial-resolution of the microscope and its multi-modality imaging capabilities enabled us to observe the internal ultra-structures of a thick chromosome without sectioningmore » it.« less

Structural Abnormalities on Magnetic Resonance Imaging in Patients With Patellofemoral Pain: A Cross-sectional Case-Control Study.

PubMed

van der Heijden, Rianne A; de Kanter, Janneke L M; Bierma-Zeinstra, Sita M A; Verhaar, Jan A N; van Veldhoven, Peter L J; Krestin, Gabriel P; Oei, Edwin H G; van Middelkoop, Marienke

2016-09-01

Structural abnormalities of the patellofemoral joint might play a role in the pathogenesis of patellofemoral pain (PFP), a common knee problem among young and physically active individuals. No previous study has investigated if PFP is associated with structural abnormalities of the patellofemoral joint using high-resolution magnetic resonance imaging (MRI). To investigate the presence of structural abnormalities of the patellofemoral joint on high-resolution MRI in patients with PFP compared with healthy control subjects. Cross-sectional study; Level of evidence, 3. Patients with PFP and healthy control subjects between 14 and 40 years of age underwent high-resolution 3-T MRI. All images were scored using the Magnetic Resonance Imaging Osteoarthritis Knee Score with the addition of specific patellofemoral features. Associations between PFP and the presence of structural abnormalities were analyzed using logistic regression analyses adjusted for age, body mass index (BMI), sex, and sports participation. A total of 64 patients and 70 control subjects were included in the study. Mean ± SD age was 23.2 ± 6.4 years, mean BMI ± SD was 22.9 ± 3.4 kg/m(2), and 56.7% were female. Full-thickness cartilage loss was not present. Minor patellar cartilage defects, patellar bone marrow lesions, and high signal intensity of the Hoffa fat pad were frequently seen in both patients (23%, 53%, and 58%, respectively) and control subjects (21%, 51%, and 51%, respectively). After adjustment for age, BMI, sex, and sports participation, none of the structural abnormalities were statistically significantly associated with PFP. Structural abnormalities of the patellofemoral joint have been hypothesized as a factor in the pathogenesis of PFP, but the study findings suggest that structural abnormalities of the patellofemoral joint on MRI are not associated with PFP. © 2016 The Author(s).

Discovery of Finely Structured Dynamic Solar Corona Observed in the Hi-C Telescope

NASA Technical Reports Server (NTRS)

Winebarger, A.; Cirtain, J.; Golub, L.; DeLuca, E.; Savage, S.; Alexander, C.; Schuler, T.

2014-01-01

In the summer of 2012, the High-resolution Coronal Imager (Hi-C) flew aboard a NASA sounding rocket and collected the highest spatial resolution images ever obtained of the solar corona. One of the goals of the Hi-C flight was to characterize the substructure of the solar corona. We therefore examine how the intensity scales from AIA resolution to Hi-C resolution. For each low-resolution pixel, we calculate the standard deviation in the contributing high-resolution pixel intensities and compare that to the expected standard deviation calculated from the noise. If these numbers are approximately equal, the corona can be assumed to be smoothly varying, i.e. have no evidence of substructure in the Hi-C image to within Hi-C's ability to measure it given its throughput and readout noise. A standard deviation much larger than the noise value indicates the presence of substructure. We calculate these values for each low-resolution pixel for each frame of the Hi-C data. On average, 70 percent of the pixels in each Hi-C image show no evidence of substructure. The locations where substructure is prevalent is in the moss regions and in regions of sheared magnetic field. We also find that the level of substructure varies significantly over the roughly 160 s of the Hi-C data analyzed here. This result indicates that the finely structured corona is concentrated in regions of heating and is highly time dependent.

DISCOVERY OF FINELY STRUCTURED DYNAMIC SOLAR CORONA OBSERVED IN THE Hi-C TELESCOPE

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

Winebarger, Amy R.; Cirtain, Jonathan; Savage, Sabrina

In the Summer of 2012, the High-resolution Coronal Imager (Hi-C) flew on board a NASA sounding rocket and collected the highest spatial resolution images ever obtained of the solar corona. One of the goals of the Hi-C flight was to characterize the substructure of the solar corona. We therefore examine how the intensity scales from AIA resolution to Hi-C resolution. For each low-resolution pixel, we calculate the standard deviation in the contributing high-resolution pixel intensities and compare that to the expected standard deviation calculated from the noise. If these numbers are approximately equal, the corona can be assumed to bemore » smoothly varying, i.e., have no evidence of substructure in the Hi-C image to within Hi-C's ability to measure it given its throughput and readout noise. A standard deviation much larger than the noise value indicates the presence of substructure. We calculate these values for each low-resolution pixel for each frame of the Hi-C data. On average, 70% of the pixels in each Hi-C image show no evidence of substructure. The locations where substructure is prevalent is in the moss regions and in regions of sheared magnetic field. We also find that the level of substructure varies significantly over the roughly 160 s of the Hi-C data analyzed here. This result indicates that the finely structured corona is concentrated in regions of heating and is highly time dependent.« less

Study of structural colour of Hebomoia glaucippe butterfly wing scales

NASA Astrophysics Data System (ADS)

Shur, V. Ya; Kuznetsov, D. K.; Pryakhina, V. I.; Kosobokov, M. S.; Zubarev, I. V.; Boymuradova, S. K.; Volchetskaya, K. V.

2017-10-01

Structural colours of Hebomoia glaucippe butterfly wing scales have been studied experimentally using high resolution scanning electron microscopy. Visualization of scales structures and computer simulation allowed distinguishing correlation between nanostructures on the scales and their colour.

Developmental and morphological studies in Japanese medaka with ultra-high resolution optical coherence tomography

PubMed Central

Gladys, Fanny Moses; Matsuda, Masaru; Lim, Yiheng; Jackin, Boaz Jessie; Imai, Takuto; Otani, Yukitoshi; Yatagai, Toyohiko; Cense, Barry

2015-01-01

We propose ultra-high resolution optical coherence tomography to study the morphological development of internal organs in medaka fish in the post-embryonic stages at micrometer resolution. Different stages of Japanese medaka were imaged after hatching in vivo with an axial resolution of 2.8 µm in tissue. Various morphological structures and organs identified in the OCT images were then compared with the histology. Due to the medaka’s close resemblance to vertebrates, including humans, these morphological features play an important role in morphogenesis and can be used to study diseases that also occur in humans. PMID:25780725

Nonlinear structured-illumination enhanced temporal focusing multiphoton excitation microscopy with a digital micromirror device

PubMed Central

Cheng, Li-Chung; Lien, Chi-Hsiang; Da Sie, Yong; Hu, Yvonne Yuling; Lin, Chun-Yu; Chien, Fan-Ching; Xu, Chris; Dong, Chen Yuan; Chen, Shean-Jen

2014-01-01

In this study, the light diffraction of temporal focusing multiphoton excitation microscopy (TFMPEM) and the excitation patterning of nonlinear structured-illumination microscopy (NSIM) can be simultaneously and accurately implemented via a single high-resolution digital micromirror device. The lateral and axial spatial resolutions of the TFMPEM are remarkably improved through the second-order NSIM and projected structured light, respectively. The experimental results demonstrate that the lateral and axial resolutions are enhanced from 397 nm to 168 nm (2.4-fold) and from 2.33 μm to 1.22 μm (1.9-fold), respectively, in full width at the half maximum. Furthermore, a three-dimensionally rendered image of a cytoskeleton cell featuring ~25 nm microtubules is improved, with other microtubules at a distance near the lateral resolution of 168 nm also able to be distinguished. PMID:25136483

MPGD for breast cancer prevention: a high resolution and low dose radiation medical imaging

NASA Astrophysics Data System (ADS)

Gutierrez, R. M.; Cerquera, E. A.; Mañana, G.

2012-07-01

Early detection of small calcifications in mammograms is considered the best preventive tool of breast cancer. However, existing digital mammography with relatively low radiation skin exposure has limited accessibility and insufficient spatial resolution for small calcification detection. Micro Pattern Gaseous Detectors (MPGD) and associated technologies, increasingly provide new information useful to generate images of microscopic structures and make more accessible cutting edge technology for medical imaging and many other applications. In this work we foresee and develop an application for the new information provided by a MPGD camera in the form of highly controlled images with high dynamical resolution. We present a new Super Detail Image (S-DI) that efficiently profits of this new information provided by the MPGD camera to obtain very high spatial resolution images. Therefore, the method presented in this work shows that the MPGD camera with SD-I, can produce mammograms with the necessary spatial resolution to detect microcalcifications. It would substantially increase efficiency and accessibility of screening mammography to highly improve breast cancer prevention.

High sensitivity far infrared laser diagnostics for the C-2U advanced beam-driven field-reversed configuration plasmas

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

Deng, B. H., E-mail: bdeng@trialphaenergy.com; Beall, M.; Schroeder, J.

2016-11-15

A high sensitivity multi-channel far infrared laser diagnostics with switchable interferometry and polarimetry operation modes for the advanced neutral beam-driven C-2U field-reversed configuration (FRC) plasmas is described. The interferometer achieved superior resolution of 1 × 10{sup 16} m{sup −2} at >1.5 MHz bandwidth, illustrated by measurement of small amplitude high frequency fluctuations. The polarimetry achieved 0.04° instrument resolution and 0.1° actual resolution in the challenging high density gradient environment with >0.5 MHz bandwidth, making it suitable for weak internal magnetic field measurements in the C-2U plasmas, where the maximum Faraday rotation angle is less than 1°. The polarimetry resolution datamore » is analyzed, and high resolution Faraday rotation data in C-2U is presented together with direct evidences of field reversal in FRC magnetic structure obtained for the first time by a non-perturbative method.« less

Open data set of live cyanobacterial cells imaged using an X-ray laser

NASA Astrophysics Data System (ADS)

van der Schot, Gijs; Svenda, Martin; Maia, Filipe R. N. C.; Hantke, Max F.; Deponte, Daniel P.; Seibert, M. Marvin; Aquila, Andrew; Schulz, Joachim; Kirian, Richard A.; Liang, Mengning; Stellato, Francesco; Bari, Sadia; Iwan, Bianca; Andreasson, Jakob; Timneanu, Nicusor; Bielecki, Johan; Westphal, Daniel; Nunes de Almeida, Francisca; Odić, Duško; Hasse, Dirk; Carlsson, Gunilla H.; Larsson, Daniel S. D.; Barty, Anton; Martin, Andrew V.; Schorb, Sebastian; Bostedt, Christoph; Bozek, John D.; Carron, Sebastian; Ferguson, Ken; Rolles, Daniel; Rudenko, Artem; Epp, Sascha W.; Foucar, Lutz; Rudek, Benedikt; Erk, Benjamin; Hartmann, Robert; Kimmel, Nils; Holl, Peter; Englert, Lars; Loh, N. Duane; Chapman, Henry N.; Andersson, Inger; Hajdu, Janos; Ekeberg, Tomas

2016-08-01

Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.

Open data set of live cyanobacterial cells imaged using an X-ray laser.

PubMed

van der Schot, Gijs; Svenda, Martin; Maia, Filipe R N C; Hantke, Max F; DePonte, Daniel P; Seibert, M Marvin; Aquila, Andrew; Schulz, Joachim; Kirian, Richard A; Liang, Mengning; Stellato, Francesco; Bari, Sadia; Iwan, Bianca; Andreasson, Jakob; Timneanu, Nicusor; Bielecki, Johan; Westphal, Daniel; Nunes de Almeida, Francisca; Odić, Duško; Hasse, Dirk; Carlsson, Gunilla H; Larsson, Daniel S D; Barty, Anton; Martin, Andrew V; Schorb, Sebastian; Bostedt, Christoph; Bozek, John D; Carron, Sebastian; Ferguson, Ken; Rolles, Daniel; Rudenko, Artem; Epp, Sascha W; Foucar, Lutz; Rudek, Benedikt; Erk, Benjamin; Hartmann, Robert; Kimmel, Nils; Holl, Peter; Englert, Lars; Loh, N Duane; Chapman, Henry N; Andersson, Inger; Hajdu, Janos; Ekeberg, Tomas

2016-08-01

Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.

Open data set of live cyanobacterial cells imaged using an X-ray laser

PubMed Central

van der Schot, Gijs; Svenda, Martin; Maia, Filipe R.N.C.; Hantke, Max F.; DePonte, Daniel P.; Seibert, M. Marvin; Aquila, Andrew; Schulz, Joachim; Kirian, Richard A.; Liang, Mengning; Stellato, Francesco; Bari, Sadia; Iwan, Bianca; Andreasson, Jakob; Timneanu, Nicusor; Bielecki, Johan; Westphal, Daniel; Nunes de Almeida, Francisca; Odić, Duško; Hasse, Dirk; Carlsson, Gunilla H.; Larsson, Daniel S.D.; Barty, Anton; Martin, Andrew V.; Schorb, Sebastian; Bostedt, Christoph; Bozek, John D.; Carron, Sebastian; Ferguson, Ken; Rolles, Daniel; Rudenko, Artem; Epp, Sascha W.; Foucar, Lutz; Rudek, Benedikt; Erk, Benjamin; Hartmann, Robert; Kimmel, Nils; Holl, Peter; Englert, Lars; Loh, N. Duane; Chapman, Henry N.; Andersson, Inger; Hajdu, Janos; Ekeberg, Tomas

2016-01-01

Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences. PMID:27479514

Revealing the hidden structures of an historical bridge by high resolution geophysical methods : A case study of Pont de Coq, France

NASA Astrophysics Data System (ADS)

Antoine, R.; Fauchard, C.

2012-04-01

In the last decades, public institutions have shown an increased interest in heritage conservation and monuments protection. Geophysical methods have been used for 20 years as powerful tools to assist in the curation of buildings. Ancient masonry bridges usually exhibit a complex structure/geometry. This complexity makes the use of combined geophysical methods highly necessary to obtain a meaningful model of the internal structure of such constructions and their environment. A high resolution geophysical survey was carried out at a stone arch bridge called Pont de Coq and located near Menerval, Normandy (France) in 2011. This decameter-sized bridge was built 400 years ago and crosses the Epte river, which is a tributary of the Seine river. The main objective of this work was to evaluate the structural state of the bridge and its vicinities. Two complementary methods were used : Electrical Resistivity tomography (ERT) and Ground Penetrating radar (GPR). Several profiles were realized along the road crossing the bridge and transversally to the construction, as well as on the two banks of the Epte river. High resolution electrical resistivity data were obtained both in the horizontal and vertical direction up to 8 meter-depth by two ERT methods (Wenner/Schlumberger and dipole-dipole). The GPR was used with shielded antennas at three different frequencies (200 MHz, 400 MHz and 1.5 GHz). This approach lead to the investigation of the subsurface up to approximately 6 meters-depth, with a resolution in the range of 0.04 m-0.40m. An excellent correlation is obtained between the ERT and the GPR methods, allowing us to propose a precise structural model of the Pont de Coq and to characterize the soil under the building. Several anomalies are observed within the roadway of the bridge at 50 cm-depth, as well as within the vaulting, corresponding to the presence of voids and a root network which lead to the slow destruction of the structure.

High resolution 3D laboratory x-ray tomography data of femora from young, 1-14 day old C57BL/6 mice.

PubMed

Bortel, Emely L; Duda, Georg N; Mundlos, Stefan; Willie, Bettina M; Fratzl, Peter; Zaslansky, Paul

2015-09-01

This data article contains high resolution (1.2 µm effective pixel size) lab-based micro-computed tomography (µCT) reconstructed volume data of the femoral mid-shafts from young C57BL/6 mice. This data formed the basis for the analyses of bone structural development in healthy mice, including closed and open porosity as reported in Bortel et al. [1]. The data reveals changes seen in bone material and porosity distribution observed when mouse bones transform from porous scaffolds into solid structures during normal organogenesis.

Soot Nanostructure: Using Fringe Analysis Software on High Resolution Transmission Electron Microscopy of Carbon Soot

NASA Technical Reports Server (NTRS)

King, James D.

2004-01-01

Using high resolution transmission electron images of carbon nanotubes and carbon particles, we are able to use image analysis program to determine several carbon fringe properties, including length, separation, curvature and orientation. Results are shown in the form of histograms for each of those quantities. The combination of those measurements can give a better indication of the graphic structure within nanotubes and particles of carbon and can distinguish carbons based upon fringe properties. Carbon with longer, straighter and closer spaced fringes are considered graphite, while amorphous carbon contain shorter, less structured fringes.

Assessing resolution in live cell structured illumination microscopy

NASA Astrophysics Data System (ADS)

Pospíšil, Jakub; Fliegel, Karel; Klíma, Miloš

2017-12-01

Structured Illumination Microscopy (SIM) is a powerful super-resolution technique, which is able to enhance the resolution of optical microscope beyond the Abbe diffraction limit. In the last decade, numerous SIM methods that achieve the resolution of 100 nm in the lateral dimension have been developed. The SIM setups with new high-speed cameras and illumination pattern generators allow rapid acquisition of the live specimen. Therefore, SIM is widely used for investigation of the live structures in molecular and live cell biology. Quantitative evaluation of resolution enhancement in a real sample is essential to describe the efficiency of super-resolution microscopy technique. However, measuring the resolution of a live cell sample is a challenging task. Based on our experimental findings, the widely used Fourier ring correlation (FRC) method does not seem to be well suited for measuring the resolution of SIM live cell video sequences. Therefore, the resolution assessing methods based on Fourier spectrum analysis are often used. We introduce a measure based on circular average power spectral density (PSDca) estimated from a single SIM image (one video frame). PSDca describes the distribution of the power of a signal with respect to its spatial frequency. Spatial resolution corresponds to the cut-off frequency in Fourier space. In order to estimate the cut-off frequency from a noisy signal, we use a spectral subtraction method for noise suppression. In the future, this resolution assessment approach might prove useful also for single-molecule localization microscopy (SMLM) live cell imaging.

4D electron microscopy: principles and applications.

PubMed

Flannigan, David J; Zewail, Ahmed H

2012-10-16

The transmission electron microscope (TEM) is a powerful tool enabling the visualization of atoms with length scales smaller than the Bohr radius at a factor of only 20 larger than the relativistic electron wavelength of 2.5 pm at 200 keV. The ability to visualize matter at these scales in a TEM is largely due to the efforts made in correcting for the imperfections in the lens systems which introduce aberrations and ultimately limit the achievable spatial resolution. In addition to the progress made in increasing the spatial resolution, the TEM has become an all-in-one characterization tool. Indeed, most of the properties of a material can be directly mapped in the TEM, including the composition, structure, bonding, morphology, and defects. The scope of applications spans essentially all of the physical sciences and includes biology. Until recently, however, high resolution visualization of structural changes occurring on sub-millisecond time scales was not possible. In order to reach the ultrashort temporal domain within which fundamental atomic motions take place, while simultaneously retaining high spatial resolution, an entirely new approach from that of millisecond-limited TEM cameras had to be conceived. As shown below, the approach is also different from that of nanosecond-limited TEM, whose resolution cannot offer the ultrafast regimes of dynamics. For this reason "ultrafast electron microscopy" is reserved for the field which is concerned with femtosecond to picosecond resolution capability of structural dynamics. In conventional TEMs, electrons are produced by heating a source or by applying a strong extraction field. Both methods result in the stochastic emission of electrons, with no control over temporal spacing or relative arrival time at the specimen. The timing issue can be overcome by exploiting the photoelectric effect and using pulsed lasers to generate precisely timed electron packets of ultrashort duration. The spatial and temporal resolutions achievable with short intense pulses containing a large number of electrons, however, are limited to tens of nanometers and nanoseconds, respectively. This is because Coulomb repulsion is significant in such a pulse, and the electrons spread in space and time, thus limiting the beam coherence. It is therefore not possible to image the ultrafast elementary dynamics of complex transformations. The challenge was to retain the high spatial resolution of a conventional TEM while simultaneously enabling the temporal resolution required to visualize atomic-scale motions. In this Account, we discuss the development of four-dimensional ultrafast electron microscopy (4D UEM) and summarize techniques and applications that illustrate the power of the approach. In UEM, images are obtained either stroboscopically with coherent single-electron packets or with a single electron bunch. Coulomb repulsion is absent under the single-electron condition, thus permitting imaging, diffraction, and spectroscopy, all with high spatiotemporal resolution, the atomic scale (sub-nanometer and femtosecond). The time resolution is limited only by the laser pulse duration and energy carried by the electron packets; the CCD camera has no bearing on the temporal resolution. In the regime of single pulses of electrons, the temporal resolution of picoseconds can be attained when hundreds of electrons are in the bunch. The applications given here are selected to highlight phenomena of different length and time scales, from atomic motions during structural dynamics to phase transitions and nanomechanical oscillations. We conclude with a brief discussion of emerging methods, which include scanning ultrafast electron microscopy (S-UEM), scanning transmission ultrafast electron microscopy (ST-UEM) with convergent beams, and time-resolved imaging of biological structures at ambient conditions with environmental cells.

Crystal structure, chemical composition, and extended defects of the high-Tc (Bi,Pb)2Sr2Ca(n)-1CunO4 + 2n + delta compounds.

PubMed

Eibl, O

1995-02-15

This paper summarizes results obtained by high-resolution transmission electron microscopy on the crystal structure and microstructure of the (Bi,Pb)2Sr2Ca(n)-1CunO4 + 2n + delta high-Tc superconducting oxides. The experimental basis for the work presented here are high-resolution structure images obtained at ultra-thin (3 nm) areas of carefully prepared transmission electron microscope (TEM) samples. The analysis was carried out on a 400 kV TEM equipped with a pole piece yielding 0.17 nm point-to-point resolution. From the images obtained the projected crystal potential of the cations can be extracted directly, as confirmed by detailed image simulation. Structural analysis of the oxygen sublattice remains an unsolved problem by high-resolution TEM (HRTEM), mainly because of the small scattering factors, and thus the contribution of the oxygen sublattice to the image contrast is small. The (BiPb)2Sr2Ca(n)-1CunO4 + 2n + delta phases are modulated structures that can be understood as an average structure plus a superimposed displacement field. The crystal structure consists of BiO double layers and perovskite-type cuboids (containing Sr, Ca, Cu, and O), which are sandwiched between the BiO double layers. The displacement field can be directly analyzed by HRTEM, and the largest displacement amplitudes of 70 pm were determined for the Bi atoms in the n = 1 compound. The chemical composition of the n = 2 and n = 3 compounds was determined by EDX in the TEM for the cation sublattice. A significant (Ca + Sr) deficiency (approximately 10%) with respect to Cu was found. The (Sr + Ca)/Cu mole fraction ratio was 1.31 for the Bi-2212 phase and 1.14 for the Bi(Pb)-2223 phase. The oxygen content cannot be determined by EDX in the TEM with the accuracy necessary for a correlation with electrical and superconducting properties. The defect structure present in these materials, that is, intergrown lamellae with different crystal structures and equal or different chemical compositions, stacking faults, and grain boundaries, is summarized. The importance of grain boundaries for understanding and improving superconducting properties is emphasized.

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

Kim, Jungho

Hard x-ray resonant inelastic x-ray scattering (RIXS) is a promising x-ray spectroscopic tool for measuring low-energy excitation spectra at high pressure which have been stymied heretofore by the technical difficulties inherent in measuring a sample held at high pressure in a diamond anvil cell. The currently available facilities of high resolution (< 200 meV) RIXS has been used to probe low-energy excitation spectra from the diamond anvil cell, by virtue of advanced photon detection instrumentations of high-brilliance synchrotron x-ray radiation sources. Compared to a structural elastic scattering and x-ray emission, RIXS is a photon hungry technique and high-resolution RIXS undermore » high pressure is at its infancy stage. In this review, the fundamentals of RIXS including instrumentation of high-resolution RIXS are presented and then experimental details of diamond anvil cell, sample preparation and measurement geometry are discussed. Experimental data of 3d and 5d transition metal oxides are presented. Finally, future improvements in high-resolution RIXS instrumentation for the high pressure experiment is discussed.« less

Molecular ecology meets remote sensing: environmental drivers to population structure of humpback dolphins in the Western Indian Ocean.

PubMed

Mendez, M; Subramaniam, A; Collins, T; Minton, G; Baldwin, R; Berggren, P; Särnblad, A; Amir, O A; Peddemors, V M; Karczmarski, L; Guissamulo, A; Rosenbaum, H C

2011-10-01

Genetic analyses of population structure can be placed in explicit environmental contexts if appropriate environmental data are available. Here, we use high-coverage and high-resolution oceanographic and genetic sequence data to assess population structure patterns and their potential environmental influences for humpback dolphins in the Western Indian Ocean. We analyzed mitochondrial DNA data from 94 dolphins from the coasts of South Africa, Mozambique, Tanzania and Oman, employing frequency-based and maximum-likelihood algorithms to assess population structure and migration patterns. The genetic data were combined with 13 years of remote sensing oceanographic data of variables known to influence cetacean dispersal and population structure. Our analyses show strong and highly significant genetic structure between all putative populations, except for those in South Africa and Mozambique. Interestingly, the oceanographic data display marked environmental heterogeneity between all sampling areas and a degree of overlap between South Africa and Mozambique. Our combined analyses therefore suggest the occurrence of genetically isolated populations of humpback dolphins in areas that are environmentally distinct. This study highlights the utility of molecular tools in combination with high-resolution and high-coverage environmental data to address questions not only pertaining to genetic population structure, but also to relevant ecological processes in marine species.

Molecular ecology meets remote sensing: environmental drivers to population structure of humpback dolphins in the Western Indian Ocean

PubMed Central

Mendez, M; Subramaniam, A; Collins, T; Minton, G; Baldwin, R; Berggren, P; Särnblad, A; Amir, O A; Peddemors, V M; Karczmarski, L; Guissamulo, A; Rosenbaum, H C

2011-01-01

Genetic analyses of population structure can be placed in explicit environmental contexts if appropriate environmental data are available. Here, we use high-coverage and high-resolution oceanographic and genetic sequence data to assess population structure patterns and their potential environmental influences for humpback dolphins in the Western Indian Ocean. We analyzed mitochondrial DNA data from 94 dolphins from the coasts of South Africa, Mozambique, Tanzania and Oman, employing frequency-based and maximum-likelihood algorithms to assess population structure and migration patterns. The genetic data were combined with 13 years of remote sensing oceanographic data of variables known to influence cetacean dispersal and population structure. Our analyses show strong and highly significant genetic structure between all putative populations, except for those in South Africa and Mozambique. Interestingly, the oceanographic data display marked environmental heterogeneity between all sampling areas and a degree of overlap between South Africa and Mozambique. Our combined analyses therefore suggest the occurrence of genetically isolated populations of humpback dolphins in areas that are environmentally distinct. This study highlights the utility of molecular tools in combination with high-resolution and high-coverage environmental data to address questions not only pertaining to genetic population structure, but also to relevant ecological processes in marine species. PMID:21427750

3D high-resolution radar imaging of small body interiors

NASA Astrophysics Data System (ADS)

Sava, Paul; Asphaug, Erik

2017-10-01

Answering fundamental questions about the origin and evolution of small planetary bodies hinges on our ability to image their interior structure in detail and at high resolution (Asphaug, 2009). We often infer internal structure from surface observations, e.g. that comet 67P/Churyumov-Gerasimenko is a primordial agglomeration of cometesimals (Massironi et al., 2015). However, the interior structure is not easily accessible without systematic imaging using, e.g., radar transmission and reflection data, as suggested by the CONSERT experiment on Rosetta. Interior imaging depends on observations from multiple viewpoints, as in medical tomography.We discuss radar imaging using methodology adapted from terrestrial exploration seismology (Sava et al., 2015). We primarily focus on full wavefield methods that facilitate high quality imaging of small body interiors characterized by complex structure and large contrasts of physical properties. We consider the case of a monostatic system (co-located transmitters and receivers) operated at two frequency bands, centered around 5 and 15 MHz, from a spacecraft in slow polar orbit around a spinning comet nucleus. Assuming that the spin period is significantly (e.g. 5x) faster than the orbital period, this configuration allows repeated views from multiple directions (Safaeinili et al., 2002)Using realistic numerical experiments, we argue that (1) the comet/asteroid imaging problem is intrinsically 3D and conventional SAR methodology does not satisfy imaging, sampling and resolution requirements; (2) imaging at different frequency bands can provide information about internal surfaces (through migration) and internal volumes (through tomography); (3) interior imaging can be accomplished progressively as data are being acquired through successive orbits around the studied object; (4) imaging resolution can go beyond the apparent radar frequency band by deconvolution of the point-spread-function characterizing the imaging system; and (5) exploiting the known (and complex) exterior shape of the studied body facilitates high-resolution imaging and tomography comparable with what could be accomplished by bi/multi-static systems.

High-resolution studies of the structure of the solar atmosphere using a new imaging algorithm

NASA Technical Reports Server (NTRS)

Karovska, Margarita; Habbal, Shadia Rifai

1991-01-01

The results of the application of a new image restoration algorithm developed by Ayers and Dainty (1988) to the multiwavelength EUV/Skylab observations of the solar atmosphere are presented. The application of the algorithm makes it possible to reach a resolution better than 5 arcsec, and thus study the structure of the quiet sun on that spatial scale. The results show evidence for discrete looplike structures in the network boundary, 5-10 arcsec in size, at temperatures of 100,000 K.

Painting Supramolecular Polymers in Organic Solvents by Super-resolution Microscopy

PubMed Central

2018-01-01

Despite the rapid development of complex functional supramolecular systems, visualization of these architectures under native conditions at high resolution has remained a challenging endeavor. Super-resolution microscopy was recently proposed as an effective tool to unveil one-dimensional nanoscale structures in aqueous media upon chemical functionalization with suitable fluorescent probes. Building upon our previous work, which enabled photoactivation localization microscopy in organic solvents, herein, we present the imaging of one-dimensional supramolecular polymers in their native environment by interface point accumulation for imaging in nanoscale topography (iPAINT). The noncovalent staining, typical of iPAINT, allows the investigation of supramolecular polymers’ structure in situ without any chemical modification. The quasi-permanent adsorption of the dye to the polymer is exploited to identify block-like arrangements within supramolecular fibers, which were obtained upon mixing homopolymers that were prestained with different colors. The staining of the blocks, maintained by the lack of exchange of the dyes, permits the imaging of complex structures for multiple days. This study showcases the potential of PAINT-like strategies such as iPAINT to visualize multicomponent dynamic systems in their native environment with an easy, synthesis-free approach and high spatial resolution. PMID:29697958

Fast, label-free super-resolution live-cell imaging using rotating coherent scattering (ROCS) microscopy

NASA Astrophysics Data System (ADS)

Jünger, Felix; Olshausen, Philipp V.; Rohrbach, Alexander

2016-07-01

Living cells are highly dynamic systems with cellular structures being often below the optical resolution limit. Super-resolution microscopes, usually based on fluorescence cell labelling, are usually too slow to resolve small, dynamic structures. We present a label-free microscopy technique, which can generate thousands of super-resolved, high contrast images at a frame rate of 100 Hertz and without any post-processing. The technique is based on oblique sample illumination with coherent light, an approach believed to be not applicable in life sciences because of too many interference artefacts. However, by circulating an incident laser beam by 360° during one image acquisition, relevant image information is amplified. By combining total internal reflection illumination with dark-field detection, structures as small as 150 nm become separable through local destructive interferences. The technique images local changes in refractive index through scattered laser light and is applied to living mouse macrophages and helical bacteria revealing unexpected dynamic processes.

