The rate of cis-trans conformation errors is increasing in low-resolution crystal structures.

PubMed

Croll, Tristan Ian

2015-03-01

Cis-peptide bonds (with the exception of X-Pro) are exceedingly rare in native protein structures, yet a check for these is not currently included in the standard workflow for some common crystallography packages nor in the automated quality checks that are applied during submission to the Protein Data Bank. This appears to be leading to a growing rate of inclusion of spurious cis-peptide bonds in low-resolution structures both in absolute terms and as a fraction of solved residues. Most concerningly, it is possible for structures to contain very large numbers (>1%) of spurious cis-peptide bonds while still achieving excellent quality reports from MolProbity, leading to concerns that ignoring such errors is allowing software to overfit maps without producing telltale errors in, for example, the Ramachandran plot.

A super resolution framework for low resolution document image OCR

NASA Astrophysics Data System (ADS)

Ma, Di; Agam, Gady

2013-01-01

Optical character recognition is widely used for converting document images into digital media. Existing OCR algorithms and tools produce good results from high resolution, good quality, document images. In this paper, we propose a machine learning based super resolution framework for low resolution document image OCR. Two main techniques are used in our proposed approach: a document page segmentation algorithm and a modified K-means clustering algorithm. Using this approach, by exploiting coherence in the document, we reconstruct from a low resolution document image a better resolution image and improve OCR results. Experimental results show substantial gain in low resolution documents such as the ones captured from video.

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.

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.

On the creation of high spatial resolution imaging spectroscopy data from multi-temporal low spatial resolution imagery

NASA Astrophysics Data System (ADS)

Yao, Wei; van Aardt, Jan; Messinger, David

2017-05-01

The Hyperspectral Infrared Imager (HyspIRI) mission aims to provide global imaging spectroscopy data to the benefit of especially ecosystem studies. The onboard spectrometer will collect radiance spectra from the visible to short wave infrared (VSWIR) regions (400-2500 nm). The mission calls for fine spectral resolution (10 nm band width) and as such will enable scientists to perform material characterization, species classification, and even sub-pixel mapping. However, the global coverage requirement results in a relatively low spatial resolution (GSD 30m), which restricts applications to objects of similar scales. We therefore have focused on the assessment of sub-pixel vegetation structure from spectroscopy data in past studies. In this study, we investigate the development or reconstruction of higher spatial resolution imaging spectroscopy data via fusion of multi-temporal data sets to address the drawbacks implicit in low spatial resolution imagery. The projected temporal resolution of the HyspIRI VSWIR instrument is 15 days, which implies that we have access to as many as six data sets for an area over the course of a growth season. Previous studies have shown that select vegetation structural parameters, e.g., leaf area index (LAI) and gross ecosystem production (GEP), are relatively constant in summer and winter for temperate forests; we therefore consider the data sets collected in summer to be from a similar, stable forest structure. The first step, prior to fusion, involves registration of the multi-temporal data. A data fusion algorithm then can be applied to the pre-processed data sets. The approach hinges on an algorithm that has been widely applied to fuse RGB images. Ideally, if we have four images of a scene which all meet the following requirements - i) they are captured with the same camera configurations; ii) the pixel size of each image is x; and iii) at least r2 images are aligned on a grid of x/r - then a high-resolution image, with a pixel

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

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.

A High-resolution Study of Presupernova Core Structure

NASA Astrophysics Data System (ADS)

Sukhbold, Tuguldur; Woosley, S. E.; Heger, Alexander

2018-06-01

The density structure surrounding the iron core of a massive star when it dies is known to have a major effect on whether or not the star explodes. Here we repeat previous surveys of presupernova evolution with some important corrections to code physics and four to 10 times better mass resolution in each star. The number of presupernova masses considered is also much larger. Over 4000 models are calculated in the range from 12 to 60 M ⊙ with varying mass loss rates. The core structure is not greatly affected by the increased spatial resolution. The qualitative patterns of compactness measures and their extrema are the same, but with the increased number of models, the scatter seen in previous studies is replaced by several localized branches. More physics-based analyses by Ertl et al. and Müller et al. show these branches with less scatter than the single-parameter characterization of O’Connor & Ott. These branches are particularly apparent for stars in the mass ranges 14–19 and 22–24 M ⊙. The multivalued solutions are a consequence of interference between several carbon- and oxygen-burning shells during the late stages of evolution. For a relevant range of masses, whether a star explodes or not may reflect the small, almost random differences in its late evolution more than its initial mass. The large number of models allows statistically meaningful statements about the radius, luminosity, and effective temperatures of presupernova stars, their core structures, and their remnant mass distributions.

High Resolution Image Reconstruction from Projection of Low Resolution Images DIffering in Subpixel Shifts

NASA Technical Reports Server (NTRS)

Mareboyana, Manohar; Le Moigne-Stewart, Jacqueline; Bennett, Jerome

2016-01-01

In this paper, we demonstrate a simple algorithm that projects low resolution (LR) images differing in subpixel shifts on a high resolution (HR) also called super resolution (SR) grid. The algorithm is very effective in accuracy as well as time efficiency. A number of spatial interpolation techniques using nearest neighbor, inverse-distance weighted averages, Radial Basis Functions (RBF) etc. used in projection yield comparable results. For best accuracy of reconstructing SR image by a factor of two requires four LR images differing in four independent subpixel shifts. The algorithm has two steps: i) registration of low resolution images and (ii) shifting the low resolution images to align with reference image and projecting them on high resolution grid based on the shifts of each low resolution image using different interpolation techniques. Experiments are conducted by simulating low resolution images by subpixel shifts and subsampling of original high resolution image and the reconstructing the high resolution images from the simulated low resolution images. The results of accuracy of reconstruction are compared by using mean squared error measure between original high resolution image and reconstructed image. The algorithm was tested on remote sensing images and found to outperform previously proposed techniques such as Iterative Back Projection algorithm (IBP), Maximum Likelihood (ML), and Maximum a posterior (MAP) algorithms. The algorithm is robust and is not overly sensitive to the registration inaccuracies.

Low-Resolution Structure of the Full-Length Barley (Hordeum vulgare) SGT1 Protein in Solution, Obtained Using Small-Angle X-Ray Scattering

PubMed Central

Taube, Michał; Pieńkowska, Joanna R.; Jarmołowski, Artur; Kozak, Maciej

2014-01-01

SGT1 is an evolutionarily conserved eukaryotic protein involved in many important cellular processes. In plants, SGT1 is involved in resistance to disease. In a low ionic strength environment, the SGT1 protein tends to form dimers. The protein consists of three structurally independent domains (the tetratricopeptide repeats domain (TPR), the CHORD- and SGT1-containing domain (CS), and the SGT1-specific domain (SGS)), and two less conserved variable regions (VR1 and VR2). In the present study, we provide the low-resolution structure of the barley (Hordeum vulgare) SGT1 protein in solution and its dimer/monomer equilibrium using small-angle scattering of synchrotron radiation, ab-initio modeling and circular dichroism spectroscopy. The multivariate curve resolution least-square method (MCR-ALS) was applied to separate the scattering data of the monomeric and dimeric species from a complex mixture. The models of the barley SGT1 dimer and monomer were formulated using rigid body modeling with ab-initio structure prediction. Both oligomeric forms of barley SGT1 have elongated shapes with unfolded inter-domain regions. Circular dichroism spectroscopy confirmed that the barley SGT1 protein had a modular architecture, with an α-helical TPR domain, a β-sheet sandwich CS domain, and a disordered SGS domain separated by VR1 and VR2 regions. Using molecular docking and ab-initio protein structure prediction, a model of dimerization of the TPR domains was proposed. PMID:24714665

Super-resolution optical microscopy study of telomere structure.

PubMed

Phipps, Mary Lisa; Goodwin, Peter M; Martinez, Jennifer S; Goodwin, Edwin H

2016-09-01

Chromosome ends are shielded from exonucleolytic attack and inappropriate end-joining by terminal structures called telomeres; these structures are potential targets for anticancer drugs. Telomeres are composed of a simple DNA sequence (5?-TTAGGG-3? in humans) repeated more than a thousand times, a short 3? single-stranded overhang, and numerous proteins. Electron microscopy has shown that the 3? overhang pairs with the complementary strand at an internal site creating a small displacement loop and a large double-stranded “t-loop.” Our goal is to determine whether all telomeres adopt the t-loop configuration, or whether there are two or more distinct configurations. Progress in optimizing super-resolution (SR) microscopy for this ongoing investigation is reported here. Results suggest that under certain conditions sample preparation procedures may disrupt chromatin by causing loss of nucleosomes. This finding may limit the use of SR microscopy in telomere studies.

Super-resolution optical microscopy study of telomere structure

NASA Astrophysics Data System (ADS)

Phipps, Mary Lisa; Goodwin, Peter M.; Martinez, Jennifer S.; Goodwin, Edwin H.

2016-09-01

Chromosome ends are shielded from exonucleolytic attack and inappropriate end-joining by terminal structures called telomeres; these structures are potential targets for anticancer drugs. Telomeres are composed of a simple DNA sequence (5‧-TTAGGG-3‧ in humans) repeated more than a thousand times, a short 3‧ single-stranded overhang, and numerous proteins. Electron microscopy has shown that the 3‧ overhang pairs with the complementary strand at an internal site creating a small displacement loop and a large double-stranded "t-loop." Our goal is to determine whether all telomeres adopt the t-loop configuration, or whether there are two or more distinct configurations. Progress in optimizing super-resolution (SR) microscopy for this ongoing investigation is reported here. Results suggest that under certain conditions sample preparation procedures may disrupt chromatin by causing loss of nucleosomes. This finding may limit the use of SR microscopy in telomere studies.

Local structure and lattice dynamics study of low dimensional materials using atomic pair distribution function and high energy resolution inelastic x-ray scattering

NASA Astrophysics Data System (ADS)

Shi, Chenyang

Structure and dynamics lie at the heart of the materials science. A detailed knowledge of both subjects would be foundational in understanding the materials' properties and predicting their potential applications. However, the task becomes increasingly dicult as the particle size is reduced to the nanometer scale. For nanostructured materials their laboratory x-ray scattering patterns are overlapped and broadened, making structure determination impossible. Atomic pair distribution function technique based on either synchrotron x-ray or neutron scattering data is known as the tool of choice for probing local structures. However, to solve the "structure problem" in low-dimensional materials with PDF is still challenging. For example for 2D materials of interest in this thesis the crystallographic modeling approach often yields unphysical thermal factors along stacking direction where new chemical intuitions about their actual structures and new modeling methodology/program are needed. Beyond this, lattice dynamical investigations on nanosized particles are extremely dicult. Laboratory tools such as Raman and infra-red only probe phonons at Brillouin zone center. Although in literature there are a great number of theoretical studies of their vibrational properties based on either empirical force elds or density functional theory, various approximations made in theories make the theoretical predictions less reliable. Also, there lacks the direct experiment result to validate the theory against. In this thesis, we studied the structure and dynamics of a wide variety of technologically relevant low-dimensional materials through synchrotron based x-ray PDF and high energy resolution inelastic x-ray scattering (HERIX) techniques. By collecting PDF data and employing advanced modeling program such as DiPy-CMI, we successfully determined the atomic structures of (i) emerging Ti3C2, Nb4C3 MXenes (transition metal carbides and/or nitrides) that are promising for energy storage

High-Resolution Data for a Low-Resolution World

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

Brady, Brendan Williams

2016-05-10

In the past 15 years, the upper section of Cañon de Valle has been severely altered by wildfires and subsequent runoff events. Loss of root structures on high-angle slopes results in debris flow and sediment accumulation in the narrow canyon bottom. The original intent of the study described here was to better understand the changes occurring in watershed soil elevations over the course of several post-fire years. An elevation dataset from 5 years post-Cerro Grande fire was compared to high-resolution LiDAR data from 14 years post-Cerro Grande fire (also 3 years post-Las Conchas fire). The following analysis was motivated bymore » a problematic comparison of these datasets of unlike resolution, and therefore focuses on what the data reveals of itself. The objective of this study is to highlight the effects vegetation can have on remote sensing data that intends to read ground surface elevation.« less

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.

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.

Modeling shape and topology of low-resolution density maps of biological macromolecules.

PubMed Central

De-Alarcón, Pedro A; Pascual-Montano, Alberto; Gupta, Amarnath; Carazo, Jose M

2002-01-01

In the present work we develop an efficient way of representing the geometry and topology of volumetric datasets of biological structures from medium to low resolution, aiming at storing and querying them in a database framework. We make use of a new vector quantization algorithm to select the points within the macromolecule that best approximate the probability density function of the original volume data. Connectivity among points is obtained with the use of the alpha shapes theory. This novel data representation has a number of interesting characteristics, such as 1) it allows us to automatically segment and quantify a number of important structural features from low-resolution maps, such as cavities and channels, opening the possibility of querying large collections of maps on the basis of these quantitative structural features; 2) it provides a compact representation in terms of size; 3) it contains a subset of three-dimensional points that optimally quantify the densities of medium resolution data; and 4) a general model of the geometry and topology of the macromolecule (as opposite to a spatially unrelated bunch of voxels) is easily obtained by the use of the alpha shapes theory. PMID:12124252

SAPHIRE (scintillator avalanche photoconductor with high resolution emitter readout) for low dose x-ray imaging: Spatial resolution

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

Li Dan; Zhao Wei

2008-07-15

An indirect flat panel imager (FPI) with programmable avalanche gain and field emitter array (FEA) readout is being investigated for low-dose and high resolution x-ray imaging. It is made by optically coupling a structured x-ray scintillator, e.g., thallium (Tl) doped cesium iodide (CsI), to an amorphous selenium (a-Se) avalanche photoconductor called high-gain avalanche rushing amorphous photoconductor (HARP). The charge image created by the scintillator/HARP (SHARP) combination is read out by the electron beams emitted from the FEA. The proposed detector is called scintillator avalanche photoconductor with high resolution emitter readout (SAPHIRE). The programmable avalanche gain of HARP can improve themore » low dose performance of indirect FPI while the FEA can be made with pixel sizes down to 50 {mu}m. Because of the avalanche gain, a high resolution type of CsI (Tl), which has not been widely used in indirect FPI due to its lower light output, can be used to improve the high spatial frequency performance. The purpose of the present article is to investigate the factors affecting the spatial resolution of SAPHIRE. Since the resolution performance of the SHARP combination has been well studied, the focus of the present work is on the inherent resolution of the FEA readout method. The lateral spread of the electron beam emitted from a 50 {mu}mx50 {mu}m pixel FEA was investigated with two different electron-optical designs: mesh-electrode-only and electrostatic focusing. Our results showed that electrostatic focusing can limit the lateral spread of electron beams to within the pixel size of down to 50 {mu}m. Since electrostatic focusing is essentially independent of signal intensity, it will provide excellent spatial uniformity.« less

Low-resolution simulations of vesicle suspensions in 2D

NASA Astrophysics Data System (ADS)

Kabacaoğlu, Gökberk; Quaife, Bryan; Biros, George

2018-03-01

Vesicle suspensions appear in many biological and industrial applications. These suspensions are characterized by rich and complex dynamics of vesicles due to their interaction with the bulk fluid, and their large deformations and nonlinear elastic properties. Many existing state-of-the-art numerical schemes can resolve such complex vesicle flows. However, even when using provably optimal algorithms, these simulations can be computationally expensive, especially for suspensions with a large number of vesicles. These high computational costs can limit the use of simulations for parameter exploration, optimization, or uncertainty quantification. One way to reduce the cost is to use low-resolution discretizations in space and time. However, it is well-known that simply reducing the resolution results in vesicle collisions, numerical instabilities, and often in erroneous results. In this paper, we investigate the effect of a number of algorithmic empirical fixes (which are commonly used by many groups) in an attempt to make low-resolution simulations more stable and more predictive. Based on our empirical studies for a number of flow configurations, we propose a scheme that attempts to integrate these fixes in a systematic way. This low-resolution scheme is an extension of our previous work [51,53]. Our low-resolution correction algorithms (LRCA) include anti-aliasing and membrane reparametrization for avoiding spurious oscillations in vesicles' membranes, adaptive time stepping and a repulsion force for handling vesicle collisions and, correction of vesicles' area and arc-length for maintaining physical vesicle shapes. We perform a systematic error analysis by comparing the low-resolution simulations of dilute and dense suspensions with their high-fidelity, fully resolved, counterparts. We observe that the LRCA enables both efficient and statistically accurate low-resolution simulations of vesicle suspensions, while it can be 10× to 100× faster.

Avalanche statistics from data with low time resolution

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

LeBlanc, Michael; Nawano, Aya; Wright, Wendelin J.

Extracting avalanche distributions from experimental microplasticity data can be hampered by limited time resolution. We compute the effects of low time resolution on avalanche size distributions and give quantitative criteria for diagnosing and circumventing problems associated with low time resolution. We show that traditional analysis of data obtained at low acquisition rates can lead to avalanche size distributions with incorrect power-law exponents or no power-law scaling at all. Furthermore, we demonstrate that it can lead to apparent data collapses with incorrect power-law and cutoff exponents. We propose new methods to analyze low-resolution stress-time series that can recover the size distributionmore » of the underlying avalanches even when the resolution is so low that naive analysis methods give incorrect results. We test these methods on both downsampled simulation data from a simple model and downsampled bulk metallic glass compression data and find that the methods recover the correct critical exponents.« less

Avalanche statistics from data with low time resolution

DOE PAGES

LeBlanc, Michael; Nawano, Aya; Wright, Wendelin J.; ...

2016-11-22

Extracting avalanche distributions from experimental microplasticity data can be hampered by limited time resolution. We compute the effects of low time resolution on avalanche size distributions and give quantitative criteria for diagnosing and circumventing problems associated with low time resolution. We show that traditional analysis of data obtained at low acquisition rates can lead to avalanche size distributions with incorrect power-law exponents or no power-law scaling at all. Furthermore, we demonstrate that it can lead to apparent data collapses with incorrect power-law and cutoff exponents. We propose new methods to analyze low-resolution stress-time series that can recover the size distributionmore » of the underlying avalanches even when the resolution is so low that naive analysis methods give incorrect results. We test these methods on both downsampled simulation data from a simple model and downsampled bulk metallic glass compression data and find that the methods recover the correct critical exponents.« less

Crystal structure of low-molecular-weight protein tyrosine phosphatase from Mycobacterium tuberculosis at 1.9-A resolution.

PubMed

Madhurantakam, Chaithanya; Rajakumara, Eerappa; Mazumdar, Pooja Anjali; Saha, Baisakhee; Mitra, Devrani; Wiker, Harald G; Sankaranarayanan, Rajan; Das, Amit Kumar

2005-03-01

The low-molecular-weight protein tyrosine phosphatase (LMWPTPase) belongs to a distinctive class of phosphotyrosine phosphatases widely distributed among prokaryotes and eukaryotes. We report here the crystal structure of LMWPTPase of microbial origin, the first of its kind from Mycobacterium tuberculosis. The structure was determined to be two crystal forms at 1.9- and 2.5-A resolutions. These structural forms are compared with those of the LMWPTPases of eukaryotes. Though the overall structure resembles that of the eukaryotic LMWPTPases, there are significant changes around the active site and the protein tyrosine phosphatase (PTP) loop. The variable loop forming the wall of the crevice leading to the active site is conformationally unchanged from that of mammalian LMWPTPase; however, differences are observed in the residues involved, suggesting that they have a role in influencing different substrate specificities. The single amino acid substitution (Leu12Thr [underlined below]) in the consensus sequence of the PTP loop, CTGNICRS, has a major role in the stabilization of the PTP loop, unlike what occurs in mammalian LMWPTPases. A chloride ion and a glycerol molecule were modeled in the active site where the chloride ion interacts in a manner similar to that of phosphate with the main chain nitrogens of the PTP loop. This structural study, in addition to identifying specific mycobacterial features, may also form the basis for exploring the mechanism of the substrate specificities of bacterial LMWPTPases.

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

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.

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.

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.

High resolution and low altitude magnetic surveys for structural geology mapping in the Seabee mine, Saskatchewan, Canada, using UAV-MAG™ technology.

NASA Astrophysics Data System (ADS)

Braun, A.; Parvar, K.; Burns, M.

2017-12-01

Uninhabited Aerial Vehicles (UAV) provide the operational flexibility and ease of use which makes them ideal tools for low altitude and high resolution magnetic surveys. Being able to fly at lower altitudes compared to manned aircrafts provides the proximity to the target needed to increase the sensitivity to detect smaller and less magnetic targets. Considering the same sensor specifications, this further increases the signal to noise ratio. However, to increase spatial resolution, a tighter line spacing is needed which increases the survey time. We describe a case study in the Seabee mine in Saskatchewan, Canada. Using Pioneer Exploration Ltd. UAV-MAG™ technology, we emphasize the importance of altitude and line spacing in magnetic surveys with UAVs in order to resolve smaller and less magnetic targets compared to conventional manned airborne magnetic surveys. Mapping lithological or stratigraphic changes along the target structure requires an existing gradient in magnetic susceptibility. Mostly, this criterium is either not presented or the is weaker than the sensor's signal to noise ratio at a certain flying altitude. However, the folded structure in the study region shows high susceptibility changes in rock formations in high altitude regional magnetic surveys. In order to confirm that there are no missed structural elements in the target region, a UAV magnetic survey using a GEM Systems GSMP-35A potassium vapor magnetometer on Pioneer Exploration's UAV-MAG™ platform was conducted to exploit the structure in detail and compare the gain in spatial resolution from flying at lower altitude and with denser flight lines. The survey was conducted at 25 meters above ground level (AGL). Line spacing was set to 15 meters and a total of 550 kilometers was covered using an autonomous UAV. The collected data were compared to the regional airborne data which were collected at 150 meters AGL with a line spacing of 100 meters. Comparison revealed an anticline with plunge

Higher-Resolution Structure of the Human Insulin Receptor Ectodomain: Multi-Modal Inclusion of the Insert Domain.

PubMed

Croll, Tristan I; Smith, Brian J; Margetts, Mai B; Whittaker, Jonathan; Weiss, Michael A; Ward, Colin W; Lawrence, Michael C

2016-03-01

Insulin receptor (IR) signaling is critical to controlling nutrient uptake and metabolism. However, only a low-resolution (3.8 Å) structure currently exists for the IR ectodomain, with some segments ill-defined or unmodeled due to disorder. Here, we revise this structure using new diffraction data to 3.3 Å resolution that allow improved modeling of the N-linked glycans, the first and third fibronectin type III domains, and the insert domain. A novel haptic interactive molecular dynamics strategy was used to aid fitting to low-resolution electron density maps. The resulting model provides a foundation for investigation of structural transitions in IR upon ligand binding. Copyright © 2016 Elsevier Ltd. All rights reserved.

Improving Measurement of Forest Structural Parameters by Co-Registering of High Resolution Aerial Imagery and Low Density LiDAR Data

PubMed Central

Huang, Huabing; Gong, Peng; Cheng, Xiao; Clinton, Nick; Li, Zengyuan

2009-01-01

Forest structural parameters, such as tree height and crown width, are indispensable for evaluating forest biomass or forest volume. LiDAR is a revolutionary technology for measurement of forest structural parameters, however, the accuracy of crown width extraction is not satisfactory when using a low density LiDAR, especially in high canopy cover forest. We used high resolution aerial imagery with a low density LiDAR system to overcome this shortcoming. A morphological filtering was used to generate a DEM (Digital Elevation Model) and a CHM (Canopy Height Model) from LiDAR data. The LiDAR camera image is matched to the aerial image with an automated keypoints search algorithm. As a result, a high registration accuracy of 0.5 pixels was obtained. A local maximum filter, watershed segmentation, and object-oriented image segmentation are used to obtain tree height and crown width. Results indicate that the camera data collected by the integrated LiDAR system plays an important role in registration with aerial imagery. The synthesis with aerial imagery increases the accuracy of forest structural parameter extraction when compared to only using the low density LiDAR data. PMID:22573971

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

Low-loss electron energy loss spectroscopy: An atomic-resolution complement to optical spectroscopies and application to graphene

DOE PAGES

Kapetanakis, Myron; Zhou, Wu; Oxley, Mark P.; ...

2015-09-25

Photon-based spectroscopies have played a central role in exploring the electronic properties of crystalline solids and thin films. They are a powerful tool for probing the electronic properties of nanostructures, but they are limited by lack of spatial resolution. On the other hand, electron-based spectroscopies, e.g., electron energy loss spectroscopy (EELS), are now capable of subangstrom spatial resolution. Core-loss EELS, a spatially resolved analog of x-ray absorption, has been used extensively in the study of inhomogeneous complex systems. In this paper, we demonstrate that low-loss EELS in an aberration-corrected scanning transmission electron microscope, which probes low-energy excitations, combined with amore » theoretical framework for simulating and analyzing the spectra, is a powerful tool to probe low-energy electron excitations with atomic-scale resolution. The theoretical component of the method combines density functional theory–based calculations of the excitations with dynamical scattering theory for the electron beam. We apply the method to monolayer graphene in order to demonstrate that atomic-scale contrast is inherent in low-loss EELS even in a perfectly periodic structure. The method is a complement to optical spectroscopy as it probes transitions entailing momentum transfer. The theoretical analysis identifies the spatial and orbital origins of excitations, holding the promise of ultimately becoming a powerful probe of the structure and electronic properties of individual point and extended defects in both crystals and inhomogeneous complex nanostructures. The method can be extended to probe magnetic and vibrational properties with atomic resolution.« less

High Resolution, Low Altitude Aeromagnetic and Electromagnetic Survey of Mt Rainier

USGS Publications Warehouse

Rystrom, V.L.; Finn, C.; Deszcz-Pan, Maryla

2000-01-01

In October 1996, the USGS conducted a high resolution airborne magnetic and electromagnetic survey in order to discern through-going sections of exposed altered rocks and those obscured beneath snow, vegetation and surficial unaltered rocks. Hydrothermally altered rocks weaken volcanic edifices, creating the potential for catastrophic sector collapses and ensuing formation of destructive volcanic debris flows. This data once compiled and interpreted, will be used to examine the geophysical properties of the Mt. Rainier volcano, and help assist the USGS in its Volcanic Hazards Program and at its Cascades Volcano Observatory. Aeromagnetic and electromagnetic data provide a means for seeing through surficial layers and have been tools for delineating structures within volcanoes. However, previously acquired geophysical data were not useful for small-scale geologic mapping. In this report, we present the new aeromagnetic and electromagnetic data, compare results from previously obtained, low-resolution aeromagnetic data with new data collected at a low-altitude and closely spaced flightlines, and provide information on potential problems with using high-resolution data.

Live CLEM imaging to analyze nuclear structures at high resolution.

PubMed

Haraguchi, Tokuko; Osakada, Hiroko; Koujin, Takako

2015-01-01

Fluorescence microscopy (FM) and electron microscopy (EM) are powerful tools for observing molecular components in cells. FM can provide temporal information about cellular proteins and structures in living cells. EM provides nanometer resolution images of cellular structures in fixed cells. We have combined FM and EM to develop a new method of correlative light and electron microscopy (CLEM), called "Live CLEM." In this method, the dynamic behavior of specific molecules of interest is first observed in living cells using fluorescence microscopy (FM) and then cellular structures in the same cell are observed using electron microscopy (EM). Following image acquisition, FM and EM images are compared to enable the fluorescent images to be correlated with the high-resolution images of cellular structures obtained using EM. As this method enables analysis of dynamic events involving specific molecules of interest in the context of specific cellular structures at high resolution, it is useful for the study of nuclear structures including nuclear bodies. Here we describe Live CLEM that can be applied to the study of nuclear structures in mammalian cells.

Structure from motion, a low cost, very high resolution method for surveying glaciers using GoPros and opportunistic helicopter flights

NASA Astrophysics Data System (ADS)

Girod, L.; Nuth, C.; Schellenberger, T.

2014-12-01

The capability of structure from motion techniques to survey glaciers with a very high spatial and temporal resolution is a promising tool for better understanding the dynamic changes of glaciers. Modern software and computing power allow us to produce accurate data sets from low cost surveys, thus improving the observational capabilities on a wider range of glaciers and glacial processes. In particular, highly accurate glacier volume change monitoring and 3D movement computations will be possible Taking advantage of the helicopter flight needed to survey the ice stakes on Kronenbreen, NW Svalbard, we acquired high resolution photogrammetric data over the well-studied Midre Lovénbreen in September 2013. GoPro Hero 2 cameras were attached to the landing gear of the helicopter, acquiring two images per second. A C/A code based GPS was used for registering the stereoscopic model. Camera clock calibration is obtained through fitting together the shapes of the flight given by both the GPS logger and the relative orientation of the images. A DEM and an ortho-image are generated at 30cm resolution from 300 images collected. The comparison with a 2005 LiDAR DEM (5 meters resolution) shows an absolute error in the direct registration of about 6±3m in 3D which could be easily reduced to 1,5±1m by using fine point cloud alignment algorithms on stable ground. Due to the different nature of the acquisition method, it was not possible to use tie point based co-registration. A combination of the DEM and ortho-image is shown with the point cloud in figure below. A second photogrammetric data set will be acquired in September 2014 to survey the annual volume change and movement. These measurements will then be compared to the annual resolution glaciological stake mass balance and velocity measurements to assess the precision of the method to monitor at an annual resolution.

Construction of pixel-level resolution DEMs from monocular images by shape and albedo from shading constrained with low-resolution DEM

NASA Astrophysics Data System (ADS)

Wu, Bo; Liu, Wai Chung; Grumpe, Arne; Wöhler, Christian

2018-06-01

Lunar Digital Elevation Model (DEM) is important for lunar successful landing and exploration missions. Lunar DEMs are typically generated by photogrammetry or laser altimetry approaches. Photogrammetric methods require multiple stereo images of the region of interest and it may not be applicable in cases where stereo coverage is not available. In contrast, reflectance based shape reconstruction techniques, such as shape from shading (SfS) and shape and albedo from shading (SAfS), apply monocular images to generate DEMs with pixel-level resolution. We present a novel hierarchical SAfS method that refines a lower-resolution DEM to pixel-level resolution given a monocular image with known light source. We also estimate the corresponding pixel-wise albedo map in the process and based on that to regularize the shape reconstruction with pixel-level resolution based on the low-resolution DEM. In this study, a Lunar-Lambertian reflectance model is applied to estimate the albedo map. Experiments were carried out using monocular images from the Lunar Reconnaissance Orbiter Narrow Angle Camera (LRO NAC), with spatial resolution of 0.5-1.5 m per pixel, constrained by the Selenological and Engineering Explorer and LRO Elevation Model (SLDEM), with spatial resolution of 60 m. The results indicate that local details are well recovered by the proposed algorithm with plausible albedo estimation. The low-frequency topographic consistency depends on the quality of low-resolution DEM and the resolution difference between the image and the low-resolution DEM.

Signal Characteristics of Super-Resolution Near-Field Structure Disks with 100 GB Capacity

NASA Astrophysics Data System (ADS)

Kim, Jooho; Hwang, Inoh; Kim, Hyunki; Park, Insik; Tominaga, Junji

2005-05-01

We report the basic characteristics of super resolution near-field structure (Super-RENS) media at a blue laser optical system (laser wavelength 405 nm, numerical aperture 0.85). Using a novel write once read many (WORM) structure for a blue laser system, we obtained a carrier-to-noise ratio (CNR) above 33 dB from the signal of the 37.5 nm mark length, which is equivalent to a 100 GB capacity with a 0.32 micrometer track pitch, and an eye pattern for 50 GB (2T: 75 nm) capacity using a patterned signal. Using a novel super-resolution material (tellurium, Te) with low super-resolution readout power, we also improved the read stability.

Structure and Evolution of Hawaii's Loihi Seamount from High-resolution Mapping

NASA Astrophysics Data System (ADS)

Clague, D. A.; Paduan, J. B.; Moyer, C. L.; Glazer, B. T.; Caress, D. W.; Yoerger, D.; Kaiser, C. L.

2016-12-01

Loihi Seamount has been mapped repeatedly using shipboard multibeam sonars with improving resolution over time. Simrad EM302 data with 25m resolution at the 950m summit and 90m at the 5000m base of the volcano were collected from Schmidt Ocean Institute's R/V Falkor in 2014. A contracted multibeam survey in 1997 employing a deep-towed vehicle has 7m resolution for the summit and upper north and south rift zones, but suffered from poor navigation. Woods Hole Oceanographic Institution's AUV Sentry surveyed most of the summit and low-T hydrothermal vents on the base of the south rift in 2013 and 2014. The 2m resolution of most data is more precise than the navigation. The 6 summit surveys were reprocessed using MB-System to remove abundant bad bottom picks and adjust the navigation to produce a spatially accurate map. The 3 summit pits, including Pele's Pit that formed in 1996, are complex collapse structures and nested inside a larger caldera that was modified by large landslides on the east and west summit flanks. The pits cut low shields that once formed a complex of overlapping summit shields, similar to Kilauea before the current caldera formed 1500 to 1790 CE. An 11m section of ash deposits crops out on the east rim of the summit along a caldera-bounding fault and is analogous to Kilauea where the caldera-bounding faults expose ash erupted as the present caldera formed. Most of the Loihi ash section is 3300 to 5880 yr BP, indicating that the larger caldera structure at Loihi is younger than 3300 yr BP. The landslides on the east and west edges of the summit are therefore younger 3300 yr BP. The uppermost south rift has several small pit craters between cones and pillow ridges, also analogous to Kilauea. Two cones near the deep low-T vents are steep pillow mounds with slopes of talus. High-resolution mapping reveals, for the first time, the many similarities between the structure and evolution of submarine Loihi Seamount and subaerial Kilauea Volcano.

From lows to highs: using low-resolution models to phase X-ray data

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

Stuart, David I.; Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot; Abrescia, Nicola G. A., E-mail: nabrescia@cicbiogune.es

2013-11-01

An unusual example of how virus structure determination pushes the limits of the molecular replacement method is presented. The study of virus structures has contributed to methodological advances in structural biology that are generally applicable (molecular replacement and noncrystallographic symmetry are just two of the best known examples). Moreover, structural virology has been instrumental in forging the more general concept of exploiting phase information derived from multiple structural techniques. This hybridization of structural methods, primarily electron microscopy (EM) and X-ray crystallography, but also small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy, is central to integrative structural biology. Here,more » the interplay of X-ray crystallography and EM is illustrated through the example of the structural determination of the marine lipid-containing bacteriophage PM2. Molecular replacement starting from an ∼13 Å cryo-EM reconstruction, followed by cycling density averaging, phase extension and solvent flattening, gave the X-ray structure of the intact virus at 7 Å resolution This in turn served as a bridge to phase, to 2.5 Å resolution, data from twinned crystals of the major coat protein (P2), ultimately yielding a quasi-atomic model of the particle, which provided significant insights into virus evolution and viral membrane biogenesis.« less

High-resolution land cover classification using low resolution global data

NASA Astrophysics Data System (ADS)

Carlotto, Mark J.

2013-05-01

A fusion approach is described that combines texture features from high-resolution panchromatic imagery with land cover statistics derived from co-registered low-resolution global databases to obtain high-resolution land cover maps. The method does not require training data or any human intervention. We use an MxN Gabor filter bank consisting of M=16 oriented bandpass filters (0-180°) at N resolutions (3-24 meters/pixel). The size range of these spatial filters is consistent with the typical scale of manmade objects and patterns of cultural activity in imagery. Clustering reduces the complexity of the data by combining pixels that have similar texture into clusters (regions). Texture classification assigns a vector of class likelihoods to each cluster based on its textural properties. Classification is unsupervised and accomplished using a bank of texture anomaly detectors. Class likelihoods are modulated by land cover statistics derived from lower resolution global data over the scene. Preliminary results from a number of Quickbird scenes show our approach is able to classify general land cover features such as roads, built up area, forests, open areas, and bodies of water over a wide range of scenes.

Structural atlas of dynein motors at atomic resolution.

PubMed

Toda, Akiyuki; Tanaka, Hideaki; Kurisu, Genji

2018-04-01

Dynein motors are biologically important bio-nanomachines, and many atomic resolution structures of cytoplasmic dynein components from different organisms have been analyzed by X-ray crystallography, cryo-EM, and NMR spectroscopy. This review provides a historical perspective of structural studies of cytoplasmic and axonemal dynein including accessory proteins. We describe representative structural studies of every component of dynein and summarize them as a structural atlas that classifies the cytoplasmic and axonemal dyneins. Based on our review of all dynein structures in the Protein Data Bank, we raise two important points for understanding the two types of dynein motor and discuss the potential prospects of future structural studies.

Micron-Resolution X-ray Structural Microscopy Studies of 3-D Grain Growth in Polycrystalline Aluminum

NASA Astrophysics Data System (ADS)

Budai, J. D.; Yang, W.; Tischler, J. Z.; Liu, W.; Larson, B. C.; Ice, G. E.

2004-03-01

We describe a new polychromatic x-ray microdiffraction technique providing 3D measurements of lattice structure, orientation and strain with submicron point-to-point spatial resolution. The instrument is located on the UNI-CAT II undulator beamline at the Advanced Photon Source and uses Kirkpatrick-Baez focusing mirrors, differential aperture CCD measurements and automated analysis of spatially-resolved Laue patterns. 3D x-ray structural microscopy is applicable to a wide range of materials investigations and here we describe 3D thermal grain growth studies in polycrystalline aluminum ( ˜1% Fe,Si) from Alcoa. The morphology and orientations of the grains in a hot-rolled aluminum sample were initially mapped. The sample was then annealed to induce grain growth, cooled to room temperature, and the same volume region was re-mapped to determine the thermal migration of all grain boundaries. Significant grain growth was observed after annealing above ˜350^oC where both low-angle and high-angle boundaries were mobile. These measurements will provide the detailed 3D experimental input needed for testing theories and computer models of 3D grain growth in bulk materials.

High-resolution coded-aperture design for compressive X-ray tomography using low resolution detectors

NASA Astrophysics Data System (ADS)

Mojica, Edson; Pertuz, Said; Arguello, Henry

2017-12-01

One of the main challenges in Computed Tomography (CT) is obtaining accurate reconstructions of the imaged object while keeping a low radiation dose in the acquisition process. In order to solve this problem, several researchers have proposed the use of compressed sensing for reducing the amount of measurements required to perform CT. This paper tackles the problem of designing high-resolution coded apertures for compressed sensing computed tomography. In contrast to previous approaches, we aim at designing apertures to be used with low-resolution detectors in order to achieve super-resolution. The proposed method iteratively improves random coded apertures using a gradient descent algorithm subject to constraints in the coherence and homogeneity of the compressive sensing matrix induced by the coded aperture. Experiments with different test sets show consistent results for different transmittances, number of shots and super-resolution factors.

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.

Fine-structure-resolution for Rovibrational Excitation of CN Due to H2

NASA Astrophysics Data System (ADS)

Byrd, Nat; Yang, Benhui H.; Stancil, Phillip C.

2018-06-01

Diatomic molecules can be readily excited in interstellar environments exposed to intense UV radiation, such as the inner rim of a protoplanetary disk. Non-thermal populations of excited rovibrational levels can result, for example, following decay from electronically excited states to the electronic ground state. Competition between radiative decay and collisional processes, mostly due to H2, determine the resulting rovibrational emission spectrum. For CN, and other open-shell molecules, the resulting spectrum will be complicated due to fine-structure splitting of the rotational levels. In some cases, fine-structure resolution has been previously computed for rotational transitions in atom- or diatom-diatom collisional processes. Here we present the first fine-structure resolution for vibrational deexcitation for CN colliding with H2. The collisional cross sections were computed using a 6D potential energy surface with a full close-coupling approach. Fine-structure resolution is obtained by adopting an angular momentum recoupling scheme to transform the scattering matrices to a recoupled basis. Here we present low-energy calculations for the v=1 to 0 transition.This work was supported by NASA Grant NNX16AF09G.

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

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.

Facial identification in very low-resolution images simulating prosthetic vision.

PubMed

Chang, M H; Kim, H S; Shin, J H; Park, K S

2012-08-01

Familiar facial identification is important to blind or visually impaired patients and can be achieved using a retinal prosthesis. Nevertheless, there are limitations in delivering the facial images with a resolution sufficient to distinguish facial features, such as eyes and nose, through multichannel electrode arrays used in current visual prostheses. This study verifies the feasibility of familiar facial identification under low-resolution prosthetic vision and proposes an edge-enhancement method to deliver more visual information that is of higher quality. We first generated a contrast-enhanced image and an edge image by applying the Sobel edge detector and blocked each of them by averaging. Then, we subtracted the blocked edge image from the blocked contrast-enhanced image and produced a pixelized image imitating an array of phosphenes. Before subtraction, every gray value of the edge images was weighted as 50% (mode 2), 75% (mode 3) and 100% (mode 4). In mode 1, the facial image was blocked and pixelized with no further processing. The most successful identification was achieved with mode 3 at every resolution in terms of identification index, which covers both accuracy and correct response time. We also found that the subjects recognized a distinctive face especially more accurately and faster than the other given facial images even under low-resolution prosthetic vision. Every subject could identify familiar faces even in very low-resolution images. And the proposed edge-enhancement method seemed to contribute to intermediate-stage visual prostheses.

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.

Packing of sidechains in low-resolution models for proteins.

PubMed

Keskin, O; Bahar, I

1998-01-01

Atomic level rotamer libraries for sidechains in proteins have been proposed by several groups. Conformations of side groups in coarse-grained models, on the other hand, have not yet been analyzed, although low resolution approaches are the only efficient way to explore global structural features. A residue-specific backbone-dependent library for sidechain isomers, compatible with a coarse-grained model, is proposed. The isomeric states are utilized in packing sidechains of known backbone structures. Sidechain positions are predicted with a root-mean-square deviation (r.m.s.d.) of 2.40 A with respect to crystal structure for 50 test proteins. The rmsd for core residues is 1.60 A and decreases to 1.35 A when conformational correlations and directional effects in inter-residue couplings are considered. An automated method for assigning sidechain positions in coarse-grained model proteins is proposed and made available on the internet; the method accounts satisfactorily for sidechain packing, particularly in the core.

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

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

Low-Resolution Raman-Spectroscopy Combustion Thermometry

NASA Technical Reports Server (NTRS)

Nguyen, Quang-Viet; Kojima, Jun

2008-01-01

A method of optical thermometry, now undergoing development, involves low-resolution measurement of the spectrum of spontaneous Raman scattering (SRS) from N2 and O2 molecules. The method is especially suitable for measuring temperatures in high pressure combustion environments that contain N2, O2, or N2/O2 mixtures (including air). Methods based on SRS (in which scattered light is shifted in wavelength by amounts that depend on vibrational and rotational energy levels of laser-illuminated molecules) have been popular means of probing flames because they are almost the only methods that provide spatially and temporally resolved concentrations and temperatures of multiple molecular species in turbulent combustion. The present SRS-based method differs from prior SRS-based methods that have various drawbacks, a description of which would exceed the scope of this article. Two main differences between this and prior SRS-based methods are that it involves analysis in the frequency (equivalently, wavelength) domain, in contradistinction to analysis in the intensity domain in prior methods; and it involves low-resolution measurement of what amounts to predominantly the rotational Raman spectra of N2 and O2, in contradistinction to higher-resolution measurement of the vibrational Raman spectrum of N2 only in prior methods.

IRAS low resolution spectra of 26 symbiotic stars

NASA Technical Reports Server (NTRS)

Stencel, Robert E.; Brugel, Edward W.; Goodwill, Michael E.

1990-01-01

Data related to the spectral scans for 26 symbiotic stars are described which were extracted from the IRAS low resolution database. Data from the 8-15- and 15-23-micron bands are merged in a program that scales the longer wavelength and produces a weighted average of the spectral scans for each source. The survey shows that active dust producers can probably be isolated and some theories related to the presence of dust emission features are discussed in terms of source variability for measurements made with low resolution spectra.

Dependence of Hurricane intensity and structures on vertical resolution and time-step size

NASA Astrophysics Data System (ADS)

Zhang, Da-Lin; Wang, Xiaoxue

2003-09-01

In view of the growing interests in the explicit modeling of clouds and precipitation, the effects of varying vertical resolution and time-step sizes on the 72-h explicit simulation of Hurricane Andrew (1992) are studied using the Pennsylvania State University/National Center for Atmospheric Research (PSU/NCAR) mesoscale model (i.e., MM5) with the finest grid size of 6 km. It is shown that changing vertical resolution and time-step size has significant effects on hurricane intensity and inner-core cloud/precipitation, but little impact on the hurricane track. In general, increasing vertical resolution tends to produce a deeper storm with lower central pressure and stronger three-dimensional winds, and more precipitation. Similar effects, but to a less extent, occur when the time-step size is reduced. It is found that increasing the low-level vertical resolution is more efficient in intensifying a hurricane, whereas changing the upper-level vertical resolution has little impact on the hurricane intensity. Moreover, the use of a thicker surface layer tends to produce higher maximum surface winds. It is concluded that the use of higher vertical resolution, a thin surface layer, and smaller time-step sizes, along with higher horizontal resolution, is desirable to model more realistically the intensity and inner-core structures and evolution of tropical storms as well as the other convectively driven weather systems.

The Lithospheric Structure of the Solonker Suture Zone and Adjacent Areas: Crustal Structure Revealed by a High-Resolution Magnetotelluric Study

NASA Astrophysics Data System (ADS)

Ye, Gaofeng; Jin, Sheng; Wei, Wenbo; Jing, Jian'en

2017-04-01

The closure of the Paleo-Asian Ocean along the Solonker Suture Zone (SSZ) during the Late Permian and Triassic represented the final stage in the formation of the Central Asian Orogenic Belt between the Siberian Craton and the North China Craton. In order to better understand the structure and formation of this ancient subduction zone, a high-resolution magnetotelluric (MT) profile was collected with both broadband and long-period MT data. The high resolution mapping of the lithosphere achieved in this study is due to the closely spaced MT stations (2-3 km). With the 2-D resistivity model, a south-dipping conductor was detected and extends through the entire crust. The geometry of this feature provides evidence that a southward directed subduction zone formed the Solonker suture. The enhanced conductivity was interpreted to subducted sulfide-bearing graphitic sediments. The resistive body beneath the northern margin of the North China Craton indicates a thickened lithosphere caused by the southward subduction at this region, and the resistive body beneath the Solonker Suture Zone indicates the subducted oceanic lithosphere. North-dipping low resistivity features were also detected in the crust of both the North China Craton and Central Asian Orogenic Belt, and were interpreted as post-collisional thrust faults. Strong anisotropy was found beneath the suture zone, and can be explained if the high strain rate has rotated the fold axes into the dip direction.

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.

The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra

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

Vasilatou, K.; Michaud, J. M.; Baykusheva, D.

2014-08-14

The cyclopropene radical cation (c-C{sub 3}H{sub 4}{sup +}) is an important but poorly characterized three-membered-ring hydrocarbon. We report on a measurement of the high-resolution photoelectron and photoionization spectra of cyclopropene and several deuterated isotopomers, from which we have determined the rovibrational energy level structure of the X{sup ~+} {sup 2}B{sub 2} ground electronic state of c-C{sub 3}H{sub 4}{sup +} at low energies for the first time. The synthesis of the partially deuterated isotopomers always resulted in mixtures of several isotopomers, differing in their number of D atoms and in the location of these atoms, so that the photoelectron spectra ofmore » deuterated samples are superpositions of the spectra of several isotopomers. The rotationally resolved spectra indicate a C{sub 2v}-symmetric R{sub 0} structure for the ground electronic state of c-C{sub 3}H{sub 4}{sup +}. Two vibrational modes of c-C{sub 3}H{sub 4}{sup +} are found to have vibrational wave numbers below 300 cm{sup −1}, which is surprising for such a small cyclic hydrocarbon. The analysis of the isotopic shifts of the vibrational levels enabled the assignment of the lowest-frequency mode (fundamental wave number of ≈110 cm{sup −1} in c-C{sub 3}H{sub 4}{sup +}) to the CH{sub 2} torsional mode (ν{sub 8}{sup +}, A{sub 2} symmetry) and of the second-lowest-frequency mode (≈210 cm{sup −1} in c-C{sub 3}H{sub 4}{sup +}) to a mode combining a CH out-of-plane with a CH{sub 2} rocking motion (ν{sub 15}{sup +}, B{sub 2} symmetry). The potential energy along the CH{sub 2} torsional coordinate is flat near the equilibrium structure and leads to a pronounced anharmonicity.« less

High-resolution low-dose scanning transmission electron microscopy.

PubMed

Buban, James P; Ramasse, Quentin; Gipson, Bryant; Browning, Nigel D; Stahlberg, Henning

2010-01-01

During the past two decades instrumentation in scanning transmission electron microscopy (STEM) has pushed toward higher intensity electron probes to increase the signal-to-noise ratio of recorded images. While this is suitable for robust specimens, biological specimens require a much reduced electron dose for high-resolution imaging. We describe here protocols for low-dose STEM image recording with a conventional field-emission gun STEM, while maintaining the high-resolution capability of the instrument. Our findings show that a combination of reduced pixel dwell time and reduced gun current can achieve radiation doses comparable to low-dose TEM.

Human Mobility Monitoring in Very Low Resolution Visual Sensor Network

PubMed Central

Bo Bo, Nyan; Deboeverie, Francis; Eldib, Mohamed; Guan, Junzhi; Xie, Xingzhe; Niño, Jorge; Van Haerenborgh, Dirk; Slembrouck, Maarten; Van de Velde, Samuel; Steendam, Heidi; Veelaert, Peter; Kleihorst, Richard; Aghajan, Hamid; Philips, Wilfried

2014-01-01

This paper proposes an automated system for monitoring mobility patterns using a network of very low resolution visual sensors (30 × 30 pixels). The use of very low resolution sensors reduces privacy concern, cost, computation requirement and power consumption. The core of our proposed system is a robust people tracker that uses low resolution videos provided by the visual sensor network. The distributed processing architecture of our tracking system allows all image processing tasks to be done on the digital signal controller in each visual sensor. In this paper, we experimentally show that reliable tracking of people is possible using very low resolution imagery. We also compare the performance of our tracker against a state-of-the-art tracking method and show that our method outperforms. Moreover, the mobility statistics of tracks such as total distance traveled and average speed derived from trajectories are compared with those derived from ground truth given by Ultra-Wide Band sensors. The results of this comparison show that the trajectories from our system are accurate enough to obtain useful mobility statistics. PMID:25375754

LORES: Low resolution shape program for the calculation of small angle scattering profiles for biological macromolecules in solution

NASA Astrophysics Data System (ADS)

Zhou, J.; Deyhim, A.; Krueger, S.; Gregurick, S. K.

2005-08-01

A program for determining the low resolution shape of biological macromolecules, based on the optimization of a small angle neutron scattering profile to experimental data, is presented. This program, termed LORES, relies on a Monte Carlo optimization procedure and will allow for multiple scattering length densities of complex structures. It is therefore more versatile than utilizing a form factor approach to produce low resolution structural models. LORES is easy to compile and use, and allows for structural modeling of biological samples in real time. To illustrate the effectiveness and versatility of the program, we present four specific biological examples, Apoferritin (shell model), Ribonuclease S (ellipsoidal model), a 10-mer dsDNA (duplex helix) and a construct of a 10-mer DNA/PNA duplex helix (heterogeneous structure). These examples are taken from protein and nucleic acid SANS studies, of both large and small scale structures. We find, in general, that our program will accurately reproduce the geometric shape of a given macromolecule, when compared with the known crystallographic structures. We also present results to illustrate the lower limit of the experimental resolution which the LORES program is capable of modeling. Program summaryTitle of program:LORES Catalogue identifier: ADVC Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVC Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer:SGI Origin200, SGI Octane, SGI Linux, Intel Pentium PC Operating systems:UNIX64 6.5 and LINUX 2.4.7 Programming language used:C Memory required to execute with typical data:8 MB No. of lines in distributed program, including test data, etc.:2270 No. of bytes in distributed program, including test data, etc.:13 302 Distribution format:tar.gz External subprograms used:The entire code must be linked with the MATH library

Impacts of model spatial resolution on the vertical structure of convection in the tropics

NASA Astrophysics Data System (ADS)

Bui, Hien Xuan; Yu, Jia-Yuh; Chou, Chia

2018-02-01

This study examined the impacts of model horizontal resolution on vertical structures of convection in the tropics by performing sensitivity experiments with the NCAR CESM1. It was found that contributions to the total precipitation between top-heavy and bottom-heavy convection are different among various resolutions. A coarser resolution tends to produce a greater contribution from top-heavy convection and, as a result, stronger precipitation in the western Pacific ITCZ; while there is less contribution from bottom-heavy convection and weaker precipitation in the eastern Pacific ITCZ. In the western Pacific ITCZ, where the convection is dominated by a top-heavy structure, the stronger precipitation in coarser resolution experiments is due to changes in temperature and moisture profiles associated with a warmer environment (i.e., thermodynamical effect). In the eastern Pacific ITCZ, where the convection is dictated by a bottom-heavy structure, the stronger precipitation in finer resolution experiments comes from changes in convection structure (i.e., dynamic effect) which favors a greater contribution of bottom-heavy convection as the model resolution goes higher. The moisture budget analysis further suggested that the very different behavior in precipitation tendencies in response to model resolution changes between the western and eastern Pacific ITCZs are determined mainly by changes in convective structure rather than changes in convective strength. This study pointed out the importance of model spatial resolution in reproducing a reasonable contribution to the total precipitation between top-heavy and bottom-heavy structure of convection in the tropical Pacific ITCZs.

Uncertainty of global summer precipitation in the CMIP5 models: a comparison between high-resolution and low-resolution models

NASA Astrophysics Data System (ADS)

Huang, Danqing; Yan, Peiwen; Zhu, Jian; Zhang, Yaocun; Kuang, Xueyuan; Cheng, Jing

2018-04-01

The uncertainty of global summer precipitation simulated by the 23 CMIP5 CGCMs and the possible impacts of model resolutions are investigated in this study. Large uncertainties exist over the tropical and subtropical regions, which can be mainly attributed to convective precipitation simulation. High-resolution models (HRMs) and low-resolution models (LRMs) are further investigated to demonstrate their different contributions to the uncertainties of the ensemble mean. It shows that the high-resolution model ensemble means (HMME) and low-resolution model ensemble mean (LMME) mitigate the biases between the MME and observation over most continents and oceans, respectively. The HMME simulates more precipitation than the LMME over most oceans, but less precipitation over some continents. The dominant precipitation category in the HRMs (LRMs) is the heavy precipitation (moderate precipitation) over the tropic regions. The combinations of convective and stratiform precipitation are also quite different: the HMME has much higher ratio of stratiform precipitation while the LMME has more convective precipitation. Finally, differences in precipitation between the HMME and LMME can be traced to their differences in the SST simulations via the local and remote air-sea interaction.

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

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.

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

Integration of High-Resolution Laser Displacement Sensors and 3D Printing for Structural Health Monitoring

PubMed Central

Chang, Shu-Wei; Kuo, Shih-Yu; Huang, Ting-Hsuan

2017-01-01

This paper presents a novel experimental design for complex structural health monitoring (SHM) studies achieved by integrating 3D printing technologies, high-resolution laser displacement sensors, and multiscale entropy SHM theory. A seven-story structure with a variety of composite bracing systems was constructed using a dual-material 3D printer. A wireless Bluetooth vibration speaker was used to excite the ground floor of the structure, and high-resolution laser displacement sensors (1-μm resolution) were used to monitor the displacement history on different floors. Our results showed that the multiscale entropy SHM method could detect damage on the 3D-printed structures. The results of this study demonstrate that integrating 3D printing technologies and high-resolution laser displacement sensors enables the design of cheap, fast processing, complex, small-scale civil structures for future SHM studies. The novel experimental design proposed in this study provides a suitable platform for investigating the validity and sensitivity of SHM in different composite structures and damage conditions for real life applications in the future. PMID:29271937

Integration of High-Resolution Laser Displacement Sensors and 3D Printing for Structural Health Monitoring.

PubMed

Chang, Shu-Wei; Lin, Tzu-Kang; Kuo, Shih-Yu; Huang, Ting-Hsuan

2017-12-22

This paper presents a novel experimental design for complex structural health monitoring (SHM) studies achieved by integrating 3D printing technologies, high-resolution laser displacement sensors, and multiscale entropy SHM theory. A seven-story structure with a variety of composite bracing systems was constructed using a dual-material 3D printer. A wireless Bluetooth vibration speaker was used to excite the ground floor of the structure, and high-resolution laser displacement sensors (1-μm resolution) were used to monitor the displacement history on different floors. Our results showed that the multiscale entropy SHM method could detect damage on the 3D-printed structures. The results of this study demonstrate that integrating 3D printing technologies and high-resolution laser displacement sensors enables the design of cheap, fast processing, complex, small-scale civil structures for future SHM studies. The novel experimental design proposed in this study provides a suitable platform for investigating the validity and sensitivity of SHM in different composite structures and damage conditions for real life applications in the future.

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.

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.

Low-Cost Ultra-High Spatial and Temporal Resolution Mapping of Intertidal Rock Platforms

NASA Astrophysics Data System (ADS)

Bryson, M.; Johnson-Roberson, M.; Murphy, R.

2012-07-01

Intertidal ecosystems have primarily been studied using field-based sampling; remote sensing offers the ability to collect data over large areas in a snapshot of time which could compliment field-based sampling methods by extrapolating them into the wider spatial and temporal context. Conventional remote sensing tools (such as satellite and aircraft imaging) provide data at relatively course, sub-meter resolutions or with limited temporal resolutions and relatively high costs for small-scale environmental science and ecology studies. In this paper, we describe a low-cost, kite-based imaging system and photogrammetric pipeline that was developed for constructing highresolution, 3D, photo-realistic terrain models of intertidal rocky shores. The processing pipeline uses automatic image feature detection and matching, structure-from-motion and photo-textured terrain surface reconstruction algorithms that require minimal human input and only a small number of ground control points and allow the use of cheap, consumer-grade digital cameras. The resulting maps combine colour and topographic information at sub-centimeter resolutions over an area of approximately 100m, thus enabling spatial properties of the intertidal environment to be determined across a hierarchy of spatial scales. Results of the system are presented for an intertidal rock platform at Cape Banks, Sydney, Australia. Potential uses of this technique include mapping of plant (micro- and macro-algae) and animal (e.g. gastropods) assemblages at multiple spatial and temporal scales.

Structure of Sputnik, a virophage, at 3.5-Å resolution

PubMed Central

Zhang, Xinzheng; Sun, Siyang; Xiang, Ye; Wong, Jimson; Klose, Thomas; Raoult, Didier; Rossmann, Michael G.

2012-01-01

“Sputnik” is a dsDNA virus, referred to as a virophage, that is coassembled with Mimivirus in the host amoeba. We have used cryo-EM to produce an electron density map of the icosahedral Sputnik virus at 3.5-Å resolution, sufficient to verify the identity of most amino acids in the capsid proteins and to establish the identity of the pentameric protein forming the fivefold vertices. It was also shown that the virus lacks an internal membrane. The capsid is organized into a T = 27 lattice in which there are 260 trimeric capsomers and 12 pentameric capsomers. The trimeric capsomers consist of three double “jelly-roll” major capsid proteins creating pseudohexameric capsomer symmetry. The pentameric capsomers consist of five single jelly-roll proteins. The release of the genome by displacing one or more of the pentameric capsomers may be the result of a low-pH environment. These results suggest a mechanism of Sputnik DNA ejection that probably also occurs in other big icosahedral double jelly-roll viruses such as Adenovirus. In this study, the near-atomic resolution structure of a virus has been established where crystallization for X-ray crystallography was not feasible. PMID:23091035

Structure of Sputnik, a virophage, at 3.5-Å resolution.

PubMed

Zhang, Xinzheng; Sun, Siyang; Xiang, Ye; Wong, Jimson; Klose, Thomas; Raoult, Didier; Rossmann, Michael G

2012-11-06

"Sputnik" is a dsDNA virus, referred to as a virophage, that is coassembled with Mimivirus in the host amoeba. We have used cryo-EM to produce an electron density map of the icosahedral Sputnik virus at 3.5-Å resolution, sufficient to verify the identity of most amino acids in the capsid proteins and to establish the identity of the pentameric protein forming the fivefold vertices. It was also shown that the virus lacks an internal membrane. The capsid is organized into a T = 27 lattice in which there are 260 trimeric capsomers and 12 pentameric capsomers. The trimeric capsomers consist of three double "jelly-roll" major capsid proteins creating pseudohexameric capsomer symmetry. The pentameric capsomers consist of five single jelly-roll proteins. The release of the genome by displacing one or more of the pentameric capsomers may be the result of a low-pH environment. These results suggest a mechanism of Sputnik DNA ejection that probably also occurs in other big icosahedral double jelly-roll viruses such as Adenovirus. In this study, the near-atomic resolution structure of a virus has been established where crystallization for X-ray crystallography was not feasible.

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.

Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods.

PubMed

Patel, Trushar R; Chojnowski, Grzegorz; Astha; Koul, Amit; McKenna, Sean A; Bujnicki, Janusz M

2017-04-15

The diverse functional cellular roles played by ribonucleic acids (RNA) have emphasized the need to develop rapid and accurate methodologies to elucidate the relationship between the structure and function of RNA. Structural biology tools such as X-ray crystallography and Nuclear Magnetic Resonance are highly useful methods to obtain atomic-level resolution models of macromolecules. However, both methods have sample, time, and technical limitations that prevent their application to a number of macromolecules of interest. An emerging alternative to high-resolution structural techniques is to employ a hybrid approach that combines low-resolution shape information about macromolecules and their complexes from experimental hydrodynamic (e.g. analytical ultracentrifugation) and solution scattering measurements (e.g., solution X-ray or neutron scattering), with computational modeling to obtain atomic-level models. While promising, scattering methods rely on aggregation-free, monodispersed preparations and therefore the careful development of a quality control pipeline is fundamental to an unbiased and reliable structural determination. This review article describes hydrodynamic techniques that are highly valuable for homogeneity studies, scattering techniques useful to study the low-resolution shape, and strategies for computational modeling to obtain high-resolution 3D structural models of RNAs, proteins, and RNA-protein complexes. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

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.

High Resolution X-ray Scattering Studies of Structural Phase Transitions in BaFe2-x Cr x As 2

NASA Astrophysics Data System (ADS)

Gaulin, B. D.; Clancy, J. P.; Wagman, J. J.; Sefat, A. S.

2011-03-01

While the effects of electron-doping on the parent compounds of the 122 family of Fe-based superconductors have been extremely well-studied in recent years, far less is known about the influence of hole-doping in compounds such as BaFe 2-x Cr x As 2 . In contrast to the electron-doped 122 systems, the hole-doped compounds do not become superconducting. Furthermore, while the hole-doped compounds exhibit similar structural and magnetic phase transitions, they appear to be much less sensitive to dopant concentration. We have performed high resolution x-ray scattering and magnetic susceptibility measurements on single crystal samples of BaFe 2-x Cr x As 2 for Cr concentrations ranging from 0 <= x <= 0.67 . These measurements allow us to determine the magnetic and structural phase transitions for this series and map out the low temperature phase diagram as a function of doping. In particular, we have carried out detailed measurements of the tetragonal (I4/mmm) to orthorhombic (Fmmm) structural phase transition which reveal how the orthorhombicity of the system evolves with increasing Cr concentration and how this correlates with the values of Ts and Tm .

Identifying Li-rich giants from low-resolution spectroscopic survey

NASA Astrophysics Data System (ADS)

Kumar, Yerra Bharat; Reddy, Bacham Eswar; Zhao, Gang

2018-04-01

In this paper we discuss our choice of a large unbiased sample used for the survey of red giant branch stars for finding Li-rich K giants, and the method used for identifying Li-rich candidates using low-resolution spectra. The sample has 2000 giants within a mass range of 0.8 to 3.0it{M}_{⊙}. Sample stars were selected from the Hipparcos catalogue with colour (B-V) and luminosity (it{L}/it{L}_{⊙}) in such way that the sample covers RGB evolution from its base towards RGB tip passing through first dredge-up and luminosity bump. Low-resolution (R ≈ 2000, 3500, 5000) spectra were obtained for all sample stars. Using core strength ratios of lines at Li I 6707 Å and its adjacent line Ca I 6717 Å we successfully identified 15 K giants with A(Li) > 1.5 dex, which are defined as Li-rich K giants. The results demonstrate the usefulness of low-resolution spectra to measure Li abundance and identify Li-rich giants from a large sample of stars in relatively shorter time periods.

Low resolution spectroscopic investigation of Am stars using Automated method

NASA Astrophysics Data System (ADS)

Sharma, Kaushal; Joshi, Santosh; Singh, Harinder P.

2018-04-01

The automated method of full spectrum fitting gives reliable estimates of stellar atmospheric parameters (Teff, log g and [Fe/H]) for late A, F, G, and early K type stars. Recently, the technique was further improved in the cooler regime and the validity range was extended up to a spectral type of M6 - M7 (Teff˜ 2900 K). The present study aims to explore the application of this method on the low-resolution spectra of Am stars, a class of chemically peculiar stars, to examine its robustness for these objects. We use ULySS with the Medium-resolution INT Library of Empirical Spectra (MILES) V2 spectral interpolator for parameter determination. The determined Teff and log g values are found to be in good agreement with those obtained from high-resolution spectroscopy.

Super-Resolution Person Re-Identification With Semi-Coupled Low-Rank Discriminant Dictionary Learning.

PubMed

Jing, Xiao-Yuan; Zhu, Xiaoke; Wu, Fei; Hu, Ruimin; You, Xinge; Wang, Yunhong; Feng, Hui; Yang, Jing-Yu

2017-03-01

Person re-identification has been widely studied due to its importance in surveillance and forensics applications. In practice, gallery images are high resolution (HR), while probe images are usually low resolution (LR) in the identification scenarios with large variation of illumination, weather, or quality of cameras. Person re-identification in this kind of scenarios, which we call super-resolution (SR) person re-identification, has not been well studied. In this paper, we propose a semi-coupled low-rank discriminant dictionary learning (SLD 2 L) approach for SR person re-identification task. With the HR and LR dictionary pair and mapping matrices learned from the features of HR and LR training images, SLD 2 L can convert the features of the LR probe images into HR features. To ensure that the converted features have favorable discriminative capability and the learned dictionaries can well characterize intrinsic feature spaces of the HR and LR images, we design a discriminant term and a low-rank regularization term for SLD 2 L. Moreover, considering that low resolution results in different degrees of loss for different types of visual appearance features, we propose a multi-view SLD 2 L (MVSLD 2 L) approach, which can learn the type-specific dictionary pair and mappings for each type of feature. Experimental results on multiple publicly available data sets demonstrate the effectiveness of our proposed approaches for the SR person re-identification task.

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.

Protein fiber linear dichroism for structure determination and kinetics in a low-volume, low-wavelength couette flow cell.

PubMed

Dafforn, Timothy R; Rajendra, Jacindra; Halsall, David J; Serpell, Louise C; Rodger, Alison

2004-01-01

High-resolution structure determination of soluble globular proteins relies heavily on x-ray crystallography techniques. Such an approach is often ineffective for investigations into the structure of fibrous proteins as these proteins generally do not crystallize. Thus investigations into fibrous protein structure have relied on less direct methods such as x-ray fiber diffraction and circular dichroism. Ultraviolet linear dichroism has the potential to provide additional information on the structure of such biomolecular systems. However, existing systems are not optimized for the requirements of fibrous proteins. We have designed and built a low-volume (200 microL), low-wavelength (down to 180 nm), low-pathlength (100 microm), high-alignment flow-alignment system (couette) to perform ultraviolet linear dichroism studies on the fibers formed by a range of biomolecules. The apparatus has been tested using a number of proteins for which longer wavelength linear dichroism spectra had already been measured. The new couette cell has also been used to obtain data on two medically important protein fibers, the all-beta-sheet amyloid fibers of the Alzheimer's derived protein Abeta and the long-chain assemblies of alpha1-antitrypsin polymers.

Can low-resolution airborne laser scanning data be used to model stream rating curves?

USGS Publications Warehouse

Lyon, Steve; Nathanson, Marcus; Lam, Norris; Dahlke, Helen; Rutzinger, Martin; Kean, Jason W.; Laudon, Hjalmar

2015-01-01

This pilot study explores the potential of using low-resolution (0.2 points/m2) airborne laser scanning (ALS)-derived elevation data to model stream rating curves. Rating curves, which allow the functional translation of stream water depth into discharge, making them integral to water resource monitoring efforts, were modeled using a physics-based approach that captures basic geometric measurements to establish flow resistance due to implicit channel roughness. We tested synthetically thinned high-resolution (more than 2 points/m2) ALS data as a proxy for low-resolution data at a point density equivalent to that obtained within most national-scale ALS strategies. Our results show that the errors incurred due to the effect of low-resolution versus high-resolution ALS data were less than those due to flow measurement and empirical rating curve fitting uncertainties. As such, although there likely are scale and technical limitations to consider, it is theoretically possible to generate rating curves in a river network from ALS data of the resolution anticipated within national-scale ALS schemes (at least for rivers with relatively simple geometries). This is promising, since generating rating curves from ALS scans would greatly enhance our ability to monitor streamflow by simplifying the overall effort required.

Detection of grapes in natural environment using HOG features in low resolution images

NASA Astrophysics Data System (ADS)

Škrabánek, Pavel; Majerík, Filip

2017-07-01

Detection of grapes in real-life images has importance in various viticulture applications. A grape detector based on an SVM classifier, in combination with a HOG descriptor, has proven to be very efficient in detection of white varieties in high-resolution images. Nevertheless, the high time complexity of such utilization was not suitable for its real-time applications, even when a detector of a simplified structure was used. Thus, we examined possibilities of the simplified version application on images of lower resolutions. For this purpose, we designed a method aimed at search for a detector’s setting which gives the best time complexity vs. performance ratio. In order to provide precise evaluation results, we formed new extended datasets. We discovered that even applied on low-resolution images, the simplified detector, with an appropriate setting of all tuneable parameters, was competitive with other state of the art solutions. We concluded that the detector is qualified for real-time detection of grapes in real-life images.

Improved image reconstruction of low-resolution multichannel phase contrast angiography

PubMed Central

P. Krishnan, Akshara; Joy, Ajin; Paul, Joseph Suresh

2016-01-01

Abstract. In low-resolution phase contrast magnetic resonance angiography, the maximum intensity projected channel images will be blurred with consequent loss of vascular details. The channel images are enhanced using a stabilized deblurring filter, applied to each channel prior to combining the individual channel images. The stabilized deblurring is obtained by the addition of a nonlocal regularization term to the reverse heat equation, referred to as nonlocally stabilized reverse diffusion filter. Unlike reverse diffusion filter, which is highly unstable and blows up noise, nonlocal stabilization enhances intensity projected parallel images uniformly. Application to multichannel vessel enhancement is illustrated using both volunteer data and simulated multichannel angiograms. Robustness of the filter applied to volunteer datasets is shown using statistically validated improvement in flow quantification. Improved performance in terms of preserving vascular structures and phased array reconstruction in both simulated and real data is demonstrated using structureness measure and contrast ratio. PMID:26835501

High resolution x-ray diffraction analysis of annealed low-temperature gallium arsenide

NASA Astrophysics Data System (ADS)

Matyi, R. J.; Melloch, M. R.; Woodall, J. M.

1992-05-01

High resolution x-ray diffraction methods have been used to characterize GaAs grown at low substrate temperatures by molecular beam epitaxy and to examine the effects of post-growth annealing on the structure of the layers. Double crystal rocking curves from the as-deposited epitaxial layer show well-defined interference fringes, indicating a high level of structural perfection despite the presence of excess arsenic. Annealing at temperatures from 700 to 900 °C resulted in a decrease in the perpendicular lattice mismatch between the GaAs grown at low temperature and the substrate from 0.133% to 0.016% and a decrease (but not total elimination) of the visibility of the interference fringes. Triple-crystal diffraction scans around the 004 point in reciprocal space exhibited an increase in the apparent mosaic spread of the epitaxial layer with increasing anneal temperature. The observations are explained in terms of the growth of arsenic precipitates in the epitaxial layer.

Evaluation of resolution-precision relationships when using Structure-from-Motion to measure low intensity erosion processes, within a laboratory setting.

NASA Astrophysics Data System (ADS)

Benaud, Pia; Anderson, Karen; Quine, Timothy; James, Mike; Quinton, John; Brazier, Richard E.

2017-04-01

The accessibility of Structure-from-Motion Multi-Stereo View (SfM) and the potential for multi-temporal applications, offers an exciting opportunity to quantify soil erosion spatially. Accordingly, published research provides examples of the successful quantification of large erosion features and events, to centimetre accuracy. Through rigorous control of the camera and image network geometry, the centimetre accuracy achievable at the field scale, can translate to sub-millimetre accuracies within a laboratory environment. The broad aim of this study, therefore, was to understand how ultra-high-resolution spatial information on soil surface topography, derived from SfM, can be utilised to develop a spatially explicit, mechanistic understanding of rill and inter-rill erosion, under experimental conditions. A rainfall simulator was used to create three soil surface conditions; compaction and rainsplash erosion, inter-rill erosion, and rill erosion. Total sediment capture was the primary validation for the experiments, allowing the comparison between structurally and volumetrically derived change, and true soil loss. A Terrestrial Laser Scanner (resolution of ca. 0.8mm) was employed to assess spatial discrepancies within the SfM datasets and to provide an alternative measure of volumetric change. The body of work will present the workflow that has been developed for the laboratory-scale studies and provide information on the importance of DTM resolution for volumetric calculations of soil loss, under different soil surface conditions. To-date, using the methodology presented, point clouds with ca. 3.38 x 107 points per m2, and RMSE values of 0.17 to 0.43 mm (relative precision 1:2023-5117), were constructed. Preliminary results suggest a decrease in DTM resolution from 0.5 to 10 mm does not result in a significant change in volumetric calculations (p = 0.088), while affording a 24-fold decrease in processing times, but may impact negatively on mechanistic understanding

Improved accuracy of quantitative parameter estimates in dynamic contrast-enhanced CT study with low temporal resolution

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

Kim, Sun Mo, E-mail: Sunmo.Kim@rmp.uhn.on.ca; Haider, Masoom A.; Jaffray, David A.

Purpose: A previously proposed method to reduce radiation dose to patient in dynamic contrast-enhanced (DCE) CT is enhanced by principal component analysis (PCA) filtering which improves the signal-to-noise ratio (SNR) of time-concentration curves in the DCE-CT study. The efficacy of the combined method to maintain the accuracy of kinetic parameter estimates at low temporal resolution is investigated with pixel-by-pixel kinetic analysis of DCE-CT data. Methods: The method is based on DCE-CT scanning performed with low temporal resolution to reduce the radiation dose to the patient. The arterial input function (AIF) with high temporal resolution can be generated with a coarselymore » sampled AIF through a previously published method of AIF estimation. To increase the SNR of time-concentration curves (tissue curves), first, a region-of-interest is segmented into squares composed of 3 × 3 pixels in size. Subsequently, the PCA filtering combined with a fraction of residual information criterion is applied to all the segmented squares for further improvement of their SNRs. The proposed method was applied to each DCE-CT data set of a cohort of 14 patients at varying levels of down-sampling. The kinetic analyses using the modified Tofts’ model and singular value decomposition method, then, were carried out for each of the down-sampling schemes between the intervals from 2 to 15 s. The results were compared with analyses done with the measured data in high temporal resolution (i.e., original scanning frequency) as the reference. Results: The patients’ AIFs were estimated to high accuracy based on the 11 orthonormal bases of arterial impulse responses established in the previous paper. In addition, noise in the images was effectively reduced by using five principal components of the tissue curves for filtering. Kinetic analyses using the proposed method showed superior results compared to those with down-sampling alone; they were able to maintain the accuracy in the

High-resolution neutron diffraction study of CuNCN: New evidence of structure anomalies at low temperature

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

Jacobs, Philipp; Houben, Andreas; Dronskowski, Richard, E-mail: drons@HAL9000.ac.rwth-aachen.de

Copper carbodiimide (CuNCN) is the nitrogen-containing analogue of cupric oxide. Based on high-resolution neutron-diffraction data, CuNCN's lattice parameters are derived as a function of the temperature. In accordance with a recent synchrotron study, a clear trend in the cell parameter a is observed accompanying the changing magnetic behavior. With decreasing temperature, a slowly decreases to a minimum at ∼100 K after which it rises again. The same trend—albeit more pronounced—is observed for the c lattice parameter at ∼35 K. The herein presented neutron powder-diffraction data also support the conjectured sequence of transitions from the high-temperature one-dimensional resonating valence-bond (RVB) statemore » to a transient two-dimensional RVB state and eventually, at lowest temperatures, into another two-dimensional RVB state, presumably the ground state.« less

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.

Survey of predictors of propensity for protein production and crystallization with application to predict resolution of crystal structures

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

Gao, Jianzhao; Wu, Zhonghua; Hu, Gang

Selection of proper targets for the X-ray crystallography will benefit biological research community immensely. Several computational models were proposed to predict propensity of successful protein production and diffraction quality crystallization from protein sequences. We reviewed a comprehensive collection of 22 such predictors that were developed in the last decade. We found that almost all of these models are easily accessible as webservers and/or standalone software and we demonstrated that some of them are widely used by the research community. We empirically evaluated and compared the predictive performance of seven representative methods. The analysis suggests that these methods produce quite accuratemore » propensities for the diffraction-quality crystallization. We also summarized results of the first study of the relation between these predictive propensities and the resolution of the crystallizable proteins. We found that the propensities predicted by several methods are significantly higher for proteins that have high resolution structures compared to those with the low resolution structures. Moreover, we tested a new meta-predictor, MetaXXC, which averages the propensities generated by the three most accurate predictors of the diffraction-quality crystallization. MetaXXC generates putative values of resolution that have modest levels of correlation with the experimental resolutions and it offers the lowest mean absolute error when compared to the seven considered methods. We conclude that protein sequences can be used to fairly accurately predict whether their corresponding protein structures can be solved using X-ray crystallography. Moreover, we also ascertain that sequences can be used to reasonably well predict the resolution of the resulting protein crystals.« less

Sequence requirements of oligonucleotide chiral selectors for the capillary electrophoresis resolution of low-affinity DNA binders.

PubMed

Tohala, Luma; Oukacine, Farid; Ravelet, Corinne; Peyrin, Eric

2017-05-01

We recently reported that a great variety of DNA oligonucleotides (ONs) used as chiral selectors in partial-filling capillary electrophoresis (CE) exhibited interesting enantioresolution properties toward low-affinity DNA binders. Herein, the sequence prerequisites of ONs for the CE enantioseparation process were studied. First, the chiral resolution properties of a series of homopolymeric sequences (Poly-dT) of different lengths (from 5 to 60-mer) were investigated. It was shown that the size increase-dependent random coil-like conformation of Poly-dT favorably acted on the apparent selectivity and resolution. The base-unpairing state constituted also an important factor in the chiral resolution ability of ONs as the switch from the single-stranded to double-stranded structure was responsible for a significant decrease in the analyte selectivity range. Finally, the chemical diversity enhanced the enantioresolution ability of single-stranded ONs. The present work could lay the foundation for the design of performant ON chiral selectors for the CE separation of weak DNA binder enantiomers. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Theoretical Models of Low-Resolution Microwave Rotational Spectra of Ethane- and Propanethiol

NASA Astrophysics Data System (ADS)

Kadjar, Ch. O.; Kazimova, S. B.; Hasanova, A. S.; Ismailzadeh, G. I.; Menzeleyev, M. R.

2018-05-01

Additive modeling of low-resolution microwave spectra of heteroisomeric substituted hydrocarbons produced theoretical spectra of ethanethiol and propanethiol in the range 0-2 THz with maxima at 465 ± 20 and 240 ± 20 GHz. More precise calculations in a narrow frequency band of these ranges used spectral line half-widths of 1.5, 0.8, and 0.5 MHz that modeled conditions in different layers of Earth's troposphere. The strongest extrema of the low-resolution spectra of the studied molecules were found at 486 ± 5, 446 ± 5, and 436 ± 5 (ethanethiol) and at 257 ± 5, 239 ± 5, and 234 ± 5 GHz (propanethiol). Various aspects of the application of the results were discussed.

Neural network application for thermal image recognition of low-resolution objects

NASA Astrophysics Data System (ADS)

Fang, Yi-Chin; Wu, Bo-Wen

2007-02-01

In the ever-changing situation on a battle field, accurate recognition of a distant object is critical to a commander's decision-making and the general public's safety. Efficiently distinguishing between an enemy's armoured vehicles and ordinary civilian houses under all weather conditions has become an important research topic. This study presents a system for recognizing an armoured vehicle by distinguishing marks and contours. The characteristics of 12 different shapes and 12 characters are used to explore thermal image recognition under the circumstance of long distance and low resolution. Although the recognition capability of human eyes is superior to that of artificial intelligence under normal conditions, it tends to deteriorate substantially under long-distance and low-resolution scenarios. This study presents an effective method for choosing features and processing images. The artificial neural network technique is applied to further improve the probability of accurate recognition well beyond the limit of the recognition capability of human eyes.

Resolution of a Low-Lying Placenta and Placenta Previa Diagnosed at the Midtrimester Anatomy Scan.

PubMed

Durst, Jennifer K; Tuuli, Methodius G; Temming, Lorene A; Hamilton, Owen; Dicke, Jeffrey M

2018-02-05

To identify the incidence and resolution rates of a low-lying placenta or placenta previa and to assess the optimal time to perform follow-up ultrasonography (US) to assess for resolution. We conducted a retrospective cohort study of women with a diagnosis of a low-lying placenta or placenta previa at routine anatomic screening. Follow-up US examinations were reviewed to estimate the proportion of women who had resolution. A Kaplan-Meier survival curve was generated to estimate the median time to resolution. The distance of the placental edge from the internal cervical os was used to categorize the placenta as previa or low-lying (0.1-10 or ≥ 10-20 mm). A time-to-event analysis was used to estimate predictive factors and the time to resolution by distance from the os. A total of 1663 (8.7%) women had a diagnosis of a low-lying placenta or placenta previa. The cumulative resolution for women who completed 1 or more additional US examinations was 91.9% (95% confidence interval, 90.2%-93.3%). The median time to resolution was 10 (interquartile range [IQR], 7-13) weeks. The distance from the internal cervical os was known for 658 (51.0%) women. The probability of resolution was inversely proportional to the distance from the internal os: 99.5% (≥10-20 mm), 95.4% (0.1-10 mm), and 72.3% (placenta previa; P < .001). The median times to resolution were 9 (IQR, 7-12) weeks for 10 to 20 mm, 10 (IQR, 7-13) weeks for 0.1 to 10 mm, and 12 (IQR, 9-15) weeks for placenta previa (P = .0003, log rank test). A low-lying placenta or placenta previa diagnosed at the midtrimester anatomy survey resolves in most patients. Resolution is near universal in patients with an initial distance from the internal os of 10 mm or greater. © 2018 by the American Institute of Ultrasound in Medicine.

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.

Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set.

PubMed

Eyrich, V A; Standley, D M; Friesner, R A

1999-05-14

We report the tertiary structure predictions for 95 proteins ranging in size from 17 to 160 residues starting from known secondary structure. Predictions are obtained from global minimization of an empirical potential function followed by the application of a refined atomic overlap potential. The minimization strategy employed represents a variant of the Monte Carlo plus minimization scheme of Li and Scheraga applied to a reduced model of the protein chain. For all of the cases except beta-proteins larger than 75 residues, a native-like structure, usually 4-6 A root-mean-square deviation from the native, is located. For beta-proteins larger than 75 residues, the energy gap between native-like structures and the lowest energy structures produced in the simulation is large, so that low RMSD structures are not generated starting from an unfolded state. This is attributed to the lack of an explicit hydrogen bond term in the potential function, which we hypothesize is necessary to stabilize large assemblies of beta-strands. Copyright 1999 Academic Press.

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.

Low-resolution ship detection from high-altitude aerial images

NASA Astrophysics Data System (ADS)

Qi, Shengxiang; Wu, Jianmin; Zhou, Qing; Kang, Minyang

2018-02-01

Ship detection from optical images taken by high-altitude aircrafts such as unmanned long-endurance airships and unmanned aerial vehicles has broad applications in marine fishery management, ship monitoring and vessel salvage. However, the major challenge is the limited capability of information processing on unmanned high-altitude platforms. Furthermore, in order to guarantee the wide detection range, unmanned aircrafts generally cruise at high altitudes, resulting in imagery with low-resolution targets and strong clutters suffered by heavy clouds. In this paper, we propose a low-resolution ship detection method to extract ships from these high-altitude optical images. Inspired by a recent research on visual saliency detection indicating that small salient signals could be well detected by a gradient enhancement operation combined with Gaussian smoothing, we propose the facet kernel filtering to rapidly suppress cluttered backgrounds and delineate candidate target regions from the sea surface. Then, the principal component analysis (PCA) is used to compute the orientation of the target axis, followed by a simplified histogram of oriented gradient (HOG) descriptor to characterize the ship shape property. Finally, support vector machine (SVM) is applied to discriminate real targets and false alarms. Experimental results show that the proposed method actually has high efficiency in low-resolution ship detection.

Spatial Structure of a Braided River: Metric Resolution Hydrodynamic Modeling Reveals What SWOT Might See

NASA Astrophysics Data System (ADS)

Schubert, J.; Sanders, B. F.; Andreadis, K.

2013-12-01

The Surface Water and Ocean Topography (SWOT) mission, currently under study by NASA (National Aeronautics and Space Administration) and CNES (Centre National d'Etudes Spatiales), is designed to provide global spatial measurements of surface water properties at resolutions better than 10 m and with centimetric accuracy. The data produced by SWOT will include irregularly spaced point clouds of the water surface height, with point spacings from roughly 2-50 m depending on a point's location within SWOT's swath. This could offer unprecedented insight into the spatial structure of rivers. Features that may be resolved include backwater profiles behind dams, drawdown profiles, uniform flow sections, critical flow sections, and even riffle-pool flow structures. In the event that SWOT scans a river during a major flood, it becomes possible to delineate the limits of the flood as well as the spatial structure of the water surface elevation, yielding insight into the dynamic interaction of channels and flood plains. The Platte River in Nebraska, USA, is a braided river with a width and slope of approximately 100 m and 100 cm/km, respectively. A 1 m resolution Digital Terrain Model (DTM) of the river basin, based on airborne lidar collected during low-flow conditions, was used to parameterize a two-dimensional, variable resolution, unstructured grid, hydrodynamic model that uses 3 m resolution triangles in low flow channels and 10 m resolution triangles in the floodplain. Use of a fine resolution mesh guarantees that local variability in topography is resolved, and after applying the hydrodynamic model, the effects of topographic variability are expressed as variability in the water surface height, depth-averaged velocity and flow depth. Flow is modeled over a reach length of 10 km for multi-day durations to capture both frequent (diurnal variations associated with regulated flow) and infrequent (extreme flooding) flow phenomena. Model outputs reveal a number of interesting

Modeling protein structure at near atomic resolutions with Gorgon.

PubMed

Baker, Matthew L; Abeysinghe, Sasakthi S; Schuh, Stephen; Coleman, Ross A; Abrams, Austin; Marsh, Michael P; Hryc, Corey F; Ruths, Troy; Chiu, Wah; Ju, Tao

2011-05-01

Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure. Copyright © 2011 Elsevier Inc. All rights reserved.

MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping.

PubMed

Zhang, Chengxin; Zheng, Wei; Freddolino, Peter L; Zhang, Yang

2018-03-10

Homology-based transferal remains the major approach to computational protein function annotations, but it becomes increasingly unreliable when the sequence identity between query and template decreases below 30%. We propose a novel pipeline, MetaGO, to deduce Gene Ontology attributes of proteins by combining sequence homology-based annotation with low-resolution structure prediction and comparison, and partner's homology-based protein-protein network mapping. The pipeline was tested on a large-scale set of 1000 non-redundant proteins from the CAFA3 experiment. Under the stringent benchmark conditions where templates with >30% sequence identity to the query are excluded, MetaGO achieves average F-measures of 0.487, 0.408, and 0.598, for Molecular Function, Biological Process, and Cellular Component, respectively, which are significantly higher than those achieved by other state-of-the-art function annotations methods. Detailed data analysis shows that the major advantage of the MetaGO lies in the new functional homolog detections from partner's homology-based network mapping and structure-based local and global structure alignments, the confidence scores of which can be optimally combined through logistic regression. These data demonstrate the power of using a hybrid model incorporating protein structure and interaction networks to deduce new functional insights beyond traditional sequence homology-based referrals, especially for proteins that lack homologous function templates. The MetaGO pipeline is available at http://zhanglab.ccmb.med.umich.edu/MetaGO/. Copyright © 2018. Published by Elsevier Ltd.

[EEG source localization using LORETA (low resolution electromagnetic tomography)].

PubMed

Puskás, Szilvia

2011-03-30

Eledctroencephalography (EEG) has excellent temporal resolution, but the spatial resolution is poor. Different source localization methods exist to solve the so-called inverse problem, thus increasing the accuracy of spatial localization. This paper provides an overview of the history of source localization and the main categories of techniques are discussed. LORETA (low resolution electromagnetic tomography) is introduced in details: technical informations are discussed and localization properties of LORETA method are compared to other inverse solutions. Validation of the method with different imaging techniques is also discussed. This paper reviews several publications using LORETA both in healthy persons and persons with different neurological and psychiatric diseases. Finally future possible applications are discussed.