Solar flare microwave observations with high spectral resolution

NASA Astrophysics Data System (ADS)

Bruggmann, G.; Magun, A.; Benz, A. O.; Stehling, W.

1990-12-01

The solar flare radio emission in the 6-8 GHz range was observed with a high resolution spectrometer. The observed band corresponds to the plasma frequencies and gyrofrequencies of the transition region and the lowest part of the corona in active regions. Most of the emissions were found to be broadbanded, as expected from the gyrosynchrotron mechanism. In eight out of 46 observed events, spectral structures of three types were detected: spikes below the time resolution of 100 ms, slowly drifting broadband structures, and a narrow bandwidth patch of continuum emission. These first narrowband bursts spectrally recorded in the 6-8 GHz range are generally weak. Slowly drifting structures are the only type compatible with the gyrosynchrotron emission mechanism. A simple argument based on free-free absorption shows that plasma emission can only be propagated if the radiation originates in a dense region with a small density-scale length. The same holds for maser emission at a low harmonic of the electron gyrofrequency. Possible emission mechanisms and diagnostic capabilities are discussed.

Fast, label-free super-resolution live-cell imaging using rotating coherent scattering (ROCS) microscopy

PubMed Central

Jünger, Felix; Olshausen, Philipp v.; Rohrbach, Alexander

2016-01-01

Living cells are highly dynamic systems with cellular structures being often below the optical resolution limit. Super-resolution microscopes, usually based on fluorescence cell labelling, are usually too slow to resolve small, dynamic structures. We present a label-free microscopy technique, which can generate thousands of super-resolved, high contrast images at a frame rate of 100 Hertz and without any post-processing. The technique is based on oblique sample illumination with coherent light, an approach believed to be not applicable in life sciences because of too many interference artefacts. However, by circulating an incident laser beam by 360° during one image acquisition, relevant image information is amplified. By combining total internal reflection illumination with dark-field detection, structures as small as 150 nm become separable through local destructive interferences. The technique images local changes in refractive index through scattered laser light and is applied to living mouse macrophages and helical bacteria revealing unexpected dynamic processes. PMID:27465033

High resolution space photometry as a method to reveal structure anomalies of the lunar surface

NASA Astrophysics Data System (ADS)

Kaydash, V. G.; Shkuratov, Yu. G.; Korokhin, V. V.

2015-11-01

We have reviewed studies of disturbed primordial structure of the lunar regolith, which is caused by both artificial and natural factors. To identify such disturbances, we used orbital high resolution photometry data in conjunction with the method of phase ratios, which makes it possible to evaluate the surface roughness of the light scattering element on the scale of less than imaging resolution. In particular, this method allows the identification of soil talus; it is also an efficient way to find new craters and places of falling meteoroid streams. The reliability of the new method is proved by the photometric detection of the anomalies associated with changes in the structure of the surface layer of regolith in landing sites of manned spacecraft, i.e., where the impact of human activity on the lunar regolith is well known. The results can be used in a planning and implementation of space missions to the Moon and other atmosphereless bodies of the solar system by the space agencies

Local structure of In0.5Ga0.5As from joint high-resolution and differential pair distribution function analysis

NASA Astrophysics Data System (ADS)

Petkov, V.; Jeong, I.-K.; Mohiuddin-Jacobs, F.; Proffen, Th.; Billinge, S. J. L.; Dmowski, W.

2000-07-01

High resolution total and indium differential atomic pair distribution functions (PDFs) for In0.5Ga0.5As alloys have been obtained by high energy and anomalous x-ray diffraction experiments, respectively. The first peak in the total PDF is resolved as a doublet due to the presence of two distinct bond lengths, In-As and Ga-As. The In differential PDF, which involves only atomic pairs containing In, yields chemical specific information and helps ease the structure data interpretation. Both PDFs have been fit with structure models and the way in that the underlying cubic zinc-blende lattice of In0.5Ga0.5As semiconductor alloy distorts locally to accommodate the distinct In-As and Ga-As bond lengths present has been quantified.

Oxidized crystalline (3 × 1)-O surface phases of InAs and InSb studied by high-resolution photoelectron spectroscopy

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

Tuominen, M., E-mail: tmleir@utu.fi, E-mail: pekka.laukkanen@utu.fi; Lång, J.; Dahl, J.

2015-01-05

The pre-oxidized crystalline (3×1)-O structure of InAs(100) has been recently found to significantly improve insulator/InAs junctions for devices, but the atomic structure and formation of this useful oxide layer are not well understood. We report high-resolution photoelectron spectroscopy analysis of (3×1)-O on InAs(100) and InSb(100). The findings reveal that the atomic structure of (3×1)-O consists of In atoms with unexpected negative (between −0.64 and −0.47 eV) and only moderate positive (In{sub 2}O type) core-level shifts; highly oxidized group-V sites; and four different oxygen sites. These fingerprint shifts are compared to those of previously studied oxides of III-V to elucidate oxidation processes.

Imaging cells and sub-cellular structures with ultrahigh resolution full-field X-ray microscopy.

PubMed

Chien, C C; Tseng, P Y; Chen, H H; Hua, T E; Chen, S T; Chen, Y Y; Leng, W H; Wang, C H; Hwu, Y; Yin, G C; Liang, K S; Chen, F R; Chu, Y S; Yeh, H I; Yang, Y C; Yang, C S; Zhang, G L; Je, J H; Margaritondo, G

2013-01-01

Our experimental results demonstrate that full-field hard-X-ray microscopy is finally able to investigate the internal structure of cells in tissues. This result was made possible by three main factors: the use of a coherent (synchrotron) source of X-rays, the exploitation of contrast mechanisms based on the real part of the refractive index and the magnification provided by high-resolution Fresnel zone-plate objectives. We specifically obtained high-quality microradiographs of human and mouse cells with 29 nm Rayleigh spatial resolution and verified that tomographic reconstruction could be implemented with a final resolution level suitable for subcellular features. We also demonstrated that a phase retrieval method based on a wave propagation algorithm could yield good subcellular images starting from a series of defocused microradiographs. The concluding discussion compares cellular and subcellular hard-X-ray microradiology with other techniques and evaluates its potential impact on biomedical research. Copyright © 2012 Elsevier Inc. All rights reserved.

Optimized expression and purification of NavAb provide the structural insight into the voltage dependence.

PubMed

Irie, Katsumasa; Haga, Yukari; Shimomura, Takushi; Fujiyoshi, Yoshinori

2018-01-01

Voltage-gated sodium channels are crucial for electro-signalling in living systems. Analysis of the molecular mechanism requires both fine electrophysiological evaluation and high-resolution channel structures. Here, we optimized a dual expression system of NavAb, which is a well-established standard of prokaryotic voltage-gated sodium channels, for E. coli and insect cells using a single plasmid vector to analyse high-resolution protein structures and measure large ionic currents. Using this expression system, we evaluated the voltage dependence and determined the crystal structures of NavAb wild-type and two mutants, E32Q and N49K, whose voltage dependence were positively shifted and essential interactions were lost in voltage sensor domain. The structural and functional comparison elucidated the molecular mechanisms of the voltage dependence of prokaryotic voltage-gated sodium channels. © 2017 Federation of European Biochemical Societies.

RAPID COMMUNICATION: Study of superstructure II in multiferroic BiMnO3

NASA Astrophysics Data System (ADS)

Ge, Bing-Hui; Li, Fang-Hua; Li, Xue-Ming; Wang, Yu-Mei; Chi, Zhen-Hua; Jin, Chang-Qing

2008-09-01

The crystal structure of the minor phase, named superstructure II, existing in multiferroic compound BiMnO3 has been studied by electron diffraction and high-resolution transmission electron microscopy. Domains of major and minor phases coexisting in BiMnO3 were observed in high-resolution electron microscope images. The unit cell of minor phase was determined to be triclinic with the size 4×4×4 times as large as the distorted perovskite subcell. The [111] and [10bar 1] projected structure maps of the minor phase have been derived from the corresponding images by means of the image processing. A possible rough three-dimensional (3D) structure model was proposed based on the 3D structural information extracted from the two projected structure maps. Since there is no inversion centre in the proposed model, the minor phase may contribute to the ferroelectric property of BiMnO3.

Objective tropical cyclone extratropical transition detection in high-resolution reanalysis and climate model data

DOE PAGES

Zarzycki, Colin M.; Thatcher, Diana R.; Jablonowski, Christiane

2017-01-22

This paper describes an objective technique for detecting the extratropical transition (ET) of tropical cyclones (TCs) in high-resolution gridded climate data. The algorithm is based on previous observational studies using phase spaces to define the symmetry and vertical thermal structure of cyclones. Storm tracking is automated, allowing for direct analysis of climate data. Tracker performance in the North Atlantic is assessed using 23 years of data from the variable-resolution Community Atmosphere Model (CAM) at two different resolutions (DX 55 km and 28 km), the Climate Forecast System Reanalysis (CFSR, DX 38 km), and the ERA-Interim Reanalysis (ERA-I, DX 80 km).more » The mean spatiotemporal climatologies and seasonal cycles of objectively detected ET in the observationally constrained CFSR and ERA-I are well matched to previous observational studies, demonstrating the capability of the scheme to adequately find events. High resolution CAM reproduces TC and ET statistics that are in general agreement with reanalyses. One notable model bias, however, is significantly longer time between ET onset and ET completion in CAM, particularly for TCs that lose symmetry prior to developing a cold-core structure and becoming extratropical cyclones, demonstrating the capability of this method to expose model biases in simulated cyclones beyond the tropical phase.« less

RBS/C, HRTEM and HRXRD study of damage accumulation in irradiated SrTiO3

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

Jagielski, Jacek; Jozwik, Przemyslaw A.; Jozwik Biala, Iwona

2013-05-14

Damage accumulation in argon-irradiated SrTiO3 single crystals has been studied by using combination of Rutherford Backscattering/Channeling (RBS/C), High Resolution Transmission Electron Microscopy (HRTEM) and High Resolution X-Ray Diffraction (HRXRD) techniques. The RBS/C spectra were fitted using McChasy, a Monte Carlo simulation code allowing the quantitative analysis of amorphous-like and dislocation-like types of defects. The results were interpreted by using a Multi-Step Damage Accumulation model which assumes, that the damage accumulation occurs in a series of structural transformations, the defect transformations are triggered by a stress caused by formation of a free volume in the irradiated crystal. This assumption has beenmore » confirmed by High Resolution Transmission Electron Microscopy and High Resolution X-Ray Diffraction analysis.« less

Structural Characterisation of Acetogenins from Annona muricata by Supercritical Fluid Chromatography Coupled to High-Resolution Tandem Mass Spectrometry.

PubMed

Laboureur, Laurent; Bonneau, Natacha; Champy, Pierre; Brunelle, Alain; Touboul, David

2017-11-01

Acetogenins are plant polyketides known to be cytotoxic and proposed as antitumor candidates. They are also suspected to be alimentary neurotoxins. Their occurrence as complex mixtures renders their dereplication and structural identification difficult using liquid chromatography coupled to tandem mass spectrometry and efforts are required to improve the methodology. To develop a supercritical fluid chromatography (SFC) high-resolution tandem mass spectrometry method, involving lithium post-column cationisation, for the structural characterisation of Annonaceous acetogenins in crude extracts. The seeds of Annona muricata L. were extracted with methanol. Supercritical fluid chromatography of the extract, using a 2-ethylpyridine stationary phase column, was monitored using a high-resolution quadrupole time-of-flight mass spectrometer. Lithium iodide was added post-column in the make-up solvent. For comparison, the same extract was analysed using high-pressure liquid chromatography coupled to the same mass spectrometer, with a column based on solid core particles. Sensitivity was similar for both HPLC and SFC approaches. Retention behaviour and fragmentation pathways of three different isomer groups are described. A previously unknown group of acetogenins was also evidenced for the first time. The use of SFC-MS/MS allows the reduction of the time of analysis, of environmental impact and an increase in the chromatographic resolution, compared to liquid chromatography. This new methodology enlightened a new group of acetogenins, isomers of montanacin-D. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

High-resolution crystal structure of Streptococcus pyogenes β-NAD⁺ glycohydrolase in complex with its endogenous inhibitor IFS reveals a highly water-rich interface.

PubMed

Yoon, Ji Young; An, Doo Ri; Yoon, Hye Jin; Kim, Hyoun Sook; Lee, Sang Jae; Im, Ha Na; Jang, Jun Young; Suh, Se Won

2013-11-01

One of the virulence factors produced by Streptococcus pyogenes is β-NAD(+) glycohydrolase (SPN). S. pyogenes injects SPN into the cytosol of an infected host cell using the cytolysin-mediated translocation pathway. As SPN is toxic to bacterial cells themselves, S. pyogenes possesses the ifs gene that encodes an endogenous inhibitor for SPN (IFS). IFS is localized intracellularly and forms a complex with SPN. This intracellular complex must be dissociated during export through the cell envelope. To provide a structural basis for understanding the interactions between SPN and IFS, the complex was overexpressed between the mature SPN (residues 38-451) and the full-length IFS (residues 1-161), but it could not be crystallized. Therefore, limited proteolysis was used to isolate a crystallizable SPNct-IFS complex, which consists of the SPN C-terminal domain (SPNct; residues 193-451) and the full-length IFS. Its crystal structure has been determined by single anomalous diffraction and the model refined at 1.70 Å resolution. Interestingly, our high-resolution structure of the complex reveals that the interface between SPNct and IFS is highly rich in water molecules and many of the interactions are water-mediated. The wet interface may facilitate the dissociation of the complex for translocation across the cell envelope.

Genetics and biochemistry remain essential in the structural era of the spliceosome.

PubMed

Mayerle, Megan; Guthrie, Christine

2017-08-01

The spliceosome is not a single macromolecular machine. Rather it is a collection of dynamic heterogeneous subcomplexes that rapidly interconvert throughout the course of a typical splicing cycle. Because of this, for many years the only high resolution structures of the spliceosome available were of smaller, isolated protein or RNA components. Consequently much of our current understanding of the spliceosome derives from biochemical and genetic techniques. Now with the publication of multiple, high resolution structures of the spliceosome, some question the relevance of traditional biochemical and genetic techniques to the splicing field. We argue such techniques are not only relevant, but vital for an in depth mechanistic understanding of pre-mRNA splicing. Copyright © 2017 Elsevier Inc. All rights reserved.

High Resolution Live Cell Raman Imaging Using Subcellular Organelle-Targeting SERS-Sensitive Gold Nanoparticles with Highly Narrow Intra-Nanogap

PubMed Central

Kang, Jeon Woong; So, Peter T. C.; Dasari, Ramachandra R.; Lim, Dong-Kwon

2015-01-01

We report a method to achieve high speed and high resolution live cell Raman images using small spherical gold nanoparticles with highly narrow intra-nanogap structures responding to NIR excitation (785 nm) and high-speed confocal Raman microscopy. The three different Raman-active molecules placed in the narrow intra-nanogap showed a strong and uniform Raman intensity in solution even under transient exposure time (10 ms) and low input power of incident laser (200 μW), which lead to obtain high-resolution single cell image within 30 s without inducing significant cell damage. The high resolution Raman image showed the distributions of gold nanoparticles for their targeted sites such as cytoplasm, mitochondria, or nucleus. The high speed Raman-based live cell imaging allowed us to monitor rapidly changing cell morphologies during cell death induced by the addition of highly toxic KCN solution to cells. These results strongly suggest that the use of SERS-active nanoparticle can greatly improve the current temporal resolution and image quality of Raman-based cell images enough to obtain the detailed cell dynamics and/or the responses of cells to potential drug molecules. PMID:25646716

Turbulence sources, character, and effects in the stable boundary layer: Insights from multi-scale direct numerical simulations and new, high-resolution measurements

NASA Astrophysics Data System (ADS)

Fritts, Dave; Wang, Ling; Balsley, Ben; Lawrence, Dale

2013-04-01

A number of sources contribute to intermittent small-scale turbulence in the stable boundary layer (SBL). These include Kelvin-Helmholtz instability (KHI), gravity wave (GW) breaking, and fluid intrusions, among others. Indeed, such sources arise naturally in response to even very simple "multi-scale" superpositions of larger-scale GWs and smaller-scale GWs, mean flows, or fine structure (FS) throughout the atmosphere and the oceans. We describe here results of two direct numerical simulations (DNS) of these GW-FS interactions performed at high resolution and high Reynolds number that allow exploration of these turbulence sources and the character and effects of the turbulence that arises in these flows. Results include episodic turbulence generation, a broad range of turbulence scales and intensities, PDFs of dissipation fields exhibiting quasi-log-normal and more complex behavior, local turbulent mixing, and "sheet and layer" structures in potential temperature that closely resemble high-resolution measurements. Importantly, such multi-scale dynamics differ from their larger-scale, quasi-monochromatic gravity wave or quasi-horizontally homogeneous shear flow instabilities in significant ways. The ability to quantify such multi-scale dynamics with new, very high-resolution measurements is also advancing rapidly. New in-situ sensors on small, unmanned aerial vehicles (UAVs), balloons, or tethered systems are enabling definition of SBL (and deeper) environments and turbulence structure and dissipation fields with high spatial and temporal resolution and precision. These new measurement and modeling capabilities promise significant advances in understanding small-scale instability and turbulence dynamics, in quantifying their roles in mixing, transport, and evolution of the SBL environment, and in contributing to improved parameterizations of these dynamics in mesoscale, numerical weather prediction, climate, and general circulation models. We expect such measurement and modeling capabilities to also aid in the design of new and more comprehensive future SBL measurement programs.

Ab initio solution of macromolecular crystal structures without direct methods.

PubMed

McCoy, Airlie J; Oeffner, Robert D; Wrobel, Antoni G; Ojala, Juha R M; Tryggvason, Karl; Lohkamp, Bernhard; Read, Randy J

2017-04-04

The majority of macromolecular crystal structures are determined using the method of molecular replacement, in which known related structures are rotated and translated to provide an initial atomic model for the new structure. A theoretical understanding of the signal-to-noise ratio in likelihood-based molecular replacement searches has been developed to account for the influence of model quality and completeness, as well as the resolution of the diffraction data. Here we show that, contrary to current belief, molecular replacement need not be restricted to the use of models comprising a substantial fraction of the unknown structure. Instead, likelihood-based methods allow a continuum of applications depending predictably on the quality of the model and the resolution of the data. Unexpectedly, our understanding of the signal-to-noise ratio in molecular replacement leads to the finding that, with data to sufficiently high resolution, fragments as small as single atoms of elements usually found in proteins can yield ab initio solutions of macromolecular structures, including some that elude traditional direct methods.

Advances in Structural Biology and the Application to Biological Filament Systems.

PubMed

Popp, David; Koh, Fujiet; Scipion, Clement P M; Ghoshdastider, Umesh; Narita, Akihiro; Holmes, Kenneth C; Robinson, Robert C

2018-04-01

Structural biology has experienced several transformative technological advances in recent years. These include: development of extremely bright X-ray sources (microfocus synchrotron beamlines and free electron lasers) and the use of electrons to extend protein crystallography to ever decreasing crystal sizes; and an increase in the resolution attainable by cryo-electron microscopy. Here we discuss the use of these techniques in general terms and highlight their application for biological filament systems, an area that is severely underrepresented in atomic resolution structures. We assemble a model of a capped tropomyosin-actin minifilament to demonstrate the utility of combining structures determined by different techniques. Finally, we survey the methods that attempt to transform high resolution structural biology into more physiological environments, such as the cell. Together these techniques promise a compelling decade for structural biology and, more importantly, they will provide exciting discoveries in understanding the designs and purposes of biological machines. © 2018 The Authors. BioEssays Published by WILEY Periodicals, Inc.

Intense sub-kilometer-scale boundary layer rolls observed in hurricane fran

PubMed

Wurman; Winslow

1998-04-24

High-resolution observations obtained with the Doppler On Wheels (DOW) mobile weather radar near the point of landfall of hurricane Fran (1996) revealed the existence of intense, sub-kilometer-scale, boundary layer rolls that strongly modulated the near-surface wind speed. It is proposed that these structures are one cause of geographically varying surface damage patterns that have been observed after some landfalling hurricanes and that they cause much of the observed gustiness, bringing high-velocity air from aloft to the lowest observable levels. High-resolution DOW radar observations are contrasted with lower-resolution observations obtained with an operational weather radar, which underestimated peak low-level wind speeds.

Structure-Guided Functional Characterization of DUF1460 Reveals a Highly Specific NlpC/P60 Amidase Family

DOE PAGES

Xu, Qingping; Mengin-Lecreulx, Dominique; Patin, Delphine; ...

2014-11-20

GlcNAc-1,6-anhydro-MurNAc-tetrapeptide is a major peptidoglycan degradation intermediate and a cytotoxin. It is generated by lytic transglycosylases and further degraded and recycled by various enzymes. We have identified and characterized a novel, highly specific N-acetylmuramoyl-L-alanine amidase (AmiA) from Bacteroides uniformis, a member of the DUF1460 protein family, that hydrolyzes GlcNAc-1,6-anhydro-MurNAc-peptide into disaccharide and stem peptide. The high-resolution apo-structure at 1.15 Å resolution shows that AmiA is related to NlpC/P60 γ-D-Glu-meso-diaminopimelic acid amidases and shares a common catalytic core and cysteine peptidase-like active site. AmiA has evolved structural adaptations that reconfigure the substrate recognition site. The preferred substrates for AmiA were predictedmore » in silico based on structural and bioinformatics data, and were subsequently characterized experimentally. Ultimately, further crystal structures of AmiA in complexes with GlcNAc-1,6-anhydro-MurNAc and GlcNAc have enabled us to elucidate substrate recognition and specificity. DUF1460 is highly conserved in structure and defines a new amidase family.« less

Structure-Guided Functional Characterization of DUF1460 Reveals a Highly Specific NlpC/P60 Amidase Family

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

Xu, Qingping; Mengin-Lecreulx, Dominique; Patin, Delphine

GlcNAc-1,6-anhydro-MurNAc-tetrapeptide is a major peptidoglycan degradation intermediate and a cytotoxin. It is generated by lytic transglycosylases and further degraded and recycled by various enzymes. We have identified and characterized a novel, highly specific N-acetylmuramoyl-L-alanine amidase (AmiA) from Bacteroides uniformis, a member of the DUF1460 protein family, that hydrolyzes GlcNAc-1,6-anhydro-MurNAc-peptide into disaccharide and stem peptide. The high-resolution apo-structure at 1.15 Å resolution shows that AmiA is related to NlpC/P60 γ-D-Glu-meso-diaminopimelic acid amidases and shares a common catalytic core and cysteine peptidase-like active site. AmiA has evolved structural adaptations that reconfigure the substrate recognition site. The preferred substrates for AmiA were predictedmore » in silico based on structural and bioinformatics data, and were subsequently characterized experimentally. Ultimately, further crystal structures of AmiA in complexes with GlcNAc-1,6-anhydro-MurNAc and GlcNAc have enabled us to elucidate substrate recognition and specificity. DUF1460 is highly conserved in structure and defines a new amidase family.« less

Structure-guided functional characterization of DUF1460 reveals a highly specific NlpC/P60 amidase family.

PubMed

Xu, Qingping; Mengin-Lecreulx, Dominique; Patin, Delphine; Grant, Joanna C; Chiu, Hsiu-Ju; Jaroszewski, Lukasz; Knuth, Mark W; Godzik, Adam; Lesley, Scott A; Elsliger, Marc-André; Deacon, Ashley M; Wilson, Ian A

2014-12-02

GlcNAc-1,6-anhydro-MurNAc-tetrapeptide is a major peptidoglycan degradation intermediate and a cytotoxin. It is generated by lytic transglycosylases and further degraded and recycled by various enzymes. We have identified and characterized a highly specific N-acetylmuramoyl-L-alanine amidase (AmiA) from Bacteroides uniformis, a member of the DUF1460 protein family, that hydrolyzes GlcNAc-1,6-anhydro-MurNAc-peptide into disaccharide and stem peptide. The high-resolution apo structure at 1.15 Å resolution shows that AmiA is related to NlpC/P60 γ-D-Glu-meso-diaminopimelic acid amidases and shares a common catalytic core and cysteine peptidase-like active site. AmiA has evolved structural adaptations that reconfigure the substrate recognition site. The preferred substrates for AmiA were predicted in silico based on structural and bioinformatics data, and subsequently were characterized experimentally. Further crystal structures of AmiA in complexes with GlcNAc-1,6-anhydro-MurNAc and GlcNAc have enabled us to elucidate substrate recognition and specificity. DUF1460 is highly conserved in structure and defines another amidase family. Copyright © 2014 Elsevier Ltd. All rights reserved.

Analysis and characterization of high-resolution and high-aspect-ratio imaging fiber bundles.

PubMed

Motamedi, Nojan; Karbasi, Salman; Ford, Joseph E; Lomakin, Vitaliy

2015-11-10

High-contrast imaging fiber bundles (FBs) are characterized and modeled for wide-angle and high-resolution imaging applications. Scanning electron microscope images of FB cross sections are taken to measure physical parameters and verify the variations of irregular fibers due to the fabrication process. Modal analysis tools are developed that include irregularities in the fiber core shapes and provide results in agreement with experimental measurements. The modeling demonstrates that the irregular fibers significantly outperform a perfectly regular "ideal" array. Using this method, FBs are designed that can provide high contrast with core pitches of only a few wavelengths of the guided light. Structural modifications of the commercially available FB can reduce the core pitch by 60% for higher resolution image relay.

Physical effects of mechanical design parameters on photon sensitivity and spatial resolution performance of a breast-dedicated PET system.

PubMed

Spanoudaki, V C; Lau, F W Y; Vandenbroucke, A; Levin, C S

2010-11-01

This study aims to address design considerations of a high resolution, high sensitivity positron emission tomography scanner dedicated to breast imaging. The methodology uses a detailed Monte Carlo model of the system structures to obtain a quantitative evaluation of several performance parameters. Special focus was given to the effect of dense mechanical structures designed to provide mechanical robustness and thermal regulation to the minuscule and temperature sensitive detectors. For the energies of interest around the photopeak (450-700 keV energy window), the simulation results predict a 6.5% reduction in the single photon detection efficiency and a 12.5% reduction in the coincidence photon detection efficiency in the case that the mechanical structures are interspersed between the detectors. However for lower energies, a substantial increase in the number of detected events (approximately 14% and 7% for singles at a 100-200 keV energy window and coincidences at a lower energy threshold of 100 keV, respectively) was observed with the presence of these structures due to backscatter. The number of photon events that involve multiple interactions in various crystal elements is also affected by the presence of the structures. For photon events involving multiple interactions among various crystal elements, the coincidence photon sensitivity is reduced by as much as 20% for a point source at the center of the field of view. There is no observable effect on the intrinsic and the reconstructed spatial resolution and spatial resolution uniformity. Mechanical structures can have a considerable effect on system sensitivity, especially for systems processing multi-interaction photon events. This effect, however, does not impact the spatial resolution. Various mechanical structure designs are currently under evaluation in order to achieve optimum trade-off between temperature stability, accurate detector positioning, and minimum influence on system performance.

Physical effects of mechanical design parameters on photon sensitivity and spatial resolution performance of a breast-dedicated PET system

PubMed Central

Spanoudaki, V. C.; Lau, F. W. Y.; Vandenbroucke, A.; Levin, C. S.

2010-01-01

Purpose: This study aims to address design considerations of a high resolution, high sensitivity positron emission tomography scanner dedicated to breast imaging. Methods: The methodology uses a detailed Monte Carlo model of the system structures to obtain a quantitative evaluation of several performance parameters. Special focus was given to the effect of dense mechanical structures designed to provide mechanical robustness and thermal regulation to the minuscule and temperature sensitive detectors. Results: For the energies of interest around the photopeak (450–700 keV energy window), the simulation results predict a 6.5% reduction in the single photon detection efficiency and a 12.5% reduction in the coincidence photon detection efficiency in the case that the mechanical structures are interspersed between the detectors. However for lower energies, a substantial increase in the number of detected events (approximately 14% and 7% for singles at a 100–200 keV energy window and coincidences at a lower energy threshold of 100 keV, respectively) was observed with the presence of these structures due to backscatter. The number of photon events that involve multiple interactions in various crystal elements is also affected by the presence of the structures. For photon events involving multiple interactions among various crystal elements, the coincidence photon sensitivity is reduced by as much as 20% for a point source at the center of the field of view. There is no observable effect on the intrinsic and the reconstructed spatial resolution and spatial resolution uniformity. Conclusions: Mechanical structures can have a considerable effect on system sensitivity, especially for systems processing multi-interaction photon events. This effect, however, does not impact the spatial resolution. Various mechanical structure designs are currently under evaluation in order to achieve optimum trade-off between temperature stability, accurate detector positioning, and minimum influence on system performance. PMID:21158296

A challenge for probing the statistics of interstellar magnetic fields: beyond the Planck resolution with Herschel

NASA Astrophysics Data System (ADS)

Bracco, Andrea; André, Philippe; Boulanger, Francois

2015-08-01

The recent Planck results in polarization at sub-mm wavelengths allow us to gain insight into the Galactic magnetic field topology, revealing its statistical correlation with matter, from the diffuse interstellar medium (ISM), to molecular clouds (MCs) (Planck intermediate results. XXXII, XXXIII, XXXV). This correlation has a lot to tell us about the dynamics of the turbulent ISM, stressing the importance of considering magnetic fields in the formation of structures, some of which eventually undergo gravitational collapse producing new star-forming cores.Investigating the early phases of star formation has been a fundamental scope of the Herschel Gould Belt survey collaboration (http://gouldbelt-herschel.cea.fr), which, in the last years, has thoroughly characterized, at a resolution of few tens of arcseconds, the statistics of MCs, such as their filamentary structure, kinematics and column density.Although at lower angular resolution, the Planck maps of dust emission at 353GHz, in intensity and polarization, show that all MCs are complex environments, where we observe a non-trivial correlation between the magnetic field and their density structure. This result opens new perspectives on their formation and evolution, which we have started to explore.In this talk, I will present first results of a comparative analysis of the Herschel-Planck data, where we combine the high resolution Herschel maps of some MCs of the Gould Belt with the Planck polarization data, which sample the structure of the field weighted by the density.In particular, I will discuss the large-scale envelopes of the selected MCs, and, given the correlation between magnetic field and matter, I will show how to make use of the high resolution information of the density structure provided by Herschel to investigate the statistics of interstellar magnetic fields in the Planck data.

Resolution enhancement of low-quality videos using a high-resolution frame

NASA Astrophysics Data System (ADS)

Pham, Tuan Q.; van Vliet, Lucas J.; Schutte, Klamer

2006-01-01

This paper proposes an example-based Super-Resolution (SR) algorithm of compressed videos in the Discrete Cosine Transform (DCT) domain. Input to the system is a Low-Resolution (LR) compressed video together with a High-Resolution (HR) still image of similar content. Using a training set of corresponding LR-HR pairs of image patches from the HR still image, high-frequency details are transferred from the HR source to the LR video. The DCT-domain algorithm is much faster than example-based SR in spatial domain 6 because of a reduction in search dimensionality, which is a direct result of the compact and uncorrelated DCT representation. Fast searching techniques like tree-structure vector quantization 16 and coherence search1 are also key to the improved efficiency. Preliminary results on MJPEG sequence show promising result of the DCT-domain SR synthesis approach.

Development of a high-resolution cavity-beam position monitor

NASA Astrophysics Data System (ADS)

Inoue, Yoichi; Hayano, Hitoshi; Honda, Yosuke; Takatomi, Toshikazu; Tauchi, Toshiaki; Urakawa, Junji; Komamiya, Sachio; Nakamura, Tomoya; Sanuki, Tomoyuki; Kim, Eun-San; Shin, Seung-Hwan; Vogel, Vladimir

2008-06-01

We have developed a high-resolution cavity-beam position monitor (BPM) to be used at the focal point of the ATF2, which is a test beam line that is now being built to demonstrate stable orbit control at ˜nanometer resolution. The design of the cavity structure was optimized for the Accelerator Test Facility (ATF) beam in various ways. For example, the cavity has a rectangular shape in order to isolate two dipole modes in orthogonal directions, and a relatively thin gap that is less sensitive to trajectory inclination. A two stage homodyne mixer with highly sensitive electronics and phase-sensitive detection was also developed. Two BPM blocks, each containing two cavity BPMs, were installed in the existing ATF beam line using a rigid support frame. After testing the basic characteristics, we measured the resolution using three BPMs. The system demonstrated 8.7 nm position resolution over a dynamic range of 5μm.

Effects of voxelization on dose volume histogram accuracy

NASA Astrophysics Data System (ADS)

Sunderland, Kyle; Pinter, Csaba; Lasso, Andras; Fichtinger, Gabor

2016-03-01

PURPOSE: In radiotherapy treatment planning systems, structures of interest such as targets and organs at risk are stored as 2D contours on evenly spaced planes. In order to be used in various algorithms, contours must be converted into binary labelmap volumes using voxelization. The voxelization process results in lost information, which has little effect on the volume of large structures, but has significant impact on small structures, which contain few voxels. Volume differences for segmented structures affects metrics such as dose volume histograms (DVH), which are used for treatment planning. Our goal is to evaluate the impact of voxelization on segmented structures, as well as how factors like voxel size affects metrics, such as DVH. METHODS: We create a series of implicit functions, which represent simulated structures. These structures are sampled at varying resolutions, and compared to labelmaps with high sub-millimeter resolutions. We generate DVH and evaluate voxelization error for the same structures at different resolutions by calculating the agreement acceptance percentage between the DVH. RESULTS: We implemented tools for analysis as modules in the SlicerRT toolkit based on the 3D Slicer platform. We found that there were large DVH variation from the baseline for small structures or for structures located in regions with a high dose gradient, potentially leading to the creation of suboptimal treatment plans. CONCLUSION: This work demonstrates that labelmap and dose volume voxel size is an important factor in DVH accuracy, which must be accounted for in order to ensure the development of accurate treatment plans.

High Resolution Observations and Modeling of Small-Scale Solar Magnetic Elements

NASA Technical Reports Server (NTRS)

Berger, Thomas E.

2001-01-01

This research contract investigating the radiative transfer and dynamic physics of the smallest observable magnetic structures in the solar photosphere. Due to the lack of a high-resolution visible light satellite instrument for solar studies, all data were acquired using ground-based instrumentation. The primary goal of the investigation was to understand the formation and evolution of "G-band bright points" in relation to the associated magnetic elements. G-band bright points are small (on the order of 100 kin or less in diameter) bright signatures associated with magnetic flux elements in the photosphere. They are seen in the A2A-X2 4308 A molecular bandhead of the CH radical ill the solar spectrum and offer the highest spatial resolution and highest contrast "tracers" of small magnetic structure on the Sun.

High-resolution CT assessment of the pediatric airways: structure and function

NASA Astrophysics Data System (ADS)

Kramer, Sandra S.; Hoffman, Eric A.; Amirav, Israel

1994-05-01

The airway has always been a central focus for respiratory pathology in infants and children. Imaging of the larynx, trachea, and the central bronchi can be readily accomplished by radiographic or conventional CT techniques. Newer high resolution CT (HRCT) techniques have extended our view of the bronchi peripherally to the limits of scanner resolution, i.e., to bronchial generations 7 - 9, and rapid volumetric CT data acquisitions have made it possible to follow the same lung anatomic level through the rapidly occurring changes in a series of experimental protocols. These techniques together with a custom designed computer software program for image display and analysis have enabled us to objectively study changes in airway caliber and lung density that occurred in an animal mode of airway reactivity and thereby relate structure with function in the airways.

High-resolution ultrasound imaging of the eye – a review

PubMed Central

Silverman, Ronald H

2009-01-01

This report summarizes the physics, technology and clinical application of ultrasound biomicroscopy (UBM) of the eye, in which frequencies of 35 MHz and above provide over a threefold improvement in resolution compared with conventional ophthalmic ultrasound systems. UBM allows imaging of anatomy and pathology involving the anterior segment, including regions obscured by overlying optically opaque anatomic or pathologic structures. UBM provides diagnostically significant information in conditions such as glaucoma, cysts and neoplasms, trauma and foreign bodies. UBM also can provide crucial biometric information regarding anterior segment structures, including the cornea and its constituent layers and the anterior and posterior chambers. Although UBM has now been in use for over 15 years, new technologies, including transducer arrays, pulse encoding and combination of ultrasound with light, offer the potential for significant advances in high-resolution diagnostic imaging of the eye. PMID:19138310

High-resolution ultrasound imaging of the eye - a review.

PubMed

Silverman, Ronald H

2009-01-01

This report summarizes the physics, technology and clinical application of ultrasound biomicroscopy (UBM) of the eye, in which frequencies of 35 MHz and above provide over a threefold improvement in resolution compared with conventional ophthalmic ultrasound systems. UBM allows imaging of anatomy and pathology involving the anterior segment, including regions obscured by overlying optically opaque anatomic or pathologic structures. UBM provides diagnostically significant information in conditions such as glaucoma, cysts and neoplasms, trauma and foreign bodies. UBM also can provide crucial biometric information regarding anterior segment structures, including the cornea and its constituent layers and the anterior and posterior chambers. Although UBM has now been in use for over 15 years, new technologies, including transducer arrays, pulse encoding and combination of ultrasound with light, offer the potential for significant advances in high-resolution diagnostic imaging of the eye.

Atomic scale structure and chemistry of interfaces by Z-contrast imaging and electron energy loss spectroscopy in the stem

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

McGibbon, M.M.; Browning, N.D.; Chisholm, M.F.

The macroscopic properties of many materials are controlled by the structure and chemistry at grain boundaries. A basic understanding of the structure-property relationship requires a technique which probes both composition and chemical bonding on an atomic scale. High-resolution Z-contrast imaging in the scanning transmission electron microscope (STEM) forms an incoherent image in which changes in atomic structure and composition across an interface can be interpreted directly without the need for preconceived atomic structure models. Since the Z-contrast image is formed by electrons scattered through high angles, parallel detection electron energy loss spectroscopy (PEELS) can be used simultaneously to provide complementarymore » chemical information on an atomic scale. The fine structure in the PEEL spectra can be used to investigate the local electronic structure and the nature of the bonding across the interface. In this paper we use the complimentary techniques of high resolution Z-contrast imaging and PEELS to investigate the atomic structure and chemistry of a 25{degree} symmetric tilt boundary in a bicrystal of the electroceramic SrTiO{sub 3}.« less

Serial Femtosecond Crystallography of G Protein-Coupled Receptors

PubMed Central

Liu, Wei; Wacker, Daniel; Gati, Cornelius; Han, Gye Won; James, Daniel; Wang, Dingjie; Nelson, Garrett; Weierstall, Uwe; Katritch, Vsevolod; Barty, Anton; Zatsepin, Nadia A.; Li, Dianfan; Messerschmidt, Marc; Boutet, Sébastien; Williams, Garth J.; Koglin, Jason E.; Seibert, M. Marvin; Wang, Chong; Shah, Syed T.A.; Basu, Shibom; Fromme, Raimund; Kupitz, Christopher; Rendek, Kimberley N.; Grotjohann, Ingo; Fromme, Petra; Kirian, Richard A.; Beyerlein, Kenneth R.; White, Thomas A.; Chapman, Henry N.; Caffrey, Martin; Spence, John C.H.; Stevens, Raymond C.; Cherezov, Vadim

2014-01-01

X-ray crystallography of G protein-coupled receptors and other membrane proteins is hampered by difficulties associated with growing sufficiently large crystals that withstand radiation damage and yield high-resolution data at synchrotron sources. Here we used an x-ray free-electron laser (XFEL) with individual 50-fs duration x-ray pulses to minimize radiation damage and obtained a high-resolution room temperature structure of a human serotonin receptor using sub-10 µm microcrystals grown in a membrane mimetic matrix known as lipidic cubic phase. Compared to the structure solved by traditional microcrystallography from cryo-cooled crystals of about two orders of magnitude larger volume, the room temperature XFEL structure displays a distinct distribution of thermal motions and conformations of residues that likely more accurately represent the receptor structure and dynamics in a cellular environment. PMID:24357322

Restoring defect structures in 3C-SiC/Si (001) from spherical aberration-corrected high-resolution transmission electron microscope images by means of deconvolution processing.

PubMed

Wen, C; Wan, W; Li, F H; Tang, D

2015-04-01

The [110] cross-sectional samples of 3C-SiC/Si (001) were observed with a spherical aberration-corrected 300 kV high-resolution transmission electron microscope. Two images taken not close to the Scherzer focus condition and not representing the projected structures intuitively were utilized for performing the deconvolution. The principle and procedure of image deconvolution and atomic sort recognition are summarized. The defect structure restoration together with the recognition of Si and C atoms from the experimental images has been illustrated. The structure maps of an intrinsic stacking fault in the area of SiC, and of Lomer and 60° shuffle dislocations at the interface have been obtained at atomic level. Copyright © 2015 Elsevier Ltd. All rights reserved.

A theoretical and experimental benchmark study of core-excited states in nitrogen

DOE PAGES

Myhre, Rolf H.; Wolf, Thomas J. A.; Cheng, Lan; ...

2018-02-14

The high resolution near edge X-ray absorption fine structure spectrum of nitrogen displays the vibrational structure of the core-excited states. This makes nitrogen well suited for assessing the accuracy of different electronic structure methods for core excitations. We report high resolution experimental measurements performed at the SOLEIL synchrotron facility. These are compared with theoretical spectra calculated using coupled cluster theory and algebraic diagrammatic construction theory. The coupled cluster singles and doubles with perturbative triples model known as CC3 is shown to accurately reproduce the experimental excitation energies as well as the spacing of the vibrational transitions. In conclusion, the computationalmore » results are also shown to be systematically improved within the coupled cluster hierarchy, with the coupled cluster singles, doubles, triples, and quadruples method faithfully reproducing the experimental vibrational structure.« less

A theoretical and experimental benchmark study of core-excited states in nitrogen

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

Myhre, Rolf H.; Wolf, Thomas J. A.; Cheng, Lan

The high resolution near edge X-ray absorption fine structure spectrum of nitrogen displays the vibrational structure of the core-excited states. This makes nitrogen well suited for assessing the accuracy of different electronic structure methods for core excitations. We report high resolution experimental measurements performed at the SOLEIL synchrotron facility. These are compared with theoretical spectra calculated using coupled cluster theory and algebraic diagrammatic construction theory. The coupled cluster singles and doubles with perturbative triples model known as CC3 is shown to accurately reproduce the experimental excitation energies as well as the spacing of the vibrational transitions. In conclusion, the computationalmore » results are also shown to be systematically improved within the coupled cluster hierarchy, with the coupled cluster singles, doubles, triples, and quadruples method faithfully reproducing the experimental vibrational structure.« less

Estimating structure quality trends in the Protein Data Bank by equivalent resolution.

PubMed

Bagaria, Anurag; Jaravine, Victor; Güntert, Peter

2013-10-01

The quality of protein structures obtained by different experimental and ab-initio calculation methods varies considerably. The methods have been evolving over time by improving both experimental designs and computational techniques, and since the primary aim of these developments is the procurement of reliable and high-quality data, better techniques resulted on average in an evolution toward higher quality structures in the Protein Data Bank (PDB). Each method leaves a specific quantitative and qualitative "trace" in the PDB entry. Certain information relevant to one method (e.g. dynamics for NMR) may be lacking for another method. Furthermore, some standard measures of quality for one method cannot be calculated for other experimental methods, e.g. crystal resolution or NMR bundle RMSD. Consequently, structures are classified in the PDB by the method used. Here we introduce a method to estimate a measure of equivalent X-ray resolution (e-resolution), expressed in units of Å, to assess the quality of any type of monomeric, single-chain protein structure, irrespective of the experimental structure determination method. We showed and compared the trends in the quality of structures in the Protein Data Bank over the last two decades for five different experimental techniques, excluding theoretical structure predictions. We observed that as new methods are introduced, they undergo a rapid method development evolution: within several years the e-resolution score becomes similar for structures obtained from the five methods and they improve from initially poor performance to acceptable quality, comparable with previously established methods, the performance of which is essentially stable. Copyright © 2013 Elsevier Ltd. All rights reserved.

A generic framework for internet-based interactive applications of high-resolution 3-D medical image data.

PubMed

Liu, Danzhou; Hua, Kien A; Sugaya, Kiminobu

2008-09-01

With the advances in medical imaging devices, large volumes of high-resolution 3-D medical image data have been produced. These high-resolution 3-D data are very large in size, and severely stress storage systems and networks. Most existing Internet-based 3-D medical image interactive applications therefore deal with only low- or medium-resolution image data. While it is possible to download the whole 3-D high-resolution image data from the server and perform the image visualization and analysis at the client site, such an alternative is infeasible when the high-resolution data are very large, and many users concurrently access the server. In this paper, we propose a novel framework for Internet-based interactive applications of high-resolution 3-D medical image data. Specifically, we first partition the whole 3-D data into buckets, remove the duplicate buckets, and then, compress each bucket separately. We also propose an index structure for these buckets to efficiently support typical queries such as 3-D slicer and region of interest, and only the relevant buckets are transmitted instead of the whole high-resolution 3-D medical image data. Furthermore, in order to better support concurrent accesses and to improve the average response time, we also propose techniques for efficient query processing, incremental transmission, and client sharing. Our experimental study in simulated and realistic environments indicates that the proposed framework can significantly reduce storage and communication requirements, and can enable real-time interaction with remote high-resolution 3-D medical image data for many concurrent users.

Slit-lamp photography and videography with high magnifications

PubMed Central

Yuan, Jin; Jiang, Hong; Mao, Xinjie; Ke, Bilian; Yan, Wentao; Liu, Che; Cintrón-Colón, Hector R; Perez, Victor L; Wang, Jianhua

2015-01-01

Purpose To demonstrate the use of the slit-lamp photography and videography with extremely high magnifications for visualizing structures of the anterior segment of the eye. Methods A Canon 60D digital camera with Movie Crop Function was adapted into a Nikon FS-2 slit-lamp to capture still images and video clips of the structures of the anterior segment of the eye. Images obtained using the slit-lamp were tested for spatial resolution. The cornea of human eyes was imaged with the slit-lamp and the structures were compared with the pictures captured using the ultra-high resolution optical coherence tomography (UHR-OCT). The central thickness of the corneal epithelium and total cornea was obtained using the slit-lamp and the results were compared with the thickness obtained using UHR-OCT. Results High-quality ocular images and higher spatial resolutions were obtained by using the slit-lamp with extremely high magnifications and Movie Crop Function, rather than the traditional slit-lamp. The structures and characteristics of the cornea, such as the normal epithelium, abnormal epithelium of corneal intraepithelial neoplasia, LASIK interface, and contact lenses, were clearly visualized using this device. These features were confirmed by comparing the obtained images with those acquired using UHR-OCT. Moreover, the tear film debris on the ocular surface and the corneal nerve in the anterior corneal stroma were also visualized. The thicknesses of the corneal epithelium and total cornea were similar to that measured using UHR-OCT (P < 0.05). Conclusions We demonstrated that the slit-lamp photography and videography with extremely high magnifications allows better visualization of the anterior segment structures of the eye, especially of the epithelium, when compared with the traditional slit-lamp. PMID:26020484

The Substructure of the Solar Corona Observed in the Hi-C Telescope

NASA Technical Reports Server (NTRS)

Winebarger, A.; Cirtain, J.; Golub, L.; DeLuca, E.; Savage, S.; Alexander, C.; Schuler, T.

2014-01-01

In the summer of 2012, the High-resolution Coronal Imager (Hi-C) flew aboard a NASA sounding rocket and collected the highest spatial resolution images ever obtained of the solar corona. One of the goals of the Hi-C flight was to characterize the substructure of the solar corona. We therefore calculate how the intensity scales from a low-resolution (AIA) pixels to high-resolution (Hi-C) pixels for both the dynamic events and "background" emission (meaning, the steady emission over the 5 minutes of data acquisition time). We find there is no evidence of substructure in the background corona; the intensity scales smoothly from low-resolution to high-resolution Hi-C pixels. In transient events, however, the intensity observed with Hi-C is, on average, 2.6 times larger than observed with AIA. This increase in intensity suggests that AIA is not resolving these events. This result suggests a finely structured dynamic corona embedded in a smoothly varying background.

X-Ray Nanofocus CT: Visualising Of Internal 3D-Structures With Submicrometer Resolution

NASA Astrophysics Data System (ADS)

Weinekoetter, Christian

2008-09-01

High-resolution X-ray Computed Tomography (CT) allows the visualization and failure analysis of the internal micro structure of objects—even if they have complicated 3D-structures where 2D X-ray microscopy would give unclear information. During the past several years, computed tomography has progressed to higher resolution and quicker reconstruction of the 3D-volume. Most recently it even allows a three-dimensional look into the inside of materials with submicron resolution. With the use of nanofocus® tube technology, nanoCT®-systems are pushing forward into application fields that were exclusive to high cost and rare available synchrotron techniques. The study was performed with the new nanotom, a very compact laboratory system which allows the analysis of samples up to 120 mm in diameter and weighing up to 1 kg with exceptional voxel-resolution down to <500 nm (<0.5 microns). It is the first 180 kV nanofocus® computed tomography system in the world which is tailored specifically to the highest-resolution applications in the fields of material science, micro electronics, geology and biology. Therefore it is particularly suitable for nanoCT-examinations e.g. of synthetic materials, metals, ceramics, composite materials, mineral and organic samples. There are a few physical effects influencing the CT quality, such as beam-hardening within the sample or ring-artefacts, which can not be completely avoided. To optimize the quality of high resolution 3D volumes, the nanotom® includes a variety of effective software tools to reduce ring-artefacts and correct beam hardenings or drift effects which occurred during data acquisition. The resulting CT volume data set can be displayed in various ways, for example by virtual slicing and sectional views in any direction of the volume. By the fact that this requires only a mouse click, this technique will substitute destructive mechanical slicing and cutting in many applications. The initial CT results obtained with the nanotom® demonstrate that it is now possible to analyze the three-dimensional micro structure of materials and small objects with submicrometer resolution. Any internal difference in material, density or porosity within a sample can be visualized and data like distances can be measured. NanoCT® widely expands the spectrum of detectable micro-structures. The nanotom® opens a new dimension of 3D-microanalysis and will replace more destructive methods—saving costs and time per sample inspected.

A high-resolution cattle CNV map by population-scale genome sequencing

USDA-ARS?s Scientific Manuscript database

Copy Number Variations (CNVs) are common genomic structural variations that have been linked to human diseases and phenotypic traits. CNVs represent an important type of genetic variation among cattle breeds and even individual animals; however, only low-resolution maps of cattle CNVs currently exis...

Stochastic Downscaling of Digital Elevation Models

NASA Astrophysics Data System (ADS)

Rasera, Luiz Gustavo; Mariethoz, Gregoire; Lane, Stuart N.

2016-04-01

High-resolution digital elevation models (HR-DEMs) are extremely important for the understanding of small-scale geomorphic processes in Alpine environments. In the last decade, remote sensing techniques have experienced a major technological evolution, enabling fast and precise acquisition of HR-DEMs. However, sensors designed to measure elevation data still feature different spatial resolution and coverage capabilities. Terrestrial altimetry allows the acquisition of HR-DEMs with centimeter to millimeter-level precision, but only within small spatial extents and often with dead ground problems. Conversely, satellite radiometric sensors are able to gather elevation measurements over large areas but with limited spatial resolution. In the present study, we propose an algorithm to downscale low-resolution satellite-based DEMs using topographic patterns extracted from HR-DEMs derived for example from ground-based and airborne altimetry. The method consists of a multiple-point geostatistical simulation technique able to generate high-resolution elevation data from low-resolution digital elevation models (LR-DEMs). Initially, two collocated DEMs with different spatial resolutions serve as an input to construct a database of topographic patterns, which is also used to infer the statistical relationships between the two scales. High-resolution elevation patterns are then retrieved from the database to downscale a LR-DEM through a stochastic simulation process. The output of the simulations are multiple equally probable DEMs with higher spatial resolution that also depict the large-scale geomorphic structures present in the original LR-DEM. As these multiple models reflect the uncertainty related to the downscaling, they can be employed to quantify the uncertainty of phenomena that are dependent on fine topography, such as catchment hydrological processes. The proposed methodology is illustrated for a case study in the Swiss Alps. A swissALTI3D HR-DEM (with 5 m resolution) and a SRTM-derived LR-DEM from the Western Alps are used to downscale a SRTM-based LR-DEM from the eastern part of the Alps. The results show that the method is capable of generating multiple high-resolution synthetic DEMs that reproduce the spatial structure and statistics of the original DEM.

Beamline P02.1 at PETRA III for high-resolution and high-energy powder diffraction

PubMed Central

Dippel, Ann-Christin; Liermann, Hanns-Peter; Delitz, Jan Torben; Walter, Peter; Schulte-Schrepping, Horst; Seeck, Oliver H.; Franz, Hermann

2015-01-01

Powder X-ray diffraction techniques largely benefit from the superior beam quality provided by high-brilliance synchrotron light sources in terms of photon flux and angular resolution. The High Resolution Powder Diffraction Beamline P02.1 at the storage ring PETRA III (DESY, Hamburg, Germany) combines these strengths with the power of high-energy X-rays for materials research. The beamline is operated at a fixed photon energy of 60 keV (0.207 Å wavelength). A high-resolution monochromator generates the highly collimated X-ray beam of narrow energy bandwidth. Classic crystal structure determination in reciprocal space at standard and non-ambient conditions are an essential part of the scientific scope as well as total scattering analysis using the real space information of the pair distribution function. Both methods are complemented by in situ capabilities with time-resolution in the sub-second regime owing to the high beam intensity and the advanced detector technology for high-energy X-rays. P02.1’s efficiency in solving chemical and crystallographic problems is illustrated by presenting key experiments that were carried out within these fields during the early stage of beamline operation. PMID:25931084

Modelling and simulation of high-frequency (100 MHz) ultrasonic linear arrays based on single crystal LiNbO3.

PubMed

Zhang, J Y; Xu, W J; Carlier, J; Ji, X M; Nongaillard, B; Queste, S; Huang, Y P

2012-01-01

High-frequency ultrasonic transducer arrays are essential for high resolution imaging in clinical analysis and Non-Destructive Evaluation (NDE). However, the fabrication of conventional backing-layer structure, which requires a pitch (distance between the centers of two adjacent elements) of half wavelength in medium, is really a great challenge. Here we present an alternative buffer-layer structure with a silicon lens for volumetric imaging. The requirement for the size of the pitch is less critical for this structure, making it possible to fabricate high-frequency (100MHz) ultrasonic linear array transducers. Using silicon substrate also makes it possible to integrate the arrays with IC (Integrated Circuit). To compare with the conventional backing-layer structure, a finite element tool, COMSOL, is employed to investigate the performances of acoustic beam focusing, the influence of pitch size for the buffer-layer configuration, and to calculate the electrical properties of the arrays, including crosstalk effect and electrical impedance. For a 100MHz 10-element array of buffer-layer structure, the ultrasound beam in azimuth plane in water could be electronically focused to obtain a spatial resolution (a half-amplitude width) of 86μm at the focal depth. When decreasing from half wavelength in silicon (42μm) to half wavelength in water (7.5μm), the pitch sizes weakly affect the focal resolution. The lateral spatial resolution is increased by 4.65% when the pitch size decreases from 42μm to 7.5μm. The crosstalk between adjacent elements at the central frequency is, respectively, -95dB, -39.4dB, and -60.5dB for the 10-element buffer, 49-element buffer and 49-element backing arrays. Additionally, the electrical impedance magnitudes for each structure are, respectively, 4kΩ, 26.4kΩ, and 24.2kΩ, which is consistent with calculation results using Krimholtz, Leedom, and Matthaei (KLM) model. These results show that the buffer-layer configuration is a promising alternative for the fabrication of high-frequency ultrasonic linear arrays dedicated to volumetric imaging. Copyright © 2011 Elsevier B.V. All rights reserved.

High Resolution Stratigraphic Mapping in Complex Terrain: A Comparison of Traditional Remote Sensing Techniques with Unmanned Aerial Vehicle - Structure from Motion Photogrammetry

NASA Astrophysics Data System (ADS)

Nesbit, P. R.; Hugenholtz, C.; Durkin, P.; Hubbard, S. M.; Kucharczyk, M.; Barchyn, T.

2016-12-01

Remote sensing and digital mapping have started to revolutionize geologic mapping in recent years as a result of their realized potential to provide high resolution 3D models of outcrops to assist with interpretation, visualization, and obtaining accurate measurements of inaccessible areas. However, in stratigraphic mapping applications in complex terrain, it is difficult to acquire information with sufficient detail at a wide spatial coverage with conventional techniques. We demonstrate the potential of a UAV and Structure from Motion (SfM) photogrammetric approach for improving 3D stratigraphic mapping applications within a complex badland topography. Our case study is performed in Dinosaur Provincial Park (Alberta, Canada), mapping late Cretaceous fluvial meander belt deposits of the Dinosaur Park formation amidst a succession of steeply sloping hills and abundant drainages - creating a challenge for stratigraphic mapping. The UAV-SfM dataset (2 cm spatial resolution) is compared directly with a combined satellite and aerial LiDAR dataset (30 cm spatial resolution) to reveal advantages and limitations of each dataset before presenting a unique workflow that utilizes the dense point cloud from the UAV-SfM dataset for analysis. The UAV-SfM dense point cloud minimizes distortion, preserves 3D structure, and records an RGB attribute - adding potential value in future studies. The proposed UAV-SfM workflow allows for high spatial resolution remote sensing of stratigraphy in complex topographic environments. This extended capability can add value to field observations and has the potential to be integrated with subsurface petroleum models.

PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements.

PubMed

Tang, Yat T; Marshall, Garland R

2011-02-28

Binding affinity prediction is one of the most critical components to computer-aided structure-based drug design. Despite advances in first-principle methods for predicting binding affinity, empirical scoring functions that are fast and only relatively accurate are still widely used in structure-based drug design. With the increasing availability of X-ray crystallographic structures in the Protein Data Bank and continuing application of biophysical methods such as isothermal titration calorimetry to measure thermodynamic parameters contributing to binding free energy, sufficient experimental data exists that scoring functions can now be derived by separating enthalpic (ΔH) and entropic (TΔS) contributions to binding free energy (ΔG). PHOENIX, a scoring function to predict binding affinities of protein-ligand complexes, utilizes the increasing availability of experimental data to improve binding affinity predictions by the following: model training and testing using high-resolution crystallographic data to minimize structural noise, independent models of enthalpic and entropic contributions fitted to thermodynamic parameters assumed to be thermodynamically biased to calculate binding free energy, use of shape and volume descriptors to better capture entropic contributions. A set of 42 descriptors and 112 protein-ligand complexes were used to derive functions using partial least-squares for change of enthalpy (ΔH) and change of entropy (TΔS) to calculate change of binding free energy (ΔG), resulting in a predictive r2 (r(pred)2) of 0.55 and a standard error (SE) of 1.34 kcal/mol. External validation using the 2009 version of the PDBbind "refined set" (n = 1612) resulted in a Pearson correlation coefficient (R(p)) of 0.575 and a mean error (ME) of 1.41 pK(d). Enthalpy and entropy predictions were of limited accuracy individually. However, their difference resulted in a relatively accurate binding free energy. While the development of an accurate and applicable scoring function was an objective of this study, the main focus was evaluation of the use of high-resolution X-ray crystal structures with high-quality thermodynamic parameters from isothermal titration calorimetry for scoring function development. With the increasing application of structure-based methods in molecular design, this study suggests that using high-resolution crystal structures, separating enthalpy and entropy contributions to binding free energy, and including descriptors to better capture entropic contributions may prove to be effective strategies toward rapid and accurate calculation of binding affinity.

Retinal optical coherence tomography at 1 μm with dynamic focus control and axial motion tracking

NASA Astrophysics Data System (ADS)

Cua, Michelle; Lee, Sujin; Miao, Dongkai; Ju, Myeong Jin; Mackenzie, Paul J.; Jian, Yifan; Sarunic, Marinko V.

2016-02-01

High-resolution optical coherence tomography (OCT) retinal imaging is important to noninvasively visualize the various retinal structures to aid in better understanding of the pathogenesis of vision-robbing diseases. However, conventional OCT systems have a trade-off between lateral resolution and depth-of-focus. In this report, we present the development of a focus-stacking OCT system with automatic focus optimization for high-resolution, extended-focal-range clinical retinal imaging by incorporating a variable-focus liquid lens into the sample arm optics. Retinal layer tracking and selection was performed using a graphics processing unit accelerated processing platform for focus optimization, providing real-time layer-specific en face visualization. After optimization, multiple volumes focused at different depths were acquired, registered, and stitched together to yield a single, high-resolution focus-stacked dataset. Using this system, we show high-resolution images of the retina and optic nerve head, from which we extracted clinically relevant parameters such as the nerve fiber layer thickness and lamina cribrosa microarchitecture.

Retinal optical coherence tomography at 1 μm with dynamic focus control and axial motion tracking.

PubMed

Cua, Michelle; Lee, Sujin; Miao, Dongkai; Ju, Myeong Jin; Mackenzie, Paul J; Jian, Yifan; Sarunic, Marinko V

2016-02-01

High-resolution optical coherence tomography (OCT) retinal imaging is important to noninvasively visualize the various retinal structures to aid in better understanding of the pathogenesis of vision-robbing diseases. However, conventional OCT systems have a trade-off between lateral resolution and depth-of-focus. In this report, we present the development of a focus-stacking OCT system with automatic focus optimization for high-resolution, extended-focal-range clinical retinal imaging by incorporating a variable-focus liquid lens into the sample arm optics. Retinal layer tracking and selection was performed using a graphics processing unit accelerated processing platform for focus optimization, providing real-time layer-specific en face visualization. After optimization, multiple volumes focused at different depths were acquired, registered, and stitched together to yield a single, high-resolution focus-stacked dataset. Using this system, we show high-resolution images of the retina and optic nerve head, from which we extracted clinically relevant parameters such as the nerve fiber layer thickness and lamina cribrosa microarchitecture.