A Multi-Resolution Approach for an Automated Fusion of Different Low-Cost 3D Sensors

PubMed Central

Dupuis, Jan; Paulus, Stefan; Behmann, Jan; Plümer, Lutz; Kuhlmann, Heiner

2014-01-01

The 3D acquisition of object structures has become a common technique in many fields of work, e.g., industrial quality management, cultural heritage or crime scene documentation. The requirements on the measuring devices are versatile, because spacious scenes have to be imaged with a high level of detail for selected objects. Thus, the used measuring systems are expensive and require an experienced operator. With the rise of low-cost 3D imaging systems, their integration into the digital documentation process is possible. However, common low-cost sensors have the limitation of a trade-off between range and accuracy, providing either a low resolution of single objects or a limited imaging field. Therefore, the use of multiple sensors is desirable. We show the combined use of two low-cost sensors, the Microsoft Kinect and the David laserscanning system, to achieve low-resolved scans of the whole scene and a high level of detail for selected objects, respectively. Afterwards, the high-resolved David objects are automatically assigned to their corresponding Kinect object by the use of surface feature histograms and SVM-classification. The corresponding objects are fitted using an ICP-implementation to produce a multi-resolution map. The applicability is shown for a fictional crime scene and the reconstruction of a ballistic trajectory. PMID:24763255

A multi-resolution approach for an automated fusion of different low-cost 3D sensors.

PubMed

Dupuis, Jan; Paulus, Stefan; Behmann, Jan; Plümer, Lutz; Kuhlmann, Heiner

2014-04-24

The 3D acquisition of object structures has become a common technique in many fields of work, e.g., industrial quality management, cultural heritage or crime scene documentation. The requirements on the measuring devices are versatile, because spacious scenes have to be imaged with a high level of detail for selected objects. Thus, the used measuring systems are expensive and require an experienced operator. With the rise of low-cost 3D imaging systems, their integration into the digital documentation process is possible. However, common low-cost sensors have the limitation of a trade-off between range and accuracy, providing either a low resolution of single objects or a limited imaging field. Therefore, the use of multiple sensors is desirable. We show the combined use of two low-cost sensors, the Microsoft Kinect and the David laserscanning system, to achieve low-resolved scans of the whole scene and a high level of detail for selected objects, respectively. Afterwards, the high-resolved David objects are automatically assigned to their corresponding Kinect object by the use of surface feature histograms and SVM-classification. The corresponding objects are fitted using an ICP-implementation to produce a multi-resolution map. The applicability is shown for a fictional crime scene and the reconstruction of a ballistic trajectory.

Label-free super-resolution with coherent nonlinear structured-illumination microscopy

NASA Astrophysics Data System (ADS)

Huttunen, Mikko J.; Abbas, Aazad; Upham, Jeremy; Boyd, Robert W.

2017-08-01

Structured-illumination microscopy enables up to a two-fold lateral resolution improvement by spatially modulating the intensity profile of the illumination beam. We propose a novel way to generalize the concept of structured illumination to nonlinear widefield modalities by spatially modulating, instead of field intensities, the phase of the incident field while interferometrically measuring the complex-valued scattered field. We numerically demonstrate that for second-order and third-order processes an almost four- and six-fold increase in lateral resolution is achievable, respectively. This procedure overcomes the conventional Abbe diffraction limit and provides new possibilities for label-free super-resolution microscopy.

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 shear-wave seismic reflection as a tool to image near-surface subrosion structures - a case study in Bad Frankenhausen, Germany

NASA Astrophysics Data System (ADS)

Wadas, Sonja H.; Polom, Ulrich; Krawczyk, Charlotte M.

2016-10-01

Subrosion is the subsurface leaching of soluble rocks that results in the formation of depression and collapse structures. This global phenomenon is a geohazard in urban areas. To study near-surface subrosion structures, four shear-wave seismic reflection profiles, with a total length of ca. 332 m, were carried out around the famous leaning church tower of Bad Frankenhausen in northern Thuringia, Germany, which shows an inclination of 4.93° from the vertical. Most of the geological underground of Thuringia is characterized by soluble Permian deposits, and the Kyffhäuser Southern Margin Fault is assumed to be a main pathway for water to leach the evaporite. The seismic profiles were acquired with the horizontal micro-vibrator ELVIS, developed at Leibniz Institute for Applied Geophysics (LIAG), and a 72 m long landstreamer equipped with 72 horizontal geophones. The high-resolution seismic sections show subrosion-induced structures to a depth of ca. 100 m and reveal five features associated with the leaching of Permian deposits: (1) lateral and vertical varying reflection patterns caused by strongly heterogeneous strata, (2) discontinuous reflectors, small offsets, and faults, which show the underground is heavily fractured, (3) formation of depression structures in the near-surface, (4) diffractions in the unmigrated seismic sections that indicate increased scattering of the seismic waves, and (5) varying seismic velocities and low-velocity zones that are presumably caused by fractures and upward-migrating cavities. A previously undiscovered southward-dipping listric normal fault was also found, to the north of the church. It probably serves as a pathway for water to leach the Permian formations below the church and causes the tilting of the church tower. This case study shows the potential of horizontal shear-wave seismic reflection to image near-surface subrosion structures in an urban environment with a horizontal resolution of less than 1 m in the uppermost 10

A Multi-Resolution Data Structure for Two-Dimensional Morse Functions

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

Bremer, P-T; Edelsbrunner, H; Hamann, B

2003-07-30

The efficient construction of simplified models is a central problem in the field of visualization. We combine topological and geometric methods to construct a multi-resolution data structure for functions over two-dimensional domains. Starting with the Morse-Smale complex we build a hierarchy by progressively canceling critical points in pairs. The data structure supports mesh traversal operations similar to traditional multi-resolution representations.

Structure of human thymidylate synthase under low-salt conditions.

PubMed

Lovelace, Leslie L; Minor, Wladek; Lebioda, Lukasz

2005-05-01

Human thymidylate synthase, a target in cancer chemotherapy, was crystallized from PEG 3350 with 30 mM ammonium sulfate (AS) in the crystallization medium. The crystals are isomorphous with the high-salt crystals ( approximately 2.0 M AS) and the structure has been solved and refined (R = 22.6%, R(free) = 24.3%) at 1.8 A resolution. The high- and low-AS-concentration structures are quite similar, with loop 181-197 is in the inactive conformation. Also, residues 95-106 and 129-135 (eukaryotic inserts region) show high mobility as assessed by poor electron density and high values of crystallographic temperature factors (residues 1-25 and 108-129 are disordered in both structures). The high mobility of this region may reflect the situation at physiological ionic strength. Of the four sulfate ions observed bound at 2.0 M AS, only two are present at 30 mM AS. The inactive conformation appears to be stabilized by the side chain of Val3 or a leucine residue from the disordered regions. The low-salt conditions of these crystals should be much more suitable for the study of thymidylate synthase inhibitors, especially those that utilize sulfate-binding sites to stabilize the inactive conformation of loop 181-197.

A Multi-resolution, Multi-epoch Low Radio Frequency Survey of the Kepler K2 Mission Campaign 1 Field

NASA Astrophysics Data System (ADS)

Tingay, S. J.; Hancock, P. J.; Wayth, R. B.; Intema, H.; Jagannathan, P.; Mooley, K.

2016-10-01

We present the first dedicated radio continuum survey of a Kepler K2 mission field, Field 1, covering the North Galactic Cap. The survey is wide field, contemporaneous, multi-epoch, and multi-resolution in nature and was conducted at low radio frequencies between 140 and 200 MHz. The multi-epoch and ultra wide field (but relatively low resolution) part of the survey was provided by 15 nights of observation using the Murchison Widefield Array (MWA) over a period of approximately a month, contemporaneous with K2 observations of the field. The multi-resolution aspect of the survey was provided by the low resolution (4‧) MWA imaging, complemented by non-contemporaneous but much higher resolution (20″) observations using the Giant Metrewave Radio Telescope (GMRT). The survey is, therefore, sensitive to the details of radio structures across a wide range of angular scales. Consistent with other recent low radio frequency surveys, no significant radio transients or variables were detected in the survey. The resulting source catalogs consist of 1085 and 1468 detections in the two MWA observation bands (centered at 154 and 185 MHz, respectively) and 7445 detections in the GMRT observation band (centered at 148 MHz), over 314 square degrees. The survey is presented as a significant resource for multi-wavelength investigations of the more than 21,000 target objects in the K2 field. We briefly examine our survey data against K2 target lists for dwarf star types (stellar types M and L) that have been known to produce radio flares.

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.

Enhancing Deep-Water Low-Resolution Gridded Bathymetry Using Single Image Super-Resolution

NASA Astrophysics Data System (ADS)

Elmore, P. A.; Nock, K.; Bonanno, D.; Smith, L.; Ferrini, V. L.; Petry, F. E.

2017-12-01

We present research to employ single-image super-resolution (SISR) algorithms to enhance knowledge of the seafloor using the 1-minute GEBCO 2014 grid when 100m grids from high-resolution sonar systems are available for training. Our numerical upscaling experiments of x15 upscaling of the GEBCO grid along three areas of the Eastern Pacific Ocean along mid-ocean ridge systems where we have these 100m gridded bathymetry data sets, which we accept as ground-truth. We show that four SISR algorithms can enhance this low-resolution knowledge of bathymetry versus bicubic or Spline-In-Tension algorithms through upscaling under these conditions: 1) rough topography is present in both training and testing areas and 2) the range of depths and features in the training area contains the range of depths in the enhancement area. We quantitatively judged successful SISR enhancement versus bicubic interpolation when Student's hypothesis testing show significant improvement of the root-mean squared error (RMSE) between upscaled bathymetry and 100m gridded ground-truth bathymetry at p < 0.05. In addition, we found evidence that random forest based SISR methods may provide more robust enhancements versus non-forest based SISR algorithms.

New low-resolution spectrometer spectra for IRAS sources

NASA Astrophysics Data System (ADS)

Volk, Kevin; Kwok, Sun; Stencel, R. E.; Brugel, E.

1991-12-01

Low-resolution spectra of 486 IRAS point sources with Fnu(12 microns) in the range 20-40 Jy are presented. This is part of an effort to extract and classify spectra that were not included in the Atlas of Low-Resolution Spectra and represents an extension of the earlier work by Volk and Cohen which covers sources with Fnu(12 microns) greater than 40 Jy. The spectra have been examined by eye and classified into nine groups based on the spectral morphology. This new classification scheme is compared with the mechanical classification of the Atlas, and the differences are noted. Oxygen-rich stars of the asymptotic giant branch make up 33 percent of the sample. Solid state features dominate the spectra of most sources. It is found that the nature of the sources as implied by the present spectral classification is consistent with the classifications based on broad-band colors of the sources.

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

Remote sensing image segmentation using local sparse structure constrained latent low rank representation

NASA Astrophysics Data System (ADS)

Tian, Shu; Zhang, Ye; Yan, Yimin; Su, Nan; Zhang, Junping

2016-09-01

Latent low-rank representation (LatLRR) has been attached considerable attention in the field of remote sensing image segmentation, due to its effectiveness in exploring the multiple subspace structures of data. However, the increasingly heterogeneous texture information in the high spatial resolution remote sensing images, leads to more severe interference of pixels in local neighborhood, and the LatLRR fails to capture the local complex structure information. Therefore, we present a local sparse structure constrainted latent low-rank representation (LSSLatLRR) segmentation method, which explicitly imposes the local sparse structure constraint on LatLRR to capture the intrinsic local structure in manifold structure feature subspaces. The whole segmentation framework can be viewed as two stages in cascade. In the first stage, we use the local histogram transform to extract the texture local histogram features (LHOG) at each pixel, which can efficiently capture the complex and micro-texture pattern. In the second stage, a local sparse structure (LSS) formulation is established on LHOG, which aims to preserve the local intrinsic structure and enhance the relationship between pixels having similar local characteristics. Meanwhile, by integrating the LSS and the LatLRR, we can efficiently capture the local sparse and low-rank structure in the mixture of feature subspace, and we adopt the subspace segmentation method to improve the segmentation accuracy. Experimental results on the remote sensing images with different spatial resolution show that, compared with three state-of-the-art image segmentation methods, the proposed method achieves more accurate segmentation results.

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 NMR Reveals Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane

PubMed Central

Zook, James D.; Molugu, Trivikram R.; Jacobsen, Neil E.; Lin, Guangxin; Soll, Jürgen; Cherry, Brian R.; Brown, Michael F.; Fromme, Petra

2013-01-01

Solving high-resolution structures for membrane proteins continues to be a daunting challenge in the structural biology community. In this study we report our high-resolution NMR results for a transmembrane protein, outer envelope protein of molar mass 16 kDa (OEP16), an amino acid transporter from the outer membrane of chloroplasts. Three-dimensional, high-resolution NMR experiments on the 13C, 15N, 2H-triply-labeled protein were used to assign protein backbone resonances and to obtain secondary structure information. The results yield over 95% assignment of N, HN, CO, Cα, and Cβ chemical shifts, which is essential for obtaining a high resolution structure from NMR data. Chemical shift analysis from the assignment data reveals experimental evidence for the first time on the location of the secondary structure elements on a per residue basis. In addition T 1Z and T2 relaxation experiments were performed in order to better understand the protein dynamics. Arginine titration experiments yield an insight into the amino acid residues responsible for protein transporter function. The results provide the necessary basis for high-resolution structural determination of this important plant membrane protein. PMID:24205117

Detecting aircraft with a low-resolution infrared sensor.

PubMed

Jakubowicz, Jérémie; Lefebvre, Sidonie; Maire, Florian; Moulines, Eric

2012-06-01

Existing computer simulations of aircraft infrared signature (IRS) do not account for dispersion induced by uncertainty on input data, such as aircraft aspect angles and meteorological conditions. As a result, they are of little use to estimate the detection performance of IR optronic systems; in this case, the scenario encompasses a lot of possible situations that must be indeed addressed, but cannot be singly simulated. In this paper, we focus on low-resolution infrared sensors and we propose a methodological approach for predicting simulated IRS dispersion of poorly known aircraft and performing aircraft detection on the resulting set of low-resolution infrared images. It is based on a sensitivity analysis, which identifies inputs that have negligible influence on the computed IRS and can be set at a constant value, on a quasi-Monte Carlo survey of the code output dispersion, and on a new detection test taking advantage of level sets estimation. This method is illustrated in a typical scenario, i.e., a daylight air-to-ground full-frontal attack by a generic combat aircraft flying at low altitude, over a database of 90,000 simulated aircraft images. Assuming a white noise or a fractional Brownian background model, detection performances are very promising.

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

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

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.

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...

Ultrahigh-resolution mapping of peatland microform using ground-based structure from motion with multiview stereo

NASA Astrophysics Data System (ADS)

Mercer, Jason J.; Westbrook, Cherie J.

2016-11-01

Microform is important in understanding wetland functions and processes. But collecting imagery of and mapping the physical structure of peatlands is often expensive and requires specialized equipment. We assessed the utility of coupling computer vision-based structure from motion with multiview stereo photogrammetry (SfM-MVS) and ground-based photos to map peatland topography. The SfM-MVS technique was tested on an alpine peatland in Banff National Park, Canada, and guidance was provided on minimizing errors. We found that coupling SfM-MVS with ground-based photos taken with a point and shoot camera is a viable and competitive technique for generating ultrahigh-resolution elevations (i.e., <0.01 m, mean absolute error of 0.083 m). In evaluating 100+ viable SfM-MVS data collection and processing scenarios, vegetation was found to considerably influence accuracy. Vegetation class, when accounted for, reduced absolute error by as much as 50%. The logistic flexibility of ground-based SfM-MVS paired with its high resolution, low error, and low cost makes it a research area worth developing as well as a useful addition to the wetland scientists' toolkit.

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.

Hyperspectral Super-Resolution of Locally Low Rank Images From Complementary Multisource Data.

PubMed

Veganzones, Miguel A; Simoes, Miguel; Licciardi, Giorgio; Yokoya, Naoto; Bioucas-Dias, Jose M; Chanussot, Jocelyn

2016-01-01

Remote sensing hyperspectral images (HSIs) are quite often low rank, in the sense that the data belong to a low dimensional subspace/manifold. This has been recently exploited for the fusion of low spatial resolution HSI with high spatial resolution multispectral images in order to obtain super-resolution HSI. Most approaches adopt an unmixing or a matrix factorization perspective. The derived methods have led to state-of-the-art results when the spectral information lies in a low-dimensional subspace/manifold. However, if the subspace/manifold dimensionality spanned by the complete data set is large, i.e., larger than the number of multispectral bands, the performance of these methods mainly decreases because the underlying sparse regression problem is severely ill-posed. In this paper, we propose a local approach to cope with this difficulty. Fundamentally, we exploit the fact that real world HSIs are locally low rank, that is, pixels acquired from a given spatial neighborhood span a very low-dimensional subspace/manifold, i.e., lower or equal than the number of multispectral bands. Thus, we propose to partition the image into patches and solve the data fusion problem independently for each patch. This way, in each patch the subspace/manifold dimensionality is low enough, such that the problem is not ill-posed anymore. We propose two alternative approaches to define the hyperspectral super-resolution through local dictionary learning using endmember induction algorithms. We also explore two alternatives to define the local regions, using sliding windows and binary partition trees. The effectiveness of the proposed approaches is illustrated with synthetic and semi real data.

Wavefield complexity and stealth structures: Resolution constraints by wave physics

NASA Astrophysics Data System (ADS)

Nissen-Meyer, T.; Leng, K.

2017-12-01

Imaging the Earth's interior relies on understanding how waveforms encode information from heterogeneous multi-scale structure. This relation is given by elastodynamics, but forward modeling in the context of tomography primarily serves to deliver synthetic waveforms and gradients for the inversion procedure. While this is entirely appropriate, it depreciates a wealth of complementary inference that can be obtained from the complexity of the wavefield. Here, we are concerned with the imprint of realistic multi-scale Earth structure on the wavefield, and the question on the inherent physical resolution limit of structures encoded in seismograms. We identify parameter and scattering regimes where structures remain invisible as a function of seismic wavelength, structural multi-scale geometry, scattering strength, and propagation path. Ultimately, this will aid in interpreting tomographic images by acknowledging the scope of "forgotten" structures, and shall offer guidance for optimising the selection of seismic data for tomography. To do so, we use our novel 3D modeling method AxiSEM3D which tackles global wave propagation in visco-elastic, anisotropic 3D structures with undulating boundaries at unprecedented resolution and efficiency by exploiting the inherent azimuthal smoothness of wavefields via a coupled Fourier expansion-spectral-element approach. The method links computational cost to wavefield complexity and thereby lends itself well to exploring the relation between waveforms and structures. We will show various examples of multi-scale heterogeneities which appear or disappear in the waveform, and argue that the nature of the structural power spectrum plays a central role in this. We introduce the concept of wavefield learning to examine the true wavefield complexity for a complexity-dependent modeling framework and discriminate which scattering structures can be retrieved by surface measurements. This leads to the question of physical invisibility and the

Using high spectral resolution spectrophotometry to study broad mineral absorption features on Mars

NASA Technical Reports Server (NTRS)

Blaney, D. L.; Crisp, D.

1993-01-01

Traditionally telescopic measurements of mineralogic absorption features have been made using relatively low to moderate (R=30-300) spectral resolution. Mineralogic absorption features tend to be broad so high resolution spectroscopy (R greater than 10,000) does not provide significant additional compositional information. Low to moderate resolution spectroscopy allows an observer to obtain data over a wide wavelength range (hundreds to thousands of wavenumbers) compared to the several wavenumber intervals that are collected using high resolution spectrometers. However, spectrophotometry at high resolution has major advantages over lower resolution spectroscopy in situations that are applicable to studies of the Martian surface, i.e., at wavelengths where relatively weak surface absorption features and atmospheric gas absorption features both occur.

Subwavelength resolution from multilayered structure (Conference Presentation)

NASA Astrophysics Data System (ADS)

Cheng, Bo Han; Jen, Yi-Jun; Liu, Wei-Chih; Lin, Shan-wen; Lan, Yung-Chiang; Tsai, Din Ping

2016-10-01

Breaking optical diffraction limit is one of the most important issues needed to be overcome for the demand of high-density optoelectronic components. Here, a multilayered structure which consists of alternating semiconductor and dielectric layers for breaking optical diffraction limitation at THz frequency region are proposed and analyzed. We numerically demonstrate that such multilayered structure not only can act as a hyperbolic metamaterial but also a birefringence material via the control of the external temperature (or magnetic field). A practical approach is provided to control all the diffraction signals toward a specific direction by using transfer matrix method and effective medium theory. Numerical calculations and computer simulation (based on finite element method, FEM) are carried out, which agree well with each other. The temperature (or magnetic field) parameter can be tuned to create an effective material with nearly flat isofrequency feature to transfer (project) all the k-space signals excited from the object to be resolved to the image plane. Furthermore, this multilayered structure can resolve subwavelength structures at various incident THz light sources simultaneously. In addition, the resolution power for a fixed operating frequency also can be tuned by only changing the magnitude of external magnetic field. Such a device provides a practical route for multi-functional material, photolithography and real-time super-resolution image.

High spatial resolution detection of low-energy electrons using an event-counting method, application to point projection microscopy

NASA Astrophysics Data System (ADS)

Salançon, Evelyne; Degiovanni, Alain; Lapena, Laurent; Morin, Roger

2018-04-01

An event-counting method using a two-microchannel plate stack in a low-energy electron point projection microscope is implemented. 15 μm detector spatial resolution, i.e., the distance between first-neighbor microchannels, is demonstrated. This leads to a 7 times better microscope resolution. Compared to previous work with neutrons [Tremsin et al., Nucl. Instrum. Methods Phys. Res., Sect. A 592, 374 (2008)], the large number of detection events achieved with electrons shows that the local response of the detector is mainly governed by the angle between the hexagonal structures of the two microchannel plates. Using this method in point projection microscopy offers the prospect of working with a greater source-object distance (350 nm instead of 50 nm), advancing toward atomic resolution.

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.

BLIPPED (BLIpped Pure Phase EncoDing) high resolution MRI with low amplitude gradients

NASA Astrophysics Data System (ADS)

Xiao, Dan; Balcom, Bruce J.

2017-12-01

MRI image resolution is proportional to the maximum k-space value, i.e. the temporal integral of the magnetic field gradient. High resolution imaging usually requires high gradient amplitudes and/or long spatial encoding times. Special gradient hardware is often required for high amplitudes and fast switching. We propose a high resolution imaging sequence that employs low amplitude gradients. This method was inspired by the previously proposed PEPI (π Echo Planar Imaging) sequence, which replaced EPI gradient reversals with multiple RF refocusing pulses. It has been shown that when the refocusing RF pulse is of high quality, i.e. sufficiently close to 180°, the magnetization phase introduced by the spatial encoding magnetic field gradient can be preserved and transferred to the following echo signal without phase rewinding. This phase encoding scheme requires blipped gradients that are identical for each echo, with low and constant amplitude, providing opportunities for high resolution imaging. We now extend the sequence to 3D pure phase encoding with low amplitude gradients. The method is compared with the Hybrid-SESPI (Spin Echo Single Point Imaging) technique to demonstrate the advantages in terms of low gradient duty cycle, compensation of concomitant magnetic field effects and minimal echo spacing, which lead to superior image quality and high resolution. The 3D imaging method was then applied with a parallel plate resonator RF probe, achieving a nominal spatial resolution of 17 μm in one dimension in the 3D image, requiring a maximum gradient amplitude of only 5.8 Gauss/cm.

Three-dimensional structure of homodimeric cholesterol esterase-ligand complex at 1.4 Å resolution

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

Pletnev, V.; Addlagatta, A.; Wawrzak, Z.

2010-03-08

The three-dimensional structure of a Candida cylindracea cholesterol esterase (ChE) homodimer (534 x 2 amino acids) in complex with a ligand of proposed formula C{sub 23}H{sub 48}O{sub 2} has been determined at 1.4 {angstrom} resolution in space group P1 using synchrotron low-temperature data. The structure refined to R = 0.136 and R{sub free} = 0.169 and has revealed new stereochemical details in addition to those detected for the apo- and holo-forms at 1.9 and 2.0 {angstrom} resolution, respectively [Ghosh et al. (1995), Structure, 3, 279-288]. The cholesterol esterase structure is a dimer with four spatially separated interfacial contact areas andmore » two symmetry-related pairs of openings to an internal intradimer cavity. Hydrophobic active-site gorges in each subunit face each other across a central interfacial cavity. The ChE subunits have carbohydrate chains attached to their Asn314 and Asn351 residues, with two ordered N-acetyl-D-glucosoamine moieties visible at each site. The side chains of 14 residues have two alternative conformations with occupancy values of 0.5 {+-} 0.2. For each subunit the electron density in the enzyme active-site gorge is well modeled by a C{sub 23}-chain fatty acid.« less

Low-resolution ultraviolet spectroscopy of several hot stars observed from Apollo 17

NASA Technical Reports Server (NTRS)

Henry, R. C.; Weinstein, A.; Feldman, P. D.; Fastie, W. G.; Moos, H. W.

1975-01-01

Low-resolution ultraviolet spectra were obtained for six early-type stars in 1972 December, using an Ebert spectrometer mounted in the service module of the Apollo 17 spacecraft. The spectrometer scanned from 1180 A to 1680 A, with a speed that varied with wavelength according to a program chosen for lunar studies. Spectral resolution was 11 A. The ultraviolet absolute calibration of the instrument was determined by comparison with National Bureau of Standards calibrated photodiodes, and is believed known to plus or minus 10 percent. The absolute intensities are in good general agreement with the observations of other stars and with the predictions of stellar model-atmosphere calculations.

High-Density, High-Resolution, Low-Cost Air Quality Sensor Networks for Urban Air Monitoring

NASA Astrophysics Data System (ADS)

Mead, M. I.; Popoola, O. A.; Stewart, G.; Bright, V.; Kaye, P.; Saffell, J.

2012-12-01

Monitoring air quality in highly granular environments such as urban areas which are spatially heterogeneous with variable emission sources, measurements need to be made at appropriate spatial and temporal scales. Current routine air quality monitoring networks generally are either composed of sparse expensive installations (incorporating e.g. chemiluminescence instruments) or higher density low time resolution systems (e.g. NO2 diffusion tubes). Either approach may not accurately capture important effects such as pollutant "hot spots" or adequately capture spatial (or temporal) variability. As a result, analysis based on data from traditional low spatial resolution networks, such as personal exposure, may be inaccurate. In this paper we present details of a sophisticated, low-cost, multi species (gas phase, speciated PM, meteorology) air quality measurement network methodology incorporating GPS and GPRS which has been developed for high resolution air quality measurements in urban areas. Sensor networks developed in the Centre for Atmospheric Science (University of Cambridge) incorporated electrochemical gas sensors configured for use in urban air quality studies operating at parts-per-billion (ppb) levels. It has been demonstrated that these sensors can be used to measure key air quality gases such as CO, NO and NO2 at the low ppb mixing ratios present in the urban environment (estimated detection limits <4ppb for CO and NO and <1ppb for NO2. Mead et al (submitted Aug., 2012)). Based on this work, a state of the art multi species instrument package for deployment in scalable sensor networks has been developed which has general applicability. This is currently being employed as part of a major 3 year UK program at London Heathrow airport (the Sensor Networks for Air Quality (SNAQ) Heathrow project). The main project outcome is the creation of a calibrated, high spatial and temporal resolution data set for O3, NO, NO2, SO2, CO, CO2, VOCstotal, size-speciated PM

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.

Comparing efficacy of different taxonomic resolutions and surrogates in detecting changes in soft bottom assemblages due to coastal defence structures.

PubMed

Bertasi, Fabio; Colangelo, Marina Antonia; Colosio, Francesco; Gregorio, Gianni; Abbiati, Marco; Ceccherelli, Victor Ugo

2009-05-01

Sandy shores on the West coast of the North Adriatic Sea are extensively protected by different types of defence structures to prevent coastal erosion. Coastal defence schemes modify the hydrodynamic regime, the sediment structure and composition thus affecting the benthic assemblages. This study examines the effectiveness in detecting changes in soft bottom assemblages caused by coastal defence structures by using different levels of taxonomic resolution, polychaetes and/or bivalves as surrogates and different data transformations. A synoptic analyses of three datasets of subtidal benthic macrofauna used in studies aimed at assessing the impact of breakwaters along the North Adriatic coast has been done. Analyses of similarities and correlations between distance matrices were done using matrices with different levels of taxonomic resolution, and with polychaetes or bivalves data alone. Lentidium mediterraneum was the most abundant species in all datasets. Its abundance was not consistently related to the presence of defence structures. Moreover, distribution patterns of L. mediterraneum were masking the structure of the whole macrofaunal assemblages. Removal of L. mediterraneum from the datasets allowed the detection of changes in benthic assemblages due to coastal defences. Analyses on different levels of taxonomic resolution showed that the level of family maintained sufficient information to detect the impacts of coastal defence structures on benthic assemblages. Moreover, the outcomes depended on the transformation used. Patterns of distribution of bivalves, used as surrogates, showed low correlations with the patterns of the total macrofaunal species assemblages. Patterns of polychaetes, if identified to the species or genus level showed higher correlations with the whole dataset. However, the identification of polychaetes to species and genus level is as costly as the identification of all macrobenthic taxa at family level. This study provided additional

Interior tomography in microscopic CT with image reconstruction constrained by full field of view scan at low spatial resolution

NASA Astrophysics Data System (ADS)

Luo, Shouhua; Shen, Tao; Sun, Yi; Li, Jing; Li, Guang; Tang, Xiangyang

2018-04-01

In high resolution (microscopic) CT applications, the scan field of view should cover the entire specimen or sample to allow complete data acquisition and image reconstruction. However, truncation may occur in projection data and results in artifacts in reconstructed images. In this study, we propose a low resolution image constrained reconstruction algorithm (LRICR) for interior tomography in microscopic CT at high resolution. In general, the multi-resolution acquisition based methods can be employed to solve the data truncation problem if the project data acquired at low resolution are utilized to fill up the truncated projection data acquired at high resolution. However, most existing methods place quite strict restrictions on the data acquisition geometry, which greatly limits their utility in practice. In the proposed LRICR algorithm, full and partial data acquisition (scan) at low and high resolutions, respectively, are carried out. Using the image reconstructed from sparse projection data acquired at low resolution as the prior, a microscopic image at high resolution is reconstructed from the truncated projection data acquired at high resolution. Two synthesized digital phantoms, a raw bamboo culm and a specimen of mouse femur, were utilized to evaluate and verify performance of the proposed LRICR algorithm. Compared with the conventional TV minimization based algorithm and the multi-resolution scout-reconstruction algorithm, the proposed LRICR algorithm shows significant improvement in reduction of the artifacts caused by data truncation, providing a practical solution for high quality and reliable interior tomography in microscopic CT applications. The proposed LRICR algorithm outperforms the multi-resolution scout-reconstruction method and the TV minimization based reconstruction for interior tomography in microscopic CT.

Aquatic plant-derived changes in oil sands naphthenic acid signatures determined by low-, high- and ultrahigh-resolution mass spectrometry.

PubMed

Headley, John V; Peru, Kerry M; Armstrong, Sarah A; Han, Xiumei; Martin, Jonathan W; Mapolelo, Mmilili M; Smith, Donald F; Rogers, Ryan P; Marshall, Alan G

2009-02-01

Mass spectrometry is a common tool for studying the fate of complex organic compound mixtures in oil sands processed water (OSPW), but a comparison of low-, high- ( approximately 10 000), and ultrahigh-resolution ( approximately 400 000) instrumentation for this purpose has not previously been made. High-resolution quadrupole time-of-flight mass spectrometry (QTOF MS) and ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), with negative-ion electrospray ionization, provided evidence for the selective dissipation of components in OSPW. Dissipation of oil sands naphthenic acids (NAs with general formula C(n)H(2n+z)O(2) where n is the number of carbon atoms, and Z is zero or a negative even number describing the number of rings) was masked (by components such as fatty acids, O(3), O(5), O(6), O(7), SO(2), SO(3), SO(4), SO(5), SO(6), and NO(4) species) at low resolution (1000) when using a triple quadrupole mass spectrometer. Changes observed in the relative composition of components in OSPW appear to be due primarily to the presence of plants, specifically cattails (Typha latifolia) and their associated microorganisms. The observed dissipation included a range of heteratomic species containing O(2), O(3), O(4), and O(5), present in Athabasca oil sands acid extracts. For the heteratomic O(2) species, namely naphthenic acids, an interesting structural relationship suggests that low and high carbon number NAs are dissipated by the plants preferentially, with a minimum around C(14)/C(15). Other heteratomic species containing O(6), O(7), SO(2), SO(3), SO(4), SO(5), SO(6), and NO(4) appear to be relatively recalcitrant to the cattails and were not dissipated to the same extent in planted systems. Copyright 2009 John Wiley & Sons, Ltd.

IMPROVING THE ACCURACY OF HISTORIC SATELLITE IMAGE CLASSIFICATION BY COMBINING LOW-RESOLUTION MULTISPECTRAL DATA WITH HIGH-RESOLUTION PANCHROMATIC DATA

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

Getman, Daniel J

2008-01-01

Many attempts to observe changes in terrestrial systems over time would be significantly enhanced if it were possible to improve the accuracy of classifications of low-resolution historic satellite data. In an effort to examine improving the accuracy of historic satellite image classification by combining satellite and air photo data, two experiments were undertaken in which low-resolution multispectral data and high-resolution panchromatic data were combined and then classified using the ECHO spectral-spatial image classification algorithm and the Maximum Likelihood technique. The multispectral data consisted of 6 multispectral channels (30-meter pixel resolution) from Landsat 7. These data were augmented with panchromatic datamore » (15m pixel resolution) from Landsat 7 in the first experiment, and with a mosaic of digital aerial photography (1m pixel resolution) in the second. The addition of the Landsat 7 panchromatic data provided a significant improvement in the accuracy of classifications made using the ECHO algorithm. Although the inclusion of aerial photography provided an improvement in accuracy, this improvement was only statistically significant at a 40-60% level. These results suggest that once error levels associated with combining aerial photography and multispectral satellite data are reduced, this approach has the potential to significantly enhance the precision and accuracy of classifications made using historic remotely sensed data, as a way to extend the time range of efforts to track temporal changes in terrestrial systems.« less

Enhancing the isotropy of lateral resolution in coherent structured illumination microscopy

PubMed Central

Park, Joo Hyun; Lee, Jae Yong; Lee, Eun Seong

2014-01-01

We present a method to improve the isotropy of spatial resolution in a structured illumination microscopy (SIM) implemented for imaging non-fluorescent samples. To alleviate the problem of anisotropic resolution involved with the previous scheme of coherent SIM that employs the two orthogonal standing-wave illumination, referred to as the orthogonal SIM, we introduce a hexagonal-lattice illumination that incorporates three standing-wave fields simultaneously superimposed at the orientations equally divided in the lateral plane. A theoretical formulation is worked out rigorously for the coherent image formation with such a simultaneous multiple-beam illumination and an explicit Fourier-domain framework is derived for reconstructing an image with enhanced resolution. Using a computer-synthesized resolution target as a 2D coherent sample, we perform numerical simulations to examine the imaging characteristics of our three-angle SIM compared with the orthogonal SIM. The investigation on the 2D resolving power with the various test patterns of different periods and orientations reveal that the orientation-dependent undulation of lateral resolution can be reduced from 27% to 8% by using the three-angle SIM while the best resolution (0.54 times the resolution limit of conventional coherent imaging) in the directions of structured illumination is slightly deteriorated by 4.6% from that of the orthogonal SIM. PMID:24940548

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

Low-cost and high-resolution interrogation scheme for LPG-based temperature sensor

NASA Astrophysics Data System (ADS)

Venkata Reddy, M.; Srimannarayana, K.; Venkatappa Rao, T.; Vengal Rao, P.

2015-09-01

A low-cost and high-resolution interrogation scheme for a long-period fiber grating (LPG) temperature sensor with adjustable temperature range has been designed, developed and tested. In general LPGs are widely used as optical sensors and can be used as optical edge filters to interrogate the wavelength encoded signal from sensors such as fiber Bragg grating (FBG) by converting it into intensity modulated signal. But the interrogation of LPG sensors using FBG is a bit novel and it is to be studied experimentally. The sensor works based on measurement of shift in attenuation band of LPG corresponding to the applied temperature. The wavelength shift of LPG attenuation band is monitored using an optical spectrum analyser (OSA). Further the bulk and expensive OSA is replaced with a low-cost interrogation system that employ an FBG, photodiode and a transimpedance amplifier (TIA). The designed interrogation scheme makes the system low-cost, fast in response, and also enhances its resolution up to 0.1°C. The measurable temperature range using the proposed scheme is limited to 120 °C. However this range can be shifted within 15-450 °C by means of adjusting the Bragg wavelength of FBG.

Example-Based Super-Resolution Fluorescence Microscopy.

PubMed

Jia, Shu; Han, Boran; Kutz, J Nathan

2018-04-23

Capturing biological dynamics with high spatiotemporal resolution demands the advancement in imaging technologies. Super-resolution fluorescence microscopy offers spatial resolution surpassing the diffraction limit to resolve near-molecular-level details. While various strategies have been reported to improve the temporal resolution of super-resolution imaging, all super-resolution techniques are still fundamentally limited by the trade-off associated with the longer image acquisition time that is needed to achieve higher spatial information. Here, we demonstrated an example-based, computational method that aims to obtain super-resolution images using conventional imaging without increasing the imaging time. With a low-resolution image input, the method provides an estimate of its super-resolution image based on an example database that contains super- and low-resolution image pairs of biological structures of interest. The computational imaging of cellular microtubules agrees approximately with the experimental super-resolution STORM results. This new approach may offer potential improvements in temporal resolution for experimental super-resolution fluorescence microscopy and provide a new path for large-data aided biomedical imaging.

A history of gap junction structure: hexagonal arrays to atomic resolution.

PubMed

Grosely, Rosslyn; Sorgen, Paul L

2013-02-01

Gap junctions are specialized membrane structures that provide an intercellular pathway for the propagation and/or amplification of signaling cascades responsible for impulse propagation, cell growth, and development. Prior to the identification of the proteins that comprise gap junctions, elucidation of channel structure began with initial observations of a hexagonal nexus connecting apposed cellular membranes. Concomitant with technological advancements spanning over 50 years, atomic resolution structures are now available detailing channel architecture and the cytoplasmic domains that have helped to define mechanisms governing the regulation of gap junctions. Highlighted in this review are the seminal structural studies that have led to our current understanding of gap junction biology.

Kite Aerial Photography for Low-Cost, Ultra-high Spatial Resolution Multi-Spectral Mapping of Intertidal Landscapes

PubMed Central

Bryson, Mitch; Johnson-Roberson, Matthew; Murphy, Richard J.; Bongiorno, Daniel

2013-01-01

Intertidal ecosystems have primarily been studied using field-based sampling; remote sensing offers the ability to collect data over large areas in a snapshot of time that could complement field-based sampling methods by extrapolating them into the wider spatial and temporal context. Conventional remote sensing tools (such as satellite and aircraft imaging) provide data at limited spatial and temporal resolutions and relatively high costs for small-scale environmental science and ecologically-focussed studies. In this paper, we describe a low-cost, kite-based imaging system and photogrammetric/mapping procedure that was developed for constructing high-resolution, three-dimensional, multi-spectral terrain models of intertidal rocky shores. The processing procedure uses automatic image feature detection and matching, structure-from-motion and photo-textured terrain surface reconstruction algorithms that require minimal human input and only a small number of ground control points and allow the use of cheap, consumer-grade digital cameras. The resulting maps combine imagery at visible and near-infrared wavelengths and topographic information at sub-centimeter resolutions over an intertidal shoreline 200 m long, thus enabling spatial properties of the intertidal environment to be determined across a hierarchy of spatial scales. Results of the system are presented for an intertidal rocky shore at Jervis Bay, New South Wales, Australia. Potential uses of this technique include mapping of plant (micro- and macro-algae) and animal (e.g. gastropods) assemblages at multiple spatial and temporal scales. PMID:24069206

Kite aerial photography for low-cost, ultra-high spatial resolution multi-spectral mapping of intertidal landscapes.

PubMed

Bryson, Mitch; Johnson-Roberson, Matthew; Murphy, Richard J; Bongiorno, Daniel

2013-01-01

Intertidal ecosystems have primarily been studied using field-based sampling; remote sensing offers the ability to collect data over large areas in a snapshot of time that could complement field-based sampling methods by extrapolating them into the wider spatial and temporal context. Conventional remote sensing tools (such as satellite and aircraft imaging) provide data at limited spatial and temporal resolutions and relatively high costs for small-scale environmental science and ecologically-focussed studies. In this paper, we describe a low-cost, kite-based imaging system and photogrammetric/mapping procedure that was developed for constructing high-resolution, three-dimensional, multi-spectral terrain models of intertidal rocky shores. The processing procedure uses automatic image feature detection and matching, structure-from-motion and photo-textured terrain surface reconstruction algorithms that require minimal human input and only a small number of ground control points and allow the use of cheap, consumer-grade digital cameras. The resulting maps combine imagery at visible and near-infrared wavelengths and topographic information at sub-centimeter resolutions over an intertidal shoreline 200 m long, thus enabling spatial properties of the intertidal environment to be determined across a hierarchy of spatial scales. Results of the system are presented for an intertidal rocky shore at Jervis Bay, New South Wales, Australia. Potential uses of this technique include mapping of plant (micro- and macro-algae) and animal (e.g. gastropods) assemblages at multiple spatial and temporal scales.

Optimization of super-resolution processing using incomplete image sets in PET imaging.

PubMed

Chang, Guoping; Pan, Tinsu; Clark, John W; Mawlawi, Osama R

2008-12-01

Super-resolution (SR) techniques are used in PET imaging to generate a high-resolution image by combining multiple low-resolution images that have been acquired from different points of view (POVs). The number of low-resolution images used defines the processing time and memory storage necessary to generate the SR image. In this paper, the authors propose two optimized SR implementations (ISR-1 and ISR-2) that require only a subset of the low-resolution images (two sides and diagonal of the image matrix, respectively), thereby reducing the overall processing time and memory storage. In an N x N matrix of low-resolution images, ISR-1 would be generated using images from the two sides of the N x N matrix, while ISR-2 would be generated from images across the diagonal of the image matrix. The objective of this paper is to investigate whether the two proposed SR methods can achieve similar performance in contrast and signal-to-noise ratio (SNR) as the SR image generated from a complete set of low-resolution images (CSR) using simulation and experimental studies. A simulation, a point source, and a NEMA/IEC phantom study were conducted for this investigation. In each study, 4 (2 x 2) or 16 (4 x 4) low-resolution images were reconstructed from the same acquired data set while shifting the reconstruction grid to generate images from different POVs. SR processing was then applied in each study to combine all as well as two different subsets of the low-resolution images to generate the CSR, ISR-1, and ISR-2 images, respectively. For reference purpose, a native reconstruction (NR) image using the same matrix size as the three SR images was also generated. The resultant images (CSR, ISR-1, ISR-2, and NR) were then analyzed using visual inspection, line profiles, SNR plots, and background noise spectra. The simulation study showed that the contrast and the SNR difference between the two ISR images and the CSR image were on average 0.4% and 0.3%, respectively. Line profiles of

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

Inkjet Printing of Functional and Structural Materials: Fluid Property Requirements, Feature Stability, and Resolution

NASA Astrophysics Data System (ADS)

Derby, Brian

2010-08-01

Inkjet printing is viewed as a versatile manufacturing tool for applications in materials fabrication in addition to its traditional role in graphics output and marking. The unifying feature in all these applications is the dispensing and precise positioning of very small volumes of fluid (1-100 picoliters) on a substrate before transformation to a solid. The application of inkjet printing to the fabrication of structures for structural or functional materials applications requires an understanding as to how the physical processes that operate during inkjet printing interact with the properties of the fluid precursors used. Here we review the current state of understanding of the mechanisms of drop formation and how this defines the fluid properties that are required for a given liquid to be printable. The interactions between individual drops and the substrate as well as between adjacent drops are important in defining the resolution and accuracy of printed objects. Pattern resolution is limited by the extent to which a liquid drop spreads on a substrate and how spreading changes with the overlap of adjacent drops to form continuous features. There are clearly defined upper and lower bounds to the width of a printed continuous line, which can be defined in terms of materials and process variables. Finer-resolution features can be achieved through appropriate patterning and structuring of the substrate prior to printing, which is essential if polymeric semiconducting devices are to be fabricated. Low advancing and receding contact angles promote printed line stability but are also more prone to solute segregation or “coffee staining” on drying.

High-Resolution, Low-Altitude Helicopter-Borne Aeromagnetic Survey over Unzen Volcano, Kyushu, Japan

NASA Astrophysics Data System (ADS)

Okubo, A.; Tanaka, Y.; Utsugi, M.; Kitada, N.; Shimizu, H.; Matsushima, T.

2003-12-01

We try to use repeated high-resolution aeromagnetic surveys at low altitudes to detect the geomagnetic field changes associated with volcanic activity. Previous magnetic studies in volcanic areas using fixed station distributions have detected small temporal changes, however, they do not have the spatial resolution to detect spatial changes. It may be possible to make repeated magnetic surveys even during active volcano eruptions using, for example, unmanned helicopters. On September 18, 2002, we conducted a high-resolution and low-altitude helicopter-borne magnetic surveys in and around Unzen Volcano in Kyushu, Japan. Unzen is an active volcano that had a sequence of eruptions from November, 1990 to 1995, after a quiescence of 198 years. The first flight covers an area over the Futsu, Chijiwa, and Kanahama faults, which are major normal faults that form the Unzen graben system. The second andthird flights cover the summit area of Unzen volcano with spiral trajectories at altitudes of 1000 and 500 ft, respectively. The spacing between the survey lines is about 50 m. The total geomagnetic was recorded by an optical pumping magnetometer installed in the sensor bird and the sampling intervals are 0.1 sec. Precise positioning data of the sensor bird was obtained by a differential GPS technique, with a time resolution of 1 sec. Diurnal magnetic variations of extra-terrestrial origin were removed by subtracting the total field data recorded at a nearby temporary station. In order to eliminate the effects of topography, the average terrain magnetization was estimated using a statistical correlation method (Grauch, 1987). Finally, an inversion was carried out for the terrain corrected anomalies, after removing the linear regional trend. From the results of this inversion, a low magnetized area was seen around the lava dome, while high magnetization is distributed around Mt.Fugen. The low magnetized area suggests that the rock bodies with remanent magnetization is fractured

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.

FBG based high sensitive pressure sensor and its low-cost interrogation system with enhanced resolution

NASA Astrophysics Data System (ADS)

Pachava, Vengal Rao; Kamineni, Srimannarayana; Madhuvarasu, Sai Shankar; Putha, Kishore; Mamidi, Venkata Reddy

2015-12-01

A fiber Bragg grating (FBG) pressure sensor with high sensitivity and resolution has been designed and demonstrated. The sensor is configured by firmly fixing the FBG with a metal bellows structure. The sensor works by means of measuring the Bragg wavelength shift of the FBG with respect to pressure change. From the experimental results, the pressure sensitivity of the sensor is found to be 90.6 pm/psi, which is approximately 4000 times as that of a bare fiber Bragg grating. A very good linearity of 99.86% is observed between the Bragg wavelength of the FBG and applied pressure. The designed sensor shows good repeatability with a negligible hysteresis error of ± 0.29 psi. A low-cost interrogation system that includes a long period grating (LPG) and a photodiode (PD) accompanied with simple electronic circuitry is demonstrated for the FBG sensor, which enables the sensor to attain high resolution of up to 0.025 psi. Thermal-strain cross sensitivity of the FBG pressure sensor is compensated using a reference FBG temperature sensor. The designed sensor can be used for liquid level, specific gravity, and static/dynamic low pressure measurement applications.

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

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.

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.

Progress in low-resolution ab initio phasing with CrowdPhase

DOE PAGES

Jorda, Julien; Sawaya, Michael R.; Yeates, Todd O.

2016-03-01

Ab initio phasing by direct computational methods in low-resolution X-ray crystallography is a long-standing challenge. A common approach is to consider it as two subproblems: sampling of phase space and identification of the correct solution. While the former is amenable to a myriad of search algorithms, devising a reliable target function for the latter problem remains an open question. Here, recent developments in CrowdPhase, a collaborative online game powered by a genetic algorithm that evolves an initial population of individuals with random genetic make-up ( i.e. random phases) each expressing a phenotype in the form of an electron-density map, aremore » presented. Success relies on the ability of human players to visually evaluate the quality of these maps and, following a Darwinian survival-of-the-fittest concept, direct the search towards optimal solutions. While an initial study demonstrated the feasibility of the approach, some important crystallographic issues were overlooked for the sake of simplicity. To address these, the new CrowdPhase includes consideration of space-group symmetry, a method for handling missing amplitudes, the use of a map correlation coefficient as a quality metric and a solvent-flattening step. Lastly, performances of this installment are discussed for two low-resolution test cases based on bona fide diffraction data.« less

Progress in low-resolution ab initio phasing with CrowdPhase

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

Jorda, Julien; Sawaya, Michael R.; Yeates, Todd O.

Ab initio phasing by direct computational methods in low-resolution X-ray crystallography is a long-standing challenge. A common approach is to consider it as two subproblems: sampling of phase space and identification of the correct solution. While the former is amenable to a myriad of search algorithms, devising a reliable target function for the latter problem remains an open question. Here, recent developments in CrowdPhase, a collaborative online game powered by a genetic algorithm that evolves an initial population of individuals with random genetic make-up ( i.e. random phases) each expressing a phenotype in the form of an electron-density map, aremore » presented. Success relies on the ability of human players to visually evaluate the quality of these maps and, following a Darwinian survival-of-the-fittest concept, direct the search towards optimal solutions. While an initial study demonstrated the feasibility of the approach, some important crystallographic issues were overlooked for the sake of simplicity. To address these, the new CrowdPhase includes consideration of space-group symmetry, a method for handling missing amplitudes, the use of a map correlation coefficient as a quality metric and a solvent-flattening step. Lastly, performances of this installment are discussed for two low-resolution test cases based on bona fide diffraction data.« less

Change of spatial information under rescaling: A case study using multi-resolution image series

NASA Astrophysics Data System (ADS)

Chen, Weirong; Henebry, Geoffrey M.

portrayed by pixels are equally weighted regardless of the shape and extent of the underlying scene objects, the rescaled image retains more of the original spatial information than would occur through direct observation at a coarser sensor spatial resolution. In contrast, for the observed images, due to the effect of the modulation transfer function (MTF) of the imaging system, high frequency features like edges are blurred or lost as the pixel size increases, resulting in greater variation in spatial structure. Successive applications of a low-pass spatial convolution filter are shown to mimic a MTF. Accordingly, it is recommended that such a procedure be applied prior to rescaling by simple block averaging, if insufficient image metadata exist to replicate the net MTF of the imaging system, as might be expected in land cover change analysis studies using historical imagery.

Super resolution reconstruction of μ-CT image of rock sample using neighbour embedding algorithm

NASA Astrophysics Data System (ADS)

Wang, Yuzhu; Rahman, Sheik S.; Arns, Christoph H.

2018-03-01

X-ray computed tomography (μ-CT) is considered to be the most effective way to obtain the inner structure of rock sample without destructions. However, its limited resolution hampers its ability to probe sub-micro structures which is critical for flow transportation of rock sample. In this study, we propose an innovative methodology to improve the resolution of μ-CT image using neighbour embedding algorithm where low frequency information is provided by μ-CT image itself while high frequency information is supplemented by high resolution scanning electron microscopy (SEM) image. In order to obtain prior for reconstruction, a large number of image patch pairs contain high- and low- image patches are extracted from the Gaussian image pyramid generated by SEM image. These image patch pairs contain abundant information about tomographic evolution of local porous structures under different resolution spaces. Relying on the assumption of self-similarity of porous structure, this prior information can be used to supervise the reconstruction of high resolution μ-CT image effectively. The experimental results show that the proposed method is able to achieve the state-of-the-art performance.

Micromachined optical microphone structures with low thermal-mechanical noise levels.

PubMed

Hall, Neal A; Okandan, Murat; Littrell, Robert; Bicen, Baris; Degertekin, F Levent

2007-10-01

Micromachined microphones with diffraction-based optical displacement detection have been introduced previously [Hall et al., J. Acoust. Soc. Am. 118, 3000-3009 (2005)]. The approach has the advantage of providing high displacement detection resolution of the microphone diaphragm independent of device size and capacitance-creating an unconstrained design space for the mechanical structure itself. Micromachined microphone structures with 1.5-mm-diam polysilicon diaphragms and monolithically integrated diffraction grating electrodes are presented in this work with backplate architectures that deviate substantially from traditional perforated plate designs. These structures have been designed for broadband frequency response and low thermal mechanical noise levels. Rigorous experimental characterization indicates a diaphragm displacement detection resolution of 20 fm radicalHz and a thermal mechanical induced diaphragm displacement noise density of 60 fm radicalHz, corresponding to an A-weighted sound pressure level detection limit of 24 dB(A) for these structures. Measured thermal mechanical displacement noise spectra are in excellent agreement with simulations based on system parameters derived from dynamic frequency response characterization measurements, which show a diaphragm resonance limited bandwidth of approximately 20 kHz. These designs are substantial improvements over initial prototypes presented previously. The high performance-to-size ratio achievable with this technology is expected to have an impact on a variety of instrumentation and hearing applications.

High-resolution X-ray crystal structure of bovine H-protein using the high-pressure cryocooling method.

PubMed

Higashiura, Akifumi; Ohta, Kazunori; Masaki, Mika; Sato, Masaru; Inaka, Koji; Tanaka, Hiroaki; Nakagawa, Atsushi

2013-11-01

Recently, many technical improvements in macromolecular X-ray crystallography have increased the number of structures deposited in the Protein Data Bank and improved the resolution limit of protein structures. Almost all high-resolution structures have been determined using a synchrotron radiation source in conjunction with cryocooling techniques, which are required in order to minimize radiation damage. However, optimization of cryoprotectant conditions is a time-consuming and difficult step. To overcome this problem, the high-pressure cryocooling method was developed (Kim et al., 2005) and successfully applied to many protein-structure analyses. In this report, using the high-pressure cryocooling method, the X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. Structural comparisons between high- and ambient-pressure cryocooled crystals at ultra-high resolution illustrate the versatility of this technique. This is the first ultra-high-resolution X-ray structure obtained using the high-pressure cryocooling method.

Ultrahigh resolution radiation imaging system using an optical fiber structure scintillator plate.

PubMed

Yamamoto, Seiichi; Kamada, Kei; Yoshikawa, Akira

2018-02-16

High resolution imaging of radiation is required for such radioisotope distribution measurements as alpha particle detection in nuclear facilities or high energy physics experiments. For this purpose, we developed an ultrahigh resolution radiation imaging system using an optical fiber structure scintillator plate. We used a ~1-μm diameter fiber structured GdAlO 3 :Ce (GAP) /α-Al 2 O 3 scintillator plate to reduce the light spread. The fiber structured scintillator plate was optically coupled to a tapered optical fiber plate to magnify the image and combined with a lens-based high sensitivity CCD camera. We observed the images of alpha particles with a spatial resolution of ~25 μm. For the beta particles, the images had various shapes, and the trajectories of the electrons were clearly observed in the images. For the gamma photons, the images also had various shapes, and the trajectories of the secondary electrons were observed in some of the images. These results show that combining an optical fiber structure scintillator plate with a tapered optical fiber plate and a high sensitivity CCD camera achieved ultrahigh resolution and is a promising method to observe the images of the interactions of radiation in a scintillator.

Densely packed beta-structure at the protein-lipid interface of porin is revealed by high-resolution cryo-electron microscopy.

PubMed

Sass, H J; Büldt, G; Beckmann, E; Zemlin, F; van Heel, M; Zeitler, E; Rosenbusch, J P; Dorset, D L; Massalski, A

1989-09-05

Porin is an integral membrane protein that forms channels across the outer membrane of Escherichia coli. Electron microscopic studies of negatively stained two-dimensional porin crystals have shown three stain accumulations per porin trimer, revealing the locations of pores spanning the membrane. In this study, reconstituted porin lattices embedded in glucose were investigated using the low-dose technique on a cryo-electron microscope equipped with a helium-cooled superconducting objective lens. The specimen temperature was maintained at 5 K to yield an improved microscopic and specimen stability. Under these conditions, we obtained for the first time electron diffraction patterns from porin lattices to a resolution of 3.2 A and images showing optical diffraction up to a resolution of 4.9 A. Applying correlation averaging techniques to the digitized micrographs, we were able to reconstruct projected images of the porin trimer to a resolution of up to 3.5 A. In the final projection maps, amplitudes from electron diffraction and phases from these images were combined. The predominant feature is a high-density narrow band (about 6 A in thickness) that delineates the outer perimeter of the trimer. Since the molecule consists of almost exclusively beta-sheet structure, as revealed by spectroscopic data, we conclude that this band is a cylindrical beta-pleated sheet crossing the membrane nearly perpendicularly to its plane. Another intriguing finding is a low-density area (about 70 A2) situated in the centre of the trimer.

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.

Low Resolution Refinement of Atomic Models Against Crystallographic Data.

PubMed

Nicholls, Robert A; Kovalevskiy, Oleg; Murshudov, Garib N

2017-01-01

This review describes some of the problems encountered during low-resolution refinement and map calculation. Refinement is considered as an application of Bayes' theorem, allowing combination of information from various sources including crystallographic experimental data and prior chemical and structural knowledge. The sources of prior knowledge relevant to macromolecules include basic chemical information such as bonds and angles, structural information from reference models of known homologs, knowledge about secondary structures, hydrogen bonding patterns, and similarity of non-crystallographically related copies of a molecule. Additionally, prior information encapsulating local conformational conservation is exploited, keeping local interatomic distances similar to those in the starting atomic model. The importance of designing an accurate likelihood function-the only link between model parameters and observed data-is emphasized. The review also reemphasizes the importance of phases, and describes how the use of raw observed amplitudes could give a better correlation between the calculated and "true" maps. It is shown that very noisy or absent observations can be replaced by calculated structure factors, weighted according to the accuracy of the atomic model. This approach helps to smoothen the map. However, such replacement should be used sparingly, as the bias toward errors in the model could be too much to avoid. It is in general recommended that, whenever a new map is calculated, map quality should be judged by inspection of the parts of the map where there is no atomic model. It is also noted that it is advisable to work with multiple blurred and sharpened maps, as different parts of a crystal may exhibit different degrees of mobility. Doing so can allow accurate building of atomic models, accounting for overall shape as well as finer structural details. Some of the results described in this review have been implemented in the programs REFMAC5, Pro

Replica Exchange Improves Sampling in Low-Resolution Docking Stage of RosettaDock

PubMed Central

Zhang, Zhe; Lange, Oliver F.

2013-01-01

Many protein-protein docking protocols are based on a shotgun approach, in which thousands of independent random-start trajectories minimize the rigid-body degrees of freedom. Another strategy is enumerative sampling as used in ZDOCK. Here, we introduce an alternative strategy, ReplicaDock, using a small number of long trajectories of temperature replica exchange. We compare replica exchange sampling as low-resolution stage of RosettaDock with RosettaDock's original shotgun sampling as well as with ZDOCK. A benchmark of 30 complexes starting from structures of the unbound binding partners shows improved performance for ReplicaDock and ZDOCK when compared to shotgun sampling at equal or less computational expense. ReplicaDock and ZDOCK consistently reach lower energies and generate significantly more near-native conformations than shotgun sampling. Accordingly, they both improve typical metrics of prediction quality of complex structures after refinement. Additionally, the refined ReplicaDock ensembles reach significantly lower interface energies and many previously hidden features of the docking energy landscape become visible when ReplicaDock is applied. PMID:24009670

A Synthetic Study on the Resolution of 2D Elastic Full Waveform Inversion

NASA Astrophysics Data System (ADS)

Cui, C.; Wang, Y.

2017-12-01

Gradient based full waveform inversion is an effective method in seismic study, it makes full use of the information given by seismic records and is capable of providing a more accurate model of the interior of the earth at a relatively low computational cost. However, the strong non-linearity of the problem brings about many difficulties in the assessment of its resolution. Synthetic inversions are therefore helpful before an inversion based on real data is made. Checker-board test is a commonly used method, but it is not always reliable due to the significant difference between a checker-board and the true model. Our study aims to provide a basic understanding of the resolution of 2D elastic inversion by examining three main factors that affect the inversion result respectively: 1. The structural characteristic of the model; 2. The level of similarity between the initial model and the true model; 3. The spacial distribution of sources and receivers. We performed about 150 synthetic inversions to demonstrate how each factor contributes to quality of the result, and compared the inversion results with those achieved by checker-board tests. The study can be a useful reference to assess the resolution of an inversion in addition to regular checker-board tests, or to determine whether the seismic data of a specific region is sufficient for a successful inversion.

Projections onto Convex Sets Super-Resolution Reconstruction Based on Point Spread Function Estimation of Low-Resolution Remote Sensing Images

PubMed Central

Fan, Chong; Wu, Chaoyun; Li, Grand; Ma, Jun

2017-01-01

To solve the problem on inaccuracy when estimating the point spread function (PSF) of the ideal original image in traditional projection onto convex set (POCS) super-resolution (SR) reconstruction, this paper presents an improved POCS SR algorithm based on PSF estimation of low-resolution (LR) remote sensing images. The proposed algorithm can improve the spatial resolution of the image and benefit agricultural crop visual interpolation. The PSF of the high-resolution (HR) image is unknown in reality. Therefore, analysis of the relationship between the PSF of the HR image and the PSF of the LR image is important to estimate the PSF of the HR image by using multiple LR images. In this study, the linear relationship between the PSFs of the HR and LR images can be proven. In addition, the novel slant knife-edge method is employed, which can improve the accuracy of the PSF estimation of LR images. Finally, the proposed method is applied to reconstruct airborne digital sensor 40 (ADS40) three-line array images and the overlapped areas of two adjacent GF-2 images by embedding the estimated PSF of the HR image to the original POCS SR algorithm. Experimental results show that the proposed method yields higher quality of reconstructed images than that produced by the blind SR method and the bicubic interpolation method. PMID:28208837

Quantitative Protein Topography Analysis and High-Resolution Structure Prediction Using Hydroxyl Radical Labeling and Tandem-Ion Mass Spectrometry (MS)*

PubMed Central

Kaur, Parminder; Kiselar, Janna; Yang, Sichun; Chance, Mark R.

2015-01-01

Hydroxyl radical footprinting based MS for protein structure assessment has the goal of understanding ligand induced conformational changes and macromolecular interactions, for example, protein tertiary and quaternary structure, but the structural resolution provided by typical peptide-level quantification is limiting. In this work, we present experimental strategies using tandem-MS fragmentation to increase the spatial resolution of the technique to the single residue level to provide a high precision tool for molecular biophysics research. Overall, in this study we demonstrated an eightfold increase in structural resolution compared with peptide level assessments. In addition, to provide a quantitative analysis of residue based solvent accessibility and protein topography as a basis for high-resolution structure prediction; we illustrate strategies of data transformation using the relative reactivity of side chains as a normalization strategy and predict side-chain surface area from the footprinting data. We tested the methods by examination of Ca+2-calmodulin showing highly significant correlations between surface area and side-chain contact predictions for individual side chains and the crystal structure. Tandem ion based hydroxyl radical footprinting-MS provides quantitative high-resolution protein topology information in solution that can fill existing gaps in structure determination for large proteins and macromolecular complexes. PMID:25687570

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

Preparation of the CARMENES Input Catalogue: Low- and High-resolution Spectroscopy of M dwarfs

NASA Astrophysics Data System (ADS)

Alonso-Floriano, F. J.; Montes, D.; Caballero, J. A.; Klutsch, A.; Jeffers, S.; Reiners, A.; Zechmeister, M.; Lamert, A.; Passegger, V. M.; Mundt, R.; Amado, P. J.; Berdinas, Z. M.; Casal, E.; Cortés-Contreras, M.; Morales, J. C.; Ribas, I.; Rodríguez-López, C.; Quirrenbach, A.

2015-01-01

The identification of the most promising targets for exoplanet hunting is a crucial first step to ensure an efficient use of the CARMENES guaranteed time. To achieve this, we obtained low-resolution (R ˜ 1500) spectra of 752 M (and late K) dwarfs mostly fainter than J = 9 mag with CAFOS. For all of them, we derived spectral types with 0.5 subtypes accuracy. We also studied metallicity and surface gravity through spectral indices, and activity from pEW(Hα). Next, we observed over 600 M dwarfs at higher resolution (R = 30 000-48 000) with FEROS, CAFE and HRS. We determined rotational velocities, v sin{i} (±0.2-0.5 km s^{-1}), and radial velocities, V_r (±0.1-0.2 km s^{-1}), of the observed stars. From our observations, we identified high-activity, low-metallicity and low-gravity stars, single- and double-lined spectroscopic binaries and, specially, fast rotators, which should be discarded from any target list for exoplanet searches. Here we present preliminary results.

Equally sloped X-ray microtomography of living insects with low radiation dose and improved resolution capability

NASA Astrophysics Data System (ADS)

Yao, Shengkun; Fan, Jiadong; Zong, Yunbing; He, You; Zhou, Guangzhao; Sun, Zhibin; Zhang, Jianhua; Huang, Qingjie; Xiao, Tiqiao; Jiang, Huaidong

2016-03-01

Three-dimensional X-ray imaging of living specimens is challenging due to the limited resolution of conventional absorption contrast X-ray imaging and potential irradiation damage of biological specimens. In this letter, we present microtomography of a living specimen combining phase-contrast imaging and a Fourier-based iterative algorithm termed equally sloped tomography. Non-destructive 3D imaging of an anesthetized living yellow mealworm Tenebrio molitor was demonstrated with a relatively low dose using synchrotron generated X-rays. Based on the high-quality 3D images, branching tracheoles and different tissues of the insect in a natural state were identified and analyzed, demonstrating a significant advantage of the technique over conventional X-ray radiography or histotomy. Additionally, the insect survived without problem after a 1.92-s X-ray exposure and subsequent absorbed radiation dose of ˜1.2 Gy. No notable physiological effects were observed after reviving the insect from anesthesia. The improved static tomographic method demonstrated in this letter shows advantage in the non-destructive structural investigation of living insects in three dimensions due to the low radiation dose and high resolution capability, and offers many potential applications in biological science.

Equally sloped X-ray microtomography of living insects with low radiation dose and improved resolution capability

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

Yao, Shengkun; Fan, Jiadong; Zong, Yunbing

Three-dimensional X-ray imaging of living specimens is challenging due to the limited resolution of conventional absorption contrast X-ray imaging and potential irradiation damage of biological specimens. In this letter, we present microtomography of a living specimen combining phase-contrast imaging and a Fourier-based iterative algorithm termed equally sloped tomography. Non-destructive 3D imaging of an anesthetized living yellow mealworm Tenebrio molitor was demonstrated with a relatively low dose using synchrotron generated X-rays. Based on the high-quality 3D images, branching tracheoles and different tissues of the insect in a natural state were identified and analyzed, demonstrating a significant advantage of the technique overmore » conventional X-ray radiography or histotomy. Additionally, the insect survived without problem after a 1.92-s X-ray exposure and subsequent absorbed radiation dose of ∼1.2 Gy. No notable physiological effects were observed after reviving the insect from anesthesia. The improved static tomographic method demonstrated in this letter shows advantage in the non-destructive structural investigation of living insects in three dimensions due to the low radiation dose and high resolution capability, and offers many potential applications in biological science.« less

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.

A high-gain, low ion-backflow double micro-mesh gaseous structure for single electron detection

NASA Astrophysics Data System (ADS)

Zhang, Zhiyong; Qi, Binbin; Liu, Chengming; Feng, Jianxin; Liu, Jianbei; Shao, Ming; Zhou, Yi; Hong, Daojin; Lv, You; Song, Guofeng; Wang, Xu; You, Wenhao

2018-05-01

Application of micro-pattern gaseous detectors to gaseous photomultiplier tubes has been widely investigated over the past two decades. In this paper, we present a double micro-mesh gaseous structure that has been designed and fabricated for this application. Tests with X-rays and UV laser light indicate that this structure exhibits an excellent gas gain of > 7 × 104 and good energy resolution of 19% (full width at half maximum) for 5.9 keV X-rays. The gas gain can reach up to 106 for single electrons while maintaining a very low ion-backflow ratio down to 0.0005. This structure has good potential for other applications requiring a very low level of ion backflow.

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

Formation of nocturnal low-level jets and structure of the nocturnal boundary layer in the Southern Great Plains

NASA Astrophysics Data System (ADS)

Klein, P. M.; Bonin, T. A.; Newman, J. F.; Wainwright, C. E.; Blumberg, W. G.; Turner, D. D.; Chilson, P. B.; Wharton, S.

2014-12-01

The Lower Atmospheric Boundary Layer Experiment (LABLE) included two measurement campaigns at the Atmospheric Radiation Measurement (ARM) Southern Great Plains site in Oklahoma in 2012 and 2013. Its main objective was to study turbulent phenomena in the lowest 2-km of the atmosphere using a variety of novel atmospheric profiling techniques including a sodar, multiple Doppler wind lidars (DWL), a Raman lidar and an atmospheric emitted radiance interferometer (AERI). Several instruments from the University of Oklahoma and Lawrence Livermore National Laboratory were deployed to augment the suite of in-situ and remote sensing instruments at the ARM site. The complementary nature of the deployed instruments with respect to resolution and height coverage provides for a near-complete picture of the dynamic and thermodynamic structure of the atmospheric boundary layer. LABLE can be considered unique in that it was designed as a multi-phase, low-cost, and multi-agency collaboration. Graduate students served as principal investigators who took the lead in designing and conducting experiments aimed at examining boundary-layer processes. This presentation provides an overview of the LABLE experiments and a summary of important results. One focus area will be the dynamic and thermodynamic structure of the nocturnal boundary layer and the formation of nocturnal low-level jets. Such low-level jets were frequently observed during both LABLE campaigns and often interacted with mesoscale atmospheric disturbances such as frontal passages. The combination of high-resolution AERI temperature profiles with DWL mean wind and turbulence profiles provided new insights about the structure and evolution of low-level jets.

The 3.2 Angstrom Resolution Structure of the Polymorphic Cowpea Chlorotic Mottle Virus Ribonucleoprotein Particle

NASA Astrophysics Data System (ADS)

Speir, Jeffrey Alan

Structural studies of the polymorphic cowpea chlorotic mottle virus have resulted in high resolution structures for two distinct icosahedral ribonucleoprotein particle conformations dependent upon whether acidic or basic pH conditions prevail. CCMV is stable below pH 6.5, however metal-free particles maintain a 10% increase in hydrodynamic volume at pH >=q 7.5. Identification of this swollen' form of CCMV, which can easily be disrupted with 1M NaCl, led to the first reassembly of an icosahedral virus in vitro from purified viral protein and RNA to form infectious particles, and its assembly has been the subject of biochemical and biophysical investigations for over twenty-five years. Under well defined conditions of pH, ionic strength and divalent metal ion concentration, CCMV capsid protein or capsid protein and RNA will reassemble to form icosahedral particles of various sizes, sheets, tubes, rosettes, and a variety of laminar structures which resemble virion structures from non-related virus families. Analysis of native particles at 3.2A resolution and swollen particles at 28A resolution has suggested that the chemical basis for the formation of polymorphic icosahedral and anisometric structures is: (i) hexamers formed of beta-barrel subunits stabilized by an unusual hexameric parallel beta structure made up of their N-termini, (ii) the location of protein-RNA interactions, (iii) divalent metal cation binding sites that regulate quasi-symmetrical subunit associations, (iv) charge repulsion across the same interfaces when lacking divalent metal ions at basic pH, which induces the formation of sixty 20A diameter portals for RNA release, and (v) a novel, C-terminal-based, subunit dimer assembly unit. The use of C- and N-terminal arms in CCMV has not been observed in other icosahedral RNA virus structures determined at near atomic resolution, however, their detailed interactions and roles in stabilizing the quaternary organization of CCMV are related to that found

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

Cartography of asteroids and comet nuclei from low resolution data

NASA Technical Reports Server (NTRS)

Stooke, Philip J.

1992-01-01

High resolution images of non-spherical objects, such as Viking images of Phobos and the anticipated Galileo images of Gaspra, lend themselves to conventional planetary cartographic procedures: control network analysis, stereophotogrammetry, image mosaicking in 2D or 3D, and airbrush mapping. There remains the problem of a suitable map projection for bodies which are extremely elongated or irregular in shape. Many bodies will soon be seen at lower resolution (5-30 pixels across the disk) in images from speckle interferometry, the Hubble Space Telescope, ground-based radar, distinct spacecraft encounters, and closer images degraded by smear. Different data with similar effective resolutions are available from stellar occultations, radar or lightcurve convex hulls, lightcurve modeling of albedo variations, and cometary jet modeling. With such low resolution, conventional methods of shape determination will be less useful or will fail altogether, leaving limb and terminator topography as the principal sources of topographic information. A method for shape determination based on limb and terminator topography was developed. It has been applied to the nucleus of Comet Halley and the jovian satellite Amalthea. The Amalthea results are described to give an example of the cartographic possibilities and problems of anticipated data sets.

Compartmentalized Low-Rank Recovery for High-Resolution Lipid Unsuppressed MRSI

PubMed Central

Bhattacharya, Ipshita; Jacob, Mathews

2017-01-01

Purpose To introduce a novel algorithm for the recovery of high-resolution magnetic resonance spectroscopic imaging (MRSI) data with minimal lipid leakage artifacts, from dual-density spiral acquisition. Methods The reconstruction of MRSI data from dual-density spiral data is formulated as a compartmental low-rank recovery problem. The MRSI dataset is modeled as the sum of metabolite and lipid signals, each of which is support limited to the brain and extracranial regions, respectively, in addition to being orthogonal to each other. The reconstruction problem is formulated as an optimization problem, which is solved using iterative reweighted nuclear norm minimization. Results The comparisons of the scheme against dual-resolution reconstruction algorithm on numerical phantom and in vivo datasets demonstrate the ability of the scheme to provide higher spatial resolution and lower lipid leakage artifacts. The experiments demonstrate the ability of the scheme to recover the metabolite maps, from lipid unsuppressed datasets with echo time (TE)=55 ms. Conclusion The proposed reconstruction method and data acquisition strategy provide an efficient way to achieve high-resolution metabolite maps without lipid suppression. This algorithm would be beneficial for fast metabolic mapping and extension to multislice acquisitions. PMID:27851875

An economic prediction of the finer resolution level wavelet coefficients in electronic structure calculations.

PubMed

Nagy, Szilvia; Pipek, János

2015-12-21

In wavelet based electronic structure calculations, introducing a new, finer resolution level is usually an expensive task, this is why often a two-level approximation is used with very fine starting resolution level. This process results in large matrices to calculate with and a large number of coefficients to be stored. In our previous work we have developed an adaptively refined solution scheme that determines the indices, where the refined basis functions are to be included, and later a method for predicting the next, finer resolution coefficients in a very economic way. In the present contribution, we would like to determine whether the method can be applied for predicting not only the first, but also the other, higher resolution level coefficients. Also the energy expectation values of the predicted wave functions are studied, as well as the scaling behaviour of the coefficients in the fine resolution limit.

Low-resolution electromagnetic brain tomography (LORETA) of monozygotic twins discordant for chronic fatigue syndrome.

PubMed

Sherlin, Leslie; Budzynski, Thomas; Kogan Budzynski, Helen; Congedo, Marco; Fischer, Mary E; Buchwald, Dedra

2007-02-15

Previous work using quantified EEG has suggested that brain activity in individuals with chronic fatigue syndrome (CFS) and normal persons differs. Our objective was to investigate if specific frequency band-pass regions and spatial locations are associated with CFS using low-resolution electromagnetic brain tomography (LORETA). We conducted a co-twin control study of 17 pairs of monozygotic twins where 1 twin met criteria for CFS and the co-twin was healthy. Twins underwent an extensive battery of tests including a structured psychiatric interview and a quantified EEG. Eyes closed EEG frequency-domain analysis was computed and the entire brain volume was compared of the CFS and healthy twins using a multiple comparison procedure. Compared with their healthy co-twins, twins with CFS differed in current source density. The CFS twins had higher delta in the left uncus and parahippocampal gyrus and higher theta in the cingulate gyrus and right superior frontal gyrus. These findings suggest that neurophysiological activity in specific areas of the brain may differentiate individuals with CFS from those in good health. The study corroborates that slowing of the deeper structures of the limbic system is associated with affect. It also supports the neurobiological model that the right forebrain is associated with sympathetic activity and the left forebrain with the effective management of energy. These preliminary findings await replication.

Efficient parallel reconstruction for high resolution multishot spiral diffusion data with low rank constraint.

PubMed

Liao, Congyu; Chen, Ying; Cao, Xiaozhi; Chen, Song; He, Hongjian; Mani, Merry; Jacob, Mathews; Magnotta, Vincent; Zhong, Jianhui

2017-03-01

To propose a novel reconstruction method using parallel imaging with low rank constraint to accelerate high resolution multishot spiral diffusion imaging. The undersampled high resolution diffusion data were reconstructed based on a low rank (LR) constraint using similarities between the data of different interleaves from a multishot spiral acquisition. The self-navigated phase compensation using the low resolution phase data in the center of k-space was applied to correct shot-to-shot phase variations induced by motion artifacts. The low rank reconstruction was combined with sensitivity encoding (SENSE) for further acceleration. The efficiency of the proposed joint reconstruction framework, dubbed LR-SENSE, was evaluated through error quantifications and compared with ℓ1 regularized compressed sensing method and conventional iterative SENSE method using the same datasets. It was shown that with a same acceleration factor, the proposed LR-SENSE method had the smallest normalized sum-of-squares errors among all the compared methods in all diffusion weighted images and DTI-derived index maps, when evaluated with different acceleration factors (R = 2, 3, 4) and for all the acquired diffusion directions. Robust high resolution diffusion weighted image can be efficiently reconstructed from highly undersampled multishot spiral data with the proposed LR-SENSE method. Magn Reson Med 77:1359-1366, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

High-resolution cryo-EM proteasome structures in drug development

PubMed Central

da Fonseca, Paula C. A.

2017-01-01

With the recent advances in biological structural electron microscopy (EM), protein structures can now be obtained by cryo-EM and single-particle analysis at resolutions that used to be achievable only by crystallographic or NMR methods. We have explored their application to study protein–ligand inter­actions using the human 20S proteasome, a well established target for cancer therapy that is also being investigated as a target for an increasing range of other medical conditions. The map of a ligand-bound human 20S proteasome served as a proof of principle that cryo-EM is emerging as a realistic approach for more general structural studies of protein–ligand interactions, with the potential benefits of extending such studies to complexes that are unfavourable to other methods and allowing structure determination under conditions that are closer to physiological, preserving ligand specificity towards closely related binding sites. Subsequently, the cryo-EM structure of the Plasmodium falciparum 20S proteasome, with a new prototype specific inhibitor bound, revealed the molecular basis for the ligand specificity towards the parasite complex, which provides a framework to guide the development of highly needed new-generation antimalarials. Here, the cryo-EM analysis of the ligand-bound human and P. falciparum 20S proteasomes is reviewed, and a complete description of the methods used for structure determination is provided, including the strategy to overcome the bias orientation of the human 20S proteasome on electron-microscope grids and details of the icr3d software used for three-dimensional reconstruction. PMID:28580914

Refined structure of dimeric diphtheria toxin at 2.0 A resolution.

PubMed Central

Bennett, M. J.; Choe, S.; Eisenberg, D.

1994-01-01

The refined structure of dimeric diphtheria toxin (DT) at 2.0 A resolution, based on 37,727 unique reflections (F > 1 sigma (F)), yields a final R factor of 19.5% with a model obeying standard geometry. The refined model consists of 523 amino acid residues, 1 molecule of the bound dinucleotide inhibitor adenylyl 3'-5' uridine 3' monophosphate (ApUp), and 405 well-ordered water molecules. The 2.0-A refined model reveals that the binding motif for ApUp includes residues in the catalytic and receptor-binding domains and is different from the Rossmann dinucleotide-binding fold. ApUp is bound in part by a long loop (residues 34-52) that crosses the active site. Several residues in the active site were previously identified as NAD-binding residues. Glu 148, previously identified as playing a catalytic role in ADP-ribosylation of elongation factor 2 by DT, is about 5 A from uracil in ApUp. The trigger for insertion of the transmembrane domain of DT into the endosomal membrane at low pH may involve 3 intradomain and 4 interdomain salt bridges that will be weakened at low pH by protonation of their acidic residues. The refined model also reveals that each molecule in dimeric DT has an "open" structure unlike most globular proteins, which we call an open monomer. Two open monomers interact by "domain swapping" to form a compact, globular dimeric DT structure. The possibility that the open monomer resembles a membrane insertion intermediate is discussed. PMID:7833807

Assessment of summer rainfall forecast skill in the Intra-Americas in GFDL high and low-resolution models

NASA Astrophysics Data System (ADS)

Krishnamurthy, Lakshmi; Muñoz, Ángel G.; Vecchi, Gabriel A.; Msadek, Rym; Wittenberg, Andrew T.; Stern, Bill; Gudgel, Rich; Zeng, Fanrong

2018-05-01

The Caribbean low-level jet (CLLJ) is an important component of the atmospheric circulation over the Intra-Americas Sea (IAS) which impacts the weather and climate both locally and remotely. It influences the rainfall variability in the Caribbean, Central America, northern South America, the tropical Pacific and the continental Unites States through the transport of moisture. We make use of high-resolution coupled and uncoupled models from the Geophysical Fluid Dynamics Laboratory (GFDL) to investigate the simulation of the CLLJ and its teleconnections and further compare with low-resolution models. The high-resolution coupled model FLOR shows improvements in the simulation of the CLLJ and its teleconnections with rainfall and SST over the IAS compared to the low-resolution coupled model CM2.1. The CLLJ is better represented in uncoupled models (AM2.1 and AM2.5) forced with observed sea-surface temperatures (SSTs), emphasizing the role of SSTs in the simulation of the CLLJ. Further, we determine the forecast skill for observed rainfall using both high- and low-resolution predictions of rainfall and SSTs for the July-August-September season. We determine the role of statistical correction of model biases, coupling and horizontal resolution on the forecast skill. Statistical correction dramatically improves area-averaged forecast skill. But the analysis of spatial distribution in skill indicates that the improvement in skill after statistical correction is region dependent. Forecast skill is sensitive to coupling in parts of the Caribbean, Central and northern South America, and it is mostly insensitive over North America. Comparison of forecast skill between high and low-resolution coupled models does not show any dramatic difference. However, uncoupled models show improvement in the area-averaged skill in the high-resolution atmospheric model compared to lower resolution model. Understanding and improving the forecast skill over the IAS has important implications

High-resolution multiphoton microscopy with a low-power continuous wave laser pump.

PubMed

Chen, Xiang-Dong; Li, Shen; Du, Bo; Dong, Yang; Wang, Ze-Hao; Guo, Guang-Can; Sun, Fang-Wen

2018-02-15

Multiphoton microscopy (MPM) has been widely used for three-dimensional biological imaging. Here, based on the photon-induced charge state conversion process, we demonstrated a low-power high-resolution MPM with a nitrogen vacancy (NV) center in diamond. Continuous wave green and orange lasers were used to pump and detect the two-photon charge state conversion, respectively. The power of the laser for multiphoton excitation was 40 μW. Both the axial and lateral resolutions were improved approximately 1.5 times compared with confocal microscopy. The results can be used to improve the resolution of the NV center-based quantum sensing and biological imaging.

IRAS Low Resolution Spectra of Asteroids

NASA Technical Reports Server (NTRS)

Cohen, Martin; Walker, Russell G.

2002-01-01

Optical/near-infrared studies of asteroids are based on reflected sunlight and surface albedo variations create broad spectral features, suggestive of families of materials. There is a significant literature on these features, but there is very little work in the thermal infrared that directly probes the materials emitting on the surfaces of asteroids. We have searched for and extracted 534 thermal spectra of 245 asteroids from the original Dutch (Groningen) archive of spectra observed by the IRAS Low Resolution Spectrometer (LRS). We find that, in general, the observed shapes of the spectral continua are inconsistent with that predicted by the standard thermal model used by IRAS. Thermal models such as proposed by Harris (1998) and Harris et al.(1998) for the near-earth asteroids with the "beaming parameter" in the range of 1.0 to 1.2 best represent the observed spectral shapes. This implies that the IRAS Minor Planet Survey (IMPS, Tedesco, 1992) and the Supplementary IMPS (SIMPS, Tedesco, et al., 2002) derived asteroid diameters are systematically underestimated, and the albedos are overestimated. We have tentatively identified several spectral features that appear to be diagnostic of at least families of materials. The variation of spectral features with taxonomic class hints that thermal infrared spectra can be a valuable tool for taxonomic classification of asteroids.

Grid Resolution Study over Operability Space for a Mach 1.7 Low Boom External Compression Inlet

NASA Technical Reports Server (NTRS)

Anderson, Bernhard H.

2014-01-01

This paper presents a statistical methodology whereby the probability limits associated with CFD grid resolution of inlet flow analysis can be determined which provide quantitative information on the distribution of that error over the specified operability range. The objectives of this investigation is to quantify the effects of both random (accuracy) and systemic (biasing) errors associated with grid resolution in the analysis of the Lockheed Martin Company (LMCO) N+2 Low Boom external compression supersonic inlet. The study covers the entire operability space as defined previously by the High Speed Civil Transport (HSCT) High Speed Research (HSR) program goals. The probability limits in terms of a 95.0% confidence interval on the analysis data were evaluated for four ARP1420 inlet metrics, namely (1) total pressure recovery (PFAIP), (2) radial hub distortion (DPH/P), (3) ) radial tip distortion (DPT/P), and (4) ) circumferential distortion (DPC/P). In general, the resulting +/-0.95 delta Y interval was unacceptably large in comparison to the stated goals of the HSCT program. Therefore, the conclusion was reached that the "standard grid" size was insufficient for this type of analysis. However, in examining the statistical data, it was determined that the CFD analysis results at the outer fringes of the operability space were the determining factor in the measure of statistical uncertainty. Adequate grids are grids that are free of biasing (systemic) errors and exhibit low random (precision) errors in comparison to their operability goals. In order to be 100% certain that the operability goals have indeed been achieved for each of the inlet metrics, the Y+/-0.95 delta Y limit must fall inside the stated operability goals. For example, if the operability goal for DPC/P circumferential distortion is =0.06, then the forecast Y for DPC/P plus the 95% confidence interval on DPC/P, i.e. +/-0.95 delta Y, must all be less than or equal to 0.06.

Dimeric arrangement and structure of the membrane-bound acetylcholine receptor studied by electron microscopy.

PubMed Central

Zingsheim, H P; Neugebauer, D C; Frank, J; Hänicke, W; Barrantes, F J

1982-01-01

The acetylcholine receptor protein (AChR) from the electric organ of Torpedo marmorata is studied in its membrane-bound form by electron microscopy and single-particle image averaging. About half the molecule protrudes from the membrane surface by approximately 5 nm. The low-resolution 3-D structure of this hydrated portion, including its handedness, can be deduced from averaged axial and lateral projections and from freeze-etched membrane surfaces. In native membrane fragments, a dimeric form of the AChR is observed and the relative orientation of the AChR monomers within the dimer is established. The dimers disappear upon disulfide reduction of the membrane preparations, whereas the average axial projections of the AChR monomer remain unaffected. Since the existence of disulfide bonds linking AChR monomers between their respective delta-subunits is well documented, the approximate position of the delta-subunit within the low-resolution structure of the AChR molecule can be deduced from the structure of the dimers. Images Fig. 1. Fig. 2. Fig. 3. PMID:7188351

Effects of spatial resolution and landscape structure on land cover characterization

NASA Astrophysics Data System (ADS)

Yang, Wenli

This dissertation addressed problems in scaling, problems that are among the main challenges in remote sensing. The principal objective of the research was to investigate the effects of changing spatial scale on the representation of land cover. A second objective was to determine the relationship between such effects, characteristics of landscape structure and scaling procedures. Four research issues related to spatial scaling were examined. They included: (1) the upscaling of Normalized Difference Vegetation Index (NDVI); (2) the effects of spatial scale on indices of landscape structure; (3) the representation of land cover databases at different spatial scales; and (4) the relationships between landscape indices and land cover area estimations. The overall bias resulting from non-linearity of NDVI in relation to spatial resolution is generally insignificant as compared to other factors such as influences of aerosols and water vapor. The bias is, however, related to land surface characteristics. Significant errors may be introduced in heterogeneous areas where different land cover types exhibit strong spectral contrast. Spatially upscaled SPOT and TM NDVIs have information content comparable with the AVHRR-derived NDVI. Indices of landscape structure and spatial resolution are generally related, but the exact forms of the relationships are subject to changes in other factors including the basic patch unit constituting a landscape and the proportional area of foreground land cover under consideration. The extent of agreement between spatially aggregated coarse resolution land cover datasets and full resolution datasets changes with the properties of the original datasets, including the pixel size and class definition. There are close relationships between landscape structure and class areas estimated from spatially aggregated land cover databases. The relationships, however, do not permit extension from one area to another. Inversion calibration across different

Low Cost Large Core Vehicle Structures Assessment

NASA Technical Reports Server (NTRS)

Hahn, Steven E.