How electrostatic networks modulate specificity and stability of collagen.

PubMed

Zheng, Hongning; Lu, Cheng; Lan, Jun; Fan, Shilong; Nanda, Vikas; Xu, Fei

2018-06-12

One-quarter of the 28 types of natural collagen exist as heterotrimers. The oligomerization state of collagen affects the structure and mechanics of the extracellular matrix, providing essential cues to modulate biological and pathological processes. A lack of high-resolution structural information limits our mechanistic understanding of collagen heterospecific self-assembly. Here, the 1.77-Å resolution structure of a synthetic heterotrimer demonstrates the balance of intermolecular electrostatics and hydrogen bonding that affects collagen stability and heterospecificity of assembly. Atomistic simulations and mutagenesis based on the solved structure are used to explore the contributions of specific interactions to energetics. A predictive model of collagen stability and specificity is developed for engineering novel collagen structures.

Investigation on the separability of slums by multi-aspect TerraSAR-X dual-co-polarized high resolution spotlight images based on the multi-scale evaluation of local distributions

NASA Astrophysics Data System (ADS)

Schmitt, Andreas; Sieg, Tobias; Wurm, Michael; Taubenböck, Hannes

2018-02-01

Following recent advances in distinguishing settlements vs. non-settlement areas from latest SAR data, the question arises whether a further automatic intra-urban delineation and characterization of different structural types is possible. This paper studies the appearance of the structural type ;slums; in high resolution SAR images. Geocoded Kennaugh elements are used as backscatter information and Schmittlet indices as descriptor of local texture. Three cities with a significant share of slums (Cape Town, Manila, Mumbai) are chosen as test sites. These are imaged by TerraSAR-X in the dual-co-polarized high resolution spotlight mode in any available aspect angle. Representative distributions are estimated and fused by a robust approach. Our observations identify a high similarity of slums throughout all three test sites. The derived similarity maps are validated with reference data sets from visual interpretation and ground truth. The final validation strategy is based on completeness and correctness versus other classes in relation to the similarity. High accuracies (up to 87%) in identifying morphologic slums are reached for Cape Town. For Manila (up to 60%) and Mumbai (up to 54%), the distinction is more difficult due to their complex structural configuration. Concluding, high resolution SAR data can be suitable to automatically trace potential locations of slums. Polarimetric information and the incidence angle seem to have a negligible impact on the results whereas the intensity patterns and the passing direction of the satellite are playing a key role. Hence, the combination of intensity images (brightness) acquired from ascending and descending orbits together with Schmittlet indices (spatial pattern) promises best results. The transfer from the automatically recognized physical similarity to the semantic interpretation remains challenging.

The impact of resolution on the dynamics of the martian global atmosphere: Varying resolution studies with the MarsWRF GCM

NASA Astrophysics Data System (ADS)

Toigo, Anthony D.; Lee, Christopher; Newman, Claire E.; Richardson, Mark I.

2012-09-01

We investigate the sensitivity of the circulation and thermal structure of the martian atmosphere to numerical model resolution in a general circulation model (GCM) using the martian implementation (MarsWRF) of the planetWRF atmospheric model. We provide a description of the MarsWRF GCM and use it to study the global atmosphere at horizontal resolutions from 7.5° × 9° to 0.5° × 0.5°, encompassing the range from standard Mars GCMs to global mesoscale modeling. We find that while most of the gross-scale features of the circulation (the rough location of jets, the qualitative thermal structure, and the major large-scale features of the surface level winds) are insensitive to horizontal resolution over this range, several major features of the circulation are sensitive in detail. The northern winter polar circulation shows the greatest sensitivity, showing a continuous transition from a smooth polar winter jet at low resolution, to a distinct vertically “split” jet as resolution increases. The separation of the lower and middle atmosphere polar jet occurs at roughly 10 Pa, with the split jet structure developing in concert with the intensification of meridional jets at roughly 10 Pa and above 0.1 Pa. These meridional jets appear to represent the separation of lower and middle atmosphere mean overturning circulations (with the former being consistent with the usual concept of the “Hadley cell”). Further, the transition in polar jet structure is more sensitive to changes in zonal than meridional horizontal resolution, suggesting that representation of small-scale wave-mean flow interactions is more important than fine-scale representation of the meridional thermal gradient across the polar front. Increasing the horizontal resolution improves the match between the modeled thermal structure and the Mars Climate Sounder retrievals for northern winter high latitudes. While increased horizontal resolution also improves the simulation of the northern high latitudes at equinox, even the lowest model resolution considered here appears to do a good job for the southern winter and southern equinoctial pole (although in detail some discrepancies remain). These results suggest that studies of the northern winter jet (e.g., transient waves and cyclogenesis) will be more sensitive to global model resolution that those of the south (e.g., the confining dynamics of the southern polar vortex relevant to studies of argon transport). For surface winds, the major effect of increased horizontal resolution is in the superposition of circulations forced by local-scale topography upon the large-scale surface wind patterns. While passive predictions of dust lifting are generally insensitive to model horizontal resolution when no lifting threshold is considered, increasing the stress threshold produces significantly more lifting in higher resolution simulations with the generation of finer-scale, higher-stress winds due primarily to better-resolved topography. Considering the positive feedbacks expected for radiatively active dust lifting, we expect this bias to increase when such feedbacks are permitted.

Acoustically Mounted Microcrystals Yield High Resolution X-ray Structures†,‡

PubMed Central

Soares, Alexei S.; Engel, Matthew A.; Stearns, Richard; Datwani, Sammy; Olechno, Joe; Ellson, Richard; Skinner, John M.; Allaire, Marc; Orville, Allen M.

2011-01-01

We demonstrate a general strategy to determine structures from showers of microcrystals. It uses acoustic droplet ejection (ADE) to transfer 2.5 nanoliter droplets from the surface of microcrystal slurries, through the air, and onto mounting micromesh pins. Individual microcrystals are located by raster-scanning a several micron X-ray beam across the cryocooled micromeshes. X-ray diffraction datasets merged from several micron-sized crystals are used to solve 1.8 Å resolution crystal structures. PMID:21542590

Atomic resolution characterization of a SrTiO{sub 3} grain boundary in the STEM

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

McGibbon, M.M.; Browning, N.D.; Chisholm, M.F.

This paper uses the complementary techniques of high resolution Z-contrast imaging and PEELS (parallel detection electron energy loss spectroscopy) to investigate the atomic structure and chemistry of a 25 degree symmetric tilt boundary in a bicrystal of the electroceramic SrTiO{sub 3}. The gain boundary is composed of two different boundary structural units which occur in about equal numbers: one which contains Ti-O columns and the other without.

Super-Resolution Imaging Strategies for Cell Biologists Using a Spinning Disk Microscope

PubMed Central

Hosny, Neveen A.; Song, Mingying; Connelly, John T.; Ameer-Beg, Simon; Knight, Martin M.; Wheeler, Ann P.

2013-01-01

In this study we use a spinning disk confocal microscope (SD) to generate super-resolution images of multiple cellular features from any plane in the cell. We obtain super-resolution images by using stochastic intensity fluctuations of biological probes, combining Photoactivation Light-Microscopy (PALM)/Stochastic Optical Reconstruction Microscopy (STORM) methodologies. We compared different image analysis algorithms for processing super-resolution data to identify the most suitable for analysis of particular cell structures. SOFI was chosen for X and Y and was able to achieve a resolution of ca. 80 nm; however higher resolution was possible >30 nm, dependant on the super-resolution image analysis algorithm used. Our method uses low laser power and fluorescent probes which are available either commercially or through the scientific community, and therefore it is gentle enough for biological imaging. Through comparative studies with structured illumination microscopy (SIM) and widefield epifluorescence imaging we identified that our methodology was advantageous for imaging cellular structures which are not immediately at the cell-substrate interface, which include the nuclear architecture and mitochondria. We have shown that it was possible to obtain two coloured images, which highlights the potential this technique has for high-content screening, imaging of multiple epitopes and live cell imaging. PMID:24130668

NUMERICAL SIMULATIONS OF CORONAL HEATING THROUGH FOOTPOINT BRAIDING

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

Hansteen, V.; Pontieu, B. De; Carlsson, M.

2015-10-01

Advanced three-dimensional (3D) radiative MHD simulations now reproduce many properties of the outer solar atmosphere. When including a domain from the convection zone into the corona, a hot chromosphere and corona are self-consistently maintained. Here we study two realistic models, with different simulated areas, magnetic field strength and topology, and numerical resolution. These are compared in order to characterize the heating in the 3D-MHD simulations which self-consistently maintains the structure of the atmosphere. We analyze the heating at both large and small scales and find that heating is episodic and highly structured in space, but occurs along loop-shaped structures, andmore » moves along with the magnetic field. On large scales we find that the heating per particle is maximal near the transition region and that widely distributed opposite-polarity field in the photosphere leads to a greater heating scale height in the corona. On smaller scales, heating is concentrated in current sheets, the thicknesses of which are set by the numerical resolution. Some current sheets fragment in time, this process occurring more readily in the higher-resolution model leading to spatially highly intermittent heating. The large-scale heating structures are found to fade in less than about five minutes, while the smaller, local, heating shows timescales of the order of two minutes in one model and one minutes in the other, higher-resolution, model.« less

Evaluation of field methods for vertical high resolution aquifer characterization

NASA Astrophysics Data System (ADS)

Vienken, T.; Tinter, M.; Rogiers, B.; Leven, C.; Dietrich, P.

2012-12-01

The delineation and characterization of subsurface (hydro)-stratigraphic structures is one of the challenging tasks of hydrogeological site investigations. The knowledge about the spatial distribution of soil specific properties and hydraulic conductivity (K) is the prerequisite for understanding flow and fluid transport processes. This is especially true for heterogeneous unconsolidated sedimentary deposits with a complex sedimentary architecture. One commonly used approach to investigate and characterize sediment heterogeneity is soil sampling and lab analyses, e.g. grain size distribution. Tests conducted on 108 samples show that calculation of K based on grain size distribution is not suitable for high resolution aquifer characterization of highly heterogeneous sediments due to sampling effects and large differences of calculated K values between applied formulas (Vienken & Dietrich 2011). Therefore, extensive tests were conducted at two test sites under different geological conditions to evaluate the performance of innovative Direct Push (DP) based approaches for the vertical high resolution determination of K. Different DP based sensor probes for the in-situ subsurface characterization based on electrical, hydraulic, and textural soil properties were used to obtain high resolution vertical profiles. The applied DP based tools proved to be a suitable and efficient alternative to traditional approaches. Despite resolution differences, all of the applied methods captured the main aquifer structure. Correlation of the DP based K estimates and proxies with DP based slug tests show that it is possible to describe the aquifer hydraulic structure on less than a meter scale by combining DP slug test data and continuous DP measurements. Even though correlations are site specific and appropriate DP tools must be chosen, DP is reliable and efficient alternative for characterizing even strongly heterogeneous sites with complex structured sedimentary aquifers (Vienken et al. 2012). References: Vienken, T., Leven, C., and Dietrich, P. 2012. Use of CPT and other direct push methods for (hydro-) stratigraphic aquifer characterization — a field study. Canadian Geotechnical Journal, 49(2): 197-206. Vienken, T., and Dietrich, P. 2011. Field evaluation of methods for determining hydraulic conductivity from grain size data. Journal of Hydrology, 400(1-2): 58-71.

An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization.

PubMed

Szałaj, Przemysław; Tang, Zhonghui; Michalski, Paul; Pietal, Michal J; Luo, Oscar J; Sadowski, Michał; Li, Xingwang; Radew, Kamen; Ruan, Yijun; Plewczynski, Dariusz

2016-12-01

ChIA-PET is a high-throughput mapping technology that reveals long-range chromatin interactions and provides insights into the basic principles of spatial genome organization and gene regulation mediated by specific protein factors. Recently, we showed that a single ChIA-PET experiment provides information at all genomic scales of interest, from the high-resolution locations of binding sites and enriched chromatin interactions mediated by specific protein factors, to the low resolution of nonenriched interactions that reflect topological neighborhoods of higher-order chromosome folding. This multilevel nature of ChIA-PET data offers an opportunity to use multiscale 3D models to study structural-functional relationships at multiple length scales, but doing so requires a structural modeling platform. Here, we report the development of 3D-GNOME (3-Dimensional Genome Modeling Engine), a complete computational pipeline for 3D simulation using ChIA-PET data. 3D-GNOME consists of three integrated components: a graph-distance-based heat map normalization tool, a 3D modeling platform, and an interactive 3D visualization tool. Using ChIA-PET and Hi-C data derived from human B-lymphocytes, we demonstrate the effectiveness of 3D-GNOME in building 3D genome models at multiple levels, including the entire genome, individual chromosomes, and specific segments at megabase (Mb) and kilobase (kb) resolutions of single average and ensemble structures. Further incorporation of CTCF-motif orientation and high-resolution looping patterns in 3D simulation provided additional reliability of potential biologically plausible topological structures. © 2016 Szałaj et al.; Published by Cold Spring Harbor Laboratory Press.

Single image super-resolution via regularized extreme learning regression for imagery from microgrid polarimeters

NASA Astrophysics Data System (ADS)

Sargent, Garrett C.; Ratliff, Bradley M.; Asari, Vijayan K.

2017-08-01

The advantage of division of focal plane imaging polarimeters is their ability to obtain temporally synchronized intensity measurements across a scene; however, they sacrifice spatial resolution in doing so due to their spatially modulated arrangement of the pixel-to-pixel polarizers and often result in aliased imagery. Here, we propose a super-resolution method based upon two previously trained extreme learning machines (ELM) that attempt to recover missing high frequency and low frequency content beyond the spatial resolution of the sensor. This method yields a computationally fast and simple way of recovering lost high and low frequency content from demosaicing raw microgrid polarimetric imagery. The proposed method outperforms other state-of-the-art single-image super-resolution algorithms in terms of structural similarity and peak signal-to-noise ratio.

Sensitive sub-Doppler nonlinear spectroscopy for hyperfine-structure analysis using simple atomizers

NASA Astrophysics Data System (ADS)

Mickadeit, Fritz K.; Kemp, Helen; Schafer, Julia; Tong, William M.

1998-05-01

Laser wave-mixing spectroscopy is presented as a sub-Doppler method that offers not only high spectral resolution, but also excellent detection sensitivity. It offers spectral resolution suitable for hyperfine structure analysis and isotope ratio measurements. In a non-planar backward- scattering four-wave mixing optical configuration, two of the three input beams counter propagate and the Doppler broadening is minimized, and hence, spectral resolution is enhanced. Since the signal is a coherent beam, optical collection is efficient and signal detection is convenient. This simple multi-photon nonlinear laser method offers un usually sensitive detection limits that are suitable for trace-concentration isotope analysis using a few different types of simple analytical atomizers. Reliable measurement of hyperfine structures allows effective determination of isotope ratios for chemical analysis.

Atomic resolution structure of the E. coli YajR transporter YAM domain.

PubMed

Jiang, Daohua; Zhao, Yan; Fan, Junping; Liu, Xuehui; Wu, Yan; Feng, Wei; Zhang, Xuejun C

2014-07-25

YajR is an Escherichia coli transporter that belongs to the major facilitator superfamily. Unlike most MFS transporters, YajR contains a carboxyl terminal, cytosolic domain of 67 amino acid residues termed YAM domain. Although it is speculated that the function of this small soluble domain is to regulate the conformational change of the 12-helix transmembrane domain, its precise regulatory role remains unclear. Here, we report the crystal structure of the YAM domain at 1.07-Å resolution, along with its structure determined using nuclear magnetic resonance. Detailed analysis of the high resolution structure revealed a symmetrical dimer in which a belt of well-ordered poly-pentagonal water molecules is embedded. A mutagenesis experiment and a thermal stability assay were used to analyze the putative role of this dimerization in response to changes in halogen concentration. Copyright © 2014 Elsevier Inc. All rights reserved.

Imaging whole mouse brains with a dual resolution serial swept-source optical coherence tomography scanner

NASA Astrophysics Data System (ADS)

Lefebvre, Joël.; Castonguay, Alexandre; Lesage, Frédéric

2018-02-01

High resolution imaging of whole rodent brains using serial OCT scanners is a promising method to investigate microstructural changes in tissue related to the evolution of neuropathologies. Although micron to sub-micron sampling resolution can be obtained by using high numerical aperture objectives and dynamic focusing, such an imaging system is not adapted to whole brain imaging. This is due to the large amount of data it generates and the significant computational resources required for reconstructing such volumes. To address this limitation, a dual resolution serial OCT scanner was developed. The optical setup consists in a swept-source OCT made of two sample and reference arms, each arm being coupled with different microscope objectives (3X / 40X). Motorized flip mirrors were used to switch between each OCT arm, thus allowing low and high resolution acquisitions within the same sample. The low resolution OCT volumes acquired with the 3X arm were stitched together, providing a 3D map of the whole mouse brain. This brain can be registered to an OCT brain template to enable neurological structures localization. The high resolution volumes acquired with the 40X arm were also stitched together to create local high resolution 3D maps of the tissue microstructure. The 40X data can be acquired at any arbitrary location in the sample, thus limiting storage-heavy high resolution data to application restricted to specific regions of interest. By providing dual-resolution OCT data, this setup can be used to validate diffusion MRI with tissue microstructure derived metrics measured at any location in ex vivo brains.

Where Water Is Oxidized to Dioxygen: Structure of the Photosynthetic Mn4Ca Cluster

PubMed Central

Yano, Junko; Kern, Jan; Sauer, Kenneth; Latimer, Matthew J.; Pushkar, Yulia; Biesiadka, Jacek; Loll, Bernhard; Saenger, Wolfram; Messinger, Johannes; Zouni, Athina; Yachandra, Vittal K.

2014-01-01

The oxidation of water to dioxygen is catalyzed within photosystem II (PSII) by a Mn4Ca cluster, the structure of which remains elusive. Polarized extended x-ray absorption fine structure (EXAFS) measurements on PSII single crystals constrain the Mn4Ca cluster geometry to a set of three similar high-resolution structures. Combining polarized EXAFS and x-ray diffraction data, the cluster was placed within PSII, taking into account the overall trend of the electron density of the metal site and the putative ligands. The structure of the cluster from the present study is unlike either the 3.0 or 3.5 angstrom–resolution x-ray structures or other previously proposed models. PMID:17082458

Structure Refinement of Protein Low Resolution Models Using the GNEIMO Constrained Dynamics Method

PubMed Central

Park, In-Hee; Gangupomu, Vamshi; Wagner, Jeffrey; Jain, Abhinandan; Vaidehi, Nagara-jan

2012-01-01

The challenge in protein structure prediction using homology modeling is the lack of reliable methods to refine the low resolution homology models. Unconstrained all-atom molecular dynamics (MD) does not serve well for structure refinement due to its limited conformational search. We have developed and tested the constrained MD method, based on the Generalized Newton-Euler Inverse Mass Operator (GNEIMO) algorithm for protein structure refinement. In this method, the high-frequency degrees of freedom are replaced with hard holonomic constraints and a protein is modeled as a collection of rigid body clusters connected by flexible torsional hinges. This allows larger integration time steps and enhances the conformational search space. In this work, we have demonstrated the use of a constraint free GNEIMO method for protein structure refinement that starts from low-resolution decoy sets derived from homology methods. In the eight proteins with three decoys for each, we observed an improvement of ~2 Å in the RMSD to the known experimental structures of these proteins. The GNEIMO method also showed enrichment in the population density of native-like conformations. In addition, we demonstrated structural refinement using a “Freeze and Thaw” clustering scheme with the GNEIMO framework as a viable tool for enhancing localized conformational search. We have derived a robust protocol based on the GNEIMO replica exchange method for protein structure refinement that can be readily extended to other proteins and possibly applicable for high throughput protein structure refinement. PMID:22260550

Light sheet theta microscopy for rapid high-resolution imaging of large biological samples.

PubMed

Migliori, Bianca; Datta, Malika S; Dupre, Christophe; Apak, Mehmet C; Asano, Shoh; Gao, Ruixuan; Boyden, Edward S; Hermanson, Ola; Yuste, Rafael; Tomer, Raju

2018-05-29

Advances in tissue clearing and molecular labeling methods are enabling unprecedented optical access to large intact biological systems. These developments fuel the need for high-speed microscopy approaches to image large samples quantitatively and at high resolution. While light sheet microscopy (LSM), with its high planar imaging speed and low photo-bleaching, can be effective, scaling up to larger imaging volumes has been hindered by the use of orthogonal light sheet illumination. To address this fundamental limitation, we have developed light sheet theta microscopy (LSTM), which uniformly illuminates samples from the same side as the detection objective, thereby eliminating limits on lateral dimensions without sacrificing the imaging resolution, depth, and speed. We present a detailed characterization of LSTM, and demonstrate its complementary advantages over LSM for rapid high-resolution quantitative imaging of large intact samples with high uniform quality. The reported LSTM approach is a significant step for the rapid high-resolution quantitative mapping of the structure and function of very large biological systems, such as a clarified thick coronal slab of human brain and uniformly expanded tissues, and also for rapid volumetric calcium imaging of highly motile animals, such as Hydra, undergoing non-isomorphic body shape changes.

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

Fine structure in the m/z 121 mass chromatogram of Paraho shale oil

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

Gallegos, E.J.

1984-04-01

High-resolution gas chromatography/high-resolution mass spectrometry/computer (HRGC/HRMS/C) techniques are reported here in the provisional identification of several homologous series of alkylpuridines, phenols, terpenes, and terpanes analytically isolated from Paraho shale oil. HRGC/HRMS/C techniques were also used to follow the hydrodenitrification, HDN, procedure for the removal of the heterocompounds, as well as to monitor the effect of hydrogenation on alkenes.

Main High-Resolution Near-IR Spectrometer for the VLT

NASA Astrophysics Data System (ADS)

Piskunov, N.

2017-06-01

We present the ongoing CRISES+ project on the development of a cross-dispersed high resolution near-infrared spectrometer for the ESO Very Large Telescope. The presentation highlights the relation between science objectives, technical solutions, and the structure of the project. We also share some of the insights on the implementation and management of the project that are crucial for keeping the tight time-line through efficient interaction between consortium members.

Enantioselective Total Synthesis of Natural Isoflavans: Asymmetric Transfer Hydrogenation/Deoxygenation of Isoflavanones with Dynamic Kinetic Resolution.

PubMed

Keßberg, Anton; Lübken, Tilo; Metz, Peter

2018-05-02

A concise and highly enantioselective synthesis of structurally diverse isoflavans from a single chromone is described. The key transformation is a single-step conversion of racemic isoflavanones into virtually enantiopure isoflavans by domino asymmetric transfer hydrogenation/deoxygenation with dynamic kinetic resolution.

Development of a High-Sensitivity Wireless Accelerometer for Structural Health Monitoring

PubMed Central

Zhu, Li; Fu, Yuguang; Chow, Raymond; Spencer, Billie F.; Park, Jong Woong; Mechitov, Kirill

2018-01-01

Structural health monitoring (SHM) is playing an increasingly important role in ensuring the safety of structures. A shift of SHM research away from traditional wired methods toward the use of wireless smart sensors (WSS) has been motivated by the attractive features of wireless smart sensor networks (WSSN). The progress achieved in Micro Electro-Mechanical System (MEMS) technologies and wireless data transmission, has extended the effectiveness and range of applicability of WSSNs. One of the most common sensors employed in SHM strategies is the accelerometer; however, most accelerometers in WSS nodes have inadequate resolution for measurement of the typical accelerations found in many SHM applications. In this study, a high-resolution and low-noise tri-axial digital MEMS accelerometer is incorporated in a next-generation WSS platform, the Xnode. In addition to meeting the acceleration sensing demands of large-scale civil infrastructure applications, this new WSS node provides powerful hardware and a robust software framework to enable edge computing that can deliver actionable information. Hardware and software integration challenges are presented, and the associate resolutions are discussed. The performance of the wireless accelerometer is demonstrated experimentally through comparison with high-sensitivity wired accelerometers. This new high-sensitivity wireless accelerometer will extend the use of WSSN to a broader class of SHM applications. PMID:29342102

Development of a High-Sensitivity Wireless Accelerometer for Structural Health Monitoring.

PubMed

Zhu, Li; Fu, Yuguang; Chow, Raymond; Spencer, Billie F; Park, Jong Woong; Mechitov, Kirill

2018-01-17

Structural health monitoring (SHM) is playing an increasingly important role in ensuring the safety of structures. A shift of SHM research away from traditional wired methods toward the use of wireless smart sensors (WSS) has been motivated by the attractive features of wireless smart sensor networks (WSSN). The progress achieved in Micro Electro-Mechanical System (MEMS) technologies and wireless data transmission, has extended the effectiveness and range of applicability of WSSNs. One of the most common sensors employed in SHM strategies is the accelerometer; however, most accelerometers in WSS nodes have inadequate resolution for measurement of the typical accelerations found in many SHM applications. In this study, a high-resolution and low-noise tri-axial digital MEMS accelerometer is incorporated in a next-generation WSS platform, the Xnode. In addition to meeting the acceleration sensing demands of large-scale civil infrastructure applications, this new WSS node provides powerful hardware and a robust software framework to enable edge computing that can deliver actionable information. Hardware and software integration challenges are presented, and the associate resolutions are discussed. The performance of the wireless accelerometer is demonstrated experimentally through comparison with high-sensitivity wired accelerometers. This new high-sensitivity wireless accelerometer will extend the use of WSSN to a broader class of SHM applications.

MRI uncovers disrupted hippocampal microstructure that underlies memory impairments after early-life adversity.

PubMed

Molet, Jenny; Maras, Pamela M; Kinney-Lang, Eli; Harris, Neil G; Rashid, Faisal; Ivy, Autumn S; Solodkin, Ana; Obenaus, Andre; Baram, Tallie Z

2016-12-01

Memory and related cognitive functions are progressively impaired in a subgroup of individuals experiencing childhood adversity and stress. However, it is not possible to identify vulnerable individuals early, a crucial step for intervention. In this study, high-resolution magnetic resonance imaging (MRI) and intra-hippocampal diffusion tensor imaging (DTI) were employed to examine for structural signatures of cognitive adolescent vulnerabilities in a rodent model of early-life adversity. These methods were complemented by neuroanatomical and functional assessments of hippocampal network integrity during adolescence, adulthood and middle-age. The high-resolution MRI identified selective loss of dorsal hippocampal volume, and intra-hippocampal DTI uncovered disruption of dendritic structure, consistent with disrupted local connectivity, already during late adolescence in adversity-experiencing rats. Memory deteriorated over time, and stunting of hippocampal dendritic trees was apparent on neuroanatomical analyses. Thus, disrupted hippocampal neuronal structure and connectivity, associated with cognitive impairments, are detectable via non-invasive imaging modalities in rats experiencing early-life adversity. These high-resolution imaging approaches may constitute promising tools for prediction and assessment of at-risk individuals in the clinic. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Cryo-EM of dynamic protein complexes in eukaryotic DNA replication.

PubMed

Sun, Jingchuan; Yuan, Zuanning; Bai, Lin; Li, Huilin

2017-01-01

DNA replication in Eukaryotes is a highly dynamic process that involves several dozens of proteins. Some of these proteins form stable complexes that are amenable to high-resolution structure determination by cryo-EM, thanks to the recent advent of the direct electron detector and powerful image analysis algorithm. But many of these proteins associate only transiently and flexibly, precluding traditional biochemical purification. We found that direct mixing of the component proteins followed by 2D and 3D image sorting can capture some very weakly interacting complexes. Even at 2D average level and at low resolution, EM images of these flexible complexes can provide important biological insights. It is often necessary to positively identify the feature-of-interest in a low resolution EM structure. We found that systematically fusing or inserting maltose binding protein (MBP) to selected proteins is highly effective in these situations. In this chapter, we describe the EM studies of several protein complexes involved in the eukaryotic DNA replication over the past decade or so. We suggest that some of the approaches used in these studies may be applicable to structural analysis of other biological systems. © 2016 The Protein Society.

Bifocal computational near eye light field displays and Structure parameters determination scheme for bifocal computational display.

PubMed

Liu, Mali; Lu, Chihao; Li, Haifeng; Liu, Xu

2018-02-19

We propose a bifocal computational near eye light field display (bifocal computational display) and structure parameters determination scheme (SPDS) for bifocal computational display that achieves greater depth of field (DOF), high resolution, accommodation and compact form factor. Using a liquid varifocal lens, two single-focal computational light fields are superimposed to reconstruct a virtual object's light field by time multiplex and avoid the limitation on high refresh rate. By minimizing the deviation between reconstructed light field and original light field, we propose a determination framework to determine the structure parameters of bifocal computational light field display. When applied to different objective to SPDS, it can achieve high average resolution or uniform resolution display over scene depth range. To analyze the advantages and limitation of our proposed method, we have conducted simulations and constructed a simple prototype which comprises a liquid varifocal lens, dual-layer LCDs and a uniform backlight. The results of simulation and experiments with our method show that the proposed system can achieve expected performance well. Owing to the excellent performance of our system, we motivate bifocal computational display and SPDS to contribute to a daily-use and commercial virtual reality display.

CLICK: The new USGS center for LIDAR information coordination and knowledge

USGS Publications Warehouse

Stoker, Jason M.; Greenlee, Susan K.; Gesch, Dean B.; Menig, Jordan C.

2006-01-01

Elevation data is rapidly becoming an important tool for the visualization and analysis of geographic information. The creation and display of three-dimensional models representing bare earth, vegetation, and structures have become major requirements for geographic research in the past few years. Light Detection and Ranging (lidar) has been increasingly accepted as an effective and accurate technology for acquiring high-resolution elevation data for bare earth, vegetation, and structures. Lidar is an active remote sensing system that records the distance, or range, of a laser fi red from an airborne or space borne platform such as an airplane, helicopter or satellite to objects or features on the Earth’s surface. By converting lidar data into bare ground topography and vegetation or structural morphologic information, extremely accurate, high-resolution elevation models can be derived to visualize and quantitatively represent scenes in three dimensions. In addition to high-resolution digital elevation models (Evans et al., 2001), other lidar-derived products include quantitative estimates of vegetative features such as canopy height, canopy closure, and biomass (Lefsky et al., 2002), and models of urban areas such as building footprints and three-dimensional city models (Maas, 2001).

Helium Ion Beam Microscopy for Copper Grain Identification in BEOL Structures

NASA Astrophysics Data System (ADS)

van den Boom, Ruud J. J.; Parvaneh, Hamed; Voci, Dave; Huynh, Chuong; Stern, Lewis; Dunn, Kathleen A.; Lifshin, Eric

2009-09-01

Grain size determination in advanced metallization structures requires a technique with resolution ˜2 nm, with a high signal-to-noise ratio and high orientation-dependant contrast for unambiguous identification of grain boundaries. Ideally, such a technique would also be capable of high-throughput and rapid time-to-knowledge. The Helium Ion Microscope (HIM) offers one possibility for achieving these aims in a single platform. This article compares the performance of the HIM with Focused Ion Beam, Scanning Electron and Transmission Electron Microscopes, in terms of achievable image resolution and contrast, using plan-view and cross-sectional imaging of electroplated samples. Although the HIM is capable of sub-nanometer beam diameter, the low signal-to-noise ratio in the images necessitates signal averaging, which degrades the measured image resolution to 6-8 nm. Strategies for improving S/N are discussed in light of the trade-off between beam current and probe size, accelerating voltage, and dwell time.

Specimen preparation for high-resolution cryo-EM

PubMed Central

Passmore, Lori A.; Russo, Christopher J.

2016-01-01

Imaging a material with electrons at near-atomic resolution requires a thin specimen that is stable in the vacuum of the transmission electron microscope. For biological samples, this comprises a thin layer of frozen aqueous solution containing the biomolecular complex of interest. The process of preparing a high-quality specimen is often the limiting step in the determination of structures by single-particle electron cryomicroscopy (cryo-EM). Here we describe a systematic approach for going from a purified biomolecular complex in aqueous solution to high-resolution electron micrographs that are suitable for 3D structure determination. This includes a series of protocols for the preparation of vitrified specimens on various specimen supports, including all-gold and graphene. We also describe techniques for troubleshooting when a preparation fails to yield suitable specimens, and common mistakes to avoid during each part of the process. Finally, we include recommendations for obtaining the highest quality micrographs from prepared specimens with current microscope, detector and support technology. PMID:27572723

Modeling defect cluster evolution in irradiated structural materials: Focus on comparing to high-resolution experimental characterization studies

DOE PAGES

Wirth, Brian D.; Hu, Xunxiang; Kohnert, Aaron; ...

2015-03-02

Exposure of metallic structural materials to irradiation environments results in significant microstructural evolution, property changes, and performance degradation, which limits the extended operation of current generation light water reactors and restricts the design of advanced fission and fusion reactors. Further, it is well recognized that these irradiation effects are a classic example of inherently multiscale phenomena and that the mix of radiation-induced features formed and the corresponding property degradation depend on a wide range of material and irradiation variables. This inherently multiscale evolution emphasizes the importance of closely integrating models with high-resolution experimental characterization of the evolving radiation-damaged microstructure. Lastly,more » this article provides a review of recent models of the defect microstructure evolution in irradiated body-centered cubic materials, which provide good agreement with experimental measurements, and presents some outstanding challenges, which will require coordinated high-resolution characterization and modeling to resolve.« less

[A modified intracellular labelling technique for high-resolution staining of neuron in 500 microm-thickness brain slice].

PubMed

Zhao, Ming-liang; Liu, Guo-long; Sui, Jian-feng; Ruan, Huai-zhen; Xiong, Ying

2007-05-01

To develop simple but reliable intracellular labelling method for high-resolution visualization of the fine structure of single neurons in brain slice with thickness of 500 microm. Biocytin was introduced into neurons in 500 microm-thickness brain slices while blind whole cell recording. Following processed for histochemistry using the avidin-biotin-complex method, stained slices were mounted in glycerol on special glass slides. Labelled cells were digital photomicrographed every 30 microm and reconstructed with Adobe Photoshop software. After histochemistry, limited background staining was produced. The resolution was so high that fine structure, including branching, termination of individual axons and even spines of neurons could be identified in exquisite detail with optic microscope. With the help of software, the neurons of interest could be reconstructed from a stack of photomicrographs. The modified method provides an easy and reliable approach to revealing the detailed morphological properties of single neurons in 500 microm-thickness brain slice. Without requisition of special equipment, it is suited to be broadly applied.

Preliminary Correlations of Gravity and Topography from Mars Global Surveyor

NASA Technical Reports Server (NTRS)

Zuber, M. T.; Tyler, G. L.; Smith, D. E.; Balmino, G. S.; Johnson, G. L.; Lemoine, F. G.; Neumann, G. A.; Phillips, R. J.; Sjogren, W. L.; Solomon, S. C.

1999-01-01

The Mars Global Surveyor (MGS) spacecraft is currently in a 400-km altitude polar mapping orbit and scheduled to begin global mapping of Mars in March of 1999. Doppler tracking data collected in this Gravity Calibration Orbit prior to the nominal mapping mission combined with observations from the MGS Science Phasing Orbit in Spring - Summer 1999 and the Viking and mariner 9 orbiters has led to preliminary high resolution gravity fields. Spherical harmonic expansions have been performed to degree and order 70 and are characterized by the first high spatial resolution coverage of high latitudes. Topographic mapping by the Mars Orbiter Laser Altimeter on MGS is providing measurements of the height of the martian surface with sub-meter vertical resolution and 5-30 m absolute accuracy. Data obtained during the circular mapping phase are expected to provide the first high resolution measurements of surface heights in the southern hemisphere. The combination of gravity and topography measurements provides information on the structure of the planetary interior, i.e. the rigidity and distribution of internal density. The observations can also be used to address the mechanisms of support of surface topography. Preliminary results of correlations of gravity and topography at long planetary wavelengths will be presented and the implications for internal structure will be addressed.

Experimental evidence and structural modeling of nonstoichiometric (010) surfaces coexisting in hydroxyapatite nano-crystals.

PubMed

Ospina, C A; Terra, J; Ramirez, A J; Farina, M; Ellis, D E; Rossi, A M

2012-01-01

High-resolution transmission electron microscopy (HRTEM) and ab initio quantum-mechanical calculations of electronic structure were combined to investigate the structure of the hydroxyapatite (HA) (010) surface, which plays an important role in HA interactions with biological media. HA was synthesized by in vitro precipitation at 37°C. HRTEM images revealed thin elongated rod nanoparticles with preferential growth along the [001] direction and terminations parallel to the (010) plane. The focal series reconstruction (FSR) technique was applied to develop an atomic-scale structural model of the high-resolution images. The HRTEM simulations identified the coexistence of two structurally distinct terminations for (010) surfaces: a rather flat Ca(II)-terminated surface and a zig-zag structure with open OH channels. Density functional theory (DFT) was applied in a periodic slab plane-wave pseudopotential approach to refine details of atomic coordination and bond lengths of Ca(I) and Ca(II) sites in hydrated HA (010) surfaces, starting from the HRTEM model. Copyright © 2011 Elsevier B.V. All rights reserved.

Structural Insight into the Assembly of TRPV Channels

PubMed Central

Huynh, Kevin W.; Cohen, Matthew R.; Chakrapani, Sudha; Holdaway, Heather A.; Stewart, Phoebe L.; Moiseenkova-Bell, Vera Y.

2017-01-01

SUMMARY Transient receptor potential (TRP) proteins are a large family of polymodal nonselective cation channels. The TRP vanilloid (TRPV) subfamily consists of six homologous members with diverse functions. TRPV1–TRPV4 are nonselective cation channels proposed to play a role in nociception, while TRPV5 and TRPV6 are involved in epithelial Ca2+ homeostasis. Here we present the cryo-electron microscopy (cryo-EM) structure of functional, full-length TRPV2 at 13.6 Å resolution. The map reveals that the TRPV2 cytoplasmic domain displays a 4-fold petal-like shape in which high-resolution N-terminal ankyrin repeat domain (ARD) structures can be unambiguously fitted. Fitting of the available ARD structures for other TRPV subfamily members into the TRPV2 EM map suggests that TRPV subfamily members have highly homologous structural topologies. These results allowed us to postulate a structural explanation for the functional diversity among TRPV channels and their differential regulation by proteins and ligands. PMID:24373766

Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13 m Serpentine Path Length Structures for Lossless Ion Manipulations Module

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

Deng, Liulin; Ibrahim, Yehia M.; Hamid, Ahmed M.

We report the development and initial evaluation of a 13-m path length Structures for Lossless Manipulations (SLIM) module for achieving high resolution separations using traveling waves (TW) with ion mobility (IM) spectrometry. The TW SLIM module was fabricated using two mirror-image printed circuit boards with appropriately configured RF, DC and TW electrodes and positioned with a 2.75-mm inter-surface gap. Ions were effective confined between the surfaces by RF-generated pseudopotential fields and moved losslessly through a serpentine path including 44 “U” turns using TWs. The ion mobility resolution was characterized at different pressures, gaps between the SLIM surfaces, TW and RFmore » parameters. After initial optimization the SLIM IM-MS module provided about 5-fold higher resolution separations than present commercially available drift tube or traveling wave IM-MS platforms. Peak capacity and peak generation rates achieved were 246 and 370 s-1, respectively, at a TW speed of 148 m/s. The high resolution achieved in the TW SLIM IM-MS enabled e.g., isomeric sugars (Lacto-N-fucopentaose I and Lacto-N-fucopentaose II) to be baseline resolved, and peptides from a albumin tryptic digest much better resolved than with existing commercial IM-MS platforms. The present work also provides a foundation for the development of much higher resolution SLIM devices based upon both considerably longer path lengths and multi-pass designs.« less

Re-evaluation of low-resolution crystal structures via interactive molecular-dynamics flexible fitting (iMDFF): a case study in complement C4.

PubMed

Croll, Tristan Ian; Andersen, Gregers Rom

2016-09-01

While the rapid proliferation of high-resolution structures in the Protein Data Bank provides a rich set of templates for starting models, it remains the case that a great many structures both past and present are built at least in part by hand-threading through low-resolution and/or weak electron density. With current model-building tools this task can be challenging, and the de facto standard for acceptable error rates (in the form of atomic clashes and unfavourable backbone and side-chain conformations) in structures based on data with dmax not exceeding 3.5 Å reflects this. When combined with other factors such as model bias, these residual errors can conspire to make more serious errors in the protein fold difficult or impossible to detect. The three recently published 3.6-4.2 Å resolution structures of complement C4 (PDB entries 4fxg, 4fxk and 4xam) rank in the top quartile of structures of comparable resolution both in terms of Rfree and MolProbity score, yet, as shown here, contain register errors in six β-strands. By applying a molecular-dynamics force field that explicitly models interatomic forces and hence excludes most physically impossible conformations, the recently developed interactive molecular-dynamics flexible fitting (iMDFF) approach significantly reduces the complexity of the conformational space to be searched during manual rebuilding. This substantially improves the rate of detection and correction of register errors, and allows user-guided model building in maps with a resolution lower than 3.5 Å to converge to solutions with a stereochemical quality comparable to atomic resolution structures. Here, iMDFF has been used to individually correct and re-refine these three structures to MolProbity scores of <1.7, and strategies for working with such challenging data sets are suggested. Notably, the improved model allowed the resolution for complement C4b to be extended from 4.2 to 3.5 Å as demonstrated by paired refinement.

Combination of structured illumination and single molecule localization microscopy in one setup

NASA Astrophysics Data System (ADS)

Rossberger, Sabrina; Best, Gerrit; Baddeley, David; Heintzmann, Rainer; Birk, Udo; Dithmar, Stefan; Cremer, Christoph

2013-09-01

Understanding the positional and structural aspects of biological nanostructures simultaneously is as much a challenge as a desideratum. In recent years, highly accurate (20 nm) positional information of optically isolated targets down to the nanometer range has been obtained using single molecule localization microscopy (SMLM), while highly resolved (100 nm) spatial information has been achieved using structured illumination microscopy (SIM). In this paper, we present a high-resolution fluorescence microscope setup which combines the advantages of SMLM with SIM in order to provide high-precision localization and structural information in a single setup. Furthermore, the combination of the wide-field SIM image with the SMLM data allows us to identify artifacts produced during the visualization process of SMLM data, and potentially also during the reconstruction process of SIM images. We describe the SMLM-SIM combo and software, and apply the instrument in a first proof-of-principle to the same region of H3K293 cells to achieve SIM images with high structural resolution (in the 100 nm range) in overlay with the highly accurate position information of localized single fluorophores. Thus, with its robust control software, efficient switching between the SMLM and SIM mode, fully automated and user-friendly acquisition and evaluation software, the SMLM-SIM combo is superior over existing solutions.

Effect of Ce doping on structural, optical and photocatalytic properties of ZnO nano-structures.

PubMed

Selvam, N Clament Sagaya; Vijaya, J Judith; Kennedy, L John

2014-03-01

A novel self-assembled pure and Ce doped ZnO nano-particles (NPs) were successfully synthesized by a simple low temperature co-precipitation method. The prepared photocatalysts were characterized by X-ray diffraction (XRD), High resolution scanning electron microscopy (HR-SEM), High resolution transmission electron microscopy (HR-TEM), diffuse reflectance spectroscopy (DRS) and Photoluminescence (PL) spectroscopy. The results indicated that the prepared photocatalysts shows a novel morphology, high crystallinity, uniform size distribution, and more defects. Photocatalytic degradation (PCD) of nonylphenol, a potent endocrine disrupting chemical in aqueous medium was investigated. Higher amount of oxygen defects exhibits enhanced PCD of nonylphenol. In addition, the influence of the Ce contents on the structure, morphology, absorption, emission and photocatalytic activity of ZnO nanoparticles (NPs) were investigated systematically. The relative PCD efficiency of pure ZnO, Ce-doped ZnO NPs and commercial TiO2 (Degussa P-25) have also been discussed.

Accelerated high-resolution photoacoustic tomography via compressed sensing

NASA Astrophysics Data System (ADS)

Arridge, Simon; Beard, Paul; Betcke, Marta; Cox, Ben; Huynh, Nam; Lucka, Felix; Ogunlade, Olumide; Zhang, Edward

2016-12-01

Current 3D photoacoustic tomography (PAT) systems offer either high image quality or high frame rates but are not able to deliver high spatial and temporal resolution simultaneously, which limits their ability to image dynamic processes in living tissue (4D PAT). A particular example is the planar Fabry-Pérot (FP) photoacoustic scanner, which yields high-resolution 3D images but takes several minutes to sequentially map the incident photoacoustic field on the 2D sensor plane, point-by-point. However, as the spatio-temporal complexity of many absorbing tissue structures is rather low, the data recorded in such a conventional, regularly sampled fashion is often highly redundant. We demonstrate that combining model-based, variational image reconstruction methods using spatial sparsity constraints with the development of novel PAT acquisition systems capable of sub-sampling the acoustic wave field can dramatically increase the acquisition speed while maintaining a good spatial resolution: first, we describe and model two general spatial sub-sampling schemes. Then, we discuss how to implement them using the FP interferometer and demonstrate the potential of these novel compressed sensing PAT devices through simulated data from a realistic numerical phantom and through measured data from a dynamic experimental phantom as well as from in vivo experiments. Our results show that images with good spatial resolution and contrast can be obtained from highly sub-sampled PAT data if variational image reconstruction techniques that describe the tissues structures with suitable sparsity-constraints are used. In particular, we examine the use of total variation (TV) regularization enhanced by Bregman iterations. These novel reconstruction strategies offer new opportunities to dramatically increase the acquisition speed of photoacoustic scanners that employ point-by-point sequential scanning as well as reducing the channel count of parallelized schemes that use detector arrays.

The rationale and suggested approaches for research geosynchronous satellite measurements for severe storm and mesoscale investigations

NASA Technical Reports Server (NTRS)

Shenk, W. E.; Adler, R. F.; Chesters, D.; Susskind, J.; Uccellini, L.

1984-01-01

The measurements from current and planned geosynchronous satellites provide quantitative estimates of temperature and moisture profiles, surface temperature, wind, cloud properties, and precipitation. A number of significant observation characteristics remain, they include: (1) temperature and moisture profiles in cloudy areas; (2) high vertical profile resolution; (3) definitive precipitation area mapping and precipitation rate estimates on the convective cloud scale; (4) winds from low level cloud motions at night; (5) the determination of convective cloud structure; and (6) high resolution surface temperature determination. Four major new observing capabilities are proposed to overcome these deficiencies: a microwave sounder/imager, a high resolution visible and infrared imager, a high spectral resolution infrared sounder, and a total ozone mapper. It is suggested that the four sensors are flown together and used to support major mesoscale and short range forecasting field experiments.

High resolution positron annihilation induced Auger electron spectroscopy of the CuM 2,3VV-transition and of Cu sub-monolayers on Pd and Fe

NASA Astrophysics Data System (ADS)

Mayer, J.; Hugenschmidt, C.; Schreckenbach, K.

2010-09-01

We present a high resolution positron annihilation induced Auger Electron Spectroscopy (PAES) of the CuM 2,3VV-transition with the unprecedented energy resolution of Δ/EE <1%. This energy resolution and the highly intense positron source NEPOMUC enabled us to resolve the double peak structure with PAES for the first time within a measurement time of only 5.5 h. In addition, sub-monolayers of Cu were deposited on Fe- and Pd-samples in order to investigate the surface selectivity of PAES in comparison with EAES. The extremely high surface selectivity of PAES due to the different positron affinity of Cu and Fe lead to the result that with only 0.96 monolayer of Cu on Fe more than 55% of the emitted Auger electrons stem from Cu, whereas with EAES the Cu Auger fraction amounted to less than 6%.

High-Resolution Structural Monitoring of Ionospheric Absorption Events

DTIC Science & Technology

2013-07-01

ionospheric plasma conductivity 5 . This results in enhanced absorption of the cosmic high frequency (HF; typically 10 – 60 MHz) radio background ...7 riometry. Incorporation of an outrigger site, to enable treatment of the unknown structure of the celestial background and the effects of...riometry. Incorporation of an outrigger site, to enable treatment of the unknown structure of the celestial background and the effects of confusion

Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase from Shewanella oneidensis at 1.6 angstrom: Identification of Farnesyl pyrophosphate Trapped in a Hydrophobic Cavity

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

Ni, Shuisong; Robinson, Howard; Marsing, Gregory C.

2004-11-01

1. Introduction Enzymes in the non-mevalonate pathway for isoprenoid synthesis have gained recent attention because of their potential value as targets for antibiotic drug development. 2C-methyl-D-erythritol-2,4 cyclophosphate (MECDP) synthase is the fifth enzyme in the seven enzyme non-mevalonate pathway for synthesis of isopentenyl diphosphate. Four groups have published structures of MECDP synthase at resolutions varying from 1.6Å to 2.8Å, either in the presence or absence of substrate from Escherichia coli (Richard et al., 2002; Kemp et al., 2002; Steinbacher et al., 2002) or from Thermus thermophilus (Kishida et al., 2003). Among these structures, the protein always exists as a homotrimermore » either with a crystallographic or a non-crystallographic three-fold symmetry axis and an active site formed in a cleft between adjacent monomers. While the overall shape of the proteins is highly similar among these structures, each of the four reported structures contain different combinations of metal ions in the active site including a Zn2+ ion only (Steinbacher et al., 2002), a Mn2+ ion only (Richard et al., 2002), Zn2+ and Mn2+ ions (Kemp et al., 2002) or two Mg2+ ions (Kishida et al., 2003). Furthermore, two of the structures are reported to contain a hydrophobic channel along the three-fold symmetry axis that is capped by a cluster of three arginine side chains (one from each monomer) at one end of the cavity and a cluster of three glutamic acid side chains (one from each monomer) at the other side of the cavity. In a 1.8Å resolution structure, Kemp et al. (2002) reported a sulfate ion coordinated to the arginine cap and solvent trapped in a hydrophobic cavity. In a lower 2.8Å resolution structure, Richard et al. (2002) concluded that geranyl diphosphate, GPP, was most likely trapped by the arginine cap and hydrophobic cavity (Richard et al., 2002), however, the low resolution of the data together with the presence of the crystallographic symmetry axis prohibited a definitive analysis of the identity and mode of binding of the bound molecule. Kishida et al. (2003) reported that no cavity existed in a 1.6Å structure of the SO3437 homolog from Thermus thermophilus, presumably due to tighter packing of the protein from the thermophilic organism. Steinbacher et al. (2002) make no description of a hydrophobic cavity in a lower resolution (2.5-3.2Å) of the Escherichia coli protein. Here, we report a high-resolution (1.6Å) structure of MECDP synthase from Shewanella oneidensis in the absence of substrate in the active site. We provide unambiguous data that confirms the presence of Zn2+ in one of the metal binding sites and observe what appears to be farnesyl diphosphate (FPP) bound in the hydrophobic cavity along the non-crystallographic three-fold symmetry axis of the homotrimer. The high-resolution structure clarifies the mode of binding of the pyrophosphate of FPP in the arginine cluster that caps the hydrophobic cavity.« less

High resolution telescope and spectrograph observations of solar fine structure in the 1600 A region

NASA Technical Reports Server (NTRS)

Cook, J. W.; Brueckner, G. E.; Bartoe, J.-D. F.

1983-01-01

High spatial resolution spectroheliograms of the 1600 A region obtained during the HRTS rocket flight of 1978 February 13 are presented. The morphology, fine structure, and temporal behavior of emission bright points (BPs) in active and quiet regions are illustrated. In quiet regions, network elements persist as morphological units, although individual BPs may vary in intensity while usually lasting the flight duration. In cell centers, the BPs are highly variable on a 1 minute time scale. BPs in plages remain more constant in brightness over the observing sequence. BPs cover less than 4 percent of the quiet surface. The lifetime and degree of packing of BPs vary with the local strength of the magnetic field.

New and unconventional approaches for advancing resolution in biological transmission electron microscopy by improving macromolecular specimen preparation and preservation.

PubMed

Massover, William H

2011-02-01

Resolution in transmission electron microscopy (TEM) now is limited by the properties of specimens, rather than by those of instrumentation. The long-standing difficulties in obtaining truly high-resolution structure from biological macromolecules with TEM demand the development, testing, and application of new ideas and unconventional approaches. This review concisely describes some new concepts and innovative methodologies for TEM that deal with unsolved problems in the preparation and preservation of macromolecular specimens. The selected topics include use of better support films, a more protective multi-component matrix surrounding specimens for cryo-TEM and negative staining, and, several quite different changes in microscopy and micrography that should decrease the effects of electron radiation damage; all these practical approaches are non-traditional, but have promise to advance resolution for specimens of biological macromolecules beyond its present level of 3-10 Å (0.3-1.0 nm). The result of achieving truly high resolution will be a fulfillment of the still unrealized potential of transmission electron microscopy for directly revealing the structure of biological macromolecules down to the atomic level. Published by Elsevier Ltd.

A Miniature Fiber-Optic Sensor for High-Resolution and High-Speed Temperature Sensing in Ocean Environment

DTIC Science & Technology

2015-11-05

the SMF is superior when it comes to remote sensing in far and deep ocean. As an initial test , the real-time temperature structure within the water...4 ℃. The high resolution guarantees the visualization of subtle variation in the local water. To test the response time of the proposed sensor, the... Honey , "Optical trubulence in the sea," in Underwater Photo-optical Instrumentation Applications SPIE, 49-55 (1972). [6] J. D. Nash, D. R. Caldwell, M

Unravelling earth flow dynamics with 3-D time series derived from UAV-SfM models

NASA Astrophysics Data System (ADS)

Clapuyt, François; Vanacker, Veerle; Schlunegger, Fritz; Van Oost, Kristof

2017-12-01

Accurately assessing geo-hazards and quantifying landslide risks in mountainous environments are gaining importance in the context of the ongoing global warming. For an in-depth understanding of slope failure mechanisms, accurate monitoring of the mass movement topography at high spatial and temporal resolutions remains essential. The choice of the acquisition framework for high-resolution topographic reconstructions will mainly result from the trade-off between the spatial resolution needed and the extent of the study area. Recent advances in the development of unmanned aerial vehicle (UAV)-based image acquisition combined with the structure-from-motion (SfM) algorithm for three-dimensional (3-D) reconstruction make the UAV-SfM framework a competitive alternative to other high-resolution topographic techniques. In this study, we aim at gaining in-depth knowledge of the Schimbrig earthflow located in the foothills of the Central Swiss Alps by monitoring ground surface displacements at very high spatial and temporal resolution using the efficiency of the UAV-SfM framework. We produced distinct topographic datasets for three acquisition dates between 2013 and 2015 in order to conduct a comprehensive 3-D analysis of the landslide. Therefore, we computed (1) the sediment budget of the hillslope, and (2) the horizontal and (3) the three-dimensional surface displacements. The multitemporal UAV-SfM based topographic reconstructions allowed us to quantify rates of sediment redistribution and surface movements. Our data show that the Schimbrig earthflow is very active, with mean annual horizontal displacement ranging between 6 and 9 m. Combination and careful interpretation of high-resolution topographic analyses reveal the internal mechanisms of the earthflow and its complex rotational structure. In addition to variation in horizontal surface movements through time, we interestingly showed that the configuration of nested rotational units changes through time. Although there are major changes in the internal structure of the earthflow in the 2013-2015 period, the sediment budget of the drainage basin is nearly in equilibrium. As a consequence, our data show that the time lag between sediment mobilization by landslides and enhanced sediment fluxes in the river network can be considerable.

Human deoxyhaemoglobin-2,3-diphosphoglycerate complex low-salt structure at 2.5 A resolution.

PubMed

Richard, V; Dodson, G G; Mauguen, Y

1993-09-20

The haemoglobin-2,3-diphosphoglycerate complex structure has been solved at 2.5 A resolution using crystals grown from low-salt solutions. The results show some important differences with the precedent haemoglobin-2,3-diphosphoglycerate high-salt structure solved by Arnone. First, we observe a loss of symmetry in the binding site, secondly both of the lysine residues 82 beta interact with 2,3-diphosphoglycerate at the same time, each making two contacts. This level of interaction is in agreement with the functional behaviour of natural haemoglobin mutants with mutations at the 2,3-diphosphoglycerate binding site.

Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud

PubMed Central

Cianfrocco, Michael A; Leschziner, Andres E

2015-01-01

The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. Calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available ‘off-the-shelf’ computing environment on Amazon's elastic cloud computing infrastructure. This environment provides users with single particle cryo-EM software packages and the ability to create computing clusters with 16–480+ CPUs. We tested our computing environment using a publicly available 80S yeast ribosome dataset and estimate that laboratories could determine high-resolution cryo-EM structures for $50 to $1500 per structure within a timeframe comparable to local clusters. Our analysis shows that Amazon's cloud computing environment may offer a viable computing environment for cryo-EM. DOI: http://dx.doi.org/10.7554/eLife.06664.001 PMID:25955969

Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution

NASA Astrophysics Data System (ADS)

Schur, Florian K. M.; Hagen, Wim J. H.; Rumlová, Michaela; Ruml, Tomáš; Müller, Barbara; Kräusslich, Hans-Georg; Briggs, John A. G.

2015-01-01

Human immunodeficiency virus type 1 (HIV-1) assembly proceeds in two stages. First, the 55 kilodalton viral Gag polyprotein assembles into a hexameric protein lattice at the plasma membrane of the infected cell, inducing budding and release of an immature particle. Second, Gag is cleaved by the viral protease, leading to internal rearrangement of the virus into the mature, infectious form. Immature and mature HIV-1 particles are heterogeneous in size and morphology, preventing high-resolution analysis of their protein arrangement in situ by conventional structural biology methods. Here we apply cryo-electron tomography and sub-tomogram averaging methods to resolve the structure of the capsid lattice within intact immature HIV-1 particles at subnanometre resolution, allowing unambiguous positioning of all α-helices. The resulting model reveals tertiary and quaternary structural interactions that mediate HIV-1 assembly. Strikingly, these interactions differ from those predicted by the current model based on in vitro-assembled arrays of Gag-derived proteins from Mason-Pfizer monkey virus. To validate this difference, we solve the structure of the capsid lattice within intact immature Mason-Pfizer monkey virus particles. Comparison with the immature HIV-1 structure reveals that retroviral capsid proteins, while having conserved tertiary structures, adopt different quaternary arrangements during virus assembly. The approach demonstrated here should be applicable to determine structures of other proteins at subnanometre resolution within heterogeneous environments.

Navigating 3D electron microscopy maps with EM-SURFER.

PubMed

Esquivel-Rodríguez, Juan; Xiong, Yi; Han, Xusi; Guang, Shuomeng; Christoffer, Charles; Kihara, Daisuke

2015-05-30

The Electron Microscopy DataBank (EMDB) is growing rapidly, accumulating biological structural data obtained mainly by electron microscopy and tomography, which are emerging techniques for determining large biomolecular complex and subcellular structures. Together with the Protein Data Bank (PDB), EMDB is becoming a fundamental resource of the tertiary structures of biological macromolecules. To take full advantage of this indispensable resource, the ability to search the database by structural similarity is essential. However, unlike high-resolution structures stored in PDB, methods for comparing low-resolution electron microscopy (EM) density maps in EMDB are not well established. We developed a computational method for efficiently searching low-resolution EM maps. The method uses a compact fingerprint representation of EM maps based on the 3D Zernike descriptor, which is derived from a mathematical series expansion for EM maps that are considered as 3D functions. The method is implemented in a web server named EM-SURFER, which allows users to search against the entire EMDB in real-time. EM-SURFER compares the global shapes of EM maps. Examples of search results from different types of query structures are discussed. We developed EM-SURFER, which retrieves structurally relevant matches for query EM maps from EMDB within seconds. The unique capability of EM-SURFER to detect 3D shape similarity of low-resolution EM maps should prove invaluable in structural biology.

On a fast calculation of structure factors at a subatomic resolution.

PubMed

Afonine, P V; Urzhumtsev, A

2004-01-01

In the last decade, the progress of protein crystallography allowed several protein structures to be solved at a resolution higher than 0.9 A. Such studies provide researchers with important new information reflecting very fine structural details. The signal from these details is very weak with respect to that corresponding to the whole structure. Its analysis requires high-quality data, which previously were available only for crystals of small molecules, and a high accuracy of calculations. The calculation of structure factors using direct formulae, traditional for 'small-molecule' crystallography, allows a relatively simple accuracy control. For macromolecular crystals, diffraction data sets at a subatomic resolution contain hundreds of thousands of reflections, and the number of parameters used to describe the corresponding models may reach the same order. Therefore, the direct way of calculating structure factors becomes very time expensive when applied to large molecules. These problems of high accuracy and computational efficiency require a re-examination of computer tools and algorithms. The calculation of model structure factors through an intermediate generation of an electron density [Sayre (1951). Acta Cryst. 4, 362-367; Ten Eyck (1977). Acta Cryst. A33, 486-492] may be much more computationally efficient, but contains some parameters (grid step, 'effective' atom radii etc.) whose influence on the accuracy of the calculation is not straightforward. At the same time, the choice of parameters within safety margins that largely ensure a sufficient accuracy may result in a significant loss of the CPU time, making it close to the time for the direct-formulae calculations. The impact of the different parameters on the computer efficiency of structure-factor calculation is studied. It is shown that an appropriate choice of these parameters allows the structure factors to be obtained with a high accuracy and in a significantly shorter time than that required when using the direct formulae. Practical algorithms for the optimal choice of the parameters are suggested.

PEPSI, the High-Resolution Optical-IR Spectrograph for the LBT

NASA Astrophysics Data System (ADS)

Andersen, Michael; Strassmeier, Klaus; Hoffman, Axel; Woche, Manfred; Spano, Paolo

PEPSI is a high resolution fibre feed optical-IR polarimetric echelle spectrograph for the Large Binocular Telescope (LBT). PEPSI utilizes the two 8.4m LBT apertures to simultaneously record four polarization states at a resolution of 120.000. The extension of the coverage towards the IR is mainly motivated by the larger Zeeman splitting of IR lines, which would allow to study weaker/fainter magnetic structures on stars. The two optical arms, which also have an integral light mode with R up to 300.000, are under construction, while the IR arm is being designed.