1998-01-01

Boeing Information, Space, and Defense Systems executed a Low Cost Large Core Vehicle Structures Assessment (LCLCVSA) under contract to NASA Marshall Space Flight Center (MSFC) between November 1997 and March 1998. NASA is interested in a low-cost launch vehicle, code named Magnum, to place heavy payloads into low earth orbit for missions such as a manned mission to Mars, a Next Generation Space Telescope, a lunar-based telescope, the Air Force's proposed space based laser, and large commercial satellites. In this study, structural concepts with the potential to reduce fabrication costs were evaluated in application to the Magnum Launch Vehicle (MLV) and the Liquid Fly Back Booster (LFBB) shuttle upgrade program. Seventeen concepts were qualitatively evaluated to select four concepts for more in-depth study. The four structural concepts selected were: an aluminum-lithium monocoque structure, an aluminum-lithium machined isogrid structure, a unitized composite sandwich structure, and a unitized composite grid structure. These were compared against a baseline concept based on the Space Shuttle External Tank (ET) construction. It was found that unitized composite structures offer significant cost and weight benefits to MLV structures. The limited study of application to LFBB structures indicated lower, but still significant benefits. Technology and facilities development roadmaps to prepare the approaches studied for application to MLV and LFBB were constructed. It was found that the cost and schedule to develop these approaches were in line with both MLV and LFBB development schedules. Current Government and Boeing programs which address elements of the development of the technologies identified are underway. It is recommended that NASA devote resources in a timely fashion to address the specific elements related to MLV and LFBB structures.

Interactive local super-resolution reconstruction of whole-body MRI mouse data: a pilot study with applications to bone and kidney metastases.

PubMed

Dzyubachyk, Oleh; Khmelinskii, Artem; Plenge, Esben; Kok, Peter; Snoeks, Thomas J A; Poot, Dirk H J; Löwik, Clemens W G M; Botha, Charl P; Niessen, Wiro J; van der Weerd, Louise; Meijering, Erik; Lelieveldt, Boudewijn P F

2014-01-01

In small animal imaging studies, when the locations of the micro-structures of interest are unknown a priori, there is a simultaneous need for full-body coverage and high resolution. In MRI, additional requirements to image contrast and acquisition time will often make it impossible to acquire such images directly. Recently, a resolution enhancing post-processing technique called super-resolution reconstruction (SRR) has been demonstrated to improve visualization and localization of micro-structures in small animal MRI by combining multiple low-resolution acquisitions. However, when the field-of-view is large relative to the desired voxel size, solving the SRR problem becomes very expensive, in terms of both memory requirements and computation time. In this paper we introduce a novel local approach to SRR that aims to overcome the computational problems and allow researchers to efficiently explore both global and local characteristics in whole-body small animal MRI. The method integrates state-of-the-art image processing techniques from the areas of articulated atlas-based segmentation, planar reformation, and SRR. A proof-of-concept is provided with two case studies involving CT, BLI, and MRI data of bone and kidney tumors in a mouse model. We show that local SRR-MRI is a computationally efficient complementary imaging modality for the precise characterization of tumor metastases, and that the method provides a feasible high-resolution alternative to conventional MRI.

Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase

PubMed Central

2013-01-01

Background Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms. Results A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed. Conclusions A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism. PMID:23915572

High resolution telescope

DOEpatents

Massie, Norbert A.; Oster, Yale

1992-01-01

A large effective-aperture, low-cost optical telescope with diffraction-limited resolution enables ground-based observation of near-earth space objects. The telescope has a non-redundant, thinned-aperture array in a center-mount, single-structure space frame. It employs speckle interferometric imaging to achieve diffraction-limited resolution. The signal-to-noise ratio problem is mitigated by moving the wavelength of operation to the near-IR, and the image is sensed by a Silicon CCD. The steerable, single-structure array presents a constant pupil. The center-mount, radar-like mount enables low-earth orbit space objects to be tracked as well as increases stiffness of the space frame. In the preferred embodiment, the array has elemental telescopes with subaperture of 2.1 m in a circle-of-nine configuration. The telescope array has an effective aperture of 12 m which provides a diffraction-limited resolution of 0.02 arc seconds. Pathlength matching of the telescope array is maintained by an electro-optical system employing laser metrology. Speckle imaging relaxes pathlength matching tolerance by one order of magnitude as compared to phased arrays. Many features of the telescope contribute to substantial reduction in costs. These include eliminating the conventional protective dome and reducing on-site construction activites. The cost of the telescope scales with the first power of the aperture rather than its third power as in conventional telescopes.

Enhanced Exoplanet Biosignature from an Interferometer Addition to Low Resolution Spectrographs

NASA Astrophysics Data System (ADS)

Erskine, D. J.; Muirhead, P. S.; Vanderburg, A. M.; Szentgyorgyi, A.

2017-12-01

The absorption spectral signature of many atmospheric molecules consists of a group of 40 or so lines that are approximately periodic due to the physics of molecular vibration. This is fortuitous for detecting atmospheric features in an exoEarth, since it has a similar periodic nature as an interferometer's transmission, which is sinusoidal. The period (in wavenumbers) of the interferometer is selectable, being inversely proportional to the delay (in cm). We show that the addition of a small interferometer of 0.6 cm delay to an existing dispersive spectrograph can greatly enhance the detection of molecular features, by several orders of magnitude for initially low resolution spectrographs. We simulate the Gemini Planet Imager measuring a telluric spectrum having native resolution of 40 and 70 in the 1.65 micron and 2 micron bands. These low resolutions are insufficient to resolve the fine features of the molecular feature group. However, the addition of a 0.6 cm delay outside the spectrograph and in series with it increases the local amplitude of the signal to a level similar to a R=4400 (at 1.65 micron) or R=3900 (at 2 micron) classical spectrograph. Prepared by LLNL under Contract DE-AC52-07NA27344.

Structural and semantic constraints on the resolution of pronouns and reflexives

PubMed Central

Kaiser, Elsi; Runner, Jeffrey T.; Sussman, Rachel S.; Tanenhaus, Michael K.

2009-01-01

We present four experiments on the interpretation of pronouns and reflexives in picture noun phrases with and without possessors (e.g. Andrew’s picture of him/himself, the picture of him/himself). The experiments (two off-line studies and two visual-world eye-tracking experiments) investigate how syntactic and semantic factors guide the interpretation of pronouns and reflexives and how different kinds of information are integrated during real-time reference resolution. The results show that the interpretation of pronouns and reflexives in picture NP constructions is sensitive not only to purely structural information, as is commonly assumed in syntactically-oriented theories of anaphor resolution, but also to semantic information (see Kuno, 1987; Tenny, 2003). Moreover, the results show that pronouns and reflexives differ in the degree of sensitivity they exhibit to different kinds of information. This finding indicates that the form-specific multiple-constraints approach (see Kaiser, 2003; Kaiser, 2005; Kaiser & Trueswell, 2008; Brown-Schmidt, Byron & Tanenhaus, 2005), which states that referential forms can exhibit asymmetrical sensitivities to the different constraints guiding reference resolution, also applies in the within-sentence domain. PMID:19426968

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.

LITE microscopy: Tilted light-sheet excitation of model organisms offers high resolution and low photobleaching

PubMed Central

Gerbich, Therese M.; Rana, Kishan; Suzuki, Aussie; Schaefer, Kristina N.; Heppert, Jennifer K.; Boothby, Thomas C.; Allbritton, Nancy L.; Gladfelter, Amy S.; Maddox, Amy S.

2018-01-01

Fluorescence microscopy is a powerful approach for studying subcellular dynamics at high spatiotemporal resolution; however, conventional fluorescence microscopy techniques are light-intensive and introduce unnecessary photodamage. Light-sheet fluorescence microscopy (LSFM) mitigates these problems by selectively illuminating the focal plane of the detection objective by using orthogonal excitation. Orthogonal excitation requires geometries that physically limit the detection objective numerical aperture (NA), thereby limiting both light-gathering efficiency (brightness) and native spatial resolution. We present a novel live-cell LSFM method, lateral interference tilted excitation (LITE), in which a tilted light sheet illuminates the detection objective focal plane without a sterically limiting illumination scheme. LITE is thus compatible with any detection objective, including oil immersion, without an upper NA limit. LITE combines the low photodamage of LSFM with high resolution, high brightness, and coverslip-based objectives. We demonstrate the utility of LITE for imaging animal, fungal, and plant model organisms over many hours at high spatiotemporal resolution. PMID:29490939

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

Atomic-resolution structure of the CAP-Gly domain of dynactin on polymeric microtubules determined by magic angle spinning NMR spectroscopy.

PubMed

Yan, Si; Guo, Changmiao; Hou, Guangjin; Zhang, Huilan; Lu, Xingyu; Williams, John Charles; Polenova, Tatyana

2015-11-24

Microtubules and their associated proteins perform a broad array of essential physiological functions, including mitosis, polarization and differentiation, cell migration, and vesicle and organelle transport. As such, they have been extensively studied at multiple levels of resolution (e.g., from structural biology to cell biology). Despite these efforts, there remain significant gaps in our knowledge concerning how microtubule-binding proteins bind to microtubules, how dynamics connect different conformational states, and how these interactions and dynamics affect cellular processes. Structures of microtubule-associated proteins assembled on polymeric microtubules are not known at atomic resolution. Here, we report a structure of the cytoskeleton-associated protein glycine-rich (CAP-Gly) domain of dynactin motor on polymeric microtubules, solved by magic angle spinning NMR spectroscopy. We present the intermolecular interface of CAP-Gly with microtubules, derived by recording direct dipolar contacts between CAP-Gly and tubulin using double rotational echo double resonance (dREDOR)-filtered experiments. Our results indicate that the structure adopted by CAP-Gly varies, particularly around its loop regions, permitting its interaction with multiple binding partners and with the microtubules. To our knowledge, this study reports the first atomic-resolution structure of a microtubule-associated protein on polymeric microtubules. Our approach lays the foundation for atomic-resolution structural analysis of other microtubule-associated motors.

High-Resolution Images of Retinal Structure in Patients with Choroideremia

PubMed Central

Syed, Reema; Sundquist, Sanna M.; Ratnam, Kavitha; Zayit-Soudry, Shiri; Zhang, Yuhua; Crawford, J. Brooks; MacDonald, Ian M.; Godara, Pooja; Rha, Jungtae; Carroll, Joseph; Roorda, Austin; Stepien, Kimberly E.; Duncan, Jacque L.

2013-01-01

Purpose. To study retinal structure in choroideremia patients and carriers using high-resolution imaging techniques. Methods. Subjects from four families (six female carriers and five affected males) with choroideremia (CHM) were characterized with best-corrected visual acuity (BCVA), kinetic and static perimetry, full-field electroretinography, and fundus autofluorescence (FAF). High-resolution macular images were obtained with adaptive optics scanning laser ophthalmoscopy (AOSLO) and spectral domain optical coherence tomography (SD-OCT). Coding regions of the CHM gene were sequenced. Results. Molecular analysis of the CHM gene identified a deletion of exons 9 to 15 in family A, a splice site mutation at position 79+1 of exon 1 in family B, deletion of exons 6 to 8 in family C, and a substitution at position 106 causing a premature stop in family D. BCVA ranged from 20/16 to 20/63 in carriers and from 20/25 to 5/63 in affected males. FAF showed abnormalities in all subjects. SD-OCT showed outer retinal layer loss, outer retinal tubulations at the margin of outer retinal loss, and inner retinal microcysts. Patchy cone loss was present in two symptomatic carriers. In two affected males, cone mosaics were disrupted with increased cone spacing near the fovea but more normal cone spacing near the edge of atrophy. Conclusions. High-resolution retinal images in CHM carriers and affected males demonstrated RPE and photoreceptor cell degeneration. As both RPE and photoreceptor cells were affected, these cell types may degenerate simultaneously in CHM. These findings provide insight into the effect of CHM mutations on macular retinal structure, with implications for the development of treatments for CHM. (ClinicalTrials.gov number, NCT00254605.) PMID:23299470

High-resolution images of retinal structure in patients with choroideremia.

PubMed

Syed, Reema; Sundquist, Sanna M; Ratnam, Kavitha; Zayit-Soudry, Shiri; Zhang, Yuhua; Crawford, J Brooks; MacDonald, Ian M; Godara, Pooja; Rha, Jungtae; Carroll, Joseph; Roorda, Austin; Stepien, Kimberly E; Duncan, Jacque L

2013-02-01

To study retinal structure in choroideremia patients and carriers using high-resolution imaging techniques. Subjects from four families (six female carriers and five affected males) with choroideremia (CHM) were characterized with best-corrected visual acuity (BCVA), kinetic and static perimetry, full-field electroretinography, and fundus autofluorescence (FAF). High-resolution macular images were obtained with adaptive optics scanning laser ophthalmoscopy (AOSLO) and spectral domain optical coherence tomography (SD-OCT). Coding regions of the CHM gene were sequenced. Molecular analysis of the CHM gene identified a deletion of exons 9 to 15 in family A, a splice site mutation at position 79+1 of exon 1 in family B, deletion of exons 6 to 8 in family C, and a substitution at position 106 causing a premature stop in family D. BCVA ranged from 20/16 to 20/63 in carriers and from 20/25 to 5/63 in affected males. FAF showed abnormalities in all subjects. SD-OCT showed outer retinal layer loss, outer retinal tubulations at the margin of outer retinal loss, and inner retinal microcysts. Patchy cone loss was present in two symptomatic carriers. In two affected males, cone mosaics were disrupted with increased cone spacing near the fovea but more normal cone spacing near the edge of atrophy. High-resolution retinal images in CHM carriers and affected males demonstrated RPE and photoreceptor cell degeneration. As both RPE and photoreceptor cells were affected, these cell types may degenerate simultaneously in CHM. These findings provide insight into the effect of CHM mutations on macular retinal structure, with implications for the development of treatments for CHM. (ClinicalTrials.gov number, NCT00254605.).

Charge-density analysis of a protein structure at subatomic resolution: the human aldose reductase case.

PubMed

Guillot, Benoît; Jelsch, Christian; Podjarny, Alberto; Lecomte, Claude

2008-05-01

The valence electron density of the protein human aldose reductase was analyzed at 0.66 angstroms resolution. The methodological developments in the software MoPro to adapt standard charge-density techniques from small molecules to macromolecular structures are described. The deformation electron density visible in initial residual Fourier difference maps was significantly enhanced after high-order refinement. The protein structure was refined after transfer of the experimental library multipolar atom model (ELMAM). The effects on the crystallographic statistics, on the atomic thermal displacement parameters and on the structure stereochemistry are analyzed. Constrained refinements of the transferred valence populations Pval and multipoles Plm were performed against the X-ray diffraction data on a selected substructure of the protein with low thermal motion. The resulting charge densities are of good quality, especially for chemical groups with many copies present in the polypeptide chain. To check the effect of the starting point on the result of the constrained multipolar refinement, the same charge-density refinement strategy was applied but using an initial neutral spherical atom model, i.e. without transfer from the ELMAM library. The best starting point for a protein multipolar refinement is the structure with the electron density transferred from the database. This can be assessed by the crystallographic statistical indices, including Rfree, and the quality of the static deformation electron-density maps, notably on the oxygen electron lone pairs. The analysis of the main-chain bond lengths suggests that stereochemical dictionaries would benefit from a revision based on recently determined unrestrained atomic resolution protein structures.

Inferring Biological Structures from Super-Resolution Single Molecule Images Using Generative Models

PubMed Central

Maji, Suvrajit; Bruchez, Marcel P.

2012-01-01

Localization-based super resolution imaging is presently limited by sampling requirements for dynamic measurements of biological structures. Generating an image requires serial acquisition of individual molecular positions at sufficient density to define a biological structure, increasing the acquisition time. Efficient analysis of biological structures from sparse localization data could substantially improve the dynamic imaging capabilities of these methods. Using a feature extraction technique called the Hough Transform simple biological structures are identified from both simulated and real localization data. We demonstrate that these generative models can efficiently infer biological structures in the data from far fewer localizations than are required for complete spatial sampling. Analysis at partial data densities revealed efficient recovery of clathrin vesicle size distributions and microtubule orientation angles with as little as 10% of the localization data. This approach significantly increases the temporal resolution for dynamic imaging and provides quantitatively useful biological information. PMID:22629348

High resolution imaging studies into the formation of laser-induced periodic surface structures.

PubMed

Kerr, N C; Clark, S E; Emmony, D C

1989-09-01

We report the results of an investigation into the formation mechanism of laser-induced ripple structures based on obtaining direct images of a surface while the transient heating induced by a KrF excimer laser is still present. These images reveal transient but well-defined periodic heating patterns which, if enough subsequent excimer pulses are incident on the surface, become permanently induced ripple structures. It is evident from these transient images that the surface heating is confined to the induced structures, thus strongly supporting the idea that at low fluences the ripples are formed by localizing surface melting.

[Can the local energy minimization refine the PDB structures of different resolution universally?].

PubMed

Godzi, M G; Gromova, A P; Oferkin, I V; Mironov, P V

2009-01-01

The local energy minimization was statistically validated as the refinement strategy for PDB structure pairs of different resolution. Thirteen pairs of structures with the only difference in resolution were extracted from PDB, and the structures of 11 identical proteins obtained by different X-ray diffraction techniques were represented. The distribution of RMSD value was calculated for these pairs before and after the local energy minimization of each structure. The MMFF94 field was used for energy calculations, and the quasi-Newton method was used for local energy minimization. By comparison of these two RMSD distributions, the local energy minimization was proved to statistically increase the structural differences in pairs so that it cannot be used for refinement purposes. To explore the prospects of complex refinement strategies based on energy minimization, randomized structures were obtained by moving the initial PDB structures as far as the minimized structures had been moved in a multidimensional space of atomic coordinates. For these randomized structures, the RMSD distribution was calculated and compared with that for minimized structures. The significant differences in their mean values proved the energy surface of the protein to have only few minima near the conformations of different resolution obtained by X-ray diffraction for PDB. Some other results obtained by exploring the energy surface near these conformations are also presented. These results are expected to be very useful for the development of new protein refinement strategies based on energy minimization.

Classification of Volcanic Eruptions on Io and Earth Using Low-Resolution Remote Sensing Data

NASA Technical Reports Server (NTRS)

Davies, A. G.; Keszthelyi, L. P.

2005-01-01

Two bodies in the Solar System exhibit high-temperature active volcanism: Earth and Io. While there are important differences in the eruptions on Earth and Io, in low-spatial-resolution data (corresponding to the bulk of available and foreseeable data of Io), similar styles of effusive and explosive volcanism yield similar thermal flux densities. For example, a square metre of an active pahoehoe flow on Io looks very similar to a square metre of an active pahoehoe flow on Earth. If, from observed thermal emission as a function of wavelength and change in thermal emission with time, the eruption style of an ionian volcano can be constrained, estimates of volumetric fluxes can be made and compared with terrestrial volcanoes using techniques derived for analysing terrestrial remotely-sensed data. In this way we find that ionian volcanoes fundamentally differ from their terrestrial counterparts only in areal extent, with Io volcanoes covering larger areas, with higher volumetric flux. Io outbursts eruptions have enormous implied volumetric fluxes, and may scale with terrestrial flood basalt eruptions. Even with the low-spatial resolution data available it is possible to sometimes constrain and classify eruption style both on Io and Earth from the integrated thermal emission spectrum. Plotting 2 and 5 m fluxes reveals the evolution of individual eruptions of different styles, as well as the relative intensity of eruptions, allowing comparison to be made from individual eruptions on both planets. Analyses like this can be used for interpretation of low-resolution data until the next mission to the jovian system. For a number of Io volcanoes (including Pele, Prometheus, Amirani, Zamama, Culann, Tohil and Tvashtar) we do have high/moderate resolution imagery to aid determination of eruption mode from analyses based only on low spatial-resolution data.

High resolution three-dimensional magnetization mapping in Tokachidake Volcano using low altitude airborne magnetic survey data

NASA Astrophysics Data System (ADS)

Iwata, M.; Mogi, T.; Okuma, S.; Nakatsuka, T.

2016-12-01

Tokachidake Volcano, central Hokkaido, Japan erupted in 1926, 1962 and 1988-1989 in the 20th century from the central part. In recent years, expansions of the edifice of the volcano at shallow depth and increases of the volcanic smoke in the Taisho crater were observed (Meteorological Agency of Japan, 2014). Magnetic changes were observed at the 62-2 crater by repeated magnetic measurements in 2008-2009, implying a demagnetization beneath the crater (Hashimoto at al., 2010). Moreover, a very low resistivity part was found right under the 62-2 crater from an AMT survey (Yamaya et al., 2010). However, since the station numbers of the survey are limited, the area coverage is not sufficient. In this study, we have re-analyzed high-resolution aeromagnetic data to delineate the three-dimensional magnetic structure of the volcano to understand the nature of other craters.A low altitude airborne magnetic survey was conducted in 2014 mainly over the active areas of the volcano by the Ministry of Land, Infrastructure, Transport and Tourism to manage land slide risk in the volcano. The survey was flown at an altitude of 60 m above ground by a helicopter with a Cesium magnetometer in the towed-bird 30m below the helicopter. The low altitude survey enables us to delineate the detailed magnetic structure. We calculated magnetic anomaly distribution on a smooth surface assuming equivalent anomalies below the observation surface. Then the 3D magnetic imaging method (Nakatsuka and Okuma, 2014) was applied to the magnetic anomalies to reveal the three-dimensional magnetic structure.As a result, magnetization highs were seen beneath the Ground crater, Suribachi crater and Kitamuki crater. This implies that magmatic activity occurred in the past at these craters. These magma should have already solidified and acquired strong remanent magnetization. Relative magnetization lows were seen beneath the 62-2 crater and the Taisho crater where fumarolic activity is active. However a

Low-temperature magnetic resonance imaging with 2.8 μm isotropic resolution

NASA Astrophysics Data System (ADS)

Chen, Hsueh-Ying; Tycko, Robert

2018-02-01

We demonstrate the feasibility of high-resolution 1H magnetic resonance imaging (MRI) at low temperatures by obtaining an MRI image of 20 μm diameter glass beads in glycerol/water at 28 K with 2.8 μm isotropic resolution. The experiments use a recently-described MRI apparatus (Moore and Tycko, 2015) with minor modifications. The sample is contained within a radio-frequency microcoil with 150 μm inner diameter. Sensitivity is additionally enhanced by paramagnetic doping, optimization of the sample temperature, three-dimensional phase-encoding of k-space data, pulsed spin-lock detection of 1H nuclear magnetic resonance signals, and spherical sampling of k-space. We verify that the actual image resolution is 2.7 ± 0.3 μm by quantitative comparisons of experimental and calculated images. Our imaging approach is compatible with dynamic nuclear polarization, providing a path to significantly higher resolution in future experiments.

A high resolution gas scintillation proportional counter for studying low energy cosmic X-ray sources

NASA Technical Reports Server (NTRS)

Hamilton, T. T.; Hailey, C. J.; Ku, W. H.-M.; Novick, R.

1980-01-01

In recent years much effort has been devoted to the development of large area gas scintillation proportional counters (GSPCs) suitable for use in X-ray astronomy. The paper deals with a low-energy GSPC for use in detecting sub-keV X-rays from cosmic sources. This instrument has a measured energy resolution of 85 eV (FWHM) at 149 eV over a sensitive area of 5 sq cm. The development of imaging capability for this instrument is discussed. Tests are performed on the feasibility of using an arrangement of several phototubes placed adjacent to one another to determine event locations in a large flat counter. A simple prototype has been constructed and successfully operated.

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

Air-Sea Interaction Processes in Low and High-Resolution Coupled Climate Model Simulations for the Southeast Pacific

NASA Astrophysics Data System (ADS)

Porto da Silveira, I.; Zuidema, P.; Kirtman, B. P.

2017-12-01

The rugged topography of the Andes Cordillera along with strong coastal upwelling, strong sea surface temperatures (SST) gradients and extensive but geometrically-thin stratocumulus decks turns the Southeast Pacific (SEP) into a challenge for numerical modeling. In this study, hindcast simulations using the Community Climate System Model (CCSM4) at two resolutions were analyzed to examine the importance of resolution alone, with the parameterizations otherwise left unchanged. The hindcasts were initialized on January 1 with the real-time oceanic and atmospheric reanalysis (CFSR) from 1982 to 2003, forming a 10-member ensemble. The two resolutions are (0.1o oceanic and 0.5o atmospheric) and (1.125o oceanic and 0.9o atmospheric). The SST error growth in the first six days of integration (fast errors) and those resulted from model drift (saturated errors) are assessed and compared towards evaluating the model processes responsible for the SST error growth. For the high-resolution simulation, SST fast errors are positive (+0.3oC) near the continental borders and negative offshore (-0.1oC). Both are associated with a decrease in cloud cover, a weakening of the prevailing southwesterly winds and a reduction of latent heat flux. The saturated errors possess a similar spatial pattern, but are larger and are more spatially concentrated. This suggests that the processes driving the errors already become established within the first week, in contrast to the low-resolution simulations. These, instead, manifest too-warm SSTs related to too-weak upwelling, driven by too-strong winds and Ekman pumping. Nevertheless, the ocean surface tends to be cooler in the low-resolution simulation than the high-resolution due to a higher cloud cover. Throughout the integration, saturated SST errors become positive and could reach values up to +4oC. These are accompanied by upwelling dumping and a decrease in cloud cover. High and low resolution models presented notable differences in how SST

Diagnostic accuracy of cone-beam computed tomography scans with high- and low-resolution modes for the detection of root perforations.

PubMed

Shokri, Abbas; Eskandarloo, Amir; Norouzi, Marouf; Poorolajal, Jalal; Majidi, Gelareh; Aliyaly, Alireza

2018-03-01

This study compared the diagnostic accuracy of cone-beam computed tomography (CBCT) scans obtained with 2 CBCT systems with high- and low-resolution modes for the detection of root perforations in endodontically treated mandibular molars. The root canals of 72 mandibular molars were cleaned and shaped. Perforations measuring 0.2, 0.3, and 0.4 mm in diameter were created at the furcation area of 48 roots, simulating strip perforations, or on the external surfaces of 48 roots, simulating root perforations. Forty-eight roots remained intact (control group). The roots were filled using gutta-percha (Gapadent, Tianjin, China) and AH26 sealer (Dentsply Maillefer, Ballaigues, Switzerland). The CBCT scans were obtained using the NewTom 3G (QR srl, Verona, Italy) and Cranex 3D (Soredex, Helsinki, Finland) CBCT systems in high- and low-resolution modes, and were evaluated by 2 observers. The chi-square test was used to assess the nominal variables. In strip perforations, the accuracies of low- and high-resolution modes were 75% and 83% for NewTom 3G and 67% and 69% for Cranex 3D. In root perforations, the accuracies of low- and high-resolution modes were 79% and 83% for NewTom 3G and was 56% and 73% for Cranex 3D. The accuracy of the 2 CBCT systems was different for the detection of strip and root perforations. The Cranex 3D had non-significantly higher accuracy than the NewTom 3G. In both scanners, the high-resolution mode yielded significantly higher accuracy than the low-resolution mode. The diagnostic accuracy of CBCT scans was not affected by the perforation diameter.

Low-cost structured-light based 3D capture system design

NASA Astrophysics Data System (ADS)

Dong, Jing; Bengtson, Kurt R.; Robinson, Barrett F.; Allebach, Jan P.

2014-03-01

Most of the 3D capture products currently in the market are high-end and pricey. They are not targeted for consumers, but rather for research, medical, or industrial usage. Very few aim to provide a solution for home and small business applications. Our goal is to fill in this gap by only using low-cost components to build a 3D capture system that can satisfy the needs of this market segment. In this paper, we present a low-cost 3D capture system based on the structured-light method. The system is built around the HP TopShot LaserJet Pro M275. For our capture device, we use the 8.0 Mpixel camera that is part of the M275. We augment this hardware with two 3M MPro 150 VGA (640 × 480) pocket projectors. We also describe an analytical approach to predicting the achievable resolution of the reconstructed 3D object based on differentials and small signal theory, and an experimental procedure for validating that the system under test meets the specifications for reconstructed object resolution that are predicted by our analytical model. By comparing our experimental measurements from the camera-projector system with the simulation results based on the model for this system, we conclude that our prototype system has been correctly configured and calibrated. We also conclude that with the analytical models, we have an effective means for specifying system parameters to achieve a given target resolution for the reconstructed object.

Three-dimensional printing and deformation behavior of low-density target structures by two-photon polymerization

NASA Astrophysics Data System (ADS)

Liu, Ying; Stein, Ori; Campbell, John H.; Jiang, Lijia; Petta, Nicole; Lu, Yongfeng

2017-08-01

Two-photon polymerization (2PP), a 3D nano to microscale additive manufacturing process, is being used for the first time to fabricate small custom experimental packages ("targets") to support laser-driven high-energy-density (HED) physics research. Of particular interest is the use of 2PP to deterministically print low-density, low atomic-number (CHO) polymer matrices ("foams") at millimeter scale with sub-micrometer resolution. Deformation during development and drying of the foam structures remains a challenge when using certain commercial photo-resins; here we compare use of acrylic resins IP-S and IP-Dip. The mechanical strength of polymeric beam and foam structures is examined particularly the degree of deformation that occurs during the development and drying processes. The magnitude of the shrinkage in the two resins in quantified by printing sample structures and by use of FEA to simulate the deformation. Capillary drying forces are shown to be small and likely below the elastic limit of the core foam structure. In contrast the substantial shrinkage in IP-Dip ( 5-10%) cause large shear stresses and associated plastic deformation particularly near constrained boundaries such as the substrate and locations with sharp density variation. The inherent weakness of stitching boundaries is also evident and in certain cases can lead to delamination. Use of IP-S shows marked reduction in deformation with a minor loss of print resolution

Low-Resolution Spectroscopy of Primitive Asteroids: Progress Report for SARA/VSU Survey

NASA Technical Reports Server (NTRS)

Leake, M. A.; Nogues, J. P.; Gaines, J. K.; Looper, J. K.; Freitas, K. A.

2001-01-01

Progress on a low-resolution survey of primitive C-class asteroids continues using new equipment (and its associated problems) to understand aqueous alteration in the solar system. Additional information is contained in the original extended abstract.

Pixel decomposition for tracking in low resolution videos

NASA Astrophysics Data System (ADS)

Govinda, Vivekanand; Ralph, Jason F.; Spencer, Joseph W.; Goulermas, John Y.; Yang, Lihua; Abbas, Alaa M.

2008-04-01

This paper describes a novel set of algorithms that allows indoor activity to be monitored using data from very low resolution imagers and other non-intrusive sensors. The objects are not resolved but activity may still be determined. This allows the use of such technology in sensitive environments where privacy must be maintained. Spectral un-mixing algorithms from remote sensing were adapted for this environment. These algorithms allow the fractional contributions from different colours within each pixel to be estimated and this is used to assist in the detection and monitoring of small objects or sub-pixel motion.

Low-light-level image super-resolution reconstruction based on iterative projection photon localization algorithm

NASA Astrophysics Data System (ADS)

Ying, Changsheng; Zhao, Peng; Li, Ye

2018-01-01

The intensified charge-coupled device (ICCD) is widely used in the field of low-light-level (LLL) imaging. The LLL images captured by ICCD suffer from low spatial resolution and contrast, and the target details can hardly be recognized. Super-resolution (SR) reconstruction of LLL images captured by ICCDs is a challenging issue. The dispersion in the double-proximity-focused image intensifier is the main factor that leads to a reduction in image resolution and contrast. We divide the integration time into subintervals that are short enough to get photon images, so the overlapping effect and overstacking effect of dispersion can be eliminated. We propose an SR reconstruction algorithm based on iterative projection photon localization. In the iterative process, the photon image is sliced by projection planes, and photons are screened under the constraints of regularity. The accurate position information of the incident photons in the reconstructed SR image is obtained by the weighted centroids calculation. The experimental results show that the spatial resolution and contrast of our SR image are significantly improved.

Resolution of low-velocity control in golf putting differentiates professionals from amateurs.

PubMed

Hasegawa, Yumiko; Fujii, Keisuke; Miura, Akito; Yamamoto, Yuji

2017-07-01

It is difficult for humans to apply small amounts of force precisely during motor control. However, experts who have undergone extended training are thought to be able to control low-velocity movement with precision. We investigated the resolution of motor control in golf putting. A total of 10 professional and 10 high-level amateur golfers participated. Putting distances were 0.6-3.3 m, in increments of 0.3 m. We measured the impact velocity and the club-face angle at impact, and the acceleration profile of the downswing. The professionals showed significantly smaller coefficients of variation with respect to impact velocity and smaller root mean square errors in relation to acceleration profiles than did the amateurs. To examine the resolution of motor control for impact velocity, we investigated intra-participant differences in the impact velocity of the club head at two adjacent distances. We found that professionals had higher velocity precision when putting small distance intervals than did amateurs. That is, professionals had higher resolution of low-velocity control than did high-level amateurs. Our results suggest that outstanding performance at a task involves the ability to recognise small distinctions and to produce appropriate movements.

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.

Structural resolution of inorganic nanotubes with complex stoichiometry.

PubMed

Monet, Geoffrey; Amara, Mohamed S; Rouzière, Stéphan; Paineau, Erwan; Chai, Ziwei; Elliott, Joshua D; Poli, Emiliano; Liu, Li-Min; Teobaldi, Gilberto; Launois, Pascale

2018-05-23

Determination of the atomic structure of inorganic single-walled nanotubes with complex stoichiometry remains elusive due to the too many atomic coordinates to be fitted with respect to X-ray diffractograms inherently exhibiting rather broad features. Here we introduce a methodology to reduce the number of fitted variables and enable resolution of the atomic structure for inorganic nanotubes with complex stoichiometry. We apply it to recently synthesized methylated aluminosilicate and aluminogermanate imogolite nanotubes of nominal composition (OH) 3 Al 2 O 3 Si(Ge)CH 3 . Fitting of X-ray scattering diagrams, supported by Density Functional Theory simulations, reveals an unexpected rolling mode for these systems. The transferability of the approach opens up for improved understanding of structure-property relationships of inorganic nanotubes to the benefit of fundamental and applicative research in these systems.

Analysis of the structure of complex networks at different resolution levels

NASA Astrophysics Data System (ADS)

Arenas, A.; Fernández, A.; Gómez, S.

2008-05-01

Modular structure is ubiquitous in real-world complex networks, and its detection is important because it gives insights into the structure-functionality relationship. The standard approach is based on the optimization of a quality function, modularity, which is a relative quality measure for the partition of a network into modules. Recently, some authors (Fortunato and Barthélemy 2007 Proc. Natl Acad. Sci. USA 104 36 and Kumpula et al 2007 Eur. Phys. J. B 56 41) have pointed out that the optimization of modularity has a fundamental drawback: the existence of a resolution limit beyond which no modular structure can be detected even though these modules might have their own entity. The reason is that several topological descriptions of the network coexist at different scales, which is, in general, a fingerprint of complex systems. Here, we propose a method that allows for multiple resolution screening of the modular structure. The method has been validated using synthetic networks, discovering the predefined structures at all scales. Its application to two real social networks allows us to find the exact splits reported in the literature, as well as the substructure beyond the actual split.

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.

Structural analysis of as-deposited and annealed low-temperature gallium arsenide

NASA Astrophysics Data System (ADS)

Matyi, R. J.; Melloch, M. R.; Woodall, J. M.

1993-04-01

The structure of GaAs grown at low substrate temperatures (LT-GaAs) by molecular beam epitaxy has been studied using high resolution X-ray diffraction methods. Double crystal rocking curves from the as-deposited LT-GaAs show well defined interference fringes, indicating a high level of structural perfection. Triple crystal diffraction analysis of the as-deposited sample showed significantly less diffuse scattering near the LT-GaAs 004 reciprocal lattice point compared with the substrate 004 reciprocal lattice point, suggesting that despite the incorporation of approximately 1% excess arsenic, the epitaxial layer had superior crystalline perfection than did the GaAs substrate. Triple crystal scans of annealed LT-GaAs showed an increase in the integrated diffuse intensity by approximately a factor of three as the anneal temperature was increased from 700 to 900°C. Analogous to the effects of SiO2 precipitates in annealed Czochralski silicon, the diffuse intensity is attributed to distortions in the epitaxial LT-GaAs lattice by arsenic precipitates.

High resolution micro-CT of low attenuating organic materials using large area photon-counting detector

NASA Astrophysics Data System (ADS)

Kumpová, I.; Vavřík, D.; Fíla, T.; Koudelka, P.; Jandejsek, I.; Jakůbek, J.; Kytýř, D.; Zlámal, P.; Vopálenský, M.; Gantar, A.

2016-02-01

To overcome certain limitations of contemporary materials used for bone tissue engineering, such as inflammatory response after implantation, a whole new class of materials based on polysaccharide compounds is being developed. Here, nanoparticulate bioactive glass reinforced gelan-gum (GG-BAG) has recently been proposed for the production of bone scaffolds. This material offers promising biocompatibility properties, including bioactivity and biodegradability, with the possibility of producing scaffolds with directly controlled microgeometry. However, to utilize such a scaffold with application-optimized properties, large sets of complex numerical simulations using the real microgeometry of the material have to be carried out during the development process. Because the GG-BAG is a material with intrinsically very low attenuation to X-rays, its radiographical imaging, including tomographical scanning and reconstructions, with resolution required by numerical simulations might be a very challenging task. In this paper, we present a study on X-ray imaging of GG-BAG samples. High-resolution volumetric images of investigated specimens were generated on the basis of micro-CT measurements using a large area flat-panel detector and a large area photon-counting detector. The photon-counting detector was composed of a 010× 1 matrix of Timepix edgeless silicon pixelated detectors with tiling based on overlaying rows (i.e. assembled so that no gap is present between individual rows of detectors). We compare the results from both detectors with the scanning electron microscopy on selected slices in transversal plane. It has been shown that the photon counting detector can provide approx. 3× better resolution of the details in low-attenuating materials than the integrating flat panel detectors. We demonstrate that employment of a large area photon counting detector is a good choice for imaging of low attenuating materials with the resolution sufficient for numerical simulations.

High resolution microendoscopy with structured illumination and Lugol's iodine staining for evaluation of breast cancer architecture

NASA Astrophysics Data System (ADS)

Dobbs, Jessica; Kyrish, Matthew; Krishnamurthy, Savitri; Grant, Benjamin; Kuerer, Henry; Yang, Wei; Tkaczyk, Tomasz; Richards-Kortum, Rebecca

2016-03-01

Intraoperative margin assessment to evaluate resected tissue margins for neoplastic tissue is performed to prevent reoperations following breast-conserving surgery. High resolution microendoscopy (HRME) can rapidly acquire images of fresh tissue specimens, but is limited by low image contrast in tissues with high optical scattering. In this study we evaluated two techniques to reduce out-of-focus light: HRME image acquisition with structured illumination (SI-HRME) and topical application of Lugol's Iodine. Fresh breast tissue specimens from 19 patients were stained with proflavine alone or Lugol's Iodine and proflavine. Images of tissue specimens were acquired using a confocal microscope and an HRME system with and without structured illumination. Images were evaluated based on visual and quantitative assessment of image contrast. The highest mean contrast was measured in confocal images stained with proflavine. Contrast was significantly lower in HRME images stained with proflavine; however, incorporation of structured illumination significantly increased contrast in HRME images to levels comparable to that in confocal images. The addition of Lugol's Iodine did not increase mean contrast significantly for HRME or SI-HRME images. These findings suggest that structured illumination could potentially be used to increase contrast in HRME images of breast tissue for rapid image acquisition.

High Resolution Shear-Wave Velocity Structure of Greenland from Surface Wave Analysis

NASA Astrophysics Data System (ADS)

Pourpoint, M.; Anandakrishnan, S.; Ammon, C. J.

2016-12-01

We present a high resolution seismic tomography model of Greenland's lithosphere from the analysis of fundamental mode Rayleigh-wave group velocity dispersion measurements. Regional and teleseismic events recorded by the GLISN, GSN and CN seismic networks over the last 20 years were used. In order to better constrain the crustal structure of Greenland, we also collected and processed several years of ambient noise data. We developed a new group velocity correction method that helps to alleviate the limitations of the sparse Greenland station network and the relatively few local events. The global dispersion model GDM52 from Ekström [2011] was used to calculate group delays from the earthquake to the boundaries of our study area. An iterative reweighted generalized least-square approach was used to invert for the group velocity maps between periods of 5 s and 180 s. A Markov chain Monte Carlo technique was then applied to invert for a 3-D shear wave velocity model of Greenland up to a depth of 200 km and estimate the uncertainties in the model. Our method results in relatively uniform azimuthal coverage and high resolution length ( 200 to 400 km) in west and east Greenland. We detect a deep high velocity zone extending from northwestern to southwestern Greenland and a low velocity zone (LVZ) between central-eastern and northeastern Greenland. The location of the LVZ correlates well with a previously measured high geothermal heat flux and could provide valuable information about its source. We expect the results of the ambient noise tomography to cross-validate the earthquake tomography results and give us a better estimate of the spatial extent and amplitude of the LVZ at shallow depths. A refined regional model of Greenland's lithospheric structure should eventually help better understand how underlying geological and geophysical processes may impact the dynamics of the ice sheet and influence its potential contribution to future sea level changes.

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.

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.

Low resolution radar digital interface. [with data recorder for precipitation measurements

NASA Technical Reports Server (NTRS)

1973-01-01

This document describes the design and operation of a low resolution radar data recording system for precipitation measurements. This system records a full azimuth scan on seven track magnetic tapes every five minutes. It is designed to operate on a continuous basis with operator intervention required only for changing tape reels and calibration.

Recovery of Sparse Positive Signals on the Sphere from Low Resolution Measurements

NASA Astrophysics Data System (ADS)

Bendory, Tamir; Eldar, Yonina C.

2015-12-01

This letter considers the problem of recovering a positive stream of Diracs on a sphere from its projection onto the space of low-degree spherical harmonics, namely, from its low-resolution version. We suggest recovering the Diracs via a tractable convex optimization problem. The resulting recovery error is proportional to the noise level and depends on the density of the Diracs. We validate the theory by numerical experiments.

Magnetic lens apparatus for a low-voltage high-resolution electron microscope

DOEpatents

Crewe, Albert V.

1996-01-01

A lens apparatus in which a beam of charged particles of low accelerating voltage is brought to a focus by a magnetic field, the lens being situated behind the target position. The lens comprises an electrically-conducting coil arranged around the axis of the beam and a magnetic pole piece extending along the axis of the beam at least within the space surrounded by the coil. The lens apparatus comprises the sole focusing lens for high-resolution imaging in a low-voltage scanning electron microscope.

Quantifying vegetation distribution and structure using high resolution drone-based structure-from-motion photogrammetry

NASA Astrophysics Data System (ADS)

Zhang, J.; Okin, G.

2017-12-01

Vegetation is one of the most important driving factors of different ecosystem processes in drylands. The structure of vegetation controls the spatial distribution of moisture and heat in the canopy and the surrounding area. Also, the structure of vegetation influences both airflow and boundary layer resistance above the land surface. Multispectral satellite remote sensing has been widely used to monitor vegetation coverage and its change; however, it can only capture 2D images, which do not contain the vertical information of vegetation. In situ observation uses different methods to measure the structure of vegetation, and their results are accurate; however, these methods are laborious and time-consuming, and susceptible to undersampling in spatial heterogeneity. Drylands are sparsely covered by short plants, which allows the drone fly at a relatively low height to obtain ultra-high resolution images. Structure-from-motion (SfM) is a photogrammetric method that was proved to produce 3D model based on 2D images. Drone-based remote sensing can obtain the multiangle images for one object, which can be used to constructed 3D models of vegetation in drylands. Using these images detected by the drone, the orthomosaics and digital surface model (DSM) can be built. In this study, the drone-based remote sensing was conducted in Jornada Basin, New Mexico, in the spring of 2016 and 2017, and three derived vegetation parameters (i.e., canopy size, bare soil gap size, and plant height) were compared with those obtained with field measurement. The correlation coefficient of canopy size, bare soil gap size, and plant height between drone images and field data are 0.91, 0.96, and 0.84, respectively. The two-year averaged root-mean-square error (RMSE) of canopy size, bare soil gap size, and plant height between drone images and field data are 0.61 m, 1.21 m, and 0.25 cm, respectively. The two-year averaged measure error (ME) of canopy size, bare soil gap size, and plant height

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

PubMed Central

Zhang, Lei; Ren, Gang

2012-01-01

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

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.

Structured illumination microscopy for dual-modality 3D sub-diffraction resolution fluorescence and refractive-index reconstruction

PubMed Central

Chowdhury, Shwetadwip; Eldridge, Will J.; Wax, Adam; Izatt, Joseph A.