Objectives and Layout of a High-Resolution X-ray Imaging Crystal Spectrometer for the Large Helical Device (LHD)

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

Bitter, M; Gates, D; Monticello, D

A high-resolution X-ray imaging crystal spectrometer, whose concept was tested on NSTX and Alcator C-Mod, is being designed for LHD. This instrument will record spatially resolved spectra of helium-like Ar16+ and provide ion temperature profiles with spatial and temporal resolutions of < 2 cm and ≥ 10 ms. The stellarator equilibrium reconstruction codes, STELLOPT and PIES, will be used for the tomographic inversion of the spectral data. The spectrometer layout and instrumental features are largely determined by the magnetic field structure of LHD.

Multiscale assessment of landscape structure in heterogeneous forested area

NASA Astrophysics Data System (ADS)

Simoniello, T.; Pignatti, S.; Carone, M. T.; Fusilli, L.; Lanfredi, M.; Coppola, R.; Santini, F.

2010-05-01

The characterization of landscape structure in space or time is fundamental to infer ecological processes (Ingegnoli, 2002). Landscape pattern arrangements strongly influence forest ecological functioning and biodiversity, as an example landscape fragmentation can induce habitat degradation reducing forest species populations or limiting their recolonization. Such arrangements are spatially correlated and scale-dependent, therefore they have distinctive operational-scales at which they can be best characterized (Wu, 2004). In addition, the detail of the land cover classification can have substantial influences on resulting pattern quantification (Greenberg et al.2001). In order to evaluate the influence of the observational scales and labelling details, we investigated a forested area (Pollino National Park; southern Italy) by analyzing the patch arrangement derived from three remote sensing sensors having different spectral and spatial resolutions. In particular, we elaborated data from the hyperspectral MIVIS (102 bands; ~7m) and Hyperion (220 bands; 30m), and the multispectral Landsat-TM (7 bands; 30m). Moreover, to assess the landscape evolution we investigated the hierarchical structure of the study area (landscape, class, patch) by elaborating two Landsat-TM acquired in 1987 and 1998. Preprocessed data were classified by adopting a supervised procedure based on the Minimum Distance classifier. The obtained labelling correspond to Corine level 5 for the high resolution MIVIS data, to Corine level 4 for Hyperion and to an intermediate level 4-3 for TM data. The analysis was performed by taking into account patch density, diversity and evenness at landscape level; mean patch size and interdispersion at class level; patch structure and perimeter regularity at patch level. The three sensors described a landscape with a quite high level of richness and distribution. The high spectral and spatial resolution of MIVIS data provided the highest diversity level (SHDI = 2.05), even if the results obtained for TM were not so different (1.93), Hyperion showed the lowest value (1.79). The obtained evenness index was similar for all the landscapes (~ 0.72). At class level, the interdispersion increases as the spatial and spectral resolution power decrease. Due to the low labelling detail, TM classes represent an aggregation of MIVIS and Hyperion classes; therefore they result larger and more diffused over the territory favouring higher interspersion values in the computation. The investigation of the patch structure highlighted the highest MIVIS capability in describing the patch articulation; Hyperion and TM showed quite similar situation. The historical analysis based on TM imagery showed a fragmentation process for some forested patches (mainly beeches): an increase of structure complexity (higher FRACT) is coupled with a higher patch number and an extension reduction. On the whole, the obtained results showed that the multispectral Landsat-TM images represent a good data source for supporting studies on landscape structure of forested areas and that for analyzing the articulation of particular species the high spectral resolution needs to be coupled with a high spatial resolution, i.e. Hyperion sampling is not adequate for such a purpose.

High-resolution, anthropomorphic, computational breast phantom: fusion of rule-based structures with patient-based anatomy

NASA Astrophysics Data System (ADS)

Chen, Xinyuan; Gong, Xiaolin; Graff, Christian G.; Santana, Maira; Sturgeon, Gregory M.; Sauer, Thomas J.; Zeng, Rongping; Glick, Stephen J.; Lo, Joseph Y.

2017-03-01

While patient-based breast phantoms are realistic, they are limited by low resolution due to the image acquisition and segmentation process. The purpose of this study is to restore the high frequency components for the patient-based phantoms by adding power law noise (PLN) and breast structures generated based on mathematical models. First, 3D radial symmetric PLN with β=3 was added at the boundary between adipose and glandular tissue to connect broken tissue and create a high frequency contour of the glandular tissue. Next, selected high-frequency features from the FDA rule-based computational phantom (Cooper's ligaments, ductal network, and blood vessels) were fused into the phantom. The effects of enhancement in this study were demonstrated by 2D mammography projections and digital breast tomosynthesis (DBT) reconstruction volumes. The addition of PLN and rule-based models leads to a continuous decrease in β. The new β is 2.76, which is similar to what typically found for reconstructed DBT volumes. The new combined breast phantoms retain the realism from segmentation and gain higher resolution after restoration.

Additive manufacturing of microfluidic glass chips

NASA Astrophysics Data System (ADS)

Kotz, F.; Helmer, D.; Rapp, B. E.

2018-02-01

Additive manufacturing has gained great interest in the microfluidic community due to the numerous channel designs which can be tested in the early phases of a lab-on-a-chip device development. High resolution additive manufacturing like microstereolithography is largely associated with polymers. Polymers are at a disadvantage compared to other materials due to their softness and low chemical resistance. Whenever high chemical and thermal resistance combined with high optical transparency is needed, glasses become the material of choice. However, glasses are difficult to structure at the microscale requiring hazardous chemicals for etching processes. In this work we present additive manufacturing and high resolution patterning of microfluidic chips in transparent fused silica glass using stereolithography and microlithography. We print an amorphous silica nanocomposite at room temperature using benchtop stereolithography printers and a custom built microlithography system based on a digital mirror device. Using microlithography we printed structures with tens of micron resolution. The printed part is then converted to a transparent fused silica glass using thermal debinding and sintering. Printing of a microfluidic chip can be done within 30 minutes. The heat treatment can be done within two days.

Criteria to Extract High-Quality Protein Data Bank Subsets for Structure Users.

PubMed

Carugo, Oliviero; Djinović-Carugo, Kristina

2016-01-01

It is often necessary to build subsets of the Protein Data Bank to extract structural trends and average values. For this purpose it is mandatory that the subsets are non-redundant and of high quality. The first problem can be solved relatively easily at the sequence level or at the structural level. The second, on the contrary, needs special attention. It is not sufficient, in fact, to consider the crystallographic resolution and other feature must be taken into account: the absence of strings of residues from the electron density maps and from the files deposited in the Protein Data Bank; the B-factor values; the appropriate validation of the structural models; the quality of the electron density maps, which is not uniform; and the temperature of the diffraction experiments. More stringent criteria produce smaller subsets, which can be enlarged with more tolerant selection criteria. The incessant growth of the Protein Data Bank and especially of the number of high-resolution structures is allowing the use of more stringent selection criteria, with a consequent improvement of the quality of the subsets of the Protein Data Bank.

Near-atomic-resolution cryo-EM analysis of the Salmonella T3S injectisome basal body.

PubMed

Worrall, L J; Hong, C; Vuckovic, M; Deng, W; Bergeron, J R C; Majewski, D D; Huang, R K; Spreter, T; Finlay, B B; Yu, Z; Strynadka, N C J

2016-12-14

The type III secretion (T3S) injectisome is a specialized protein nanomachine that is critical for the pathogenicity of many Gram-negative bacteria, including purveyors of plague, typhoid fever, whooping cough, sexually transmitted infections and major nosocomial infections. This syringe-shaped 3.5-MDa macromolecular assembly spans both bacterial membranes and that of the infected host cell. The internal channel formed by the injectisome allows for the direct delivery of partially unfolded virulence effectors into the host cytoplasm. The structural foundation of the injectisome is the basal body, a molecular lock-nut structure composed predominantly of three proteins that form highly oligomerized concentric rings spanning the inner and outer membranes. Here we present the structure of the prototypical Salmonella enterica serovar Typhimurium pathogenicity island 1 basal body, determined using single-particle cryo-electron microscopy, with the inner-membrane-ring and outer-membrane-ring oligomers defined at 4.3 Å and 3.6 Å resolution, respectively. This work presents the first, to our knowledge, high-resolution structural characterization of the major components of the basal body in the assembled state, including that of the widespread class of outer-membrane portals known as secretins.

Submicron-resolution photoacoustic microscopy of endogenous light-absorbing biomolecules

NASA Astrophysics Data System (ADS)

Zhang, Chi

Photoacoustic imaging in biomedicine has the unique advantage of probing endogenous light absorbers at various length scales with a 100% relative sensitivity. Among the several modalities of photoacoustic imaging, optical-resolution photoacoustic microscopy (OR-PAM) can achieve high spatial resolution, on the order of optical wavelength, at <1 mm depth in biological tissue (the optical ballistic regime). OR-PAM has been applied successfully to structural and functional imaging of blood vasculature and red blood cells in vivo. Any molecules which absorb sufficient light at certain wavelengths can potentially be imaged by PAM. Compared with pure optical imaging, which typically targets fluorescent markers, label-free PAM avoids the major concerns that the fluorescent labeling probes may disturb the function of biomolecules and may have an insufficient density. This dissertation aims to advance label-free OR-PAM to the subcellular scale. The first part of this dissertation describes the technological advancement of PAM yielding high spatial resolution in 3D. The lateral resolution was improved by using optical objectives with high numerical apertures for optical focusing. The axial resolution was improved by using broadband ultrasonic transducers for ultrasound detection. We achieved 220 nm lateral resolution in transmission mode, 0.43 microm lateral resolution in reflection mode, 7.6 microm axial resolution in normal tissue, and 5.8 microm axial resolution with silicone oil immersion/injection. The achieved lateral resolution and axial resolution were the finest reported at the time. With high-resolution in 3D, PAM was demonstrated to resolve cellular and subcellular structures in vivo, such as red blood cells and melanosomes in melanoma cells. Compared with previous PAM systems, our high-resolution PAM could resolve capillaries in mouse ears more clearly. As an example application, we demonstrated intracellular temperature imaging, assisted by fluorescence signal detection, with sub-degree temperature resolution and sub-micron lateral resolution. The second part of this dissertation describes the exploration of endogenous light-absorbing biomolecules for PAM. We demonstrated cytochromes and myoglobin as new absorption contrasts for PAM and identified the corresponding optimal wavelengths for imaging. Fixed fibroblasts on slides and mouse ear sections were imaged by PAM at 422 nm and 250 nm wavelengths to reveal cytoplasms and nuclei, respectively, as confirmed by standard hematoxylin and eosin (H&E) histology. By imaging a blood-perfused mouse heart at 532 nm down to 150 microm in depth, we derived the myocardial sheet thickness and the cleavage height from an undehydrated heart for the first time. The findings promote PAM at new wavelengths and open up new possibilities for characterizing biological tissue. Of particular interest, dual-wavelength PAM around 250 nm and 420 nm wavelengths is analogous to H&E histology. The last part of this dissertation describes the development of sectioning photoacoustic microscopy (SPAM), based on the advancement in spatial resolution and new contrasts for PAM, with applications in brain histology. Label-free SPAM, assisted by a microtome, acquires serial distortion-free images of a specimen on the surface. By exciting cell nuclei at 266 nm wavelength with high resolution, SPAM could pinpoint cell nuclei sensitively and specifically in the mouse brain section, as confirmed by H&E histology. SPAM was demonstrated to generate high-resolution 3D images, highlighting cell nuclei, of formalin-fixed paraffin-embedded mouse brains without tissue staining or clearing. SPAM can potentially serve as a high-throughput and minimal-artifact substitute for histology, probe many other biomolecules and cells, and become a universal tool for animal or human whole-organ microscopy, with diverse applications in life sciences.

3D hierarchical geometric modeling and multiscale FE analysis as a base for individualized medical diagnosis of bone structure.

PubMed

Podshivalov, L; Fischer, A; Bar-Yoseph, P Z

2011-04-01

This paper describes a new alternative for individualized mechanical analysis of bone trabecular structure. This new method closes the gap between the classic homogenization approach that is applied to macro-scale models and the modern micro-finite element method that is applied directly to micro-scale high-resolution models. The method is based on multiresolution geometrical modeling that generates intermediate structural levels. A new method for estimating multiscale material properties has also been developed to facilitate reliable and efficient mechanical analysis. What makes this method unique is that it enables direct and interactive analysis of the model at every intermediate level. Such flexibility is of principal importance in the analysis of trabecular porous structure. The method enables physicians to zoom-in dynamically and focus on the volume of interest (VOI), thus paving the way for a large class of investigations into the mechanical behavior of bone structure. This is one of the very few methods in the field of computational bio-mechanics that applies mechanical analysis adaptively on large-scale high resolution models. The proposed computational multiscale FE method can serve as an infrastructure for a future comprehensive computerized system for diagnosis of bone structures. The aim of such a system is to assist physicians in diagnosis, prognosis, drug treatment simulation and monitoring. Such a system can provide a better understanding of the disease, and hence benefit patients by providing better and more individualized treatment and high quality healthcare. In this paper, we demonstrate the feasibility of our method on a high-resolution model of vertebra L3. Copyright © 2010 Elsevier Inc. All rights reserved.

Fabrication of 3D SiO x structures using patterned PMMA sacrificial layer

NASA Astrophysics Data System (ADS)

Li, Zhiqin; Xiang, Quan; Zheng, Mengjie; Bi, Kaixi; Chen, Yiqin; Chen, Keqiu; Duan, Huigao

2018-02-01

Three-dimensional (3D) nanofabrication based on electron-beam lithography (EBL) has drawn wide attention for various applications with its high patterning resolution and design flexibility. In this work, we present a bilayer EBL process to obtain 3D freestanding SiO x structures via the release of the bottom sacrificial layer. This new kind of bilayer process enables us to define various 3D freestanding SiO x structures with high resolution and low edge roughness. As a proof of concept for applications, metal-coated freestanding SiO x microplates with an underlying air gap were fabricated to form asymmetric Fabry-Perot resonators, which can be utilized for colorimetric refractive index sensing and thus also have application potential for biochemical detection, anti-counterfeiting and smart active nano-optical devices.

A 3D puzzle approach to building protein-DNA structures.

PubMed

Hinton, Deborah M

2017-03-15

Despite recent advances in structural analysis, it is still challenging to obtain a high-resolution structure for a complex of RNA polymerase, transcriptional factors, and DNA. However, using biochemical constraints, 3D printed models of available structures, and computer modeling, one can build biologically relevant models of such supramolecular complexes.

High resolution simulations of energy absorption in dynamically loaded cellular structures

NASA Astrophysics Data System (ADS)

Winter, R. E.; Cotton, M.; Harris, E. J.; Eakins, D. E.; McShane, G.

2017-03-01

Cellular materials have potential application as absorbers of energy generated by high velocity impact. CTH, a Sandia National Laboratories Code which allows very severe strains to be simulated, has been used to perform very high resolution simulations showing the dynamic crushing of a series of two-dimensional, stainless steel metal structures with varying architectures. The structures are positioned to provide a cushion between a solid stainless steel flyer plate with velocities ranging from 300 to 900 m/s, and an initially stationary stainless steel target. Each of the alternative architectures under consideration was formed by an array of identical cells each of which had a constant volume and a constant density. The resolution of the simulations was maximised by choosing a configuration in which one-dimensional conditions persisted for the full period over which the specimen densified, a condition which is most readily met by impacting high density specimens at high velocity. It was found that the total plastic flow and, therefore, the irreversible energy dissipated in the fully densified energy absorbing cell, increase (a) as the structure becomes more rodlike and less platelike and (b) as the impact velocity increases. Sequential CTH images of the deformation processes show that the flow of the cell material may be broadly divided into macroscopic flow perpendicular to the compression direction and jetting-type processes (microkinetic flow) which tend to predominate in rod and rodlike configurations and also tend to play an increasing role at increased strain rates. A very simple analysis of a configuration in which a solid flyer impacts a solid target provides a baseline against which to compare and explain features seen in the simulations. The work provides a basis for the development of energy absorbing structures for application in the 200-1000 m/s impact regime.

Investigation of skin structures based on infrared wave parameter indirect microscopic imaging

NASA Astrophysics Data System (ADS)

Zhao, Jun; Liu, Xuefeng; Xiong, Jichuan; Zhou, Lijuan

2017-02-01

Detailed imaging and analysis of skin structures are becoming increasingly important in modern healthcare and clinic diagnosis. Nanometer resolution imaging techniques such as SEM and AFM can cause harmful damage to the sample and cannot measure the whole skin structure from the very surface through epidermis, dermis to subcutaneous. Conventional optical microscopy has the highest imaging efficiency, flexibility in onsite applications and lowest cost in manufacturing and usage, but its image resolution is too low to be accepted for biomedical analysis. Infrared parameter indirect microscopic imaging (PIMI) uses an infrared laser as the light source due to its high transmission in skins. The polarization of optical wave through the skin sample was modulated while the variation of the optical field was observed at the imaging plane. The intensity variation curve of each pixel was fitted to extract the near field polarization parameters to form indirect images. During the through-skin light modulation and image retrieving process, the curve fitting removes the blurring scattering from neighboring pixels and keeps only the field variations related to local skin structures. By using the infrared PIMI, we can break the diffraction limit, bring the wide field optical image resolution to sub-200nm, in the meantime of taking advantage of high transmission of infrared waves in skin structures.

Structural Information Detection Based Filter for GF-3 SAR Images

NASA Astrophysics Data System (ADS)

Sun, Z.; Song, Y.

2018-04-01

GF-3 satellite with high resolution, large swath, multi-imaging mode, long service life and other characteristics, can achieve allweather and all day monitoring for global land and ocean. It has become the highest resolution satellite system in the world with the C-band multi-polarized synthetic aperture radar (SAR) satellite. However, due to the coherent imaging system, speckle appears in GF-3 SAR images, and it hinders the understanding and interpretation of images seriously. Therefore, the processing of SAR images has big challenges owing to the appearance of speckle. The high-resolution SAR images produced by the GF-3 satellite are rich in information and have obvious feature structures such as points, edges, lines and so on. The traditional filters such as Lee filter and Gamma MAP filter are not appropriate for the GF-3 SAR images since they ignore the structural information of images. In this paper, the structural information detection based filter is constructed, successively including the point target detection in the smallest window, the adaptive windowing method based on regional characteristics, and the most homogeneous sub-window selection. The despeckling experiments on GF-3 SAR images demonstrate that compared with the traditional filters, the proposed structural information detection based filter can well preserve the points, edges and lines as well as smooth the speckle more sufficiently.

Large and small-scale structures in Saturn's rings

NASA Astrophysics Data System (ADS)

Albers, N.; Rehnberg, M. E.; Brown, Z. L.; Sremcevic, M.; Esposito, L. W.

2017-09-01

Observations made by the Cassini spacecraft have revealed both large and small scale structures in Saturn's rings in unprecedented detail. Analysis of high-resolution measurements by the Cassini Ultraviolet Spectrograph (UVIS) High Speed Photometer (HSP) and the Imaging Science Subsystem (ISS) show an abundance of intrinsic small-scale structures (or clumping) seen across the entire ring system. These include self-gravity wakes (50-100m), sub-km structure at the A and B ring edges, and "straw"/"ropy" structures (1-3km).

HATS (High Altitude Thermal Sounder): a passive sensor solution to 3D high-resolution mapping of upper atmosphere dynamics (Conference Presentation)

NASA Astrophysics Data System (ADS)

Gordley, Larry; Marshall, Benjamin T.; Lachance, Richard L.

2016-10-01

This presentation introduces a High Altitude Thermal Sensor (HATS) that has the potential to resolve the thermal structure of the upper atmosphere (cloud top to 100km) with both horizontal and vertical resolution of 5-7 km or better. This would allow the complete characterization of the wave structures that carry weather signature from the underlying atmosphere. Using a novel gas correlation technique, an extremely high-resolution spectral scan is accomplished by measuring a Doppler modulated signal as the atmospheric thermal scene passes through the HATS 2D FOV. This high spectral resolution, difficult to impossible to achieve with any other passive technique, enables the separation of radiation emanating at high altitudes from that emanating at low altitudes. A principal component analysis of these modulation signals then exposes the complete thermal structure of the upper atmosphere. We show that nadir sounding from low earth orbit, using various branches of CO2 emission in the 17 to 15 micron region, with sufficient spectral resolution and spectral measurement range, can distinguish thermal energy that peaks at various altitudes. By observing the up-welling atmospheric emission through a low pressure (Doppler broadened) gas cell, as the scene passes through our FOV, a modulation signal is created as the atmospheric emission lines are shifted through the spectral position of the gas cell absorption lines. The modulation signal is shown to be highly correlated to the emission coming from the spectral location of the gas cell lines relative to the atmospheric emission lines. This effectively produces a scan of the atmospheric emission with a Doppler line resolution. Similar to thermal sounding of the troposphere, a principal component analysis of the modulation signal can be used to produce an altitude resolved profile, given a reasonable a priori temperature profile. It is then shown that with the addition of a limb observation with one CO2 broadband channel (similar to methods employed with sensors like LIMS on Nimbus 7, HIRDLS on Aura, and SABER on TIMED), a limb temperature profile can be retrieved and used as the a priori profile, nearly eliminating uncertainty due to a priori inaccuracy. Feasibility studies and proposed instrument designs are presented. A tutorial for a similar technique proposed for measuring winds and temperature with limb observations can be found at http://www.gats-inc.com/future_missions.html

Atomic Resolution Cryo-EM Structure of β-Galactosidase.

PubMed

Bartesaghi, Alberto; Aguerrebere, Cecilia; Falconieri, Veronica; Banerjee, Soojay; Earl, Lesley A; Zhu, Xing; Grigorieff, Nikolaus; Milne, Jacqueline L S; Sapiro, Guillermo; Wu, Xiongwu; Subramaniam, Sriram

2018-05-10

The advent of direct electron detectors has enabled the routine use of single-particle cryo-electron microscopy (EM) approaches to determine structures of a variety of protein complexes at near-atomic resolution. Here, we report the development of methods to account for local variations in defocus and beam-induced drift, and the implementation of a data-driven dose compensation scheme that significantly improves the extraction of high-resolution information recorded during exposure of the specimen to the electron beam. These advances enable determination of a cryo-EM density map for β-galactosidase bound to the inhibitor phenylethyl β-D-thiogalactopyranoside where the ordered regions are resolved at a level of detail seen in X-ray maps at ∼ 1.5 Å resolution. Using this density map in conjunction with constrained molecular dynamics simulations provides a measure of the local flexibility of the non-covalently bound inhibitor and offers further opportunities for structure-guided inhibitor design. Published by Elsevier Ltd.

High-resolution NMR spectroscopy of encapsulated proteins dissolved in low-viscosity fluids

PubMed Central

Nucci, Nathaniel V.; Valentine, Kathleen G.; Wand, A. Joshua

2014-01-01

High-resolution multi-dimensional solution NMR is unique as a biophysical and biochemical tool in its ability to examine both the structure and dynamics of macromolecules at atomic resolution. Conventional solution NMR approaches, however, are largely limited to examinations of relatively small (< 25 kDa) molecules, mostly due to the spectroscopic consequences of slow rotational diffusion. Encapsulation of macromolecules within the protective nanoscale aqueous interior of reverse micelles dissolved in low viscosity fluids has been developed as a means through which the ‘slow tumbling problem’ can be overcome. This approach has been successfully applied to diverse proteins and nucleic acids ranging up to 100 kDa, considerably widening the range of biological macromolecules to which conventional solution NMR methodologies may be applied. Recent advances in methodology have significantly broadened the utility of this approach in structural biology and molecular biophysics. PMID:24656086

Atomic resolution ADF-STEM imaging of organic molecular crystal of halogenated copper phthalocyanine.

PubMed

Haruta, Mitsutaka; Yoshida, Kaname; Kurata, Hiroki; Isoda, Seiji

2008-05-01

Annular dark-field (ADF) scanning transmission electron microscopy (STEM) measurements are demonstrated for the first time to be applicable for acquiring Z-contrast images of organic molecules at atomic resolution. High-angle ADF imaging by STEM is a new technique that provides incoherent high-resolution Z-contrast images for organic molecules. In the present study, low-angle ADF-STEM is successfully employed to image the molecular crystal structure of hexadecachloro-Cu-phthalocyanine (Cl16-CuPc), an organic molecule. The structures of CuPc derivatives (polyhalogenated CuPc with Br and Cl) are determined quantitatively using the same technique to determine the occupancy of halogens at each chemical site. By comparing the image contrasts of atomic columns, the occupancy of Br is found to be ca. 56% at the inner position, slightly higher than that for random substitution and in good agreement with previous TEM results.

Ultrastable gold substrates: Properties of a support for high-resolution electron cryomicroscopy of biological specimens

PubMed Central

Russo, Christopher J.; Passmore, Lori A.

2016-01-01

Electron cryomicroscopy (cryo-EM) allows structure determination of a wide range of biological molecules and specimens. All-gold supports improve cryo-EM images by reducing radiation-induced motion and image blurring. Here we compare the mechanical and electrical properties of all-gold supports to amorphous carbon foils. Gold supports are more conductive, and have suspended foils that are not compressed by differential contraction when cooled to liquid nitrogen temperatures. These measurements show how the choice of support material and geometry can reduce specimen movement by more than an order of magnitude during low-dose imaging. We provide methods for fabrication of all-gold supports and preparation of vitrified specimens. We also analyse illumination geometry for optimal collection of high resolution, low-dose data. Together, the support structures and methods herein can improve the resolution and quality of images from any electron cryomicroscope. PMID:26592474

High Resolution Infrared Spectroscopy of Molecules of Terrestrial and Planetary Interest

NASA Technical Reports Server (NTRS)

Freedman, Richard S.

2001-01-01

In collaboration with the laboratory spectroscopy group of the Ames Atmospheric Physics Research Branch (SGP), high resolution infrared spectra of molecules that are of importance for the dynamics of the earth's and other planets' atmospheres were acquired using the SGP high resolution Fourier transform spectrometer and gas handling apparatus. That data, along with data acquired using similar instrumentation at the Kitt Peak National Observatory was analyzed to determine the spectral parameters for each of the rotationally resolved transitions for each molecule. Those parameters were incorporated into existing international databases (e.g. HITRANS and GEISA) so that field measurements could be converted into quantitative information regarding the physical and chemical structures of earth and planetary atmospheres.

Characterization of scintillator-based detectors for few-ten-keV high-spatial-resolution x-ray imaging

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

Larsson, Jakob C., E-mail: jakob.larsson@biox.kth.se; Lundström, Ulf; Hertz, Hans M.

2016-06-15

Purpose: High-spatial-resolution x-ray imaging in the few-ten-keV range is becoming increasingly important in several applications, such as small-animal imaging and phase-contrast imaging. The detector properties critically influence the quality of such imaging. Here the authors present a quantitative comparison of scintillator-based detectors for this energy range and at high spatial frequencies. Methods: The authors determine the modulation transfer function, noise power spectrum (NPS), and detective quantum efficiency for Gadox, needle CsI, and structured CsI scintillators of different thicknesses and at different photon energies. An extended analysis of the NPS allows for direct measurements of the scintillator effective absorption efficiency andmore » effective light yield as well as providing an alternative method to assess the underlying factors behind the detector properties. Results: There is a substantial difference in performance between the scintillators depending on the imaging task but in general, the CsI based scintillators perform better than the Gadox scintillators. At low energies (16 keV), a thin needle CsI scintillator has the best performance at all frequencies. At higher energies (28–38 keV), the thicker needle CsI scintillators and the structured CsI scintillator all have very good performance. The needle CsI scintillators have higher absorption efficiencies but the structured CsI scintillator has higher resolution. Conclusions: The choice of scintillator is greatly dependent on the imaging task. The presented comparison and methodology will assist the imaging scientist in optimizing their high-resolution few-ten-keV imaging system for best performance.« less

Characterization of scintillator-based detectors for few-ten-keV high-spatial-resolution x-ray imaging.

PubMed

Larsson, Jakob C; Lundström, Ulf; Hertz, Hans M

2016-06-01

High-spatial-resolution x-ray imaging in the few-ten-keV range is becoming increasingly important in several applications, such as small-animal imaging and phase-contrast imaging. The detector properties critically influence the quality of such imaging. Here the authors present a quantitative comparison of scintillator-based detectors for this energy range and at high spatial frequencies. The authors determine the modulation transfer function, noise power spectrum (NPS), and detective quantum efficiency for Gadox, needle CsI, and structured CsI scintillators of different thicknesses and at different photon energies. An extended analysis of the NPS allows for direct measurements of the scintillator effective absorption efficiency and effective light yield as well as providing an alternative method to assess the underlying factors behind the detector properties. There is a substantial difference in performance between the scintillators depending on the imaging task but in general, the CsI based scintillators perform better than the Gadox scintillators. At low energies (16 keV), a thin needle CsI scintillator has the best performance at all frequencies. At higher energies (28-38 keV), the thicker needle CsI scintillators and the structured CsI scintillator all have very good performance. The needle CsI scintillators have higher absorption efficiencies but the structured CsI scintillator has higher resolution. The choice of scintillator is greatly dependent on the imaging task. The presented comparison and methodology will assist the imaging scientist in optimizing their high-resolution few-ten-keV imaging system for best performance.

Magnetic resonance imaging of the inner ear by using a hybrid radiofrequency coil at 7 T

NASA Astrophysics Data System (ADS)

Kim, Kyoung-Nam; Heo, Phil; Kim, Young-Bo; Han, Gyu-Cheol

2015-01-01

Visualization of the membranous structures of the inner ear has been limited to the detection of the normal fluid signal intensity within the bony labyrinth by using magnetic resonance imaging (MRI) equipped with a 1.5 Tesla (T) magnet. High-field (HF) MRI has been available for more than a decade, and numerous studies have documented its significant advantages over conventional MRI with regards to its use in basic scientific research and routine clinical assessments. No previous studies of the inner ear by using HF MRI have been reported, in part because high-quality resolution of mastoid pneumatization is challenging due to artifacts generated in the HF environment and insufficient performance of radiofrequency (RF) coils. Therefore, a hybrid RF coil with integrated circuitry was developed at 7 T and was targeted for anatomical imaging to achieve a high resolution image of the structure of the human inner ear, excluding the bony portion. The inner-ear's structure is composed of soft tissues containing hydrogen ions and includes the membranous labyrinth, endolymphatic space, perilymphatic space, and cochlear-vestibular nerves. Visualization of the inner-ear's anatomy was performed in-vivo with a custom-designed hybrid RF coil and a specific imaging protocol based on an interpolated breath-held examination sequence. The comparative signal intensity value at 30-mm away from the phantom side was 88% higher for the hybrid RF coil and 24% higher for the 8-channel transmit/receive (Tx/Rx) coil than for the commercial birdcage coil. The optimized MRI protocol employed a hybrid RF coil because it enabled high-resolution imaging of the inner-ear's anatomy and accurate mapping of structures including the cochlea and the semicircular canals. These results indicate that 7 T MRI achieves high spatial resolution visualization of the inner-ear's anatomy. Therefore, MRI imaging using a hybrid RF coil at 7 T could provide a powerful tool for clinical investigations of petrous pathologies of the inner ear.