2017-01-01

Though structured illumination (SI) microscopy is a popular imaging technique conventionally associated with fluorescent super-resolution, recent works have suggested its applicability towards sub-diffraction resolution coherent imaging with quantitative endogenous biological contrast. Here, we demonstrate that SI can efficiently integrate together the principles of fluorescent super-resolution and coherent synthetic aperture to achieve 3D dual-modality sub-diffraction resolution, fluorescence and refractive-index (RI) visualizations of biological samples. We experimentally demonstrate this framework by introducing a SI microscope capable of 3D sub-diffraction resolution fluorescence and RI imaging, and verify its biological visualization capabilities by experimentally reconstructing 3D RI/fluorescence visualizations of fluorescent calibration microspheres as well as alveolar basal epithelial adenocarcinoma (A549) and human colorectal adenocarcinmoa (HT-29) cells, fluorescently stained for F-actin. This demonstration may suggest SI as an especially promising imaging technique to enable future biological studies that explore synergistically operating biophysical/biochemical and molecular mechanisms at sub-diffraction resolutions. PMID:29296504

High-resolution imaging of the low velocity layer in Alaskan subduction zone with scattered waves and interferometry

NASA Astrophysics Data System (ADS)

Kim, D.; Keranen, K. M.; Abers, G. A.; Kim, Y.; Li, J.; Shillington, D. J.; Brown, L. D.

2017-12-01

The physical factors that control the rupture process of great earthquakes at convergent plate boundaries remain incompletely understood. While recent developments in imaging using the teleseismic wavefield have led to marked advances at wavelengths of a couple kilometers to tens of kilometers, higher resolution imaging of the rupture zone would improve the resolution of imaging and thus provide improved parameter estimation, as the teleseismic wavefield is fundamentally limited by its low frequency content. This study compares and evaluates two seismic imaging techniques using the high-frequency signals from teleseismic coda versus earthquake scattered waves to image the subducting Yakutat oceanic plateau in the Alaska subduction zone. We use earthquakes recorded by the MOOS PASSCAL broadband deployment in southern Alaska. In our first method, we select local earthquakes that lie directly beneath and laterally near the recording array for imaging, and extract body wave information via a simple autocorrelation and stacking. Profiles analogous to seismic reflection profile are constructed using the near-vertically travelling waves. In our second method, we compute teleseismic receiver functions within the 0.02-1.0 Hz frequency band. Both results image interfaces that we associate with the subducting oceanic plate in Alaska-Aleutian system, with greater resolution than commonly used methods with teleseismic sources. Structural details from our results can further our understanding of the conditions and materials that characterize the subduction megathrusts, and the techniques can be employed in other regions along the Alaska-Aleutian system and at other convergent margins with suitable seismic arrays.

Fluid-Structure Interaction in a Fluid-Filled Composite Structure Subjected to Low Velocity Impact

DTIC Science & Technology

2016-06-01

for creating an E-glass composite cubic structure and a pendulum was designed and built to provide a repeatable low velocity impact. The behavior of...structure and a pendulum was designed and built to provide a repeatable low velocity impact. The behavior of the composite structure was studied at various...SET-UP .......................................................31  1.  Impact Pendulum

Structural Mapping and Geomorphology of Ireland's Southwest Continental Shelf Using High Resolution Sonar

NASA Astrophysics Data System (ADS)

Bowden, S.; Wireman, R.

2016-02-01

Bathymetric surveys were conducted on the continental shelf off the southwest coast of County Cork, Ireland by the Marine Institute of Ireland, the Geological Survey of Ireland, and the INFOMAR project. Data were collected from July 2006 through September 2014 using a Kongsberg EM2040 multibeam echosounder aboard the R/Vs Celtic Voyager and Keary, and a Kongsberg EM1002 on the R/V Celtic Explorer. Sonar data were post-processed with CARIS HIPS and SIPS 9.0 to create 2D and 3D bathymetric and backscatter intensity surfaces with a resolution of 1 m. The offshore study site is part of the 286 Ma western Variscian orogenic front and has several massive outcrops, exhibiting 5 to 20 m of near-vertical relief. These outcrops were structurally mapped and relatively aged, and exhibit significant folding, rotation, tilting, and joint systems. Google Earth, ArcGIS, and previous terrestrial studies were used to further analyze how geomorphology is controlled by seafloor composition and structural features. Rock type and age were interpreted by comparing fracture analysis of the joints and fold trends to similar onshore outcrops documented previously, to determine an age of 416-299 Ma for the shelf's outcropping strata and associated structural features. The oldest features observed are regional anticlines and synclines containing Upper Devonian Old Red Sandstone and Lower Carboniferous shales. Within the shale layers are NE-SW plunging parasitic chevron folds. Jointing is observed in both sandstone and shale layers and is superimposed on chevron folding, with cross joints appearing to influence shallow current patterns. Rotation of the regional folds is the youngest structural feature, as both the parasitic folds and joint systems are warped. Our study shows that high resolution sonar is an effective tool for offshore structural mapping and is an important resource for understanding the geomorphology and geologic history of submerged outcrops on continental shelf systems.

Structure of the ThDP-dependent enzyme benzaldehyde lyase refined to 1.65 Å resolution

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

Maraite, Andy; Schmidt, Thomas; Ansörge-Schumacher, Marion B.

2007-07-01

The X-ray crystal structure of the ThDP-dependent enzyme benzaldehyde lyase has been refined to 1.65 Å. Benzaldehyde lyase (BAL; EC 4.1.2.38) is a thiamine diphosphate (ThDP) dependent enzyme that catalyses the enantioselective carboligation of two molecules of benzaldehyde to form (R)-benzoin. BAL has hence aroused interest for its potential in the industrial synthesis of optically active benzoins and derivatives. The structure of BAL was previously solved to a resolution of 2.6 Å using MAD experiments on a selenomethionine derivative [Mosbacher et al. (2005 ▶), FEBS J.272, 6067–6076]. In this communication of parallel studies, BAL was crystallized in an alternative spacemore » group (P2{sub 1}2{sub 1}2{sub 1}) and its structure refined to a resolution of 1.65 Å, allowing detailed observation of the water structure, active-site interactions with ThDP and also the electron density for the co-solvent 2-methyl-2,4-pentanediol (MPD) at hydrophobic patches of the enzyme surface.« less

Volcanic Eruption Classification on Io and Earth from Low Spatial Resolution Remote-Sensing Data

NASA Astrophysics Data System (ADS)

Davies, A. G.; Keszthelyi, L. P.

2005-08-01

Earth and Io exhibit high-temperature (silicate) active volcanism. While there are important differences in the eruptions on Earth and Io, in low-spatial-resolution data (corresponding to the bulk of available and foreseeable data of Io), similar styles of effusive and explosive volcanism yield similar thermal flux densities [1-3]. If, from observed thermal emission as a function of wavelength and change in thermal emission with time, the eruption style of an ionian volcano can be constrained, estimates of volumetric fluxes can be made and compared with terrestrial volcanoes using techniques derived for analysing terrestrial remotely-sensed data. We find that ionian volcanoes fundamentally differ from their terrestrial counterparts only in areal extent, with Io volcanoes covering larger areas, with higher volumetric fluxes. Even with the low-spatial resolution data available it is possible to sometimes constrain and classify eruption style both on Io and Earth from the integrated thermal emission spectrum, and how this changes temporally. Plotting 2 and 5 μm fluxes reveals the evolution of individual eruptions of different styles, as well as the relative intensity of eruptions, allowing comparison to be made from individual eruptions on both planets. For some Ionian volcanoes, low-resolution analyses are confirmed from observations obtained at high spatial resolution Of great importance, possibly more so than spatial resolution, is temporal resolution, as this has proven diagnostic in determining style of eruption at a number of volcanoes (e.g., Prometheus, Pele, Loki Patera, Pillan 1997) [1-3]. Active lava lakes, fire-fountains and insulated flows are identified using this methodology, and this allows comparison of individual eruptions on both planets. References: [1] Davies et al. (2001) JGR, 106, 33079-33,103. [2] Keszthelyi et al. (2001) LPSC XXXII Abstract 1523. [3] Davies (2003) JGR, 108, 10.1029/2001JE001509. This work was carried out at the Jet Propulsion

A High Spatial Resolution Depth Sensing Method Based on Binocular Structured Light

PubMed Central

Yao, Huimin; Ge, Chenyang; Xue, Jianru; Zheng, Nanning

2017-01-01

Depth information has been used in many fields because of its low cost and easy availability, since the Microsoft Kinect was released. However, the Kinect and Kinect-like RGB-D sensors show limited performance in certain applications and place high demands on accuracy and robustness of depth information. In this paper, we propose a depth sensing system that contains a laser projector similar to that used in the Kinect, and two infrared cameras located on both sides of the laser projector, to obtain higher spatial resolution depth information. We apply the block-matching algorithm to estimate the disparity. To improve the spatial resolution, we reduce the size of matching blocks, but smaller matching blocks generate lower matching precision. To address this problem, we combine two matching modes (binocular mode and monocular mode) in the disparity estimation process. Experimental results show that our method can obtain higher spatial resolution depth without loss of the quality of the range image, compared with the Kinect. Furthermore, our algorithm is implemented on a low-cost hardware platform, and the system can support the resolution of 1280 × 960, and up to a speed of 60 frames per second, for depth image sequences. PMID:28397759

Direct observation and analysis of york-shell materials using low-voltage high-resolution scanning electron microscopy: Nanometal-particles encapsulated in metal-oxide, carbon, and polymer

NASA Astrophysics Data System (ADS)

Asahina, Shunsuke; Suga, Mitsuo; Takahashi, Hideyuki; Young Jeong, Hu; Galeano, Carolina; Schüth, Ferdi; Terasaki, Osamu

2014-11-01

Nanometal particles show characteristic features in chemical and physical properties depending on their sizes and shapes. For keeping and further enhancing their features, the particles should be protected from coalescence or degradation. One approach is to encapsulate the nanometal particles inside pores with chemically inert or functional materials, such as carbon, polymer, and metal oxides, which contain mesopores to allow permeation of only chemicals not the nanometal particles. Recently developed low-voltage high-resolution scanning electron microscopy was applied to the study of structural, chemical, and electron state of both nanometal particles and encapsulating materials in yolk-shell materials of Au@C, Ru/Pt@C, Au@TiO2, and Pt@Polymer. Progresses in the following categories were shown for the yolk-shell materials: (i) resolution of topographic image contrast by secondary electrons, of atomic-number contrast by back-scattered electrons, and of elemental mapping by X-ray energy dispersive spectroscopy; (ii) sample preparation for observing internal structures; and (iii) X-ray spectroscopy such as soft X-ray emission spectroscopy. Transmission electron microscopy was also used for characterization of Au@C.

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.

The application of structure from motion (SfM) to identify the geological structure and outcrop studies

NASA Astrophysics Data System (ADS)

Saputra, Aditya; Rahardianto, Trias; Gomez, Christopher

2017-07-01

Adequate knowledge of geological structure is an essential for most studies in geoscience, mineral exploration, geo-hazard and disaster management. The geological map is still one the datasets the most commonly used to obtain information about the geological structure such as fault, joint, fold, and unconformities, however in rural areas such as Central Java data is still sparse. Recent progress in data acquisition technologies and computing have increased the interest in how to capture the high-resolution geological data effectively and for a relatively low cost. Some methods such as Airborne Laser Scanning (ALS), Terrestrial Laser Scanning (TLS), and Unmanned Aerial Vehicles (UAVs) have been widely used to obtain this information, however, these methods need a significant investment in hardware, software, and time. Resolving some of those issues, the photogrammetric method structure from motion (SfM) is an image-based method, which can provide solutions equivalent to laser technologies for a relatively low-cost with minimal time, specialization and financial investment. Using SfM photogrammetry, it is possible to generate high resolution 3D images rock surfaces and outcrops, in order to improve the geological understanding of Indonesia. In the present contribution, it is shown that the information about fault and joint can be obtained at high-resolution and in a shorter time than with the conventional grid mapping and remotely sensed topographic surveying. The SfM method produces a point-cloud through image matching and computing. This task can be run with open- source or commercial image processing and 3D reconstruction software. As the point cloud has 3D information as well as RGB values, it allows for further analysis such as DEM extraction and image orthorectification processes. The present paper describes some examples of SfM to identify the fault in the outcrops and also highlight the future possibilities in terms of earthquake hazard assessment, based on

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

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

The evolution of structured illumination microscopy in studies of HIV.

PubMed

Marno, Kelly; Al'Zoubi, Lara; Pearson, Matthew; Posch, Markus; McKnight, Áine; Wheeler, Ann P

2015-10-15

The resolution limit of conventional light microscopy has proven to be limiting for many biological structures such as viruses including Human immunodeficiency virus (HIV). Individual HIV virions are impossible to study using confocal microscopy as they are well below the 200 nm resolution limit of conventional light microscopes. Structured illumination microscopy (SIM) allows a twofold enhancement in image resolution compared to standard widefield illumination and so provides an excellent tool for study of HIV. Viral capsids (CAs) vary between 110 and 146 nm so this study challenges the performance of SIM microscopes. SIM microscopy was first developed in 2000, commercialised in 2007 and rapidly developed. Here we present the changes in capabilities of the SIM microscopes for study of HIV localisation as the instrumentation for structured illumination microscopy has evolved over the past 8 years. Copyright © 2015. Published by Elsevier Inc.

Structure and chemistry of epitaxial ceria thin films on yttria-stabilized zirconia substrates, studied by high resolution electron microscopy

DOE PAGES

Sinclair, Robert; Lee, Sang Chul; Shi, Yezhou; ...

2017-03-18

Here, we have applied aberration-corrected transmission electron microscopy (TEM) imaging and electron energy loss spectroscopy (EELS) to study the structure and chemistry of epitaxial ceria thin films, grown by pulsed laser deposition onto (001) yttria-stabilized zirconia (YSZ) substrates. There are few observable defects apart from the expected mismatch interfacial dislocations and so the films would be expected to have good potential for applications. Under high electron beam dose rate (above about 6000 e-/Å 2s) domains of an ordered structure appear and these are interpreted as being created by oxygen vacancy ordering. The ordered structure does not appear at lower losemore » rates (ca. 2600 e-/Å 2s) and can be removed by imaging under 1 mbar oxygen gas in an environmental TEM. EELS confirms that there is both oxygen deficiency and the associated increase in Ce 3+ versus Ce 4+ cations in the ordered domains. In situ high resolution TEM recordings show the formation of the ordered domains as well as atomic migration along the ceria thin film (001) surface.« less

Structure and chemistry of epitaxial ceria thin films on yttria-stabilized zirconia substrates, studied by high resolution electron microscopy

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

Sinclair, Robert; Lee, Sang Chul; Shi, Yezhou

Here, we have applied aberration-corrected transmission electron microscopy (TEM) imaging and electron energy loss spectroscopy (EELS) to study the structure and chemistry of epitaxial ceria thin films, grown by pulsed laser deposition onto (001) yttria-stabilized zirconia (YSZ) substrates. There are few observable defects apart from the expected mismatch interfacial dislocations and so the films would be expected to have good potential for applications. Under high electron beam dose rate (above about 6000 e-/Å 2s) domains of an ordered structure appear and these are interpreted as being created by oxygen vacancy ordering. The ordered structure does not appear at lower losemore » rates (ca. 2600 e-/Å 2s) and can be removed by imaging under 1 mbar oxygen gas in an environmental TEM. EELS confirms that there is both oxygen deficiency and the associated increase in Ce 3+ versus Ce 4+ cations in the ordered domains. In situ high resolution TEM recordings show the formation of the ordered domains as well as atomic migration along the ceria thin film (001) surface.« less

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

Atomic resolution crystal structure of VcLMWPTP-1 from Vibrio cholerae O395: Insights into a novel mode of dimerization in the low molecular weight protein tyrosine phosphatase family

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

Nath, Seema; Banerjee, Ramanuj; Sen, Udayaditya, E-mail: udayaditya.sen@saha.ac.in

Highlights: • VcLMWPTP-1 forms dimer in solution. • The dimer is catalytically active unlike other reported dimeric LMWPTPs. • The formation of extended dimeric surface excludes the active site pocket. • The surface bears closer resemblance to eukaryotic LMWPTPs. - Abstract: Low molecular weight protein tyrosine phosphatase (LMWPTP) is a group of phosphotyrosine phosphatase ubiquitously found in a wide range of organisms ranging from bacteria to mammals. Dimerization in the LMWPTP family has been reported earlier which follows a common mechanism involving active site residues leading to an enzymatically inactive species. Here we report a novel form of dimerization inmore » a LMWPTP from Vibrio cholera 0395 (VcLMWPTP-1). Studies in solution reveal the existence of the dimer in solution while kinetic study depicts the active form of the enzyme. This indicates that the mode of dimerization in VcLMWPTP-1 is different from others where active site residues are not involved in the process. A high resolution (1.45 Å) crystal structure of VcLMWPTP-1 confirms a different mode of dimerization where the active site is catalytically accessible as evident by a tightly bound substrate mimicking ligand, MOPS at the active site pocket. Although being a member of a prokaryotic protein family, VcLMWPTP-1 structure resembles very closely to LMWPTP from a eukaryote, Entamoeba histolytica. It also delineates the diverse surface properties around the active site of the enzyme.« less

Field study of mussel impact on turbulent structure in the internal boundary layer of a low energetic deep lake

NASA Astrophysics Data System (ADS)

Wang, B.; Liao, Q.; Bootsma, H. A.; Troy, C. D.

2013-12-01

The impact of invasive mussels on Great Lake aquatic ecosystem attracted wide attentions. Their strong ability on phytoplankton consumption and impact on nutrient and oxygen dynamics greatly change the behavior of benthic communities. The hydrodynamics in the internal boundary layer (IBL) at low energetic deep lakes is of great importance on food delivery. Meantime, the filtration activities of mussels provide feedback to turbulence structure in the IBL. This filed study was carried out at the 55 meters station in Lake Michigan using an in situ PIV system to measure high resolution turbulence immediately above the mussel bed. A HR acoustic profiler was used to measure three dimensional velocities within 1 meter above the bed. Quadrant-Hole analysis method was used to identify the organized structures of turbulent motion on contributing Reynolds shear stress. Sufficiently close to the mussels, turbulence sources were mostly contributed to flow-mussel interaction and mussel filtration, rather than shear production. Bed shear stress, friction velocity and bottom roughness were also investigated. Our results suggest measurement should be made in the IBL to accurate estimate the bed friction and erodability. A particle concentration depletion layer was observed within 7~8 centimeters above the mussel bed. Significant enhancement of turbulent mixing was found due to filtration activities, which tends to help food supply for benthic mussels in low energetic aquatic systems A sample PIV image superimposed with 2-D velocity map Vertical profiles of (a) fraction for each quadrant event (b) conditional averaged Reynolds shear stress for each quadrant event. Two dash lines represent z = 1.3 cm and 3.6 cm.

Water polygons in high-resolution protein crystal structures.

PubMed

Lee, Jonas; Kim, Sung-Hou

2009-07-01

We have analyzed the interstitial water (ISW) structures in 1500 protein crystal structures deposited in the Protein Data Bank that have greater than 1.5 A resolution with less than 90% sequence similarity with each other. We observed varieties of polygonal water structures composed of three to eight water molecules. These polygons may represent the time- and space-averaged structures of "stable" water oligomers present in liquid water, and their presence as well as relative population may be relevant in understanding physical properties of liquid water at a given temperature. On an average, 13% of ISWs are localized enough to be visible by X-ray diffraction. Of those, averages of 78% are water molecules in the first water layer on the protein surface. Of the localized ISWs beyond the first layer, almost half of them form water polygons such as trigons, tetragons, as well as expected pentagons, hexagons, higher polygons, partial dodecahedrons, and disordered networks. Most of the octagons and nanogons are formed by fusion of smaller polygons. The trigons are most commonly observed. We suggest that our observation provides an experimental basis for including these water polygon structures in correlating and predicting various water properties in liquid state.

Super-resolution mapping using multi-viewing CHRIS/PROBA data

NASA Astrophysics Data System (ADS)

Dwivedi, Manish; Kumar, Vinay

2016-04-01

High-spatial resolution Remote Sensing (RS) data provides detailed information which ensures high-definition visual image analysis of earth surface features. These data sets also support improved information extraction capabilities at a fine scale. In order to improve the spatial resolution of coarser resolution RS data, the Super Resolution Reconstruction (SRR) technique has become widely acknowledged which focused on multi-angular image sequences. In this study multi-angle CHRIS/PROBA data of Kutch area is used for SR image reconstruction to enhance the spatial resolution from 18 m to 6m in the hope to obtain a better land cover classification. Various SR approaches like Projection onto Convex Sets (POCS), Robust, Iterative Back Projection (IBP), Non-Uniform Interpolation and Structure-Adaptive Normalized Convolution (SANC) chosen for this study. Subjective assessment through visual interpretation shows substantial improvement in land cover details. Quantitative measures including peak signal to noise ratio and structural similarity are used for the evaluation of the image quality. It was observed that SANC SR technique using Vandewalle algorithm for the low resolution image registration outperformed the other techniques. After that SVM based classifier is used for the classification of SRR and data resampled to 6m spatial resolution using bi-cubic interpolation. A comparative analysis is carried out between classified data of bicubic interpolated and SR derived images of CHRIS/PROBA and SR derived classified data have shown a significant improvement of 10-12% in the overall accuracy. The results demonstrated that SR methods is able to improve spatial detail of multi-angle images as well as the classification accuracy.

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.

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

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.

Improving Barotropic Tides by Two-way Nesting High and Low Resolution Domains

NASA Astrophysics Data System (ADS)

Jeon, C. H.; Buijsman, M. C.; Wallcraft, A. J.; Shriver, J. F.; Hogan, P. J.; Arbic, B. K.; Richman, J. G.

2017-12-01

In a realistically forced global ocean model, relatively large sea-surface-height root-mean-square (RMS) errors are observed in the North Atlantic near the Hudson Strait. These may be associated with large tidal resonances interacting with coastal bathymetry that are not correctly represented with a low resolution grid. This issue can be overcome by using high resolution grids, but at a high computational cost. In this paper we apply two-way nesting as an alternative solution. This approach applies high resolution to the area with large RMS errors and a lower resolution to the rest. It is expected to improve the tidal solution as well as reduce the computational cost. To minimize modification of the original source codes of the ocean circulation model (HYCOM), we apply the coupler OASIS3-MCT. This coupler is used to exchange barotropic pressures and velocity fields through its APIs (Application Programming Interface) between the parent and the child components. The developed two-way nesting framework has been validated with an idealized test case where the parent and the child domains have identical grid resolutions. The result of the idealized case shows very small RMS errors between the child and parent solutions. We plan to show results for a case with realistic tidal forcing in which the resolution of the child grid is three times that of the parent grid. The numerical results of this realistic case are compared to TPXO data.

Probabilistic description of ice-supersaturated layers in low resolution profiles of relative humidity

NASA Astrophysics Data System (ADS)

Dickson, N. C.; Gierens, K. M.; Rogers, H. L.; Jones, R. L.

2010-07-01

The global observation, assimilation and prediction in numerical models of ice super-saturated (ISS) regions (ISSR) are crucial if the climate impact of aircraft condensation trails (contrails) is to be fully understood, and if, for example, contrail formation is to be avoided through aircraft operational measures. Given their small scales compared to typical atmospheric model grid sizes, statistical representations of the spatial scales of ISSR are required, in both horizontal and vertical dimensions, if global occurrence of ISSR is to be adequately represented in climate models. This paper uses radiosonde launches made by the UK Meteorological Office, from the British Isles, Gibraltar, St. Helena and the Falkland Islands between January 2002 and December 2006, to investigate the probabilistic occurrence of ISSR. Each radiosonde profile is divided into 50- and 100-hPa pressure layers, to emulate the coarse vertical resolution of some atmospheric models. Then the high resolution observations contained within each thick pressure layer are used to calculate an average relative humidity and an ISS fraction for each individual thick pressure layer. These relative humidity pressure layer descriptions are then linked through a probability function to produce an s-shaped curve which empirically describes the ISS fraction in any average relative humidity pressure layer. Using this empirical understanding of the s-shaped relationship a mathematical model was developed to represent the ISS fraction within any arbitrary thick pressure layer. Two models were developed to represent both 50- and 100-hPa pressure layers with each reconstructing their respective s-shapes within 8-10% of the empirical curves. These new models can be used, to represent the small scale structures of ISS events, in modelled data where only low vertical resolution is available. This will be useful in understanding, and improving the global distribution, both observed and forecasted, of ice super-saturation.

The impact of the resolution of meteorological datasets on catchment-scale drought studies

NASA Astrophysics Data System (ADS)

Hellwig, Jost; Stahl, Kerstin

2017-04-01

Gridded meteorological datasets provide the basis to study drought at a range of scales, including catchment scale drought studies in hydrology. They are readily available to study past weather conditions and often serve real time monitoring as well. As these datasets differ in spatial/temporal coverage and spatial/temporal resolution, for most studies there is a tradeoff between these features. Our investigation examines whether biases occur when studying drought on catchment scale with low resolution input data. For that, a comparison among the datasets HYRAS (covering Central Europe, 1x1 km grid, daily data, 1951 - 2005), E-OBS (Europe, 0.25° grid, daily data, 1950-2015) and GPCC (whole world, 0.5° grid, monthly data, 1901 - 2013) is carried out. Generally, biases in precipitation increase with decreasing resolution. Most important variations are found during summer. In low mountain range of Central Europe the datasets of sparse resolution (E-OBS, GPCC) overestimate dry days and underestimate total precipitation since they are not able to describe high spatial variability. However, relative measures like the correlation coefficient reveal good consistencies of dry and wet periods, both for absolute precipitation values and standardized indices like the Standardized Precipitation Index (SPI) or Standardized Precipitation Evaporation Index (SPEI). Particularly the most severe droughts derived from the different datasets match very well. These results indicate that absolute values of sparse resolution datasets applied to catchment scale might be critical to use for an assessment of the hydrological drought at catchment scale, whereas relative measures for determining periods of drought are more trustworthy. Therefore, studies on drought, that downscale meteorological data, should carefully consider their data needs and focus on relative measures for dry periods if sufficient for the task.

Low-resolution expression recognition based on central oblique average CS-LBP with adaptive threshold

NASA Astrophysics Data System (ADS)

Han, Sheng; Xi, Shi-qiong; Geng, Wei-dong

2017-11-01

In order to solve the problem of low recognition rate of traditional feature extraction operators under low-resolution images, a novel algorithm of expression recognition is proposed, named central oblique average center-symmetric local binary pattern (CS-LBP) with adaptive threshold (ATCS-LBP). Firstly, the features of face images can be extracted by the proposed operator after pretreatment. Secondly, the obtained feature image is divided into blocks. Thirdly, the histogram of each block is computed independently and all histograms can be connected serially to create a final feature vector. Finally, expression classification is achieved by using support vector machine (SVM) classifier. Experimental results on Japanese female facial expression (JAFFE) database show that the proposed algorithm can achieve a recognition rate of 81.9% when the resolution is as low as 16×16, which is much better than that of the traditional feature extraction operators.

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

Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization

PubMed Central

Marti-Renom, Marc A.; Mirny, Leonid A.

2011-01-01

Over the last decade, and especially after the advent of fluorescent in situ hybridization imaging and chromosome conformation capture methods, the availability of experimental data on genome three-dimensional organization has dramatically increased. We now have access to unprecedented details of how genomes organize within the interphase nucleus. Development of new computational approaches to leverage this data has already resulted in the first three-dimensional structures of genomic domains and genomes. Such approaches expand our knowledge of the chromatin folding principles, which has been classically studied using polymer physics and molecular simulations. Our outlook describes computational approaches for integrating experimental data with polymer physics, thereby bridging the resolution gap for structural determination of genomes and genomic domains. PMID:21779160

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.

Low Resolution Picture Transmission (LRPT) Demonstration System

NASA Technical Reports Server (NTRS)

Fong, Wai; Yeh, Pen-Shu; Sank, Victor; Nyugen, Xuan; Xia, Wei; Duran, Steve; Day, John H. (Technical Monitor)

2002-01-01

Low-Resolution Picture Transmission (LRPT) is a proposed standard for direct broadcast transmission of satellite weather images. This standard is a joint effort by the European Organization for the Exploitation of Meteorological Satellites (EUMETSAT) and the National Oceanic Atmospheric Administration (NOAA). As a digital transmission scheme, its purpose is to replace the current analog Automatic Picture Transmission (APT) system for use in the Meteorological Operational (METOP) satellites. Goddard Space Flight Center has been tasked to build an LRPT Demonstration System (LDS). It's main objective is to develop or demonstrate the feasibility of a low-cost receiver utilizing a Personal Computer (PC) as the primary processing component and determine the performance of the protocol in the simulated Radio Frequency (RF) environment. The approach would consist of two phases. In the phase 1, a Commercial-off-the-Shelf (COTS) Modulator-Demodulator (MODEM) board that would perform RF demodulation would be purchased allowing the Central Processing Unit (CPU) to perform the Consultative Committee for Space Data Systems (CCSDS) protocol processing. Also since the weather images are compressed the PC would perform the decompression. Phase 1 was successfully demonstrated on December 1997. Phase 2 consists of developing a high-fidelity receiver, transmitter and environment simulator. Its goal is to find out how the METOP Specification performs in a simulated noise environment in a cost-effective receiver. The approach would be to produce a receiver using as much software as possible to perform front-end processing to take advantage of the latest high-speed PCs. Thus the COTS MODEM used in Phase 1 is performing RF demodulation along with data acquisition providing data to the receiving software. Also, environment simulator is produced using the noise patterns generated by Institute for Telecommunications Sciences (ITS) from their noise environment study.

Characterisation of transition state structures for protein folding using 'high', 'medium' and 'low' {Phi}-values.

PubMed

Geierhaas, Christian D; Salvatella, Xavier; Clarke, Jane; Vendruscolo, Michele

2008-03-01

It has been suggested that Phi-values, which allow structural information about transition states (TSs) for protein folding to be obtained, are most reliably interpreted when divided into three classes (high, medium and low). High Phi-values indicate almost completely folded regions in the TS, intermediate Phi-values regions with a detectable amount of structure and low Phi-values indicate mostly unstructured regions. To explore the extent to which this classification can be used to characterise in detail the structure of TSs for protein folding, we used Phi-values divided into these classes as restraints in molecular dynamics simulations. This type of procedure is related to that used in NMR spectroscopy to define the structure of native proteins from the measurement of inter-proton distances derived from nuclear Overhauser effects. We illustrate this approach by determining the TS ensembles of five proteins and by showing that the results are similar to those obtained by using as restraints the actual numerical Phi-values measured experimentally. Our results indicate that the simultaneous consideration of a set of low-resolution Phi-values can provide sufficient information for characterising the architecture of a TS for folding of a protein.

Xenon-plasma-light low-energy ultrahigh-resolution photoemission study of Co(S1-xSex)2 (x=0.075)

NASA Astrophysics Data System (ADS)

Sato, Takafumi; Souma, Seigo; Sugawara, Katsuaki; Nakayama, Kosuke; Raj, Satyabrata; Hiraka, Haruhiro; Takahashi, Takashi

2007-09-01

We have performed low-energy ultrahigh-resolution photoemission spectroscopy on Co(S1-xSex)2 (x=0.075) to elucidate the bulk electronic states responsible for the ferromagnetic transition. By using a newly developed plasma-driven low-energy xenon (Xe) discharge lamp (hν=8.436eV) , we clearly observed a sharp quasiparticle peak at the Fermi level together with the remarkable temperature dependence of the electron density of states across the transition temperature. Comparison with the experimental result by the HeIα resonance line (hν=21.218eV) indicates that the sharp quasiparticle is of bulk origin and is produced by the Fermi-level crossing of the Co 3d eg↓ subband.

On the utility of low resolution IUE spectroscopy of the 2800 A Mg II lines as a stellar chromosphere indicator

NASA Technical Reports Server (NTRS)

Smith, Graeme H.; Burstein, David; Fanelli, Michael N.; O'Connell, Robert W.; Wu, C.-C.

1991-01-01

Low resolution IUE spectroscopy of the 2800-A Mg II h and k lines is shown to provide a useful means for documenting chromospheric activity among relatively young dwarf stars. An index I(Mg II) has been defined which measures the integrated flux in the region 2784-2814 A relative to the flux interpolated from nearby comparison regions. Values of this index have been derived from low resolution IUE spectra for a sample of field dwarfs for which Ca II H and K line indices have been published as part of the Mount Wilson HK program. The large range in chromospheric activity among field dwarfs that is exhibited by the Mount Wilson Ca II S index is found to also be reflected by the lower resolution I(Mg II) index. Using an age calibration of Ca II emission line strengths derived by Barry, it is found that the value of I(Mg II) can be used to distinguish between dwarfs younger and older than 3 Gyr. The low resolution nature of the I(Mg II) index means that it holds potential for use as an age diagnostic for stellar population studies. Among dwarfs of age greater than 3 Gyr there is some evidence that this Mg II index is affected by line blanketing.

Employing X-ray absorption technique for better detector resolution and measurement of low cross-section events

NASA Astrophysics Data System (ADS)

Sharma, Gaurav; Puri, Nitin K.; Kumar, Pravin; Nandi, T.

2018-03-01

The versatility of X-ray absorption technique is experimentally employed for enhancing the detector resolution and to rejuvenate the low probable transitions obscured in the pile-up region, during a beam-foil spectroscopy experiment. The multiple aluminum absorber layers (10 μm each) are used to suppress the pile-up contribution drastically and to restore a weak transition which is about 1.38 × 104 times weaker than a one-electron-one-photon transitions viz. Kα and Khα. The weak line is possibly originating from a two-electron-one-photon transition in He-like Ti. Further, the transitions, which were obscured in the spectra due to high intensity ratio, are revived by dissimilar line intensity attenuation using this technique. The measured lifetimes of Kα line with and without intensity attenuation match well within error bar. The present technique finds potential implications in understanding the structure of multiple-core-vacant ions and other low cross section processes in ion-solid collisions.

An unsupervised classification method for inferring original case locations from low-resolution disease maps.

PubMed

Brownstein, John S; Cassa, Christopher A; Kohane, Isaac S; Mandl, Kenneth D

2006-12-08

Widespread availability of geographic information systems software has facilitated the use of disease mapping in academia, government and private sector. Maps that display the address of affected patients are often exchanged in public forums, and published in peer-reviewed journal articles. As previously reported, a search of figure legends in five major medical journals found 19 articles from 1994-2004 that identify over 19,000 patient addresses. In this report, a method is presented to evaluate whether patient privacy is being breached in the publication of low-resolution disease maps. To demonstrate the effect, a hypothetical low-resolution map of geocoded patient addresses was created and the accuracy with which patient addresses can be resolved is described. Through georeferencing and unsupervised classification of the original image, the method precisely re-identified 26% (144/550) of the patient addresses from a presentation quality map and 79% (432/550) from a publication quality map. For the presentation quality map, 99.8% of the addresses were within 70 meters (approximately one city block length) of the predicted patient location, 51.6% of addresses were identified within five buildings, 70.7% within ten buildings and 93% within twenty buildings. For the publication quality map, all addresses were within 14 meters and 11 buildings of the predicted patient location. This study demonstrates that lowering the resolution of a map displaying geocoded patient addresses does not sufficiently protect patient addresses from re-identification. Guidelines to protect patient privacy, including those of medical journals, should reflect policies that ensure privacy protection when spatial data are displayed or published.

Intelligence and EEG current density using low-resolution electromagnetic tomography (LORETA).

PubMed

Thatcher, R W; North, D; Biver, C

2007-02-01

The purpose of this study was to compare EEG current source densities in high IQ subjects vs. low IQ subjects. Resting eyes closed EEG was recorded from 19 scalp locations with a linked ears reference from 442 subjects ages 5 to 52 years. The Wechsler Intelligence Test was administered and subjects were divided into low IQ (< or =90), middle IQ (>90 to <120) and high IQ (> or =120) groups. Low-resolution electromagnetic tomographic current densities (LORETA) from 2,394 cortical gray matter voxels were computed from 1-30 Hz based on each subject's EEG. Differences in current densities using t tests, multivariate analyses of covariance, and regression analyses were used to evaluate the relationships between IQ and current density in Brodmann area groupings of cortical gray matter voxels. Frontal, temporal, parietal, and occipital regions of interest (ROIs) consistently exhibited a direct relationship between LORETA current density and IQ. Maximal t test differences were present at 4 Hz, 9 Hz, 13 Hz, 18 Hz, and 30 Hz with different anatomical regions showing different maxima. Linear regression fits from low to high IQ groups were statistically significant (P < 0.0001). Intelligence is directly related to a general level of arousal and to the synchrony of neural populations driven by thalamo-cortical resonances. A traveling frame model of sequential microstates is hypothesized to explain the results.

Investigation of spatial resolution and temporal performance of SAPHIRE (scintillator avalanche photoconductor with high resolution emitter readout) with integrated electrostatic focusing

NASA Astrophysics Data System (ADS)

Scaduto, David A.; Lubinsky, Anthony R.; Rowlands, John A.; Kenmotsu, Hidenori; Nishimoto, Norihito; Nishino, Takeshi; Tanioka, Kenkichi; Zhao, Wei

2014-03-01

We have previously proposed SAPHIRE (scintillator avalanche photoconductor with high resolution emitter readout), a novel detector concept with potentially superior spatial resolution and low-dose performance compared with existing flat-panel imagers. The detector comprises a scintillator that is optically coupled to an amorphous selenium photoconductor operated with avalanche gain, known as high-gain avalanche rushing photoconductor (HARP). High resolution electron beam readout is achieved using a field emitter array (FEA). This combination of avalanche gain, allowing for very low-dose imaging, and electron emitter readout, providing high spatial resolution, offers potentially superior image quality compared with existing flat-panel imagers, with specific applications to fluoroscopy and breast imaging. Through the present collaboration, a prototype HARP sensor with integrated electrostatic focusing and nano- Spindt FEA readout technology has been fabricated. The integrated electron-optic focusing approach is more suitable for fabricating large-area detectors. We investigate the dependence of spatial resolution on sensor structure and operating conditions, and compare the performance of electrostatic focusing with previous technologies. Our results show a clear dependence of spatial resolution on electrostatic focusing potential, with performance approaching that of the previous design with external mesh-electrode. Further, temporal performance (lag) of the detector is evaluated and the results show that the integrated electrostatic focusing design exhibits comparable or better performance compared with the mesh-electrode design. This study represents the first technical evaluation and characterization of the SAPHIRE concept with integrated electrostatic focusing.

Sparsity-Based Super Resolution for SEM Images.

PubMed

Tsiper, Shahar; Dicker, Or; Kaizerman, Idan; Zohar, Zeev; Segev, Mordechai; Eldar, Yonina C

2017-09-13

The scanning electron microscope (SEM) is an electron microscope that produces an image of a sample by scanning it with a focused beam of electrons. The electrons interact with the atoms in the sample, which emit secondary electrons that contain information about the surface topography and composition. The sample is scanned by the electron beam point by point, until an image of the surface is formed. Since its invention in 1942, the capabilities of SEMs have become paramount in the discovery and understanding of the nanometer world, and today it is extensively used for both research and in industry. In principle, SEMs can achieve resolution better than one nanometer. However, for many applications, working at subnanometer resolution implies an exceedingly large number of scanning points. For exactly this reason, the SEM diagnostics of microelectronic chips is performed either at high resolution (HR) over a small area or at low resolution (LR) while capturing a larger portion of the chip. Here, we employ sparse coding and dictionary learning to algorithmically enhance low-resolution SEM images of microelectronic chips-up to the level of the HR images acquired by slow SEM scans, while considerably reducing the noise. Our methodology consists of two steps: an offline stage of learning a joint dictionary from a sequence of LR and HR images of the same region in the chip, followed by a fast-online super-resolution step where the resolution of a new LR image is enhanced. We provide several examples with typical chips used in the microelectronics industry, as well as a statistical study on arbitrary images with characteristic structural features. Conceptually, our method works well when the images have similar characteristics, as microelectronics chips do. This work demonstrates that employing sparsity concepts can greatly improve the performance of SEM, thereby considerably increasing the scanning throughput without compromising on analysis quality and resolution.

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

High resolution age-structured mapping of childhood vaccination coverage in low and middle income countries.

PubMed

Utazi, C Edson; Thorley, Julia; Alegana, Victor A; Ferrari, Matthew J; Takahashi, Saki; Metcalf, C Jessica E; Lessler, Justin; Tatem, Andrew J

2018-03-14

The expansion of childhood vaccination programs in low and middle income countries has been a substantial public health success story. Indicators of the performance of intervention programmes such as coverage levels and numbers covered are typically measured through national statistics or at the scale of large regions due to survey design, administrative convenience or operational limitations. These mask heterogeneities and 'coldspots' of low coverage that may allow diseases to persist, even if overall coverage is high. Hence, to decrease inequities and accelerate progress towards disease elimination goals, fine-scale variation in coverage should be better characterized. Using measles as an example, cluster-level Demographic and Health Surveys (DHS) data were used to map vaccination coverage at 1 km spatial resolution in Cambodia, Mozambique and Nigeria for varying age-group categories of children under five years, using Bayesian geostatistical techniques built on a suite of publicly available geospatial covariates and implemented via Markov Chain Monte Carlo (MCMC) methods. Measles vaccination coverage was found to be strongly predicted by just 4-5 covariates in geostatistical models, with remoteness consistently selected as a key variable. The output 1 × 1 km maps revealed significant heterogeneities within the three countries that were not captured using province-level summaries. Integration with population data showed that at the time of the surveys, few districts attained the 80% coverage, that is one component of the WHO Global Vaccine Action Plan 2020 targets. The elimination of vaccine-preventable diseases requires a strong evidence base to guide strategies and inform efficient use of limited resources. The approaches outlined here provide a route to moving beyond large area summaries of vaccination coverage that mask epidemiologically-important heterogeneities to detailed maps that capture subnational vulnerabilities. The output datasets are built

High-resolution structure of a retroviral protease folded as a monomer

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

Gilski, Miroslaw; Polish Academy of Sciences, 61-704 Poznan; Kazmierczyk, Maciej

2011-11-01

The crystal structure of Mason–Pfizer monkey virus protease folded as a monomer has been solved by molecular replacement using a model generated by players of the online game Foldit. The structure shows at high resolution the details of a retroviral protease folded as a monomer which can guide rational design of protease dimerization inhibitors as retroviral drugs. Mason–Pfizer monkey virus (M-PMV), a D-type retrovirus assembling in the cytoplasm, causes simian acquired immunodeficiency syndrome (SAIDS) in rhesus monkeys. Its pepsin-like aspartic protease (retropepsin) is an integral part of the expressed retroviral polyproteins. As in all retroviral life cycles, release and dimerizationmore » of the protease (PR) is strictly required for polyprotein processing and virion maturation. Biophysical and NMR studies have indicated that in the absence of substrates or inhibitors M-PMV PR should fold into a stable monomer, but the crystal structure of this protein could not be solved by molecular replacement despite countless attempts. Ultimately, a solution was obtained in mr-rosetta using a model constructed by players of the online protein-folding game Foldit. The structure indeed shows a monomeric protein, with the N- and C-termini completely disordered. On the other hand, the flap loop, which normally gates access to the active site of homodimeric retropepsins, is clearly traceable in the electron density. The flap has an unusual curled shape and a different orientation from both the open and closed states known from dimeric retropepsins. The overall fold of the protein follows the retropepsin canon, but the C{sup α} deviations are large and the active-site ‘DTG’ loop (here NTG) deviates up to 2.7 Å from the standard conformation. This structure of a monomeric retropepsin determined at high resolution (1.6 Å) provides important extra information for the design of dimerization inhibitors that might be developed as drugs for the treatment of retroviral

Low Frequency Error Analysis and Calibration for High-Resolution Optical Satellite's Uncontrolled Geometric Positioning

NASA Astrophysics Data System (ADS)

Wang, Mi; Fang, Chengcheng; Yang, Bo; Cheng, Yufeng

2016-06-01

The low frequency error is a key factor which has affected uncontrolled geometry processing accuracy of the high-resolution optical image. To guarantee the geometric quality of imagery, this paper presents an on-orbit calibration method for the low frequency error based on geometric calibration field. Firstly, we introduce the overall flow of low frequency error on-orbit analysis and calibration, which includes optical axis angle variation detection of star sensor, relative calibration among star sensors, multi-star sensor information fusion, low frequency error model construction and verification. Secondly, we use optical axis angle change detection method to analyze the law of low frequency error variation. Thirdly, we respectively use the method of relative calibration and information fusion among star sensors to realize the datum unity and high precision attitude output. Finally, we realize the low frequency error model construction and optimal estimation of model parameters based on DEM/DOM of geometric calibration field. To evaluate the performance of the proposed calibration method, a certain type satellite's real data is used. Test results demonstrate that the calibration model in this paper can well describe the law of the low frequency error variation. The uncontrolled geometric positioning accuracy of the high-resolution optical image in the WGS-84 Coordinate Systems is obviously improved after the step-wise calibration.