Optimized Negative Staining: a High-throughput Protocol for Examining Small and Asymmetric Protein Structure by Electron Microscopy

DOE PAGES

Rames, Matthew; Yu, Yadong; Ren, Gang

2014-08-15

Structural determination of proteins is rather challenging for proteins with molecular masses between 40 - 200 kDa. Considering that more than half of natural proteins have a molecular mass between 40 - 200 kDa, a robust and high-throughput method with a nanometer resolution capability is needed. Negative staining (NS) electron microscopy (EM) is an easy, rapid, and qualitative approach which has frequently been used in research laboratories to examine protein structure and protein-protein interactions. Unfortunately, conventional NS protocols often generate structural artifacts on proteins, especially with lipoproteins that usually form presenting rouleaux artifacts. By using images of lipoproteins from cryo-electronmore » microscopy (cryo-EM) as a standard, the key parameters in NS specimen preparation conditions were recently screened and reported as the optimized NS protocol (OpNS), a modified conventional NS protocol. Artifacts like rouleaux can be greatly limited by OpNS, additionally providing high contrast along with reasonably high-resolution (near 1 nm) images of small and asymmetric proteins. These high-resolution and high contrast images are even favorable for an individual protein (a single object, no average) 3D reconstruction, such as a 160 kDa antibody, through the method of electron tomography. Moreover, OpNS can be a high-throughput tool to examine hundreds of samples of small proteins. For example, the previously published mechanism of 53 kDa cholesteryl ester transfer protein (CETP) involved the screening and imaging of hundreds of samples. Considering cryo-EM rarely successfully images proteins less than 200 kDa has yet to publish any study involving screening over one hundred sample conditions, it is fair to call OpNS a high-throughput method for studying small proteins. Hopefully the OpNS protocol presented here can be a useful tool to push the boundaries of EM and accelerate EM studies into small protein structure, dynamics and mechanisms.« less

3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling

PubMed Central

Segura, Joan; Sanchez-Garcia, Ruben; Tabas-Madrid, Daniel; Cuenca-Alba, Jesus; Sorzano, Carlos Oscar S.; Carazo, Jose Maria

2016-01-01

Electron microscopy (EM) is experiencing a revolution with the advent of a new generation of Direct Electron Detectors, enabling a broad range of large and flexible structures to be resolved well below 1 nm resolution. Although EM techniques are evolving to the point of directly obtaining structural data at near-atomic resolution, for many molecules the attainable resolution might not be enough to propose high-resolution structural models. However, accessing information on atomic coordinates is a necessary step toward a deeper understanding of the molecular mechanisms that allow proteins to perform specific tasks. For that reason, methods for the integration of EM three-dimensional maps with x-ray and NMR structural data are being developed, a modeling task that is normally referred to as fitting, resulting in the so called hybrid models. In this work, we present a novel application—3DIANA—specially targeted to those cases in which the EM map resolution is medium or low and additional experimental structural information is scarce or even lacking. In this way, 3DIANA statistically evaluates proposed/potential contacts between protein domains, presents a complete catalog of both structurally resolved and predicted interacting regions involving these domains and, finally, suggests structural templates to model the interaction between them. The evaluation of the proposed interactions is computed with DIMERO, a new method that scores physical binding sites based on the topology of protein interaction networks, which has recently shown the capability to increase by 200% the number of domain-domain interactions predicted in interactomes as compared to previous approaches. The new application displays the information at a sequence and structural level and is accessible through a web browser or as a Chimera plugin at http://3diana.cnb.csic.es. PMID:26772592

Inflatable Antenna Microwave Radiometer for Soil Moisture Measurement

NASA Technical Reports Server (NTRS)

Bailey, M. C.; Kendall, Bruce M.; Schroeder, Lyle C.; Harrington, Richard F.

1993-01-01

Microwave measurements of soil moisture are not being obtained at the required spatial Earth resolution with current technology. Recently, new novel designs for lightweight reflector systems have been developed using deployable inflatable antenna structures which could enable lightweight real-aperture radiometers. In consideration of this, a study was conducted at the NASA Langley Research Center (LaRC) to determine the feasibility of developing a microwave radiometer system using inflatable reflector antenna technology to obtain high spatial resolution radiometric measurements of soil moisture from low Earth orbit and which could be used with a small and cost effective launch vehicle. The required high resolution with reasonable swath width coupled with the L-band measurement frequency for soil moisture dictated the use of a large (30 meter class) real aperture antenna in conjunction with a pushbroom antenna beam configuration and noise-injection type radiometer designs at 1.4 and 4.3 GHz to produce a 370 kilometer cross-track swath with a 10 kilometer resolution that could be packaged for launch with a Titan 2 class vehicle. This study includes design of the inflatable structure, control analysis, structural and thermal analysis, antenna and feed design, radiometer design, payload packaging, orbital analysis, and electromagnetic losses in the thin membrane inflatable materials.

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

Li, Fuyu; Collins, William D.; Wehner, Michael F.

High-resolution climate models have been shown to improve the statistics of tropical storms and hurricanes compared to low-resolution models. The impact of increasing horizontal resolution in the tropical storm simulation is investigated exclusively using a series of Atmospheric Global Climate Model (AGCM) runs with idealized aquaplanet steady-state boundary conditions and a fixed operational storm-tracking algorithm. The results show that increasing horizontal resolution helps to detect more hurricanes, simulate stronger extreme rainfall, and emulate better storm structures in the models. However, increasing model resolution does not necessarily produce stronger hurricanes in terms of maximum wind speed, minimum sea level pressure, andmore » mean precipitation, as the increased number of storms simulated by high-resolution models is mainly associated with weaker storms. The spatial scale at which the analyses are conducted appears to have more important control on these meteorological statistics compared to horizontal resolution of the model grid. When the simulations are analyzed on common low-resolution grids, the statistics of the hurricanes, particularly the hurricane counts, show reduced sensitivity to the horizontal grid resolution and signs of scale invariant.« less

Information Extraction of High Resolution Remote Sensing Images Based on the Calculation of Optimal Segmentation Parameters

PubMed Central

Zhu, Hongchun; Cai, Lijie; Liu, Haiying; Huang, Wei

2016-01-01

Multi-scale image segmentation and the selection of optimal segmentation parameters are the key processes in the object-oriented information extraction of high-resolution remote sensing images. The accuracy of remote sensing special subject information depends on this extraction. On the basis of WorldView-2 high-resolution data, the optimal segmentation parameters methodof object-oriented image segmentation and high-resolution image information extraction, the following processes were conducted in this study. Firstly, the best combination of the bands and weights was determined for the information extraction of high-resolution remote sensing image. An improved weighted mean-variance method was proposed andused to calculatethe optimal segmentation scale. Thereafter, the best shape factor parameter and compact factor parameters were computed with the use of the control variables and the combination of the heterogeneity and homogeneity indexes. Different types of image segmentation parameters were obtained according to the surface features. The high-resolution remote sensing images were multi-scale segmented with the optimal segmentation parameters. Ahierarchical network structure was established by setting the information extraction rules to achieve object-oriented information extraction. This study presents an effective and practical method that can explain expert input judgment by reproducible quantitative measurements. Furthermore the results of this procedure may be incorporated into a classification scheme. PMID:27362762

Information Extraction of High Resolution Remote Sensing Images Based on the Calculation of Optimal Segmentation Parameters.

PubMed

Zhu, Hongchun; Cai, Lijie; Liu, Haiying; Huang, Wei

2016-01-01

Multi-scale image segmentation and the selection of optimal segmentation parameters are the key processes in the object-oriented information extraction of high-resolution remote sensing images. The accuracy of remote sensing special subject information depends on this extraction. On the basis of WorldView-2 high-resolution data, the optimal segmentation parameters methodof object-oriented image segmentation and high-resolution image information extraction, the following processes were conducted in this study. Firstly, the best combination of the bands and weights was determined for the information extraction of high-resolution remote sensing image. An improved weighted mean-variance method was proposed andused to calculatethe optimal segmentation scale. Thereafter, the best shape factor parameter and compact factor parameters were computed with the use of the control variables and the combination of the heterogeneity and homogeneity indexes. Different types of image segmentation parameters were obtained according to the surface features. The high-resolution remote sensing images were multi-scale segmented with the optimal segmentation parameters. Ahierarchical network structure was established by setting the information extraction rules to achieve object-oriented information extraction. This study presents an effective and practical method that can explain expert input judgment by reproducible quantitative measurements. Furthermore the results of this procedure may be incorporated into a classification scheme.

Unexpected materials in a Rembrandt painting characterized by high spatial resolution cluster-TOF-SIMS imaging.

PubMed

Sanyova, Jana; Cersoy, Sophie; Richardin, Pascale; Laprévote, Olivier; Walter, Philippe; Brunelle, Alain

2011-02-01

The painting materials of the Portrait of Nicolaes van Bambeeck (Royal Museums of Fine Arts of Belgium, Brussels, inv. 155) painted by Rembrandt van Rijn in 1641 has been studied using high resolution cluster-TOF-SIMS imaging. In the first step, a moderate spatial resolution (2 μm) was used to characterize the layer structure and the chemical composition of each layer on account of a high mass resolution. Then, in the second step, and despite a low mass resolution, the cluster primary ion beam was focused well below 1 μm in order to reveal smaller structures in the painting sample. The study confirmed the presence of starch in the second ground layer, which is quite surprising and, at least for Rembrandt paintings, has never been reported before. TOF-SIMS also indicated the presence of proteins, which, added to the size and shape of lake particles, suggests that it was manufactured from shearings (waste of textile manufacturing) of dyed wool, used as the source of the dyestuff. The analyses have also shown various lead carboxylates, being the products of the interaction between lead white and the oil of the binding medium. These findings considerably contribute to the understanding of Rembrandt's studio practice and thus demonstrate the importance and potential of cluster-TOF-SIMS imaging in the characterization on a submicrometer scale of artist painting materials.

Structure of High Latitude Currents in Magnetosphere-Ionosphere Models

NASA Astrophysics Data System (ADS)

Wiltberger, M.; Rigler, E. J.; Merkin, V.; Lyon, J. G.

2017-03-01

Using three resolutions of the Lyon-Fedder-Mobarry global magnetosphere-ionosphere model (LFM) and the Weimer 2005 empirical model we examine the structure of the high latitude field-aligned current patterns. Each resolution was run for the entire Whole Heliosphere Interval which contained two high speed solar wind streams and modest interplanetary magnetic field strengths. Average states of the field-aligned current (FAC) patterns for 8 interplanetary magnetic field clock angle directions are computed using data from these runs. Generally speaking the patterns obtained agree well with results obtained from the Weimer 2005 computing using the solar wind and IMF conditions that correspond to each bin. As the simulation resolution increases the currents become more intense and narrow. A machine learning analysis of the FAC patterns shows that the ratio of Region 1 (R1) to Region 2 (R2) currents decreases as the simulation resolution increases. This brings the simulation results into better agreement with observational predictions and the Weimer 2005 model results. The increase in R2 current strengths also results in the cross polar cap potential (CPCP) pattern being concentrated in higher latitudes. Current-voltage relationships between the R1 and CPCP are quite similar at the higher resolution indicating the simulation is converging on a common solution. We conclude that LFM simulations are capable of reproducing the statistical features of FAC patterns.

Structure of high latitude currents in global magnetospheric-ionospheric models

USGS Publications Warehouse

Wiltberger, M; Rigler, E. J.; Merkin, V; Lyon, J. G

2016-01-01

Using three resolutions of the Lyon-Fedder-Mobarry global magnetosphere-ionosphere model (LFM) and the Weimer 2005 empirical model we examine the structure of the high latitude field-aligned current patterns. Each resolution was run for the entire Whole Heliosphere Interval which contained two high speed solar wind streams and modest interplanetary magnetic field strengths. Average states of the field-aligned current (FAC) patterns for 8 interplanetary magnetic field clock angle directions are computed using data from these runs. Generally speaking the patterns obtained agree well with results obtained from the Weimer 2005 computing using the solar wind and IMF conditions that correspond to each bin. As the simulation resolution increases the currents become more intense and narrow. A machine learning analysis of the FAC patterns shows that the ratio of Region 1 (R1) to Region 2 (R2) currents decreases as the simulation resolution increases. This brings the simulation results into better agreement with observational predictions and the Weimer 2005 model results. The increase in R2 current strengths also results in the cross polar cap potential (CPCP) pattern being concentrated in higher latitudes. Current-voltage relationships between the R1 and CPCP are quite similar at the higher resolution indicating the simulation is converging on a common solution. We conclude that LFM simulations are capable of reproducing the statistical features of FAC patterns.

Taking structure searches to the next dimension.

PubMed

Schafferhans, Andrea; Rost, Burkhard

2014-07-08

Structure comparisons are now the first step when a new experimental high-resolution protein structure has been determined. In this issue of Structure, Wiederstein and colleagues describe their latest tool for comparing structures, which gives us the unprecedented power to discover crucial structural connections between whole complexes of proteins in the full structural database in real time. Copyright © 2014 Elsevier Ltd. All rights reserved.

An edge-directed interpolation method for fetal spine MR images.

PubMed

Yu, Shaode; Zhang, Rui; Wu, Shibin; Hu, Jiani; Xie, Yaoqin

2013-10-10

Fetal spinal magnetic resonance imaging (MRI) is a prenatal routine for proper assessment of fetus development, especially when suspected spinal malformations occur while ultrasound fails to provide details. Limited by hardware, fetal spine MR images suffer from its low resolution.High-resolution MR images can directly enhance readability and improve diagnosis accuracy. Image interpolation for higher resolution is required in clinical situations, while many methods fail to preserve edge structures. Edge carries heavy structural messages of objects in visual scenes for doctors to detect suspicions, classify malformations and make correct diagnosis. Effective interpolation with well-preserved edge structures is still challenging. In this paper, we propose an edge-directed interpolation (EDI) method and apply it on a group of fetal spine MR images to evaluate its feasibility and performance. This method takes edge messages from Canny edge detector to guide further pixel modification. First, low-resolution (LR) images of fetal spine are interpolated into high-resolution (HR) images with targeted factor by bi-linear method. Then edge information from LR and HR images is put into a twofold strategy to sharpen or soften edge structures. Finally a HR image with well-preserved edge structures is generated. The HR images obtained from proposed method are validated and compared with that from other four EDI methods. Performances are evaluated from six metrics, and subjective analysis of visual quality is based on regions of interest (ROI). All these five EDI methods are able to generate HR images with enriched details. From quantitative analysis of six metrics, the proposed method outperforms the other four from signal-to-noise ratio (SNR), peak signal-to-noise ratio (PSNR), structure similarity index (SSIM), feature similarity index (FSIM) and mutual information (MI) with seconds-level time consumptions (TC). Visual analysis of ROI shows that the proposed method maintains better consistency in edge structures with the original images. The proposed method classifies edge orientations into four categories and well preserves structures. It generates convincing HR images with fine details and is suitable in real-time situations. Iterative curvature-based interpolation (ICBI) method may result in crisper edges, while the other three methods are sensitive to noise and artifacts.

DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein

PubMed Central

Duan, Ming-Rui; Nan, Jie; Liang, Yu-He; Mao, Peng; Lu, Lu; Li, Lanfen; Wei, Chunhong; Lai, Luhua; Li, Yi; Su, Xiao-Dong

2007-01-01

WRKY proteins, defined by the conserved WRKYGQK sequence, are comprised of a large superfamily of transcription factors identified specifically from the plant kingdom. This superfamily plays important roles in plant disease resistance, abiotic stress, senescence as well as in some developmental processes. In this study, the Arabidopsis WRKY1 was shown to be involved in the salicylic acid signaling pathway and partially dependent on NPR1; a C-terminal domain of WRKY1, AtWRKY1-C, was constructed for structural studies. Previous investigations showed that DNA binding of the WRKY proteins was localized at the WRKY domains and these domains may define novel zinc-binding motifs. The crystal structure of the AtWRKY1-C determined at 1.6 Å resolution has revealed that this domain is composed of a globular structure with five β strands, forming an antiparallel β-sheet. A novel zinc-binding site is situated at one end of the β-sheet, between strands β4 and β5. Based on this high-resolution crystal structure and site-directed mutagenesis, we have defined and confirmed that the DNA-binding residues of AtWRKY1-C are located at β2 and β3 strands. These results provided us with structural information to understand the mechanism of transcriptional control and signal transduction events of the WRKY proteins. PMID:17264121

Study of irradiated Hadfield steel using transmission Mössbauer spectroscopy with high velocity resolution and conversion electron Mössbauer spectroscopy

NASA Astrophysics Data System (ADS)

Semionkin, V. A.; Neshev, F. G.; Tsurin, V. A.; Milder, O. B.; Oshtrakh, M. I.

2010-03-01

Proton irradiated Hadfield steel foil was studied using transmission Mössbauer spectroscopy with high velocity resolution and conversion electron Mössbauer spectroscopy. It was shown that proton irradiation leads to structural changes in the foil as well as to surface oxidation with ferric hydrous oxide formation (ferrihydrite). Moreover, oxidation on the foil underside was higher than on the foil right side.

Crossed Ga2O3/SnO2 multiwire architecture: a local structure study with nanometer resolution.

PubMed

Martínez-Criado, Gema; Segura-Ruiz, Jaime; Chu, Manh-Hung; Tucoulou, Remi; López, Iñaki; Nogales, Emilio; Mendez, Bianchi; Piqueras, Javier

2014-10-08

Crossed nanowire structures are the basis for high-density integration of a variety of nanodevices. Owing to the critical role of nanowires intersections in creating hybrid architectures, it has become a challenge to investigate the local structure in crossing points in metal oxide nanowires. Thus, if intentionally grown crossed nanowires are well-patterned, an ideal model to study the junction is formed. By combining electron and synchrotron beam nanoprobes, we show here experimental evidence of the role of impurities in the coupling formation, structural modifications, and atomic site configuration based on crossed Ga2O3/SnO2 nanowires. Our experiment opens new avenues for further local structure studies with both nanometer resolution and elemental sensitivity.

Hyperspectral classification of grassland species: towards a UAS application for semi-automatic field surveys

NASA Astrophysics Data System (ADS)

Lopatin, Javier; Fassnacht, Fabian E.; Kattenborn, Teja; Schmidtlein, Sebastian

2017-04-01

Grasslands are one of the ecosystems that have been strongly intervened during the past decades due to anthropogenic impacts, affecting their structural and functional composition. To monitor the spatial and/or temporal changes of these environments, a reliable field survey is first needed. As quality relevés are usually expensive and time consuming, the amount of information available is usually poor or not well spatially distributed at the regional scale. In the present study, we investigate the possibility of a semi-automated method used for repeated surveys of monitoring sites. We analyze the applicability of very high spatial resolution hyperspectral data to classify grassland species at the level of individuals. The AISA+ imaging spectrometer mounted on a scaffold was applied to scan 1 m2 grassland plots and assess the impact of four sources of variation on the predicted species cover: (1) the spatial resolution of the scans, (2) the species number and structural diversity, (3) the species cover, and (4) the species functional types (bryophytes, forbs and graminoids). We found that the spatial resolution and the diversity level (mainly structural diversity) were the most important source of variation for the proposed approach. A spatial resolution below 1 cm produced relatively high model performances, while predictions with pixel sizes over that threshold produced non adequate results. Areas with low interspecies overlap reached classification median values of 0.8 (kappa). On the contrary, results were not satisfactory in plots with frequent interspecies overlap in multiple layers. By means of a bootstrapping procedure, we found that areas with shadows and mixed pixels introduce uncertainties into the classification. We conclude that the application of very high resolution hyperspectral remote sensing as a robust alternative or supplement to field surveys is possible for environments with low structural heterogeneity. This study presents the first try of a full classification of grassland species at the individuum level using spectral data.

Light-sheet enhanced resolution of light field microscopy for rapid imaging of large volumes

NASA Astrophysics Data System (ADS)

Madrid Wolff, Jorge; Castro, Diego; Arbeláez, Pablo; Forero-Shelton, Manu

2018-02-01

Whole-brain imaging is challenging because it demands microscopes with high temporal and spatial resolution, which are often at odds, especially in the context of large fields of view. We have designed and built a light-sheet microscope with digital micromirror illumination and light-field detection. On the one hand, light sheets provide high resolution optical sectioning on live samples without compromising their viability. On the other hand, light field imaging makes it possible to reconstruct full volumes of relatively large fields of view from a single camera exposure; however, its enhanced temporal resolution comes at the expense of spatial resolution, limiting its applicability. We present an approach to increase the resolution of light field images using DMD-based light sheet illumination. To that end, we develop a method to produce synthetic resolution targets for light field microscopy and a procedure to correct the depth at which planes are refocused with rendering software. We measured the axial resolution as a function of depth and show a three-fold potential improvement with structured illumination, albeit by sacrificing some temporal resolution, also three-fold. This results in an imaging system that may be adjusted to specific needs without having to reassemble and realign it. This approach could be used to image relatively large samples at high rates.

Isotropic image in structured illumination microscopy patterned with a spatial light modulator.

PubMed

Chang, Bo-Jui; Chou, Li-Jun; Chang, Yun-Ching; Chiang, Su-Yu

2009-08-17

We developed a structured illumination microscopy (SIM) system that uses a spatial light modulator (SLM) to generate interference illumination patterns at four orientations - 0 degrees, 45 degrees, 90 degrees, and 135 degrees, to reconstruct a high-resolution image. The use of a SLM for pattern alterations is rapid and precise, without mechanical calibration; moreover, our design of SLM patterns allows generating the four illumination patterns of high contrast and nearly equivalent periods to achieve a near isotropic enhancement in lateral resolution. We compare the conventional image of 100-nm beads with those reconstructed from two (0 degrees +90 degrees or 45 degrees +135 degrees) and four (0 degrees +45 degrees +90 degrees +135 degrees) pattern orientations to show the differences in resolution and image, with the support of simulations. The reconstructed images of 200-nm beads at various depths and fine structures of actin filaments near the edge of a HeLa cell are presented to demonstrate the intensity distributions in the axial direction and the prospective application to biological systems. (c) 2009 Optical Society of America

Multiple capsid-stabilizing interactions revealed in a high-resolution structure of an emerging picornavirus causing neonatal sepsis

NASA Astrophysics Data System (ADS)

Shakeel, Shabih; Westerhuis, Brenda M.; Domanska, Ausra; Koning, Roman I.; Matadeen, Rishi; Koster, Abraham J.; Bakker, Arjen Q.; Beaumont, Tim; Wolthers, Katja C.; Butcher, Sarah J.

2016-07-01

The poorly studied picornavirus, human parechovirus 3 (HPeV3) causes neonatal sepsis with no therapies available. Our 4.3-Å resolution structure of HPeV3 on its own and at 15 Å resolution in complex with human monoclonal antibody Fabs demonstrates the expected picornavirus capsid structure with three distinct features. First, 25% of the HPeV3 RNA genome in 60 sites is highly ordered as confirmed by asymmetric reconstruction, and interacts with conserved regions of the capsid proteins VP1 and VP3. Second, the VP0 N terminus stabilizes the capsid inner surface, in contrast to other picornaviruses where on expulsion as VP4, it forms an RNA translocation channel. Last, VP1's hydrophobic pocket, the binding site for the antipicornaviral drug, pleconaril, is blocked and thus inappropriate for antiviral development. Together, these results suggest a direction for development of neutralizing antibodies, antiviral drugs based on targeting the RNA-protein interactions and dissection of virus assembly on the basis of RNA nucleation.

High resolution measurements of nightside ion troughs at Venus - Evidence of electrodynamic perturbations

NASA Technical Reports Server (NTRS)

Taylor, H. A., Jr.; Grebowsky, J. M.; Mayr, H. G.; Niemann, H. B.; Brace, L. H.; Cloutier, P. A.; Daniell, R. E., Jr.; Coulson, J. T.

1982-01-01

The Bennett rf ion mass spectrometer of the Pioneer Venus Orbiter was expressly designed to provide variable temporal resolution for measurements of thermal ion composition and density. The Explore-Adapt mode is used to obtain priority for measuring the most prominent ion species; in the 2/16 configuration, the two dominant ions within the available range of 16 species are selectively sampled at the highest rate of 0.2 sec/sample. The high-resolution measurements are combined with independent observations from the magnetic field, neutral mass spectrometer, and electron temperature experiments in investigating sharply structured troughs in the low-altitude nightside ion concentrations. The results suggest a close correlation between the structure in the ion distributions and the structured configuration of the magnetic field that is draped about the planet. In the regions of the ion depletions, sharp fluctuations in electron temperature and anomalous increases in the density of neutral gases suggest that the ion depletion may be associated with dynamic perturbation in the ion and neutral flows and/or local joule heating.

Bendable X-ray Optics for High Resolution Imaging

NASA Technical Reports Server (NTRS)

Gubarev, M.; Ramsey, B.; Kilaru, K.; Atkins, C.; Broadway, D.

2014-01-01

Current state-of the-art for x-ray optics fabrication calls for either the polishing of massive substrates into high-angular-resolution mirrors or the replication of thin, lower-resolution, mirrors from perfectly figured mandrels. Future X-ray Missions will require a change in this optics fabrication paradigm in order to achieve sub-arcsecond resolution in light-weight optics. One possible approach to this is to start with perfectly flat, light-weight surface, bend it into a perfect cone, form the desired mirror figure by material deposition, and insert the resulting mirror into a telescope structure. Such an approach is currently being investigated at MSFC, and a status report will be presented detailing the results of finite element analyses, bending tests and differential deposition experiments.

Imaging and reconstruction of cell cortex structures near the cell surface

NASA Astrophysics Data System (ADS)

Jin, Luhong; Zhou, Xiaoxu; Xiu, Peng; Luo, Wei; Huang, Yujia; Yu, Feng; Kuang, Cuifang; Sun, Yonghong; Liu, Xu; Xu, Yingke

2017-11-01

Total internal reflection fluorescence microscopy (TIRFM) provides high optical sectioning capability and superb signal-to-noise ratio for imaging of cell cortex structures. The development of multi-angle (MA)-TIRFM permits high axial resolution imaging and reconstruction of cellular structures near the cell surface. Cytoskeleton is composed of a network of filaments, which are important for maintenance of cell function. The high-resolution imaging and quantitative analysis of filament organization would contribute to our understanding of cytoskeleton regulation in cell. Here, we used a custom-developed MA-TIRFM setup, together with stochastic photobleaching and single molecule localization method, to enhance the lateral resolution of TIRFM imaging to about 100 nm. In addition, we proposed novel methods to perform filament segmentation and 3D reconstruction from MA-TIRFM images. Furthermore, we applied these methods to study the 3D localization of cortical actin and microtubule structures in U373 cancer cells. Our results showed that cortical actins localize ∼ 27 nm closer to the plasma membrane when compared with microtubules. We found that treatment of cells with chemotherapy drugs nocodazole and cytochalasin B disassembles cytoskeletal network and induces the reorganization of filaments towards the cell periphery. In summary, this study provides feasible approaches for 3D imaging and analyzing cell surface distribution of cytoskeletal network. Our established microscopy platform and image analysis toolkits would facilitate the study of cytoskeletal network in cells.

Three-dimensional high-resolution second-harmonic generation imaging of endogenous structural proteins in biological tissues.

PubMed Central

Campagnola, Paul J; Millard, Andrew C; Terasaki, Mark; Hoppe, Pamela E; Malone, Christian J; Mohler, William A

2002-01-01

We find that several key endogenous protein structures give rise to intense second-harmonic generation (SHG)-nonabsorptive frequency doubling of an excitation laser line. Second-harmonic imaging microscopy (SHIM) on a laser-scanning system proves, therefore, to be a powerful and unique tool for high-resolution, high-contrast, three-dimensional studies of live cell and tissue architecture. Unlike fluorescence, SHG suffers no inherent photobleaching or toxicity and does not require exogenous labels. Unlike polarization microscopy, SHIM provides intrinsic confocality and deep sectioning in complex tissues. In this study, we demonstrate the clarity of SHIM optical sectioning within unfixed, unstained thick specimens. SHIM and two-photon excited fluorescence (TPEF) were combined in a dual-mode nonlinear microscopy to elucidate the molecular sources of SHG in live cells and tissues. SHG arose not only from coiled-coil complexes within connective tissues and muscle thick filaments, but also from microtubule arrays within interphase and mitotic cells. Both polarization dependence and a local symmetry cancellation effect of SHG allowed the signal from species generating the second harmonic to be decoded, by ratiometric correlation with TPEF, to yield information on local structure below optical resolution. The physical origin of SHG within these tissues is addressed and is attributed to the laser interaction with dipolar protein structures that is enhanced by the intrinsic chirality of the protein helices. PMID:11751336

Energy flux and characteristic energy of an elemental auroral structure

NASA Technical Reports Server (NTRS)

Lanchester, B. S.; Palmer, J. R.; Rees, M. H.; Lummerzheim, D.; Kaila, K.; Turunen, T.

1994-01-01

Electron density profiles acquired with the EISCAT radar at 0.2 s time resolution, together with TV images and photometric intensities, were used to study the characteristics of thin (less than 1 km) auroral arc structures that drifted through the field of view of the instruments. It is demonstrated that both high time and space resolution are essential for deriving the input parameters of the electron flux responsible for the elemental auroral structures. One such structure required a 400 mW/sq m (erg/sq cm s) downward energy flux carried by an 8 keV monochromatic electron flux equivalent to a current density of 50 micro Angstrom/sq m.

Localization microscopy of DNA in situ using Vybrant(®) DyeCycle™ Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution.

PubMed

Żurek-Biesiada, Dominika; Szczurek, Aleksander T; Prakash, Kirti; Mohana, Giriram K; Lee, Hyun-Keun; Roignant, Jean-Yves; Birk, Udo J; Dobrucki, Jurek W; Cremer, Christoph

2016-05-01

Higher order chromatin structure is not only required to compact and spatially arrange long chromatids within a nucleus, but have also important functional roles, including control of gene expression and DNA processing. However, studies of chromatin nanostructures cannot be performed using conventional widefield and confocal microscopy because of the limited optical resolution. Various methods of superresolution microscopy have been described to overcome this difficulty, like structured illumination and single molecule localization microscopy. We report here that the standard DNA dye Vybrant(®) DyeCycle™ Violet can be used to provide single molecule localization microscopy (SMLM) images of DNA in nuclei of fixed mammalian cells. This SMLM method enabled optical isolation and localization of large numbers of DNA-bound molecules, usually in excess of 10(6) signals in one cell nucleus. The technique yielded high-quality images of nuclear DNA density, revealing subdiffraction chromatin structures of the size in the order of 100nm; the interchromatin compartment was visualized at unprecedented optical resolution. The approach offers several advantages over previously described high resolution DNA imaging methods, including high specificity, an ability to record images using a single wavelength excitation, and a higher density of single molecule signals than reported in previous SMLM studies. The method is compatible with DNA/multicolor SMLM imaging which employs simple staining methods suited also for conventional optical microscopy. Copyright © 2016. Published by Elsevier Inc.

Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase

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

Bacik, John -Paul; Mekasha, Sophanit; Forsberg, Zarah

Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1–3 mm 3) of a chitin-processing LPMO from the Gram-positive soil bacterium Jonesia denitrificans were grown and screened for their ability to diffract neutrons. In addition to the collection of neutron diffraction data, which were processed to 2.1 Å resolution, a high-resolution room-temperature X-ray diffraction data set was collected andmore » processed to 1.1 Å resolution in space group P2 12 12 1. To our knowledge, this work marks the first successful neutron crystallographic experiment on an LPMO. As a result, joint X-ray/neutron refinement of the resulting data will reveal new details of the structure and mechanism of this recently discovered class of enzymes.« less

Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase

DOE PAGES

Bacik, John -Paul; Mekasha, Sophanit; Forsberg, Zarah; ...

2015-01-01

Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1–3 mm 3) of a chitin-processing LPMO from the Gram-positive soil bacterium Jonesia denitrificans were grown and screened for their ability to diffract neutrons. In addition to the collection of neutron diffraction data, which were processed to 2.1 Å resolution, a high-resolution room-temperature X-ray diffraction data set was collected andmore » processed to 1.1 Å resolution in space group P2 12 12 1. To our knowledge, this work marks the first successful neutron crystallographic experiment on an LPMO. As a result, joint X-ray/neutron refinement of the resulting data will reveal new details of the structure and mechanism of this recently discovered class of enzymes.« less

Simultaneous observations of structure function parameter of refractive index using a high-resolution radar and the DataHawk small airborne measurement system

NASA Astrophysics Data System (ADS)

Scipión, Danny E.; Lawrence, Dale A.; Milla, Marco A.; Woodman, Ronald F.; Lume, Diego A.; Balsley, Ben B.

2016-09-01

The SOUSY (SOUnding SYstem) radar was relocated to the Jicamarca Radio Observatory (JRO) near Lima, Peru, in 2000, where the radar controller and acquisition system were upgraded with state-of-the-art parts to take full advantage of its potential for high-resolution atmospheric sounding. Due to its broad bandwidth (4 MHz), it is able to characterize clear-air backscattering with high range resolution (37.5 m). A campaign conducted at JRO in July 2014 aimed to characterize the lower troposphere with a high temporal resolution (8.1 Hz) using the DataHawk (DH) small unmanned aircraft system, which provides in situ atmospheric measurements at scales as small as 1 m in the lower troposphere and can be GPS-guided to obtain measurements within the beam of the radar. This was a unique opportunity to make coincident observations by both systems and to directly compare their in situ and remotely sensed parameters. Because SOUSY only points vertically, it is only possible to retrieve vertical radar profiles caused by changes in the refractive index within the resolution volume. Turbulent variations due to scattering are described by the structure function parameter of refractive index Cn2. Profiles of Cn2 from the DH are obtained by combining pressure, temperature, and relative humidity measurements along the helical trajectory and integrated at the same scale as the radar range resolution. Excellent agreement is observed between the Cn2 estimates obtained from the DH and SOUSY in the overlapping measurement regime from 1200 m up to 4200 m above sea level, and this correspondence provides the first accurate calibration of the SOUSY radar for measuring Cn2.

Integrating histology and MRI in the first digital brain of common squirrel monkey, Saimiri sciureus

NASA Astrophysics Data System (ADS)

Sun, Peizhen; Parvathaneni, Prasanna; Schilling, Kurt G.; Gao, Yurui; Janve, Vaibhav; Anderson, Adam; Landman, Bennett A.

2015-03-01

This effort is a continuation of development of a digital brain atlas of the common squirrel monkey, Saimiri sciureus, a New World monkey with functional and microstructural organization of central nervous system similar to that of humans. Here, we present the integration of histology with multi-modal magnetic resonance imaging (MRI) atlas constructed from the brain of an adult female squirrel monkey. The central concept of this work is to use block face photography to establish an intermediate common space in coordinate system which preserves the high resolution in-plane resolution of histology while enabling 3-D correspondence with MRI. In vivo MRI acquisitions include high resolution T2 structural imaging (300 μm isotropic) and low resolution diffusion tensor imaging (600 um isotropic). Ex vivo MRI acquisitions include high resolution T2 structural imaging and high resolution diffusion tensor imaging (both 300 μm isotropic). Cortical regions were manually annotated on the co-registered volumes based on published histological sections in-plane. We describe mapping of histology and MRI based data of the common squirrel monkey and construction of a viewing tool that enable online viewing of these datasets. The previously descried atlas MRI is used for its deformation to provide accurate conformation to the MRI, thus adding information at the histological level to the MRI volume. This paper presents the mapping of single 2D image slice in block face as a proof of concept and this can be extended to map the atlas space in 3D coordinate system as part of the future work and can be loaded to an XNAT system for further use.

High-Speed and Scalable Whole-Brain Imaging in Rodents and Primates.

PubMed

Seiriki, Kaoru; Kasai, Atsushi; Hashimoto, Takeshi; Schulze, Wiebke; Niu, Misaki; Yamaguchi, Shun; Nakazawa, Takanobu; Inoue, Ken-Ichi; Uezono, Shiori; Takada, Masahiko; Naka, Yuichiro; Igarashi, Hisato; Tanuma, Masato; Waschek, James A; Ago, Yukio; Tanaka, Kenji F; Hayata-Takano, Atsuko; Nagayasu, Kazuki; Shintani, Norihito; Hashimoto, Ryota; Kunii, Yasuto; Hino, Mizuki; Matsumoto, Junya; Yabe, Hirooki; Nagai, Takeharu; Fujita, Katsumasa; Matsuda, Toshio; Takuma, Kazuhiro; Baba, Akemichi; Hashimoto, Hitoshi

2017-06-21

Subcellular resolution imaging of the whole brain and subsequent image analysis are prerequisites for understanding anatomical and functional brain networks. Here, we have developed a very high-speed serial-sectioning imaging system named FAST (block-face serial microscopy tomography), which acquires high-resolution images of a whole mouse brain in a speed range comparable to that of light-sheet fluorescence microscopy. FAST enables complete visualization of the brain at a resolution sufficient to resolve all cells and their subcellular structures. FAST renders unbiased quantitative group comparisons of normal and disease model brain cells for the whole brain at a high spatial resolution. Furthermore, FAST is highly scalable to non-human primate brains and human postmortem brain tissues, and can visualize neuronal projections in a whole adult marmoset brain. Thus, FAST provides new opportunities for global approaches that will allow for a better understanding of brain systems in multiple animal models and in human diseases. Copyright © 2017 Elsevier Inc. All rights reserved.

Propagation Diagnostic Simulations Using High-Resolution Equatorial Plasma Bubble Simulations

NASA Astrophysics Data System (ADS)

Rino, C. L.; Carrano, C. S.; Yokoyama, T.

2017-12-01

In a recent paper, under review, equatorial-plasma-bubble (EPB) simulations were used to conduct a comparative analysis of the EPB spectra characteristics with high-resolution in-situ measurements from the C/NOFS satellite. EPB realizations sampled in planes perpendicular to magnetic field lines provided well-defined EPB structure at altitudes penetrating both high and low-density regions. The average C/NOFS structure in highly disturbed regions showed nearly identical two-component inverse-power-law spectral characteristics as the measured EPB structure. This paper describes the results of PWE simulations using the same two-dimensional cross-field EPB realizations. New Irregularity Parameter Estimation (IPE) diagnostics, which are based on two-dimensional equivalent-phase-screen theory [A theory of scintillation for two-component power law irregularity spectra: Overview and numerical results, by Charles Carrano and Charles Rino, DOI: 10.1002/2015RS005903], have been successfully applied to extract two-component inverse-power-law parameters from measured intensity spectra. The EPB simulations [Low and Midlatitude Ionospheric Plasma DensityIrregularities and Their Effects on Geomagnetic Field, by Tatsuhiro Yokoyama and Claudia Stolle, DOI 10.1007/s11214-016-0295-7] have sufficient resolution to populate the structure scales (tens of km to hundreds of meters) that cause strong scintillation at GPS frequencies. The simulations provide an ideal geometry whereby the ramifications of varying structure along the propagation path can be investigated. It is well known path-integrated one-dimensional spectra increase the one-dimensional index by one. The relation requires decorrelation along the propagation path. Correlated structure would be interpreted as stochastic total-electron-content (TEC). The simulations are performed with unmodified structure. Because the EPB structure is confined to the central region of the sample planes, edge effects are minimized. Consequently, the propagated signal phase can be comparted to path-integrated phase for evaluating TEC extraction. Only the frequency dependence of phase scintillation distinguishes phase scintillation. The simulations allow scale-dependent exploration of remote-sensing diagnostics.

High spatial resolution imaging for structural health monitoring based on virtual time reversal

NASA Astrophysics Data System (ADS)

Cai, Jian; Shi, Lihua; Yuan, Shenfang; Shao, Zhixue

2011-05-01

Lamb waves are widely used in structural health monitoring (SHM) of plate-like structures. Due to the dispersion effect, Lamb wavepackets will be elongated and the resolution for damage identification will be strongly affected. This effect can be automatically compensated by the time reversal process (TRP). However, the time information of the compensated waves is also removed at the same time. To improve the spatial resolution of Lamb wave detection, virtual time reversal (VTR) is presented in this paper. In VTR, a changing-element excitation and reception mechanism (CERM) rather than the traditional fixed excitation and reception mechanism (FERM) is adopted for time information conservation. Furthermore, the complicated TRP procedure is replaced by simple signal operations which can make savings in the hardware cost for recording and generating the time-reversed Lamb waves. After the effects of VTR for dispersive damage scattered signals are theoretically analyzed, the realization of VTR involving the acquisition of the transfer functions of damage detecting paths under step pulse excitation is discussed. Then, a VTR-based imaging method is developed to improve the spatial resolution of the delay-and-sum imaging with a sparse piezoelectric (PZT) wafer array. Experimental validation indicates that the damage scattered wavepackets of A0 mode in an aluminum plate are partly recompressed and focalized with their time information preserved by VTR. Both the single damage and the dual adjacent damages in the plate can be clearly displayed with high spatial resolution by the proposed VTR-based imaging method.

Water molecules in the antibody-antigen interface of the structure of the Fab HyHEL-5-lysozyme complex at 1.7 A resolution: comparison with results from isothermal titration calorimetry.

PubMed

Cohen, Gerson H; Silverton, Enid W; Padlan, Eduardo A; Dyda, Fred; Wibbenmeyer, Jamie A; Willson, Richard C; Davies, David R

2005-05-01

The structure of the complex between hen egg-white lysozyme and the Fab HyHEL-5 at 2.7 A resolution has previously been reported [Cohen et al. (1996), Acta Cryst. D52, 315-326]. With the availability of recombinant Fab, the X-ray structure of the complex has been re-evaluated at 1.7 A resolution. The refined structure has yielded a detailed picture of the Fab-lysozyme interface, showing the high complementarity of the protein surfaces as well as several water molecules within the interface that complete the good fit. The model of the full complex has improved significantly, yielding an R(work) of 19.5%. With this model, the structural results can be compared with the results of isothermal titration calorimetry. An attempt has been made to estimate the changes in bound waters that accompany complex formation and the difficulties inherent in using the crystal structures to provide the information necessary to make this calculation are discussed.

Are X-rays the key to integrated computational materials engineering?

DOE PAGES

Ice, Gene E.

2015-11-01

The ultimate dream of materials science is to predict materials behavior from composition and processing history. Owing to the growing power of computers, this long-time dream has recently found expression through worldwide excitement in a number of computation-based thrusts: integrated computational materials engineering, materials by design, computational materials design, three-dimensional materials physics and mesoscale physics. However, real materials have important crystallographic structures at multiple length scales, which evolve during processing and in service. Moreover, real materials properties can depend on the extreme tails in their structural and chemical distributions. This makes it critical to map structural distributions with sufficient resolutionmore » to resolve small structures and with sufficient statistics to capture the tails of distributions. For two-dimensional materials, there are high-resolution nondestructive probes of surface and near-surface structures with atomic or near-atomic resolution that can provide detailed structural, chemical and functional distributions over important length scales. Furthermore, there are no nondestructive three-dimensional probes with atomic resolution over the multiple length scales needed to understand most materials.« less

Visualizing impact structures using high-resolution LiDAR-derived DEMs: A case study of two structures in Missouri

USGS Publications Warehouse

Finn, Michael P.; Krizanich, Gary W.; Evans, Kevin R.; Cox, Melissa R.; Yamamoto, Kristina H.

2015-01-01

Evidence suggests that a crypto-explosive hypothesis and a meteorite impact hypothesis may be partly correct in explaining several anomalous geological features in the middle of the United States. We used a primary geographic information science (GIScience) technique of creating a digital elevation model (DEM) of two of these features that occur in Missouri. The DEMs were derived from airborne light detection and ranging, or LiDAR. Using these DEMs, we characterized the Crooked Creek structure in southern Crawford County and the Weaubleau structure in southeastern St. Clair County, Missouri. The mensuration and study of exposed and buried impact craters implies that the craters may have intrinsic dimensions which could only be produced by collision. The results show elevations varying between 276 and 348 m for Crooked Creek and between 220 and 290 m for Weaubleau structure. These new high- resolution DEMs are accurate enough to allow for precise measurements and better interpretations of geological structures, particularly jointing in the carbonate rocks, and they show greater definition of the central uplift area in the Weaubleau structure than publicly available DEMs.

A Consensus Model of Human Apolipoprotein A-I in its Monomeric and Lipid-free State

PubMed Central

Melchior, John T.; Walker, Ryan G.; Cooke, Allison L.; Morris, Jamie; Castleberry, Mark; Thompson, Thomas B.; Jones, Martin K.; Song, Hyun D.; Rye, Kerry-Anne; Oda, Mike N.; Sorci-Thomas, Mary G.; Thomas, Michael J.; Heinecke, Jay W.; Mei, Xiaohu; Atkinson, David; Segrest, Jere P.; Lund-Katz, Sissel; Phillips, Michael C.; Davidson, W. Sean

2017-01-01

Apolipoprotein (apo)A-I is an organizing scaffold protein that is critical to high density lipoprotein (HDL) structure and metabolism, likely mediating many of its cardioprotective properties. However, HDL biogenesis is poorly understood as lipid-free apoA-I has been notoriously resistant to high resolution structural study. Published models from low resolution techniques share certain features but vary considerably in shape and secondary structure. To tackle this central issue in lipoprotein biology, we assembled an unprecedented team of lipoprotein structural biologists and set out to build a consensus model of monomeric lipid-free human apoA-I. Combining novel and published cross-link constraints, small angle X-ray scattering (SAXS), hydrogen-deuterium exchange (H-DX) and crystallography data, we propose a time averaged model consistent with much of the experimental data published over the last 40 years. The model provides a long sought platform for understanding and testing details of HDL biogenesis, structure and function. PMID:29131142

Classification of high resolution remote sensing image based on geo-ontology and conditional random fields

NASA Astrophysics Data System (ADS)

Hong, Liang

2013-10-01

The availability of high spatial resolution remote sensing data provides new opportunities for urban land-cover classification. More geometric details can be observed in the high resolution remote sensing image, Also Ground objects in the high resolution remote sensing image have displayed rich texture, structure, shape and hierarchical semantic characters. More landscape elements are represented by a small group of pixels. Recently years, the an object-based remote sensing analysis methodology is widely accepted and applied in high resolution remote sensing image processing. The classification method based on Geo-ontology and conditional random fields is presented in this paper. The proposed method is made up of four blocks: (1) the hierarchical ground objects semantic framework is constructed based on geoontology; (2) segmentation by mean-shift algorithm, which image objects are generated. And the mean-shift method is to get boundary preserved and spectrally homogeneous over-segmentation regions ;(3) the relations between the hierarchical ground objects semantic and over-segmentation regions are defined based on conditional random fields framework ;(4) the hierarchical classification results are obtained based on geo-ontology and conditional random fields. Finally, high-resolution remote sensed image data -GeoEye, is used to testify the performance of the presented method. And the experimental results have shown the superiority of this method to the eCognition method both on the effectively and accuracy, which implies it is suitable for the classification of high resolution remote sensing image.

Evaluation of the sparse coding super-resolution method for improving image quality of up-sampled images in computed tomography

NASA Astrophysics Data System (ADS)

Ota, Junko; Umehara, Kensuke; Ishimaru, Naoki; Ohno, Shunsuke; Okamoto, Kentaro; Suzuki, Takanori; Shirai, Naoki; Ishida, Takayuki

2017-02-01

As the capability of high-resolution displays grows, high-resolution images are often required in Computed Tomography (CT). However, acquiring high-resolution images takes a higher radiation dose and a longer scanning time. In this study, we applied the Sparse-coding-based Super-Resolution (ScSR) method to generate high-resolution images without increasing the radiation dose. We prepared the over-complete dictionary learned the mapping between low- and highresolution patches and seek a sparse representation of each patch of the low-resolution input. These coefficients were used to generate the high-resolution output. For evaluation, 44 CT cases were used as the test dataset. We up-sampled images up to 2 or 4 times and compared the image quality of the ScSR scheme and bilinear and bicubic interpolations, which are the traditional interpolation schemes. We also compared the image quality of three learning datasets. A total of 45 CT images, 91 non-medical images, and 93 chest radiographs were used for dictionary preparation respectively. The image quality was evaluated by measuring peak signal-to-noise ratio (PSNR) and structure similarity (SSIM). The differences of PSNRs and SSIMs between the ScSR method and interpolation methods were statistically significant. Visual assessment confirmed that the ScSR method generated a high-resolution image with sharpness, whereas conventional interpolation methods generated over-smoothed images. To compare three different training datasets, there were no significance between the CT, the CXR and non-medical datasets. These results suggest that the ScSR provides a robust approach for application of up-sampling CT images and yields substantial high image quality of extended images in CT.

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy.

PubMed

Chen, Shaoxia; McMullan, Greg; Faruqi, Abdul R; Murshudov, Garib N; Short, Judith M; Scheres, Sjors H W; Henderson, Richard

2013-12-01

Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3D map. Because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3D map, which can give a false impression of the resolution attained. The balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. There is a growing awareness in the cryoEM community of how to avoid such over-fitting and over-estimation of resolution. Equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. Here we describe a simple test that is compatible with any image processing protocol. The test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3D map. We have applied the method to two different sets of cryoEM images of the enzyme beta-galactosidase using several image processing packages. Our procedure involves substituting the Fourier components of the initial particle image stack beyond a chosen resolution by either the Fourier components from an adjacent area of background, or by simple randomisation of the phases of the particle structure factors. This substituted noise thus has the same spectral power distribution as the original data. Comparison of the Fourier Shell Correlation (FSC) plots from the 3D map obtained using the experimental data with that from the same data with high-resolution noise (HR-noise) substituted allows an unambiguous measurement of the amount of overfitting and an accompanying resolution assessment. A simple formula can be used to calculate an unbiased FSC from the two curves, even when a substantial amount of overfitting is present. The approach is software independent. The user is therefore completely free to use any established method or novel combination of methods, provided the HR-noise test is carried out in parallel. Applying this procedure to cryoEM images of beta-galactosidase shows how overfitting varies greatly depending on the procedure, but in the best case shows no overfitting and a resolution of ~6 Å. (382 words). © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

High resolution microtomography for density and spatial infomation about wood structures

Treesearch

Barbara Illman; Betsy Dowd

1999-01-01

Microtomography has successfully been used to characterize loss of structural integrity of wood. Tomographic images were generated with the newly developed third generation x-ray computed microtomography (XCMT) instrument at the X27A beamline at the national Synchrotron Light source (NSLS). The beamline is equipped with high-flux x-ray monochromator based on multilayer...

Alleviating tropical Atlantic sector biases in the Kiel climate model by enhancing horizontal and vertical atmosphere model resolution: climatology and interannual variability

NASA Astrophysics Data System (ADS)

Harlaß, Jan; Latif, Mojib; Park, Wonsun

2018-04-01

We investigate the quality of simulating tropical Atlantic (TA) sector climatology and interannual variability in integrations of the Kiel climate model (KCM) with varying atmosphere model resolution. The ocean model resolution is kept fixed. A reasonable simulation of TA sector annual-mean climate, seasonal cycle and interannual variability can only be achieved at sufficiently high horizontal and vertical atmospheric resolution. Two major reasons for the improvements are identified. First, the western equatorial Atlantic westerly surface wind bias in spring can be largely eliminated, which is explained by a better representation of meridional and especially vertical zonal momentum transport. The enhanced atmospheric circulation along the equator in turn greatly improves the thermal structure of the upper equatorial Atlantic with much reduced warm sea surface temperature (SST) biases. Second, the coastline in the southeastern TA and steep orography are better resolved at high resolution, which improves wind structure and in turn reduces warm SST biases in the Benguela upwelling region. The strongly diminished wind and SST biases at high atmosphere model resolution allow for a more realistic latitudinal position of the intertropical convergence zone. Resulting stronger cross-equatorial winds, in conjunction with a shallower thermocline, enable a rapid cold tongue development in the eastern TA in boreal spring. This enables simulation of realistic interannual SST variability and its seasonal phase locking in the KCM, which primarily is the result of a stronger thermocline feedback. Our findings suggest that enhanced atmospheric resolution, both vertical and horizontal, could be a key to achieving more realistic simulation of TA climatology and interannual variability in climate models.

Local X-ray Computed Tomography Imaging for Mineralogical and Pore Characterization

NASA Astrophysics Data System (ADS)

Mills, G.; Willson, C. S.

2015-12-01

Sample size, material properties and image resolution are all tradeoffs that must be considered when imaging porous media samples with X-ray computed tomography. In many natural and engineered samples, pore and throat sizes span several orders of magnitude and are often correlated with the material composition. Local tomography is a nondestructive technique that images a subvolume, within a larger specimen, at high resolution and uses low-resolution tomography data from the larger specimen to reduce reconstruction error. The high-resolution, subvolume data can be used to extract important fine-scale properties but, due to the additional noise associated with the truncated dataset, it makes segmentation of different materials and mineral phases a challenge. The low-resolution data of a larger specimen is typically of much higher-quality making material characterization much easier. In addition, the imaging of a larger domain, allows for mm-scale bulk properties and heterogeneities to be determined. In this research, a 7 mm diameter and ~15 mm in length sandstone core was scanned twice. The first scan was performed to cover the entire diameter and length of the specimen at an image voxel resolution of 4.1 μm. The second scan was performed on a subvolume, ~1.3 mm in length and ~2.1 mm in diameter, at an image voxel resolution of 1.08 μm. After image processing and segmentation, the pore network structure and mineralogical features were extracted from the low-resolution dataset. Due to the noise in the truncated high-resolution dataset, several image processing approaches were applied prior to image segmentation and extraction of the pore network structure and mineralogy. Results from the different truncated tomography segmented data sets are compared to each other to evaluate the potential of each approach in identifying the different solid phases from the original 16 bit data set. The truncated tomography segmented data sets were also compared to the whole-core tomography segmented data set in two ways: (1) assessment of the porosity and pore size distribution at different scales; and (2) comparison of the mineralogical composition and distribution. Finally, registration of the two datasets will be used to show how the pore structure and mineralogy details at the two scales can be used to supplement each other.

Multi-resolution voxel phantom modeling: a high-resolution eye model for computational dosimetry

NASA Astrophysics Data System (ADS)

Caracappa, Peter F.; Rhodes, Ashley; Fiedler, Derek

2014-09-01

Voxel models of the human body are commonly used for simulating radiation dose with a Monte Carlo radiation transport code. Due to memory limitations, the voxel resolution of these computational phantoms is typically too large to accurately represent the dimensions of small features such as the eye. Recently reduced recommended dose limits to the lens of the eye, which is a radiosensitive tissue with a significant concern for cataract formation, has lent increased importance to understanding the dose to this tissue. A high-resolution eye model is constructed using physiological data for the dimensions of radiosensitive tissues, and combined with an existing set of whole-body models to form a multi-resolution voxel phantom, which is used with the MCNPX code to calculate radiation dose from various exposure types. This phantom provides an accurate representation of the radiation transport through the structures of the eye. Two alternate methods of including a high-resolution eye model within an existing whole-body model are developed. The accuracy and performance of each method is compared against existing computational phantoms.

An Assessment of Stream Confluence Flow Dynamics using Large Scale Particle Image Velocimetry Captured from Unmanned Aerial Systems

NASA Astrophysics Data System (ADS)

Lewis, Q. W.; Rhoads, B. L.

2017-12-01

The merging of rivers at confluences results in complex three-dimensional flow patterns that influence sediment transport, bed morphology, downstream mixing, and physical habitat conditions. The capacity to characterize comprehensively flow at confluences using traditional sensors, such as acoustic Doppler velocimeters and profiles, is limited by the restricted spatial resolution of these sensors and difficulties in measuring velocities simultaneously at many locations within a confluence. This study assesses two-dimensional surficial patterns of flow structure at a small stream confluence in Illinois, USA, using large scale particle image velocimetry (LSPIV) derived from videos captured by unmanned aerial systems (UAS). The method captures surface velocity patterns at high spatial and temporal resolution over multiple scales, ranging from the entire confluence to details of flow within the confluence mixing interface. Flow patterns at high momentum ratio are compared to flow patterns when the two incoming flows have nearly equal momentum flux. Mean surface flow patterns during the two types of events provide details on mean patterns of surface flow in different hydrodynamic regions of the confluence and on changes in these patterns with changing momentum flux ratio. LSPIV data derived from the highest resolution imagery also reveal general characteristics of large-scale vortices that form along the shear layer between the flows during the high-momentum ratio event. The results indicate that the use of LSPIV and UAS is well-suited for capturing in detail mean surface patterns of flow at small confluences, but that characterization of evolving turbulent structures is limited by scale considerations related to structure size, image resolution, and camera instability. Complementary methods, including camera platforms mounted at fixed positions close to the water surface, provide opportunities to accurately characterize evolving turbulent flow structures in confluences.

Pure optical photoacoustic microscopy

PubMed Central

Xie, Zhixing; Chen, Sung-Liang; Ling, Tao; Guo, L. Jay; Carson, Paul L.; Wang, Xueding

2011-01-01

The concept of pure optical photoacoustic microscopy(POPAM) was proposed based on optical rastering of a focused excitation beam and optically sensing the photoacoustic signal using a microring resonator fabricated by a nanoimprinting technique. After the refinements of the microring’s working wavelength and in the resonator structure and mold fabrication, an ultrahigh Q factor of 3.0×105 was achieved which provided high sensitivity with a noise equivalent detectable pressure(NEDP) value of 29Pa. This NEDP is much lower than the hundreds of Pascals achieved with existing optical resonant structures such as etalons, fiber gratings and dielectric multilayer interference filters available for acoustic measurement. The featured high sensitivity allowed the microring resonator to detect the weak photoacoustic signals from micro- or submicroscale objects. The inherent superbroad bandwidth of the optical microring resonator combined with an optically focused scanning beam provided POPAM with high resolution in the axial as well as both lateral directions while the axial resolution of conventional photoacoustic microscopy (PAM) suffers from the limited bandwidth of PZT detectors. Furthermore, the broadband microring resonator showed similar sensitivity to that of our most sensitive PZT detector. The current POPAM system provides a lateral resolution of 5 μm and an axial resolution of 8 μm, comparable to that achieved by optical microscopy while presenting the unique contrast of optical absorption and functional information complementing other optical modalities. The 3D structure of microvasculature, including capillary networks, and even individual red blood cells have been discerned successfully in the proof-of-concept experiments on mouse bladders ex vivo and mouse ears in vivo. The potential of approximately GHz bandwidth of the microring resonator also might allow much higher resolution than shown here in microscopy of optical absorption and acoustic propagation properties at depths in unfrozen tissue specimens or thicker tissue sections, which is not now imageable with current optical or acoustic microscopes of comparable resolution. PMID:21643156

To the Application of LiDAR to Detect the Geological Structures in Sulphurets Property, British Columbia, Canada

NASA Astrophysics Data System (ADS)

Koohzare, A.; Rezaeian, M.; McIntosh, A.

2009-05-01

The Kerr Sulphurets property in North Western British Columbia has been explored primarily as a placer gold holding since the 1880s; and, potentially includes one of Canada's largest gold deposits (e.g. the Mitchell Zone). The Sulphurets camp has been classified by Taylor in 2007 as a prominent global epithermal high-sulphidation subtype with 10 million tonnes of ore (reserves + production) containing approximately 10 g/t gold. The geological and geophysical observations of this deposit indicate intrusion- related mineralized veins which are known to overlap as the result of structural complexities. Faulting predates mineralization and alteration and dramatically dominates the location of the mineralization for this porphyry- epithermal high-sulphidation deposit (Britton and Alldrick 1988, British Columbia Ministry of Energy, Mines and Petroleum Resources, 1992; Margolis, 1993). However, the surface trace of these structures and lineaments within the site is obscured by vegetation, glacial cover and steep topographic relief. We used high resolution LiDAR airborne bare-earth sensing (vegetative data deleted) in an effort to detect the surface geological features and lineaments in the Kerr Sulphurets site. The LiDAR flight was designed to acquire high density data with 2 points per square meter using a 150 kHz multipulse system. High resolution LiDAR data provides a level of detail not achievable by other digital terrain modelling techniques, whether extracted from aerial photography, low-resolution topographic contour maps, 10-30 meter USGS, or SRTM digital elevation models. LiDAR bare-earth data spectacularly revealed hidden geological structures within the property district, which in turn assisted in identifying the high potential zones for mineralization in Sulphurets.

Lunar apennine-hadley region: geological inplications of Earth-based radar and infrared measurements.

PubMed

Zisk, S H; Carr, M H; Masursky, H; Shorthill, R W; Thompson, T W

1971-08-27

Recently completed high-resolution radar maps of the moon contain information on the decimeter-scale structure of the surface. When this information is combined with eclipse thermal-enhancement data and with high-resolution Lunar Orbiter photography, the surface morphology is revealed in some detail. A geological history for certain features and subareas can be developed, which provides one possible framework for the interpretation of the findings from the Apollo 15 landing. Frequency of decimeter-and meter-size blocks in and around lunar craters, given by the remote-sensed data, supports a multilayer structure in the Palus Putredinis mare region, as well as a great age for the bordering Apennine Mountains scarp.

Lunar Apennine-Hadley region: Geological implications of earth-based radar and infrared measurements

USGS Publications Warehouse

Zisk, S.H.; Carr, M.H.; Masursky, H.; Shorthill, R.W.; Thompson, T.W.

1971-01-01

Recently completed high-resolution radar maps of the moon contain information on the decimeter-scale structure of the surface. When this information is combined with eclipse thermal-enhancement data and with high-resolution Lunar Orbiter photography, the surface morphology is revealed in some detail. A geological history for certain features and subareas can be developed, which provides one possible framework for the interpretation of the findings from the Apollo 15 landing. Frequency of decimeter- and meter-size blocks in and around lunar craters, given by the remote-sensed data, supports a multilayer structure in the Palus Putredinis mare region, as well as a great age for the bordering Apennins Mountains scarp.