Water polygons in high-resolution protein crystal structures

PubMed Central

Lee, Jonas; Kim, Sung-Hou

2009-01-01

We have analyzed the interstitial water (ISW) structures in 1500 protein crystal structures deposited in the Protein Data Bank that have greater than 1.5 Å resolution with less than 90% sequence similarity with each other. We observed varieties of polygonal water structures composed of three to eight water molecules. These polygons may represent the time- and space-averaged structures of “stable” water oligomers present in liquid water, and their presence as well as relative population may be relevant in understanding physical properties of liquid water at a given temperature. On an average, 13% of ISWs are localized enough to be visible by X-ray diffraction. Of those, averages of 78% are water molecules in the first water layer on the protein surface. Of the localized ISWs beyond the first layer, almost half of them form water polygons such as trigons, tetragons, as well as expected pentagons, hexagons, higher polygons, partial dodecahedrons, and disordered networks. Most of the octagons and nanogons are formed by fusion of smaller polygons. The trigons are most commonly observed. We suggest that our observation provides an experimental basis for including these water polygon structures in correlating and predicting various water properties in liquid state. PMID:19551896

High Structural Resolution Hydroxyl Radical Protein Footprinting Reveals an Extended Robo1-Heparin Binding Interface*

PubMed Central

Li, Zixuan; Moniz, Heather; Wang, Shuo; Ramiah, Annapoorani; Zhang, Fuming; Moremen, Kelley W.; Linhardt, Robert J.; Sharp, Joshua S.

2015-01-01

Interaction of transmembrane receptors of the Robo family and the secreted protein Slit provides important signals in the development of the central nervous system and regulation of axonal midline crossing. Heparan sulfate, a sulfated linear polysaccharide modified in a complex variety of ways, serves as an essential co-receptor in Slit-Robo signaling. Previous studies have shown that closely related heparin octasaccharides bind to Drosophila Robo directly, and surface plasmon resonance analysis revealed that Robo1 binds more tightly to full-length unfractionated heparin. For the first time, we utilized electron transfer dissociation-based high spatial resolution hydroxyl radical protein footprinting to identify two separate binding sites for heparin interaction with Robo1: one binding site at the previously identified site for heparin dp8 and a second binding site at the N terminus of Robo1 that is disordered in the x-ray crystal structure. Mutagenesis of the identified N-terminal binding site exhibited a decrease in binding affinity as measured by surface plasmon resonance and heparin affinity chromatography. Footprinting also indicated that heparin binding induces a minor change in the conformation and/or dynamics of the Ig2 domain, but no major conformational changes were detected. These results indicate a second low affinity binding site in the Robo-Slit complex as well as suggesting the role of the Ig2 domain of Robo1 in heparin-mediated signal transduction. This study also marks the first use of electron transfer dissociation-based high spatial resolution hydroxyl radical protein footprinting, which shows great utility for the characterization of protein-carbohydrate complexes. PMID:25752613

Structure of dehaloperoxidase B at 1.58 Å resolution and structural characterization of the AB dimer from Amphitrite ornata

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

Serrano, Vesna de; D’Antonio, Jennifer; Franzen, Stefan

2010-05-01

The crystal structure of dehaloperoxidase (DHP) isoenzyme B from the terebellid polychaete A. ornata, which exhibits both hemoglobin and peroxidase functions, has been determined at 1.58 Å resolution. As members of the globin superfamily, dehaloperoxidase (DHP) isoenzymes A and B from the marine annelid Amphitrite ornata possess hemoglobin function, but they also exhibit a biologically relevant peroxidase activity that is capable of converting 2,4,6-trihalophenols to the corresponding 2,6-dihaloquinones in the presence of hydrogen peroxide. Here, a comprehensive structural study of recombinant DHP B, both by itself and cocrystallized with isoenzyme A, using X-ray diffraction is presented. The structure of DHPmore » B refined to 1.58 Å resolution exhibits the same distal histidine (His55) conformational flexibility as that observed in isoenzyme A, as well as additional changes to the distal and proximal hydrogen-bonding networks. Furthermore, preliminary characterization of the DHP AB heterodimer is presented, which exhibits differences in the AB interface that are not observed in the A-only or B-only homodimers. These structural investigations of DHP B provide insights that may relate to the mechanistic details of the H{sub 2}O{sub 2}-dependent oxidative dehalogenation reaction catalyzed by dehaloperoxidase, present a clearer description of the function of specific residues in DHP at the molecular level and lead to a better understanding of the paradigms of globin structure–function relationships.« less

First high resolution P wave velocity structure beneath Tenerife Island, (Canary Islands, Spain)

NASA Astrophysics Data System (ADS)

Garcia-Yeguas, Araceli; Ivan, Koulakov; Ibañez Jesus, M.; Valenti, Sallarès.

2010-05-01

3D velocity structure distribution has been imaged for first time using high resolution traveltime seismic tomography of the active volcano of Tenerife Island (Canary Islands, Spain). It is located in the Atlantic Ocean. In this island is situated the Teide stratovolcano (3718 m high) that is part of the Cañadas-Teide-Pico Viejo volcanic complex. Las Cañadas is a caldera system more than 20 kilometers wide where at least four distinct caldera processes have been identified. Evidence for many explosive eruptions in the volcanic complex has been found; the last noticeable explosive eruption (sub-plinean) occurred at Montaña Blanca around 2000 years ago. During the last 300 years, six effusive eruptions have been reported, the last of which took place at Chinyero Volcano on 18 November 1909. In January 2007, a seismic active experiment was carried out as part of the TOM-TEIDEVS project. About 6850 air gun shots were fired on the sea and recorded on a dense local seismic land network consisting of 150 independent (three component) seismic stations. The good quality of the recorded data allowed identifying P-wave arrivals up to offsets of 30-40 km obtaining more than 63000 traveltimes used in the tomographic inversion. The images have been obtained using ATOM-3D code (Koulakov, 2009). This code uses ray bending algorithms in the ray tracing for the forward modelling and in the inversion step it uses gradient methods. The velocity models show a very heterogeneous upper crust that is usual in similar volcanic environment. The tomographic images points out the no-existence of a magmatic chamber near to the surface and below Pico Teide. The ancient Las Cañadas caldera borders are clearly imaged featuring relatively high seismic velocity. Moreover, we have found a big low velocity anomaly in the northwest dorsal of the island. The last eruption took place in 1909 in this area. Furthermore, in the southeast another low velocity anomaly has been imaged. Several resolution

Impact of low-frequency sound on historic structures

NASA Astrophysics Data System (ADS)

Sutherland, Louis C.; Horonjeff, Richard D.

2005-09-01

In common usage, the term soundscape usually refers to portions of the sound spectrum audible to human observers, and perhaps more broadly other members of the animal kingdom. There is, however, a soundscape regime at the low end of the frequency spectrum (e.g., 10-25 Hz), which is inaudible to humans, where nonindigenous sound energy may cause noise-induced vibrations in structures. Such low frequency components may be of sufficient magnitude to pose damage risk potential to historic structures and cultural resources. Examples include Anasazi cliff and cave dwellings, and pueblo structures of vega type roof construction. Both are susceptible to noise induced vibration from low-frequency sound pressures that excite resonant frequencies in these structures. The initial damage mechanism is usually fatigue cracking. Many mechanisms are subtle, temporally multiphased, and not initially evident to the naked eye. This paper reviews the types of sources posing the greatest potential threat, their low-frequency spectral characteristics, typical structural responses, and the damage risk mechanisms involved. Measured sound and vibration levels, case history studies, and conditions favorable to damage risk are presented. The paper concludes with recommendations for increasing the damage risk knowledge base to better protect these resources.

Low resolution crystal structure of Arenicola erythrocruorin: influence of coiled coils on the architecture of a megadalton respiratory protein.

PubMed

Royer, William E; Omartian, Michael N; Knapp, James E

2007-01-05

Annelid erythrocruorins are extracellular respiratory complexes assembled from 180 subunits into hexagonal bilayers. Cryo-electron microscopic experiments have identified two different architectural classes. In one, designated type I, the vertices of the two hexagonal layers are partially staggered, with one hexagonal layer rotated by about 16 degrees relative to the other layer, whereas in the other class, termed type II, the vertices are essentially eclipsed. We report here the first crystal structure of a type II erythrocruorin, that from Arenicola marina, at 6.2 A resolution. The structure reveals the presence of long continuous triple-stranded coiled-coil "spokes" projecting towards the molecular center from each one-twelfth unit; interdigitation of these spokes provides the only contacts between the two hexagonal layers of the complex. This arrangement contrasts with that of a type I erythrocruorin from Lumbricus terrestris in which the spokes are broken into two triple-stranded coiled coils with a disjointed connection. The disjointed connection allows formation of a more compact structure in the type I architecture, with the two hexagonal layers closer together and additional extensive contacts between the layers. Comparison of sequences of the coiled-coil regions of various linker subunits shows that the linker subunits from type II erythrocruorins possess continuous heptad repeats, whereas a sequence gap places these repeats out of register in the type I linker subunits, consistent with a disjointed coiled-coil arrangement.

Structure of the CFA/III major pilin subunit CofA from human enterotoxigenic Escherichia coli determined at 0.90 Å resolution by sulfur-SAD phasing.

PubMed

Fukakusa, Shunsuke; Kawahara, Kazuki; Nakamura, Shota; Iwashita, Takaki; Baba, Seiki; Nishimura, Mitsuhiro; Kobayashi, Yuji; Honda, Takeshi; Iida, Tetsuya; Taniguchi, Tooru; Ohkubo, Tadayasu

2012-10-01

CofA, a major pilin subunit of colonization factor antigen III (CFA/III), forms pili that mediate small-intestinal colonization by enterotoxigenic Escherichia coli (ETEC). In this study, the crystal structure of an N-terminally truncated version of CofA was determined by single-wavelength anomalous diffraction (SAD) phasing using five sulfurs in the protein. Given the counterbalance between anomalous signal strength and the undesired X-ray absorption of the solvent, diffraction data were collected at 1.5 Å resolution using synchrotron radiation. These data were sufficient to elucidate the sulfur substructure at 1.38 Å resolution. The low solvent content (29%) of the crystal necessitated that density modification be performed with an additional 0.9 Å resolution data set to reduce the phase error caused by the small sulfur anomalous signal. The CofA structure showed the αβ-fold typical of type IVb pilins and showed high structural homology to that of TcpA for toxin-coregulated pili of Vibrio cholerae, including spatial distribution of key residues critical for pilin self-assembly. A pilus-filament model of CofA was built by computational docking and molecular-dynamics simulation using the previously reported filament model of TcpA as a structural template. This model revealed that the CofA filament surface was highly negatively charged and that a 23-residue-long loop between the α1 and α2 helices filled the gap between the pilin subunits. These characteristics could provide a unique binding epitope for the CFA/III pili of ETEC compared with other type IVb pili.

Low-Resolution Vision-at the Hub of Eye Evolution.

PubMed

Nilsson, Dan-E; Bok, Michael J

2017-11-01

Simple roles for photoreception are likely to have preceded more demanding ones such as vision. The driving force behind this evolution is the improvement and elaboration of animal behaviors using photoreceptor input. Because the basic role for all senses aimed at the external world is to guide behavior, we argue here that understanding this "behavioral drive" is essential for unraveling the evolutionary past of the senses. Photoreception serves many different types of behavior, from simple shadow responses to visual communication. Based on minimum performance requirements for different types of tasks, photoreceptors have been argued to have evolved from non-directional receptors, via directional receptors, to low-resolution vision, and finally to high-resolution vision. Through this sequence, the performance requirements on the photoreceptors have gradually changed from broad to narrow angular sensitivity, from slow to fast response, and from low to high contrast sensitivity during the evolution from simple to more advanced and demanding behaviors. New behaviors would only evolve if their sensory performance requirements to some degree overlap with the requirements of already existing behaviors. This need for sensory "performance continuity" must have determined the order by which behaviors have evolved and thus been an important factor guiding animal evolution. Naturally, new behaviors are most likely to evolve from already existing behaviors with similar neural processing needs and similar motor responses, pointing to "neural continuity" as another guiding factor in sensory evolution. Here we use these principles to derive an evolutionary tree for behaviors driven by photoreceptor input. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

How low can you go? Changing the resolution of novel complex objects in visual working memory according to task demands

PubMed Central

Allon, Ayala S.; Balaban, Halely; Luria, Roy

2014-01-01

In three experiments we manipulated the resolution of novel complex objects in visual working memory (WM) by changing task demands. Previous studies that investigated the trade-off between quantity and resolution in visual WM yielded mixed results for simple familiar stimuli. We used the contralateral delay activity as an electrophysiological marker to directly track the deployment of visual WM resources while participants preformed a change-detection task. Across three experiments we presented the same novel complex items but changed the task demands. In Experiment 1 we induced a medium resolution task by using change trials in which a random polygon changed to a different type of polygon and replicated previous findings showing that novel complex objects are represented with higher resolution relative to simple familiar objects. In Experiment 2 we induced a low resolution task that required distinguishing between polygons and other types of stimulus categories, but we failed in finding a corresponding decrease in the resolution of the represented item. Finally, in Experiment 3 we induced a high resolution task that required discriminating between highly similar polygons with somewhat different contours. This time, we observed an increase in the item’s resolution. Our findings indicate that the resolution for novel complex objects can be increased but not decreased according to task demands, suggesting that minimal resolution is required in order to maintain these items in visual WM. These findings support studies claiming that capacity and resolution in visual WM reflect different mechanisms. PMID:24734026

Molecular structure of leucine aminopeptidase at 2. 7- angstrom resolution

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

Burley, S.K.; David, P.R.; Lipscomb, W.N.

1990-09-01

The three-dimensional structure of bovine lens leucine aminopeptidase complexed with bestatin, a slow-binding inhibitor, has been solved to 3.0-{angstrom} resolution by the multiple isomorphous replacement method with phase combination and density modification. In addition, the structure of the isomorphous native enzyme has been refined at 2.7-{angstrom} resolution, and the current crystallographic R factor is 0.169 for a model that includes the two zinc ions and all 487 amino acid residues comprising the asymmetric unit. The enzyme is physiologically active as a hexamer, which has 32 symmetry and is triangular in shape with a triangle edge length of 115 {angstrom} andmore » maximal thickness of 90 {angstrom}. The monomers are crystallographically equivalent and each is folded into two unequal {alpha}/{beta} domains connected by an {alpha}-helix to give a comma-like shape with approximate maximal dimensions of 90 x 55 x 55 {angstrom}{sup 3}. The secondary structural composition is 40% {alpha}-helix and 19% {beta}-strand. The active site also contains two positively charged residues, Lys-250 and Arg-336. The six active sites are themselves located in the interior of the hexamer, where they line a disk-shaped cavity of radius 15 {angstrom} and thickness 10 {angstrom}. Access to this cavity is provided by solvent channels that run along the twofold symmetry axes.« less

Nocturnal low-level clouds over southern West Africa analysed using high-resolution simulations

NASA Astrophysics Data System (ADS)

Adler, Bianca; Kalthoff, Norbert; Gantner, Leonhard

2017-01-01

We performed a high-resolution numerical simulation to study the development of extensive low-level clouds that frequently form over southern West Africa during the monsoon season. This study was made in preparation for a field campaign in 2016 within the Dynamics-aerosol-chemistry-cloud interactions in West Africa (DACCIWA) project and focuses on an area around the city of Savè in southern Benin. Nocturnal low-level clouds evolve a few hundred metres above the ground around the same level as a distinct low-level jet. Several processes are found to determine the spatio-temporal evolution of these clouds including (i) significant cooling of the nocturnal atmosphere caused by horizontal advection with the south-westerly monsoon flow during the first half of the night, (ii) vertical cold air advection due to gravity waves leading to clouds in the wave crests and (iii) enhanced convergence and upward motion upstream of existing clouds that trigger new clouds. The latter is caused by an upward shift of the low-level jet in cloudy areas leading to horizontal convergence in the lower part and to horizontal divergence in the upper part of the cloud layer. Although this single case study hardly allows for a generalisation of the processes found, the results added to the optimisation of the measurements strategy for the field campaign and the observations will be used to test the hypotheses for cloud formation resulting from this study.

Low resolution ultraviolet and optical spectrophotometry of symbiotic stars

NASA Technical Reports Server (NTRS)

Slovak, M. H.

1982-01-01

Low resolution International Ultraviolet Explorer spectra combined with optical spectrophotometry provide absolute flux distributions for seven symbiotic variables from 1200 to 6450 A. For five stars (EG And, BF Cyg, CI Cyg, AG Peg, and Z And) the data are representative of the quiescent/out-of-eclipse energy distributions; for CH Cyg and AX Per, the observations were obtained following their atest outburst in 1977 and 1978, respectively. The de-reddened distributions reveal a remarkable diversity of both line spectra and continua. While the optical and near infrared regions lambda = 5500 A) are well represented by single component stellar models, multicomponent flux distributions are required to reproduce the ultraviolet continua.

Timing resolution and time walk in super low K factor single-photon avalanche diode-measurement and optimization

NASA Astrophysics Data System (ADS)

Fong, Bernicy S.; Davies, Murray; Deschamps, Pierre

2018-01-01

Timing resolution (or timing jitter) and time walk are separate parameters associated with a detector's response time. Studies have been done mostly on the time resolution of various single-photon detectors. As the designer and manufacturer of the ultra-low noise (ƙ-factor) silicon avalanche photodiode the super low K factor (SLiK) single-photon avalanche diode (SPAD), which is used in many single-photon counting applications, we often get inquiries from customers to better understand how this detector behaves under different operating conditions. Hence, here, we will be focusing on the study of these time-related parameters specifically for the SLiK SPAD, as a way to provide the most direct information for users of this detector to help with its use more efficiently and effectively. We will be providing the study data on how these parameters can be affected by temperature (both intrinsic to the detector chip and environmental input based on operating conditions), operating voltage, photon wavelength, as well as light spot size. How these parameters can be optimized and the trade-offs from optimization from the desired performance will be presented?

Troublesome Crystal Structures: Prevention, Detection, and Resolution

PubMed Central

Harlow, Richard L.

1996-01-01

A large number of incorrect crystal structures is being published today. These structures are proving to be a particular problem to those of us who are interested in comparing structural moieties found in the databases in order to develop structure-property relationships. Problems can reside in the input data, e.g., wrong unit cell or low quality intensity data, or in the structural model, e.g., wrong space group or atom types. Many of the common mistakes are, however, relatively easy to detect and thus should be preventable; at the very least, suspicious structures can be flagged, if not by the authors then by the referees and, ultimately, the crystallographic databases. This article describes some of the more common mistakes and their effects on the resulting structures, lists a series of tests that can be used to detect incorrect structures, and makes a strong plea for the publication of higher quality structures. PMID:27805169

Testing high resolution numerical models for analysis of contaminant storage and release from low permeability zones

NASA Astrophysics Data System (ADS)

Chapman, Steven W.; Parker, Beth L.; Sale, Tom C.; Doner, Lee Ann

2012-08-01

It is now widely recognized that contaminant release from low permeability zones can sustain plumes long after primary sources are depleted, particularly for chlorinated solvents where regulatory limits are orders of magnitude below source concentrations. This has led to efforts to appropriately characterize sites and apply models for prediction incorporating these effects. A primary challenge is that diffusion processes are controlled by small-scale concentration gradients and capturing mass distribution in low permeability zones requires much higher resolution than commonly practiced. This paper explores validity of using numerical models (HydroGeoSphere, FEFLOW, MODFLOW/MT3DMS) in high resolution mode to simulate scenarios involving diffusion into and out of low permeability zones: 1) a laboratory tank study involving a continuous sand body with suspended clay layers which was 'loaded' with bromide and fluorescein (for visualization) tracers followed by clean water flushing, and 2) the two-layer analytical solution of Sale et al. (2008) involving a relatively simple scenario with an aquifer and underlying low permeability layer. All three models are shown to provide close agreement when adequate spatial and temporal discretization are applied to represent problem geometry, resolve flow fields and capture advective transport in the sands and diffusive transfer with low permeability layers and minimize numerical dispersion. The challenge for application at field sites then becomes appropriate site characterization to inform the models, capturing the style of the low permeability zone geometry and incorporating reasonable hydrogeologic parameters and estimates of source history, for scenario testing and more accurate prediction of plume response, leading to better site decision making.

Optimizing the position resolution of a Z-stack microchannel plate resistive anode detector for low intensity signals

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

Wiggins, B. B.; Richardson, E.; Siwal, D.

A method for achieving good position resolution of low-intensity electron signals using a microchannel plate resistive anode detector is demonstrated. Electron events at a rate of 7 counts s{sup −1} are detected using a Z-stack microchannel plate. The dependence of position resolution on both the distance and the potential difference between the microchannel plate and resistive anode is investigated. Using standard commercial electronics, a measured position resolution of 170 μm (FWHM) is obtained, which corresponds to an intrinsic resolution of 157 μm (FWHM)

Label-free imaging of the dynamics of cell-to-cell string-like structure bridging in the free-space by low-coherent quantitative phase microscopy

NASA Astrophysics Data System (ADS)

Yamauchi, Toyohiko; Iwai, Hidenao; Yamashita, Yutaka

2013-03-01

We succeeded in utilizing our low-coherent quantitative phase microscopy (LC-QPM) to achieve label-free and three-dimensional imaging of string-like structures bridging the free-space between live cells. In past studies, three dimensional morphology of the string-like structures between cells had been investigated by electron microscopies and fluorescence microscopies and these structures were called "membrane nanotubes" or "tunneling nanotubes." However, use of electron microscopy inevitably kills these cells and fluorescence microscopy is itself a potentially invasive method. To achieve noninvasive imaging of live cells, we applied our LC-QPM which is a reflection-type, phase resolved and full-field interference microscope employing a low-coherent light source. LC-QPM is able to visualize the three-dimensional morphology of live cells without labeling by means of low-coherence interferometry. The lateral (diffraction limit) and longitudinal (coherence-length) spatial resolution of LC-QPM were respectively 0.49 and 0.93 micrometers and the repeatability of the phase measurement was 0.02 radians (1.0 nm). We successfully obtained three-dimensional morphology of live cultured epithelial cells (cell type: HeLa, derived from cervix cancer) and were able to clearly observe the individual string-like structures interconnecting the cells. When we performed volumetric imaging, a 80 micrometer by 60 micrometer by 6.5 micrometer volume was scanned every 5.67 seconds and 70 frames of a three-dimensional movie were recorded for a duration of 397 seconds. Moreover, the optical phase images gave us detailed information about the three-dimensional morphology of the string-like structure at sub-wavelength resolution. We believe that our LC-QPM will be a useful tool for the study of three-dimensional morphology of live cells.

Impact of low-frequency hotspot mutation R282Q on the structure of p53 DNA-binding domain as revealed by crystallography at 1.54 Å resolution

PubMed Central

Tu, Chao; Tan, Yu-Hong; Shaw, Gary; Zhou, Zheng; Bai, Yawen; Luo, Ray; Ji, Xinhua

2008-01-01

Tumor suppressor p53 is a sequence-specific DNA-binding protein and its central DNA-binding domain (DBD) harbors six hotspots (Arg175, Gly245, Arg248, Arg249, Arg273 and Arg282) for human cancers. Here, the crystal structure of a low-frequency hotspot mutant, p53DBD(R282Q), is reported at 1.54 Å resolution together with the results of molecular-dynamics simulations on the basis of the structure. In addition to eliminating a salt bridge, the R282Q mutation has a significant impact on the properties of two DNA-binding loops (L1 and L3). The L1 loop is flexible in the wild type, but it is not flexible in the mutant. The L3 loop of the wild type is not flexible, whereas it assumes two conformations in the mutant. Molecular-dynamics simulations indicated that both conformations of the L3 loop are accessible under biological conditions. It is predicted that the elimination of the salt bridge and the inversion of the flexibility of L1 and L3 are directly or indirectly responsible for deactivating the tumor suppressor p53. PMID:18453682

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

Spatially encoded phase-contrast MRI-3D MRI movies of 1D and 2D structures at millisecond resolution.

PubMed

Merboldt, Klaus-Dietmar; Uecker, Martin; Voit, Dirk; Frahm, Jens

2011-10-01

This work demonstrates that the principles underlying phase-contrast MRI may be used to encode spatial rather than flow information along a perpendicular dimension, if this dimension contains an MRI-visible object at only one spatial location. In particular, the situation applies to 3D mapping of curved 2D structures which requires only two projection images with different spatial phase-encoding gradients. These phase-contrast gradients define the field of view and mean spin-density positions of the object in the perpendicular dimension by respective phase differences. When combined with highly undersampled radial fast low angle shot (FLASH) and image reconstruction by regularized nonlinear inversion, spatial phase-contrast MRI allows for dynamic 3D mapping of 2D structures in real time. First examples include 3D MRI movies of the acting human hand at a temporal resolution of 50 ms. With an even simpler technique, 3D maps of curved 1D structures may be obtained from only three acquisitions of a frequency-encoded MRI signal with two perpendicular phase encodings. Here, 3D MRI movies of a rapidly rotating banana were obtained at 5 ms resolution or 200 frames per second. In conclusion, spatial phase-contrast 3D MRI of 2D or 1D structures is respective two or four orders of magnitude faster than conventional 3D MRI. Copyright © 2011 Wiley-Liss, Inc.

Sparse PDF Volumes for Consistent Multi-Resolution Volume Rendering.

PubMed

Sicat, Ronell; Krüger, Jens; Möller, Torsten; Hadwiger, Markus

2014-12-01

This paper presents a new multi-resolution volume representation called sparse pdf volumes, which enables consistent multi-resolution volume rendering based on probability density functions (pdfs) of voxel neighborhoods. These pdfs are defined in the 4D domain jointly comprising the 3D volume and its 1D intensity range. Crucially, the computation of sparse pdf volumes exploits data coherence in 4D, resulting in a sparse representation with surprisingly low storage requirements. At run time, we dynamically apply transfer functions to the pdfs using simple and fast convolutions. Whereas standard low-pass filtering and down-sampling incur visible differences between resolution levels, the use of pdfs facilitates consistent results independent of the resolution level used. We describe the efficient out-of-core computation of large-scale sparse pdf volumes, using a novel iterative simplification procedure of a mixture of 4D Gaussians. Finally, our data structure is optimized to facilitate interactive multi-resolution volume rendering on GPUs.

Sparse PDF Volumes for Consistent Multi-Resolution Volume Rendering

PubMed Central

Sicat, Ronell; Krüger, Jens; Möller, Torsten; Hadwiger, Markus

2015-01-01

This paper presents a new multi-resolution volume representation called sparse pdf volumes, which enables consistent multi-resolution volume rendering based on probability density functions (pdfs) of voxel neighborhoods. These pdfs are defined in the 4D domain jointly comprising the 3D volume and its 1D intensity range. Crucially, the computation of sparse pdf volumes exploits data coherence in 4D, resulting in a sparse representation with surprisingly low storage requirements. At run time, we dynamically apply transfer functions to the pdfs using simple and fast convolutions. Whereas standard low-pass filtering and down-sampling incur visible differences between resolution levels, the use of pdfs facilitates consistent results independent of the resolution level used. We describe the efficient out-of-core computation of large-scale sparse pdf volumes, using a novel iterative simplification procedure of a mixture of 4D Gaussians. Finally, our data structure is optimized to facilitate interactive multi-resolution volume rendering on GPUs. PMID:26146475

Study on the Spatial Resolution of Single and Multiple Coincidences Compton Camera

NASA Astrophysics Data System (ADS)

Andreyev, Andriy; Sitek, Arkadiusz; Celler, Anna

2012-10-01

In this paper we study the image resolution that can be obtained from the Multiple Coincidences Compton Camera (MCCC). The principle of MCCC is based on a simultaneous acquisition of several gamma-rays emitted in cascade from a single nucleus. Contrary to a standard Compton camera, MCCC can theoretically provide the exact location of a radioactive source (based only on the identification of the intersection point of three cones created by a single decay), without complicated tomographic reconstruction. However, practical implementation of the MCCC approach encounters several problems, such as low detection sensitivities result in very low probability of coincident triple gamma-ray detection, which is necessary for the source localization. It is also important to evaluate how the detection uncertainties (finite energy and spatial resolution) influence identification of the intersection of three cones, thus the resulting image quality. In this study we investigate how the spatial resolution of the reconstructed images using the triple-cone reconstruction (TCR) approach compares to images reconstructed from the same data using standard iterative method based on single-cone. Results show, that FWHM for the point source reconstructed with TCR was 20-30% higher than the one obtained from the standard iterative reconstruction based on expectation maximization (EM) algorithm and conventional single-cone Compton imaging. Finite energy and spatial resolutions of the MCCC detectors lead to errors in conical surfaces definitions (“thick” conical surfaces) which only amplify in image reconstruction when intersection of three cones is being sought. Our investigations show that, in spite of being conceptually appealing, the identification of triple cone intersection constitutes yet another restriction of the multiple coincidence approach which limits the image resolution that can be obtained with MCCC and TCR algorithm.

Low-cost solar array structure development

NASA Astrophysics Data System (ADS)

Wilson, A. H.

1981-06-01

Early studies of flat-plate arrays have projected costs on the order of $50/square meter for installed array support structures. This report describes an optimized low-cost frame-truss structure that is estimated to cost below $25/square meter, including all markups, shipping an installation. The structure utilizes a planar frame made of members formed from light-gauge galvanized steel sheet and is supposed in the field by treated-wood trusses that are partially buried in trenches. The buried trusses use the overburden soil to carry uplift wind loads and thus to obviate reinforced-concrete foundations. Details of the concept, including design rationale, fabrication and assembly experience, structural testing and fabrication drawings are included.

Low-cost solar array structure development

NASA Technical Reports Server (NTRS)

Wilson, A. H.

1981-01-01

Early studies of flat-plate arrays have projected costs on the order of $50/square meter for installed array support structures. This report describes an optimized low-cost frame-truss structure that is estimated to cost below $25/square meter, including all markups, shipping an installation. The structure utilizes a planar frame made of members formed from light-gauge galvanized steel sheet and is supposed in the field by treated-wood trusses that are partially buried in trenches. The buried trusses use the overburden soil to carry uplift wind loads and thus to obviate reinforced-concrete foundations. Details of the concept, including design rationale, fabrication and assembly experience, structural testing and fabrication drawings are included.

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

Imaging cellular structures in super-resolution with SIM, STED and Localisation Microscopy: A practical comparison.

PubMed

Wegel, Eva; Göhler, Antonia; Lagerholm, B Christoffer; Wainman, Alan; Uphoff, Stephan; Kaufmann, Rainer; Dobbie, Ian M

2016-06-06

Many biological questions require fluorescence microscopy with a resolution beyond the diffraction limit of light. Super-resolution methods such as Structured Illumination Microscopy (SIM), STimulated Emission Depletion (STED) microscopy and Single Molecule Localisation Microscopy (SMLM) enable an increase in image resolution beyond the classical diffraction-limit. Here, we compare the individual strengths and weaknesses of each technique by imaging a variety of different subcellular structures in fixed cells. We chose examples ranging from well separated vesicles to densely packed three dimensional filaments. We used quantitative and correlative analyses to assess the performance of SIM, STED and SMLM with the aim of establishing a rough guideline regarding the suitability for typical applications and to highlight pitfalls associated with the different techniques.

Comparing high-resolution microscopy techniques for potential intraoperative use in guiding low-grade glioma resections.

PubMed

Meza, Daphne; Wang, Danni; Wang, Yu; Borwege, Sabine; Sanai, Nader; Liu, Jonathan T C

2015-04-01

Fluorescence image-guided surgery (FIGS), with contrast provided by 5-ALA-induced PpIX, has been shown to enable a higher extent of resection of high-grade gliomas. However, conventional FIGS with low-power microscopy lacks the sensitivity to aid in low-grade glioma (LGG) resection because PpIX signal is weak and sparse in such tissues. Intraoperative high-resolution microscopy of PpIX fluorescence has been proposed as a method to guide LGG resection, where sub-cellular resolution allows for the visualization of sparse and punctate mitochondrial PpIX production in tumor cells. Here, we assess the performance of three potentially portable high-resolution microscopy techniques that may be used for the intraoperative imaging of human LGG tissue samples with PpIX contrast: high-resolution fiber-optic microscopy (HRFM), high-resolution wide-field microscopy (WFM), and dual-axis confocal (DAC) microscopy. Thick unsectioned human LGG tissue samples (n = 7) with 5-ALA-induced PpIX contrast were imaged using three imaging techniques (HRFM, WFM, DAC). The average signal-to-background ratio (SBR) was then calculated for each imaging modality (5 images per tissue, per modality). HRFM provides the ease of use and portability of a flexible fiber bundle, and is simple and inexpensive to build. However, in most cases (6/7), HRFM is not capable of detecting PpIX signal from LGGs due to high autofluorescence, generated by the fiber bundle under laser illumination at 405 nm, which overwhelms the PpIX signal and impedes its visualization. WFM is a camera-based method possessing high lateral resolution but poor axial resolution, resulting in sub-optimal image contrast. Consistent successful detection of PpIX signal throughout our human LGG tissue samples (n = 7), with an acceptable image contrast (SBR >2), was only achieved using DAC microscopy, which offers superior image resolution and contrast that is comparable to histology, but requires a laser-scanning mechanism to

TandemPET-A High Resolution, Small Animal, Virtual Pinhole-Based PET Scanner: Initial Design Study

NASA Astrophysics Data System (ADS)

Raylman, Raymond R.; Stolin, Alexander V.; Martone, Peter F.; Smith, Mark F.

2016-02-01

Mice are the perhaps the most common species of rodents used in biomedical research, but many of the current generation of small animal PET scanners are non-optimal for imaging these small rodents due to their relatively low resolution. Consequently, a number of researchers have investigated the development of high-resolution scanners to address this need. In this investigation, the design of a novel, high-resolution system based on the dual-detector, virtual-pinhole PET concept was explored via Monte Carlo simulations. Specifically, this system, called TandemPET, consists of a 5 cm × 5 cm high-resolution detector made-up of a 90 × 90 array of 0.5 mm × 0.5 × 10 mm (pitch = 0.55 mm) LYSO detector elements in coincidence with a lower resolution detector consisting of a 68 × 68 array of 1.5 mm × 1.5 mm × 10 mm LYSO detector elements (total size = 10.5 cm × 10.5 cm). Analyses indicated that TandemPET's optimal geometry is to position the high-resolution detector 3 cm from the center-of-rotation, with the lower resolution detector positioned 9 cm from center. Measurements using modified NEMA NU4-2008-based protocols revealed that the spatial resolution of the system is 0.5 mm FWHM, after correction of positron range effects. Peak sensitivity is 2.1%, which is comparable to current small animal PET scanners. Images from a digital mouse brain phantom demonstrated the potential of the system for identifying important neurological structures.

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.

Active Radiation Detectors for Use in Space Beyond Low Earth Orbit: Spatial and Energy Resolution Requirements and Methods for Heavy Ion Charge Classification

NASA Astrophysics Data System (ADS)

McBeth, Rafe A.

Space radiation exposure to astronauts will need to be carefully monitored on future missions beyond low earth orbit. NASA has proposed an updated radiation risk framework that takes into account a significant amount of radiobiological and heavy ion track structure information. These models require active radiation detection systems to measure the energy and ion charge Z. However, current radiation detection systems cannot meet these demands. The aim of this study was to investigate several topics that will help next generation detection systems meet the NASA objectives. Specifically, this work investigates the required spatial resolution to avoid coincident events in a detector, the effects of energy straggling and conversion of dose from silicon to water, and methods for ion identification (Z) using machine learning. The main results of this dissertation are as follows: 1. Spatial resolution on the order of 0.1 cm is required for active space radiation detectors to have high confidence in identifying individual particles, i.e., to eliminate coincident events. 2. Energy resolution of a detector system will be limited by energy straggling effects and the conversion of dose in silicon to dose in biological tissue (water). 3. Machine learning methods show strong promise for identification of ion charge (Z) with simple detector designs.

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.

Cholesterol oxidase: ultrahigh-resolution crystal structure and multipolar atom model-based analysis.

PubMed

Zarychta, Bartosz; Lyubimov, Artem; Ahmed, Maqsood; Munshi, Parthapratim; Guillot, Benoît; Vrielink, Alice; Jelsch, Christian

2015-04-01

Examination of protein structure at the subatomic level is required to improve the understanding of enzymatic function. For this purpose, X-ray diffraction data have been collected at 100 K from cholesterol oxidase crystals using synchrotron radiation to an optical resolution of 0.94 Å. After refinement using the spherical atom model, nonmodelled bonding peaks were detected in the Fourier residual electron density on some of the individual bonds. Well defined bond density was observed in the peptide plane after averaging maps on the residues with the lowest thermal motion. The multipolar electron density of the protein-cofactor complex was modelled by transfer of the ELMAM2 charge-density database, and the topology of the intermolecular interactions between the protein and the flavin adenine dinucleotide (FAD) cofactor was subsequently investigated. Taking advantage of the high resolution of the structure, the stereochemistry of main-chain bond lengths and of C=O···H-N hydrogen bonds was analyzed with respect to the different secondary-structure elements.

Low Resolution Picture Transmission (LRPT) Demonstration System. Phase II; 1.0

NASA Technical Reports Server (NTRS)

Fong, Wai; Yeh, Pen-Shu; Duran, Steve; Sank, Victor; Nyugen, Xuan; Xia, Wei; Day, John H. (Technical Monitor)

2002-01-01

Low-Resolution Picture Transmission (LRPT) is a proposed standard for direct broadcast transmission of satellite weather images. This standard is a joint effort by the European Organization for the Exploitation of Meteorological Satellites (EUMETSAT) and NOAA. As a digital transmission scheme, its purpose is to replace the current analog Automatic Picture Transmission (APT) system for use in the Meteorological Operational (METOP) satellites. GSFC has been tasked to build an LRPT Demonstration System (LDS). Its main objective is to develop or demonstrate the feasibility of a low-cost receiver utilizing a PC as the primary processing component and determine the performance of the protocol in the simulated Radio Frequency (RF) environment. The approach would consist of two phases.

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

High resolution observations of low contrast phenomena from an Advanced Geosynchronous Platform (AGP)

NASA Technical Reports Server (NTRS)

Maxwell, M. S.

1984-01-01

Present technology allows radiometric monitoring of the Earth, ocean and atmosphere from a geosynchronous platform with good spatial, spectral and temporal resolution. The proposed system could provide a capability for multispectral remote sensing with a 50 m nadir spatial resolution in the visible bands, 250 m in the 4 micron band and 1 km in the 11 micron thermal infrared band. The diffraction limited telescope has a 1 m aperture, a 10 m focal length (with a shorter focal length in the infrared) and linear and area arrays of detectors. The diffraction limited resolution applies to scenes of any brightness but for a dark low contrast scenes, the good signal to noise ratio of the system contribute to the observation capability. The capabilities of the AGP system are assessed for quantitative observations of ocean scenes. Instrument and ground system configuration are presented and projected sensor capabilities are analyzed.

Crystal Structure Studies of Low-Ca Pyroxenes from LL-Group Chondritic Meteorites

NASA Astrophysics Data System (ADS)

Artioli, G.; Davoli, G.; Sighinolfi, G. P.

1993-07-01

One orthorhombic (Pbca) and two monoclinic (P2(sub)1/c) single crystals of low-Ca pyroxenes were extracted from unequilibrated chondritic meteorites of the LL-group. The results of the crystal structure refinements performed using x-ray diffraction data indicate that: (1) the intracrystalline Fe-Mg distribution over the M1 and M2 crystallographic sites of the Parnallee (LL-3) orthoenstatite is consistent with a temperature of 960 degrees C for the closure of the exchange equilibrium process; and (2) the structural state and intracristalline Fe-Mg order in the Soko Banja (LL-4) and Jolomba (LL-6) clinoenstatites indicate a closing temperature of at least 1000-1100 degrees C, with no significant reequilibration at lower temperatures. The present data represent the first detailed crystallographic investigation of pyroxenes from LL-chondrites and support the hypothesis that the chondrule pyroxenes bear a distinct memory of rapid cooling in the solar nebular and that thermal metamorphism in the parent body, if present, was totally unsufficient to allow reequilibration of the pyroxene minerals to the low-temperature ordered crystal structures. The data also indicate that, assuming low or mild pressure and shock effects, there is no well-defined correlation between equilibrium temperature of the mineral phases and the alleged petrologic type of the meteorites. This evidence is consistent with a rubble-pile model for the parent body accretional history, or with an onion-shell model with very low thermal-peak metamorphism, as it is assumed for a very small object.

A Low-Noise X-ray Astronomical Silicon-On-Insulator Pixel Detector Using a Pinned Depleted Diode Structure.

PubMed

Kamehama, Hiroki; Kawahito, Shoji; Shrestha, Sumeet; Nakanishi, Syunta; Yasutomi, Keita; Takeda, Ayaki; Tsuru, Takeshi Go; Arai, Yasuo

2017-12-23

This paper presents a novel full-depletion Si X-ray detector based on silicon-on-insulator pixel (SOIPIX) technology using a pinned depleted diode structure, named the SOIPIX-PDD. The SOIPIX-PDD greatly reduces stray capacitance at the charge sensing node, the dark current of the detector, and capacitive coupling between the sensing node and SOI circuits. These features of the SOIPIX-PDD lead to low read noise, resulting high X-ray energy resolution and stable operation of the pixel. The back-gate surface pinning structure using neutralized p-well at the back-gate surface and depleted n-well underneath the p-well for all the pixel area other than the charge sensing node is also essential for preventing hole injection from the p-well by making the potential barrier to hole, reducing dark current from the Si-SiO₂ interface and creating lateral drift field to gather signal electrons in the pixel area into the small charge sensing node. A prototype chip using 0.2 μm SOI technology shows very low readout noise of 11.0 e - rms , low dark current density of 56 pA/cm² at -35 °C and the energy resolution of 200 eV(FWHM) at 5.9 keV and 280 eV (FWHM) at 13.95 keV.

A Low-Noise X-ray Astronomical Silicon-On-Insulator Pixel Detector Using a Pinned Depleted Diode Structure

PubMed Central

Kamehama, Hiroki; Kawahito, Shoji; Shrestha, Sumeet; Nakanishi, Syunta; Yasutomi, Keita; Takeda, Ayaki; Tsuru, Takeshi Go

2017-01-01

This paper presents a novel full-depletion Si X-ray detector based on silicon-on-insulator pixel (SOIPIX) technology using a pinned depleted diode structure, named the SOIPIX-PDD. The SOIPIX-PDD greatly reduces stray capacitance at the charge sensing node, the dark current of the detector, and capacitive coupling between the sensing node and SOI circuits. These features of the SOIPIX-PDD lead to low read noise, resulting high X-ray energy resolution and stable operation of the pixel. The back-gate surface pinning structure using neutralized p-well at the back-gate surface and depleted n-well underneath the p-well for all the pixel area other than the charge sensing node is also essential for preventing hole injection from the p-well by making the potential barrier to hole, reducing dark current from the Si-SiO2 interface and creating lateral drift field to gather signal electrons in the pixel area into the small charge sensing node. A prototype chip using 0.2 μm SOI technology shows very low readout noise of 11.0 e−rms, low dark current density of 56 pA/cm2 at −35 °C and the energy resolution of 200 eV(FWHM) at 5.9 keV and 280 eV (FWHM) at 13.95 keV. PMID:29295523

Higher Resolution and Faster MRI of 31Phosphorus in Bone

NASA Astrophysics Data System (ADS)

Frey, Merideth; Barrett, Sean; Sethna, Zachary; Insogna, Karl; Vanhouten, Joshua

2013-03-01

Probing the internal composition of bone on the sub-100 μm length scale is important to study normal features and to look for signs of disease. However, few useful non-destructive techniques are available to evaluate changes in the bone mineral chemical structure and functional micro-architecture on the interior of bones. MRI would be an excellent candidate, but bone is a particularly challenging tissue to study given the relatively low water density, wider linewidths of its solid components leading to low spatial resolution, and the long imaging time compared to conventional 1H MRI. Our lab has recently made advances in obtaining high spatial resolution (sub-400 μm)3 three-dimensional 31Phosphorus MRI of bone through use of the quadratic echo line-narrowing sequence (1). In this talk, we describe our current results using proton decoupling to push this technique even further towards the factor of 1000 increase in spatial resolution imposed by fundamental limits. We also discuss our work to speed up imaging through novel, faster reconstruction algorithms that can reconstruct the desired image from very sparse data sets. (1) M. Frey, et al. PNAS 109: 5190 (2012).

Holography and coherent diffraction with low-energy electrons: A route towards structural biology at the single molecule level.

PubMed

Latychevskaia, Tatiana; Longchamp, Jean-Nicolas; Escher, Conrad; Fink, Hans-Werner

2015-12-01

The current state of the art in structural biology is led by NMR, X-ray crystallography and TEM investigations. These powerful tools however all rely on averaging over a large ensemble of molecules. Here, we present an alternative concept aiming at structural analysis at the single molecule level. We show that by combining electron holography and coherent diffraction imaging estimations concerning the phase of the scattered wave become needless as the phase information is extracted from the data directly and unambiguously. Performed with low-energy electrons the resolution of this lens-less microscope is just limited by the De Broglie wavelength of the electron wave and the numerical aperture, given by detector geometry. In imaging freestanding graphene, a resolution of 2Å has been achieved revealing the 660.000 unit cells of the graphene sheet from a single data set. Once applied to individual biomolecules the method shall ultimately allow for non-destructive imaging and imports the potential to distinguish between different conformations of proteins with atomic resolution. Copyright © 2015. Published by Elsevier B.V.

Optical photometry and low-resolution spectroscopy of the SN 2014J

NASA Astrophysics Data System (ADS)

Gonzalez Hernandez, Jonay I.; Genova-Santos, Ricardo; Rubiño-Martin, Jose Alberto; Ruiz-Lapuente, Pilar

2014-02-01

We have obtained low-resolution spectroscopic data and broadband (g,r,i,z) photometric images at the 4.2m-WHT equipped with the instrument ACAM at the Observatorio del Roque de los Muchachos (La Palma, Spain) on approximately January 28.13 UT. A preliminary analysis of these spectra show the strong Si II (6355A) line moving at ~12600 km/s, and CII (6580A) and SII (5468A) at ~13700km/s and 12150 km/s, respectively.

Low-temperature high-Z gamma-detectors with very high energy resolution

NASA Astrophysics Data System (ADS)

Pobes, Carlos; Brofferio, Chiara; Bucci, Carlo; Cremonesi, Oliviero; Fiorini, Ettore; Giuliani, Andrea; Nucciotti, Angelo; Pavan, Maura; Pedretti, Marisa; Pessina, Gianluigi; Pirro, Stefano; Previtali, Ezio; Sisti, Monica; Vanzini, Marco; Zanotti, Luigi

2001-12-01

High-Z low-temperature calorimeters are developed by an Italian collaboration (Milano-Como-Gran Sasso Underground Laboratories) in order to search for rare nuclear events and Dark Matter massive candidates. They exhibit an excellent energy resolution, close to that of Ge-diodes, but a much higher efficiency. Different high-Z materials were initially employed . A many-years optimisation work on tellurium oxide (TeO2) lead to impressive results: devices with total masses around 750 g present FWHM energy resolutions on gamma-ray peaks ranging from 1 KeV (close to the 5 KeV energy threshold) to 2.6 KeV at 2615 KeV (208Tl gamma line). A 3.2 KeV FWHM energy resolution was obtained at 5.4 MeV (210Po alpha line), which is by far the best one ever achieved with any alpha detector. These devices, operated at about 10 mK, consist of a TeO2 single crystal thermally coupled to a 50 mg Neutron Transmutation Doped (NTD) Ge crystal working as a temperature sensor. Special care was devoted to methods for response linearization and temporal stabilisation. Devices based on the same principle and specifically optimised could find applications in several fields like gamma-ray astrophysics, nuclear physics searches, environmental monitoring and radiation metrology.

Mini-Sosie high-resolution seismic method aids hazards studies

USGS Publications Warehouse

Stephenson, W.J.; Odum, J.; Shedlock, K.M.; Pratt, T.L.; Williams, R.A.

1992-01-01

The Mini-Sosie high-resolution seismic method has been effective in imaging shallow-structure and stratigraphic features that aid in seismic-hazard and neotectonic studies. The method is not an alternative to Vibroseis acquisition for large-scale studies. However, it has two major advantages over Vibroseis as it is being used by the USGS in its seismic-hazards program. First, the sources are extremely portable and can be used in both rural and urban environments. Second, the shifting-and-summation process during acquisition improves the signal-to-noise ratio and cancels out seismic noise sources such as cars and pedestrians. -from Authors

High-Resolution Fibre-Optic Temperature Sensing: A New Tool to Study the Two-Dimensional Structure of Atmospheric Surface-Layer Flow

NASA Astrophysics Data System (ADS)

Thomas, Christoph K.; Kennedy, Adam M.; Selker, John S.; Moretti, Ayla; Schroth, Martin H.; Smoot, Alexander R.; Tufillaro, Nicholas B.; Zeeman, Matthias J.

2012-02-01

We present a novel approach based on fibre-optic distributed temperature sensing (DTS) to measure the two-dimensional thermal structure of the surface layer at high resolution (0.25 m, ≈0.5 Hz). Air temperature observations obtained from a vertically-oriented fibre-optics array of approximate dimensions 8 m × 8 m and sonic anemometer data from two levels were collected over a short grass field located in the flat bottom of a wide valley with moderate surface heterogeneity. The objectives of the study were to evaluate the potential of the DTS technique to study small-scale processes in the surface layer over a wide range of atmospheric stability, and to analyze the space-time dynamics of transient cold-air pools in the calm boundary layer. The time response and precision of the fibre-based temperatures were adequate to resolve individual sub-metre sized turbulent and non-turbulent structures, of time scales of seconds, in the convective, neutral, and stable surface layer. Meaningful sensible heat fluxes were computed using the eddy-covariance technique when combined with vertical wind observations. We present a framework that determines the optimal environmental conditions for applying the fibre-optics technique in the surface layer and identifies areas for potentially significant improvements of the DTS performance. The top of the transient cold-air pool was highly non-stationary indicating a superposition of perturbations of different time and length scales. Vertical eddy scales in the strongly stratified transient cold-air pool derived from the DTS data agreed well with the buoyancy length scale computed using the vertical velocity variance and the Brunt-Vaisala frequency, while scales for weak stratification disagreed. The high-resolution DTS technique opens a new window into spatially sampling geophysical fluid flows including turbulent energy exchange.

Multi-disciplinary study for the exploration of deep low enthalpy geothermal reservoirs, Neuchâtel, Switzerland

NASA Astrophysics Data System (ADS)

Mauri, G.; Abdelfettah, Y.; Negro, F.; Schill, E.; Vuataz, F.

2011-12-01

The authorities of the canton of Neuchâtel, in the Western part of Switzerland, are willing to develop geothermal energy for district heating in the two main cities of the canton: Neuchâtel, located along the Lake of Neuchâtel, and La Chaux-de-Fonds situated in a high valley of the Jura Massif. The geology of both areas is linked to the Jura Range and present complex structures, where the landscape is composed of anticlines associated with overthrust faults, which are overcut by strike-slip fault and secondary faulting events. The rock formations go from the Trias, which forms the detachment layer, up to the Quaternary rock. Bedrocks are mainly composed of limestones and marls, which can reach a thickness of several hundreds meters. The three main deep aquifers investigated in this area, from the shallowest (≤ 400 m below surface) to deepest (< 2000 m), are the Malm, the Dogger and the Muschelkalk. The estimated temperatures, based on previous studies, should range between 20 to 65 oC, which are function of depth, elevation and groundwater velocity. The expected low temperature is mainly due to the presence of karstic systems, which drains the heat towards the low elevation of the basin. The present study is based on gravimetry surveys, 3D geological models and 3D gravimetry models to best characterize the underground structures and to find areas where the rock properties would be favourable to geothermal exploitation. This means targets where permeability and porosity are high in the potential aquifers, allowing a significant flow at the future production wells. The results indicate that gravity anomalies are associated with both shallow and deep geological structures in the two exploration sites and that high resolution of dense grid gravity measurements combined with realistic 3D models of the geological structures allow to characterize interesting features for deep geothermal exploration. Gravity corrections were carried out with a computing code using

Structure of a prokaryotic virtual proton pump at 3.2 Å resolution

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

Fang, Yiling; Jayaram, Hariharan; Shane, Tania

2009-09-15

To reach the mammalian gut, enteric bacteria must pass through the stomach. Many such organisms survive exposure to the harsh gastric environment (pH 1.5-4) by mounting extreme acid-resistance responses, one of which, the arginine-dependent system of Escherichia coli, has been studied at levels of cellular physiology, molecular genetics and protein biochemistry. This multiprotein system keeps the cytoplasm above pH 5 during acid challenge by continually pumping protons out of the cell using the free energy of arginine decarboxylation. At the heart of the process is a 'virtual proton pump' in the inner membrane, called AdiC, that imports L-arginine from themore » gastric juice and exports its decarboxylation product agmatine. AdiC belongs to the APC superfamily of membrane proteins, which transports amino acids, polyamines and organic cations in a multitude of biological roles, including delivery of arginine for nitric oxide synthesis, facilitation of insulin release from pancreatic {beta}-cells, and, when inappropriately overexpressed, provisioning of certain fast-growing neoplastic cells with amino acids. High-resolution structures and detailed transport mechanisms of APC transporters are currently unknown. Here we describe a crystal structure of AdiC at 3.2 {angstrom} resolution. The protein is captured in an outward-open, substrate-free conformation with transmembrane architecture remarkably similar to that seen in four other families of apparently unrelated transport proteins.« less

Measurement of replication structures at the nanometer scale using super-resolution light microscopy

PubMed Central

Baddeley, D.; Chagin, V. O.; Schermelleh, L.; Martin, S.; Pombo, A.; Carlton, P. M.; Gahl, A.; Domaing, P.; Birk, U.; Leonhardt, H.; Cremer, C.; Cardoso, M. C.

2010-01-01

DNA replication, similar to other cellular processes, occurs within dynamic macromolecular structures. Any comprehensive understanding ultimately requires quantitative data to establish and test models of genome duplication. We used two different super-resolution light microscopy techniques to directly measure and compare the size and numbers of replication foci in mammalian cells. This analysis showed that replication foci vary in size from 210 nm down to 40 nm. Remarkably, spatially modulated illumination (SMI) and 3D-structured illumination microscopy (3D-SIM) both showed an average size of 125 nm that was conserved throughout S-phase and independent of the labeling method, suggesting a basic unit of genome duplication. Interestingly, the improved optical 3D resolution identified 3- to 5-fold more distinct replication foci than previously reported. These results show that optical nanoscopy techniques enable accurate measurements of cellular structures at a level previously achieved only by electron microscopy and highlight the possibility of high-throughput, multispectral 3D analyses. PMID:19864256

A low power MICS band phase-locked loop for high resolution retinal prosthesis.

PubMed

Yang, Jiawei; Skafidas, Efstratios

2013-08-01

Ultra low power dissipation is essential in retinal prosthesis and many other biomedical implants. Extensive research has been undertaken in designing low power biomedical transceivers, however to date, most effort has been focused on low frequency inductive links. For higher frequency, more robust and more complex applications, such as Medical Implant Communication Service (MICS) band multichannel transceivers, power consumption remains high. This paper explores the design of micro-power data links at 400 MHz for a high resolution retinal prosthesis. By taking advantage of advanced small geometry CMOS technology and precise transistor-level modeling, we successfully utilized subthreshold FET operation, which has been historically limited to low frequency circuits due to the inadequate transistor operating speed in and near weak inversion; we have implemented a low power MICS transceiver. Particularly, a low power, MICS band multichannel phase-locked loop (PLL) that employs a subthreshold voltage controlled oscillator (VCO) and digital synchronous dividers has been implemented on a 65-nm CMOS. A design methodology is presented in detail with the demonstration of EKV model parameters extraction. This PLL provides 600- mVpp quadrature oscillations and exhibits a phase noise of -102 dBc/Hz at 200-kHz offset, while only consuming 430- μW from a 1-V supply. The VCO has a gain (KVCO) of 12 MHz/V and is designed to operate in the near-weak inversion region and consumes 220- μA DC current. The designed PLL has a core area of 0.54 mm(2). It satisfies all specifications of MICS band operation with the advantage of significant reduction in power which is crucial for high resolution retinal prosthesis.

Testing high resolution numerical models for analysis of contaminant storage and release from low permeability zones.

PubMed

Chapman, Steven W; Parker, Beth L; Sale, Tom C; Doner, Lee Ann

2012-08-01

It is now widely recognized that contaminant release from low permeability zones can sustain plumes long after primary sources are depleted, particularly for chlorinated solvents where regulatory limits are orders of magnitude below source concentrations. This has led to efforts to appropriately characterize sites and apply models for prediction incorporating these effects. A primary challenge is that diffusion processes are controlled by small-scale concentration gradients and capturing mass distribution in low permeability zones requires much higher resolution than commonly practiced. This paper explores validity of using numerical models (HydroGeoSphere, FEFLOW, MODFLOW/MT3DMS) in high resolution mode to simulate scenarios involving diffusion into and out of low permeability zones: 1) a laboratory tank study involving a continuous sand body with suspended clay layers which was 'loaded' with bromide and fluorescein (for visualization) tracers followed by clean water flushing, and 2) the two-layer analytical solution of Sale et al. (2008) involving a relatively simple scenario with an aquifer and underlying low permeability layer. All three models are shown to provide close agreement when adequate spatial and temporal discretization are applied to represent problem geometry, resolve flow fields and capture advective transport in the sands and diffusive transfer with low permeability layers and minimize numerical dispersion. The challenge for application at field sites then becomes appropriate site characterization to inform the models, capturing the style of the low permeability zone geometry and incorporating reasonable hydrogeologic parameters and estimates of source history, for scenario testing and more accurate prediction of plume response, leading to better site decision making. Copyright © 2012 Elsevier B.V. All rights reserved.

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

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

High Energy Resolution Hyperspectral X-Ray Imaging for Low-Dose Contrast-Enhanced Digital Mammography.

PubMed

Pani, Silvia; Saifuddin, Sarene C; Ferreira, Filipa I M; Henthorn, Nicholas; Seller, Paul; Sellin, Paul J; Stratmann, Philipp; Veale, Matthew C; Wilson, Matthew D; Cernik, Robert J

2017-09-01

Contrast-enhanced digital mammography (CEDM) is an alternative to conventional X-ray mammography for imaging dense breasts. However, conventional approaches to CEDM require a double exposure of the patient, implying higher dose, and risk of incorrect image registration due to motion artifacts. A novel approach is presented, based on hyperspectral imaging, where a detector combining positional and high-resolution spectral information (in this case based on Cadmium Telluride) is used. This allows simultaneous acquisition of the two images required for CEDM. The approach was tested on a custom breast-equivalent phantom containing iodinated contrast agent (Niopam 150®). Two algorithms were used to obtain images of the contrast agent distribution: K-edge subtraction (KES), providing images of the distribution of the contrast agent with the background structures removed, and a dual-energy (DE) algorithm, providing an iodine-equivalent image and a water-equivalent image. The high energy resolution of the detector allowed the selection of two close-by energies, maximising the signal in KES images, and enhancing the visibility of details with the low surface concentration of contrast agent. DE performed consistently better than KES in terms of contrast-to-noise ratio of the details; moreover, it allowed a correct reconstruction of the surface concentration of the contrast agent in the iodine image. Comparison with CEDM with a conventional detector proved the superior performance of hyperspectral CEDM in terms of the image quality/dose tradeoff.

Internal structure of InP/ZnS nanocrystals unraveled by high-resolution soft X-ray photoelectron spectroscopy.

PubMed

Huang, Kai; Demadrille, Renaud; Silly, Mathieu G; Sirotti, Fausto; Reiss, Peter; Renault, Olivier

2010-08-24

High-energy resolution photoelectron spectroscopy (DeltaE < 200 meV) is used to investigate the internal structure of semiconductor quantum dots containing low Z-contrast elements. In InP/ZnS core/shell nanocrystals synthesized using a single-step procedure (core and shell precursors added at the same time), a homogeneously alloyed InPZnS core structure is evidenced by quantitative analysis of their In3d(5/2) spectra recorded at variable excitation energy. When using a two-step method (core InP nanocrystal synthesis followed by subsequent ZnS shell growth), XPS analysis reveals a graded core/shell interface. We demonstrate the existence of In-S and S(x)-In-P(1-x) bonding states in both types of InP/ZnS nanocrystals, which allows a refined view on the underlying reaction mechanisms.

Studies of the field-of-view resolution tradeoff in virtual-reality systems

NASA Technical Reports Server (NTRS)

Piantanida, Thomas P.; Boman, Duane; Larimer, James; Gille, Jennifer; Reed, Charles

1992-01-01

Most virtual-reality systems use LCD-based displays that achieve a large field-of-view at the expense of resolution. A typical display will consist of approximately 86,000 pixels uniformly distributed over an 80-degree by 60-degree image. Thus, each pixel subtends about 13 minutes of arc at the retina; about the same as the resolvable features of the 20/200 line of a Snellen Eye Chart. The low resolution of LCD-based systems limits task performance in some applications. We have examined target-detection performance in a low-resolution virtual world. Our synthesized three-dimensional virtual worlds consisted of target objects that could be positioned at a fixed distance from the viewer, but at random azimuth and constrained elevation. A virtual world could be bounded by chromatic walls or by wire-frame, or it could be unbounded. Viewers scanned these worlds and indicated by appropriate gestures when they had detected the target object. By manipulating the viewer's field size and the chromatic and luminance contrast of annuli surrounding the field-of-view, we were able to assess the effect of field size on the detection of virtual objects in low-resolution synthetic worlds.

Structural perturbation of proteins in low denaturant concentrations.

PubMed

Basak, S; Debnath, D; Haque, E; Ray, S; Chakrabarti, A

2001-01-01

The presence of very low concentrations of the widely used chemical denaturants, guanidinium chloride and urea, induce changes in the tertiary structure of proteins. We have presented results on such changes in four structurally unrelated proteins to show that such structural perturbations are common irrespective of their origin. Data representative of such structural changes are shown for the monomeric globular proteins such as horseradish peroxidase (HRP) from a plant, human serum albumin (HSA) and prothrombin from ovine blood serum, and for the membrane-associated, worm-like elongated protein, spectrin, from ovine erythrocytes. Structural alterations in these proteins were reflected in quenching studies of tryptophan fluorescence using the widely used quencher acrylamide. Stern-Volmer quenching constants measured in presence of the denaturants, even at concentrations below 100 mM, were higher than those measured in absence of the denaturants. Both steady-state and time-resolved fluorescence emission properties of tryptophan and of the extrinsic probe PRODAN were used for monitoring conformational changes in the proteins in presence of different low concentrations of the denaturants. These results are consistent with earlier studies from our laboratory indicating structural perturbations in proteins at the tertiary level, keeping their native-like secondary structure and their biological activity more or less intact.

Structure of a low-population binding intermediate in protein-RNA recognition

PubMed Central

Bardaro, Michael F.; Aprile, Francesco A.; Varani, Gabriele; Vendruscolo, Michele

2016-01-01

The interaction of the HIV-1 protein transactivator of transcription (Tat) and its cognate transactivation response element (TAR) RNA transactivates viral transcription and represents a paradigm for the widespread occurrence of conformational rearrangements in protein-RNA recognition. Although the structures of free and bound forms of TAR are well characterized, the conformations of the intermediates in the binding process are still unknown. By determining the free energy landscape of the complex using NMR residual dipolar couplings in replica-averaged metadynamics simulations, we observe two low-population intermediates. We then rationally design two mutants, one in the protein and another in the RNA, that weaken specific nonnative interactions that stabilize one of the intermediates. By using surface plasmon resonance, we show that these mutations lower the release rate of Tat, as predicted. These results identify the structure of an intermediate for RNA-protein binding and illustrate a general strategy to achieve this goal with high resolution. PMID:27286828

Low-frequency noise reduction of lightweight airframe structures

NASA Technical Reports Server (NTRS)

Getline, G. L.

1976-01-01

The results of an experimental study to determine the noise attenuation characteristics of aircraft type fuselage structural panels were presented. Of particular interest was noise attenuation at low frequencies, below the fundamental resonances of the panels. All panels were flightweight structures for transport type aircraft in the 34,050 to 45,400 kg (75,000 to 100,000 pounds) gross weight range. Test data include the results of vibration and acoustic transmission loss tests on seven types of isotropic and orthotropically stiffened, flat and curved panels. The results show that stiffness controlled acoustically integrated structures can provide very high noise reductions at low frequencies without significantly affecting their high frequency noise reduction capabilities.

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

Design and performance of a high resolution, low latency stripline beam position monitor system

NASA Astrophysics Data System (ADS)

Apsimon, R. J.; Bett, D. R.; Blaskovic Kraljevic, N.; Burrows, P. N.; Christian, G. B.; Clarke, C. I.; Constance, B. D.; Dabiri Khah, H.; Davis, M. R.; Perry, C.; Resta López, J.; Swinson, C. J.

2015-03-01

A high-resolution, low-latency beam position monitor (BPM) system has been developed for use in particle accelerators and beam lines that operate with trains of particle bunches with bunch separations as low as several tens of nanoseconds, such as future linear electron-positron colliders and free-electron lasers. The system was tested with electron beams in the extraction line of the Accelerator Test Facility at the High Energy Accelerator Research Organization (KEK) in Japan. It consists of three stripline BPMs instrumented with analogue signal-processing electronics and a custom digitizer for logging the data. The design of the analogue processor units is presented in detail, along with measurements of the system performance. The processor latency is 15.6 ±0.1 ns . A single-pass beam position resolution of 291 ±10 nm has been achieved, using a beam with a bunch charge of approximately 1 nC.

Next Generation X-Ray Optics: High-Resolution, Light-Weight, and Low-Cost

NASA Technical Reports Server (NTRS)

Zhang, William W.

2012-01-01

X-ray telescopes are essential to the future of x-ray astronomy. In this talk I will describe a comprehensive program to advance the technology for x-ray telescopes well beyond the state of the art represented by the three currently operating missions: Chandra, XMM-Newton, and Suzaku. This program will address the three key issues in making an x-ray telescope: (1) angular resolution, (2) effective area per unit mass, and (3) cost per unit effective area. The objectives of this technology program are (1) in the near term, to enable Explorer-class x-ray missions and an IXO-type mission, and (2) in the long term, to enable a flagship x-ray mission with sub-arcsecond angular resolution and multi-square-meter effective area, at an affordable cost. We pursue two approaches concurrently, emphasizing the first approach in the near term (2-5 years) and the second in the long term (4-10 years). The first approach is precision slumping of borosilicate glass sheets. By design and choice at the outset, this technique makes lightweight and low-cost mirrors. The development program will continue to improve angular resolution, to enable the production of 5-arcsecond x-ray telescopes, to support Explorer-class missions and one or more missions to supersede the original IXO mission. The second approach is precision polishing and light-weighting of single-crystal silicon mirrors. This approach benefits from two recent commercial developments: (1) the inexpensive and abundant availability of large blocks of monocrystalline silicon, and (2) revolutionary advances in deterministic, precision polishing of mirrors. By design and choice at the outset, this technique is capable of producing lightweight mirrors with sub-arcsecond angular resolution. The development program will increase the efficiency and reduce the cost of the polishing and the light-weighting processes, to enable the production of lightweight sub-arcsecond x-ray telescopes. Concurrent with the fabrication of lightweight

Next Generation X-Ray Optics: High-Resolution, Light-Weight, and Low-Cost

NASA Technical Reports Server (NTRS)

Zhang, William W.

2011-01-01

X-ray telescopes are essential to the future of x-ray astronomy. This paper describes a comprehensive program to advance the technology for x-ray telescopes well beyond the state of the art represented by the three currently operating missions: Chandra, XMM-Newton , and Suzaku . This program will address the three key issues in making an x-ray telescope: (I) angular resolution, (2) effective area per unit mass, and (3) cost per unit effective area. The objectives of this technology program are (1) in the near term, to enable Explorer-class x-ray missions and an IXO type mission, and (2) in the long term, to enable a flagship x-ray mission with sub-arcsecond angular resolution and multi-square-meter effective area, at an affordable cost. We pursue two approaches concurrently, emphasizing the first approach in the near term (2-5 years) and the second in the long term (4-10 years). The first approach is precision slumping of borosilicate glass sheets. By design and choice at the outset, this technique makes lightweight and low-cost mirrors. The development program will continue to improve angular resolution, to enable the production of 5-arcsecond x-ray telescopes, to support Explorer-class missions and one or more missions to supersede the original IXO mission. The second approach is precision polishing and light-weighting of single-crystal silicon mirrors. This approach benefits from two recent commercial developments: (1) the inexpensive and abundant availability of large blocks of mono crystalline silicon, and (2) revolutionary advances in deterministic, precision polishing of mirrors. By design and choice at the outset, this technique is capable of producing lightweight mirrors with sub-arcsecond angular resolution. The development program will increase the efficiency and reduce the cost of the polishing and the lightweighting processes, to enable the production of lightweight sub-arcsecond x-ray telescopes. Concurrent with the fabrication of lightweight mirror

Cosmological parameters from a re-analysis of the WMAP 7 year low-resolution maps

NASA Astrophysics Data System (ADS)

Finelli, F.; De Rosa, A.; Gruppuso, A.; Paoletti, D.

2013-06-01

Cosmological parameters from Wilkinson Microwave Anisotropy Probe (WMAP) 7 year data are re-analysed by substituting a pixel-based likelihood estimator to the one delivered publicly by the WMAP team. Our pixel-based estimator handles exactly intensity and polarization in a joint manner, allowing us to use low-resolution maps and noise covariance matrices in T, Q, U at the same resolution, which in this work is 3.6°. We describe the features and the performances of the code implementing our pixel-based likelihood estimator. We perform a battery of tests on the application of our pixel-based likelihood routine to WMAP publicly available low-resolution foreground-cleaned products, in combination with the WMAP high-ℓ likelihood, reporting the differences on cosmological parameters evaluated by the full WMAP likelihood public package. The differences are not only due to the treatment of polarization, but also to the marginalization over monopole and dipole uncertainties present in the WMAP pixel likelihood code for temperature. The credible central value for the cosmological parameters change below the 1σ level with respect to the evaluation by the full WMAP 7 year likelihood code, with the largest difference in a shift to smaller values of the scalar spectral index nS.

Low-Mass Inflation Systems for Inflatable Structures

NASA Technical Reports Server (NTRS)

Thunnissen, Daniel P.; Webster, Mark S.; Engelbrecht, Carl S.

1995-01-01

The use of inflatable space structures has often been proposed for aerospace and planetary applications. Communication, power generation, and very-long-baseline interferometry are just three potential applications of inflatable technology. The success of inflatable structures depends on the development of an applications of inflatable technology. This paper describes two design studies performed to develop a low mass inflation system. The first study takes advantage of existing onboard propulsion gases to reduce the overall system mass. The second study assumes that there is no onboard propulsion system. Both studies employ advanced components developed for the Pluto fast flyby spacecraft to further reduce mass. The study examined four different types of systems: hydrazine, nitrogen and water, nitrogen, and xenon. This study shows that all of these systems can be built for a small space structure with masses lower than 0.5 kilograms.

CARMENES input catalogue of M dwarfs. I. Low-resolution spectroscopy with CAFOS

NASA Astrophysics Data System (ADS)

Alonso-Floriano, F. J.; Morales, J. C.; Caballero, J. A.; Montes, D.; Klutsch, A.; Mundt, R.; Cortés-Contreras, M.; Ribas, I.; Reiners, A.; Amado, P. J.; Quirrenbach, A.; Jeffers, S. V.

2015-05-01

Context. CARMENES is a stabilised, high-resolution, double-channel spectrograph at the 3.5 m Calar Alto telescope. It is optimally designed for radial-velocity surveys of M dwarfs with potentially habitable Earth-mass planets. Aims: We prepare a list of the brightest, single M dwarfs in each spectral subtype observable from the northern hemisphere, from which we will select the best planet-hunting targets for CARMENES. Methods: In this first paper on the preparation of our input catalogue, we compiled a large amount of public data and collected low-resolution optical spectroscopy with CAFOS at the 2.2 m Calar Alto telescope for 753 stars. We derived accurate spectral types using a dense grid of standard stars, a double least-squares minimisation technique, and 31 spectral indices previously defined by other authors. Additionally, we quantified surface gravity, metallicity, and chromospheric activity for all the stars in our sample. Results: We calculated spectral types for all 753 stars, of which 305 are new and 448 are revised. We measured pseudo-equivalent widths of Hα for all the stars in our sample, concluded that chromospheric activity does not affect spectral typing from our indices, and tabulated 49 stars that had been reported to be young stars in open clusters, moving groups, and stellar associations. Of the 753 stars, two are new subdwarf candidates, three are T Tauri stars, 25 are giants, 44 are K dwarfs, and 679 are M dwarfs. Many of the 261 investigated dwarfs in the range M4.0-8.0 V are among the brightest stars known in their spectral subtype. Conclusions: This collection of low-resolution spectroscopic data serves as a candidate target list for the CARMENES survey and can be highly valuable for other radial-velocity surveys of M dwarfs and for studies of cool dwarfs in the solar neighbourhood. Full Tables A.1, A.2, and A.3 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http

CARMENES science preparation: characterisation of M dwarfs with low-resolution spectroscopy and search for low-mass wide companions to young stars

NASA Astrophysics Data System (ADS)

Alonso-Floriano, F. J.

2015-11-01

This thesis is focused on the study of low-mass objects that can be targets of exoplanet searches with near-infrared spectrographs in general and CARMENES (Calar Alto high-Resolution search for M dwarfs with Exo-earths with Near-infrared and optical Echelle Spectrographs; see Quirrenbach et al. 2014) in particular. The CARMENES consortium comprises 11 institutions from Germany and Spain that are building a high-resolution spectrograph (R=82,000) with two channels, visible (0.55 - 1.05 um) and infrared (0.95 - 1.7 um), for the 3.5 m Calar Alto telescope. It will observe a sample of 300 M dwarfs in 600 nights of guaranteed time during at least three years, starting in January 2016. The final sample will be chosen from the 2200 M dwarfs included in the CARMENCITA input catalogue. For these stars, we have obtained and collected a large amount of data: spectral types, radial and rotational velocities, photometry in several bands, etc. Part of the e effort of the science preparation necessary for the final selection of targets for CARMENES and other near-infrared spectrographs has been collected in two publications, which are presented in this PhD thesis. In the first publication (Alonso-Floriano et al., 2015A&A...577A.128A), we obtained low-resolution spectra for 753 stars using the CAFOS spectrograph at the 2.2 m Calar Alto telescope. The main goal was to derive accurate spectral types, which are fundamental parameters for the sample selection. We used a grid of 49 standard stars, from spectral types K3V to M8V, together with a double least-square minimisation technique and 31 spectral indices previously defined by other authors. In addition, we quantified the surface gravity, metallicity and chromospheric activity of the sample, in order to detect low-gravity stars (giants and very young), metal-poor and very metal-poor stars (subdwarfs), and very active stars. In the second publication (Alonso-Floriano et al., 2015A&A...583A..85A), we searched for common proper

Resolution, the key to unlocking granite petrogenesis using zircon U-Pb - Lu-Hf studies

NASA Astrophysics Data System (ADS)

Tapster, Simon; Horstwood, Matthew; Roberts, Nick M. W.; Deady, Eimear; Shail, Robin

2017-04-01

Coarse-scale understanding of crustal evolution and source contributions to igneous systems has been drastically enhanced by coupled zircon U-Pb and Lu-Hf data sets. These are now common place and potentially offer advantages over whole-rock analyses by resolving heterogeneous source components in the complex crystal cargos of single hand-samples. However, the application of coupled zircon U-Pb and Lu-Hf studies to address detailed petrogenetic questions faces a crisis of resolution - On the one hand, micro-beam analytical techniques have high spatial resolution, capable of interrogating crystals with complex growth histories. Yet, the >1-2% temporal resolution of these techniques places a fundamental limitation on their utility for developing petrogenetic models. This limitation in data interpretation arises from timescales of crystal recycling or changes in source evolution that are often shorter than the U-Pb analytical precision. Conversely, high-precision CA-ID-TIMS U-Pb analysis of single whole zircons and solution MC-ICP-MS Lu-Hf isotopes of column washes (Hf masses equating to ca. 10-50 ng) have much greater temporal resolution (<0.1%), yet lack the spatial resolution to deal with complex crystal growth. Analyses homogenize any heterogeneity within the zircon and convolute the petrogenetic model. A balance must be struck between spatial and temporal resolution to address petrogenetic issues. Here, we demonstrate that micro-sampling of complex xenocryst-rich zircon crystals (e.g. <40 µm zircon tips) from the granitic post-Variscan Cornubian Batholith (SW England), in tandem with low-common Pb blank CA-ID-TIMS U-Pb chemistry, permits the analysis of zircon volumes that approach those of LA-ICPMS analyses, whilst simultaneously retaining the majority of the temporal resolution associated with the CA-ID-TIMS U-Pb technique. The low volume of zircon within these analyses may only provide <5 ng Hf, and therefore gaining useful precision from Lu-Hf isotopes is

High resolution structure of cleaved Serpin 42 Da from Drosophila melanogaster.

PubMed

Ellisdon, Andrew M; Zhang, Qingwei; Henstridge, Michelle A; Johnson, Travis K; Warr, Coral G; Law, Ruby Hp; Whisstock, James C

2014-04-24

The Drosophila melanogaster Serpin 42 Da gene (previously Serpin 4) encodes a serine protease inhibitor that is capable of remarkable functional diversity through the alternative splicing of four different reactive centre loop exons. Eight protein isoforms of Serpin 42 Da have been identified to date, targeting the protease inhibitor to both different proteases and cellular locations. Biochemical and genetic studies suggest that Serpin 42 Da inhibits target proteases through the classical serpin 'suicide' inhibition mechanism, however the crystal structure of a representative Serpin 42 Da isoform remains to be determined. We report two high-resolution crystal structures of Serpin 42 Da representing the A/B isoforms in the cleaved conformation, belonging to two different space-groups and diffracting to 1.7 Å and 1.8 Å. Structural analysis reveals the archetypal serpin fold, with the major elements of secondary structure displaying significant homology to the vertebrate serpin, neuroserpin. Key residues known to have central roles in the serpin inhibitory mechanism are conserved in both the hinge and shutter regions of Serpin 42 Da. Furthermore, these structures identify important conserved interactions that appear to be of crucial importance in allowing the Serpin 42 Da fold to act as a versatile template for multiple reactive centre loops that have different sequences and protease specificities. In combination with previous biochemical and genetic studies, these structures confirm for the first time that the Serpin 42 Da isoforms are typical inhibitory serpin family members with the conserved serpin fold and inhibitory mechanism. Additionally, these data reveal the remarkable structural plasticity of serpins, whereby the basic fold is harnessed as a template for inhibition of a large spectrum of proteases by reactive centre loop exon 'switching'. This is the first structure of a Drosophila serpin reported to date, and will provide a platform for future mutational

A measurement of the proton’s spin structure function g2 at low Q2

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

Zhu, Pengjia

2015-10-21

JLab E08-027, a measurement of g2p and the longitudinal-transverse (LT) spin polarizability, successfully collected data from March to May, 2012. Nucleon spin structure study has been an active research area, which has attracted a very large effort from both experimentalists and theorists. The spin structure study for the last 2 decades has provided us with many exciting and often surprising results. Recently, new precision results in the low-to-intermediate momentum transfer Q2 region from JLab have provided extensive information on the nucleon structure in the confinement region and the transition region between asymptotic free to confinement. In particular, the extensive comparisonsmore » of experimental results with Chiral Perturbation Theory (the effective theory of QCD at low energy) calculations show general good agreements, but strong disagreement in the case of the neutron LT spin polarizability. This experiment completed the measurements of gp2 and the LT spin polarizability on the proton in the low-to-intermediate Q2 region. The experiment used a polarized proton (NH3) target for the first time in Hall A. Scattered electrons were detected by a pair of Hall A high resolution spectrometer (HRS) with a pair of septum magnets. To avoid too much depolarization of the target, beam current was limited to 50-100 nA during the experiment. Since the existing beam current monitors (BCMs), beam position monitors (BPMs) and calibration methods did not work at such a low current range, new BPM and BCM receivers were designed and used for current condition. A pair of super-harps and a tungsten calorimeter were installed to calibrate the BPMs and BCMs. To compensate for the effect of the 2.5/5T transverse magnet field, two chicane dipole magnets were installed. A pair of slow rasters were installed for the first time in Hall A, combining with a pair of fast raster. The standard Hall A DAQ system and the improved high resolution DAQ system were used to record the

High-resolution crystal structure of copper amine oxidase from Arthrobacter globiformis: assignment of bound diatomic molecules as O2.

PubMed

Murakawa, Takeshi; Hayashi, Hideyuki; Sunami, Tomoko; Kurihara, Kazuo; Tamada, Taro; Kuroki, Ryota; Suzuki, Mamoru; Tanizawa, Katsuyuki; Okajima, Toshihide

2013-12-01

The crystal structure of a copper amine oxidase from Arthrobacter globiformis was determined at 1.08 Å resolution with the use of low-molecular-weight polyethylene glycol (LMW PEG; average molecular weight ∼200) as a cryoprotectant. The final crystallographic R factor and Rfree were 13.0 and 15.0%, respectively. Several molecules of LMW PEG were found to occupy cavities in the protein interior, including the active site, which resulted in a marked reduction in the overall B factor and consequently led to a subatomic resolution structure for a relatively large protein with a monomer molecular weight of ∼70,000. About 40% of the presumed H atoms were observed as clear electron densities in the Fo - Fc difference map. Multiple minor conformers were also identified for many residues. Anisotropic displacement fluctuations were evaluated in the active site, which contains a post-translationally derived quinone cofactor and a Cu atom. Furthermore, diatomic molecules, most likely to be molecular oxygen, are bound to the protein, one of which is located in a region that had previously been proposed as an entry route for the dioxygen substrate from the central cavity of the dimer interface to the active site.

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.

Structure of rat acidic fibroblast growth factor at 1.4 Å resolution

PubMed Central

Kulahin, Nikolaj; Kiselyov, Vladislav; Kochoyan, Arthur; Kristensen, Ole; Kastrup, Jette Sandholm; Berezin, Vladimir; Bock, Elisabeth; Gajhede, Michael

2007-01-01

Fibroblast growth factors (FGFs) constitute a family of 22 structurally related heparin-binding polypeptides that are involved in the regulation of cell growth, survival, differentiation and migration. Here, a 1.4 Å resolution X-ray structure of rat FGF1 is presented. Two molecules are present in the asymmetric unit of the crystal and they coordinate a total of five sulfate ions. The structures of human, bovine and newt FGF1 have been published previously. Human and rat FGF1 are found to have very similar structures. PMID:17277441

Deducing 2D Crystal Structure at the Solid/Liquid Interface with Atomic Resolution by Combined STM and SFG Study

NASA Astrophysics Data System (ADS)

McClelland, Arthur; Ahn, Seokhoon; Matzger, Adam J.; Chen, Zhan

2009-03-01

Supplemented by computed models, Scanning Tunneling Microscopy (STM) can provide detailed structure of 2D crystals formed at the liquid/solid interface with atomic resolution. However, some structural information such as functional group orientations in such 2D crystals needs to be tested experimentally to ensure the accuracy of the deduced structures. Due to the limited sensitivity, many other experimental techniques such as Raman and infrared spectroscopy have not been allowed to provide such structural information of 2D crystals. Here we showed that Sum Frequency Generation Vibrational Spectroscopy (SFG) can measure average orientation of functional groups in such 2D crystals, or physisorbed monolayers, providing key experimental data to aid in the modeling and interpretation of the STM images. The usefulness of combining these two techniques is demonstrated with a phthalate diesters monolayer formed at the 1-phenyloctane/ highly oriented pyrolytic graphite (HOPG) interface. The spatial orientation of the ester C=O of the monolayer was successfully determined using SFG.

Transmission function properties for multi-layered structures: application to super-resolution.

PubMed

Mattiucci, N; D'Aguanno, G; Scalora, M; Bloemer, M J; Sibilia, C

2009-09-28

We discuss the properties of the transmission function in the k-space for a generic multi-layered structure. In particular we analytically demonstrate that a transmission greater than one in the evanescent spectrum (amplification of the evanescent modes) can be directly linked to the guided modes supported by the structure. Moreover we show that the slope of the phase of the transmission function in the propagating spectrum is inversely proportional to the ability of the structure to compensate the diffraction of the propagating modes. We apply these findings to discuss several examples where super-resolution is achieved thanks to the simultaneous availability of the amplification of the evanescent modes and the diffraction compensation of the propagating modes.

Texton-based super-resolution for achieving high spatiotemporal resolution in hybrid camera system

NASA Astrophysics Data System (ADS)

Kamimura, Kenji; Tsumura, Norimichi; Nakaguchi, Toshiya; Miyake, Yoichi

2010-05-01

Many super-resolution methods have been proposed to enhance the spatial resolution of images by using iteration and multiple input images. In a previous paper, we proposed the example-based super-resolution method to enhance an image through pixel-based texton substitution to reduce the computational cost. In this method, however, we only considered the enhancement of a texture image. In this study, we modified this texton substitution method for a hybrid camera to reduce the required bandwidth of a high-resolution video camera. We applied our algorithm to pairs of high- and low-spatiotemporal-resolution videos, which were synthesized to simulate a hybrid camera. The result showed that the fine detail of the low-resolution video can be reproduced compared with bicubic interpolation and the required bandwidth could be reduced to about 1/5 in a video camera. It was also shown that the peak signal-to-noise ratios (PSNRs) of the images improved by about 6 dB in a trained frame and by 1.0-1.5 dB in a test frame, as determined by comparison with the processed image using bicubic interpolation, and the average PSNRs were higher than those obtained by the well-known Freeman’s patch-based super-resolution method. Compared with that of the Freeman’s patch-based super-resolution method, the computational time of our method was reduced to almost 1/10.

High Resolution Analysis of Meiotic Chromosome Structure and Behaviour in Barley (Hordeum vulgare L.)

PubMed Central

Phillips, Dylan; Nibau, Candida; Wnetrzak, Joanna; Jenkins, Glyn

2012-01-01

Reciprocal crossing over and independent assortment of chromosomes during meiosis generate most of the genetic variation in sexually reproducing organisms. In barley, crossovers are confined primarily to distal regions of the chromosomes, which means that a substantial proportion of the genes of this crop rarely, if ever, engage in recombination events. There is potentially much to be gained by redistributing crossovers to more proximal regions, but our ability to achieve this is dependent upon a far better understanding of meiosis in this species. This study explores the meiotic process by describing with unprecedented resolution the early behaviour of chromosomal domains, the progression of synapsis and the structure of the synaptonemal complex (SC). Using a combination of molecular cytogenetics and advanced fluorescence imaging, we show for the first time in this species that non-homologous centromeres are coupled prior to synapsis. We demonstrate that at early meiotic prophase the loading of the SC-associated structural protein ASY1, the cluster of telomeres, and distal synaptic initiation sites occupy the same polarised region of the nucleus. Through the use of advanced 3D image analysis, we show that synapsis is driven predominantly from the telomeres, and that new synaptic initiation sites arise during zygotene. In addition, we identified two different SC configurations through the use of super-resolution 3D structured illumination microscopy (3D-SIM). PMID:22761818

1.55 Å resolution X-ray crystal structure of Rv3902c from Mycobacterium tuberculosis

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

Reddy, Bharat G.; Moates, Derek B.; Kim, Heung-Bok

The 1.55 Å resolution X-ray crystal structure of Rv3902c from M. tuberculosis reveals a novel fold. The crystallographic structure of the Mycobacterium tuberculosis (TB) protein Rv3902c (176 residues; molecular mass of 19.8 kDa) was determined at 1.55 Å resolution. The function of Rv3902c is unknown, although several TB genes involved in bacterial pathogenesis are expressed from the operon containing the Rv3902c gene. The unique structural fold of Rv3902c contains two domains, each consisting of antiparallel β-sheets and α-helices, creating a hand-like binding motif with a small binding pocket in the palm. Structural homology searches reveal that Rv3902c has an overallmore » structure similar to that of the Salmonella virulence-factor chaperone InvB, with an r.m.s.d. for main-chain atoms of 2.3 Å along an aligned domain.« less

DMD-based LED-illumination super-resolution and optical sectioning microscopy.

PubMed

Dan, Dan; Lei, Ming; Yao, Baoli; Wang, Wen; Winterhalder, Martin; Zumbusch, Andreas; Qi, Yujiao; Xia, Liang; Yan, Shaohui; Yang, Yanlong; Gao, Peng; Ye, Tong; Zhao, Wei

2013-01-01

Super-resolution three-dimensional (3D) optical microscopy has incomparable advantages over other high-resolution microscopic technologies, such as electron microscopy and atomic force microscopy, in the study of biological molecules, pathways and events in live cells and tissues. We present a novel approach of structured illumination microscopy (SIM) by using a digital micromirror device (DMD) for fringe projection and a low-coherence LED light for illumination. The lateral resolution of 90 nm and the optical sectioning depth of 120 μm were achieved. The maximum acquisition speed for 3D imaging in the optical sectioning mode was 1.6×10(7) pixels/second, which was mainly limited by the sensitivity and speed of the CCD camera. In contrast to other SIM techniques, the DMD-based LED-illumination SIM is cost-effective, ease of multi-wavelength switchable and speckle-noise-free. The 2D super-resolution and 3D optical sectioning modalities can be easily switched and applied to either fluorescent or non-fluorescent specimens.

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.

Synthesis and structure resolution of RbLaF4.

PubMed

Rollet, Anne-Laure; Allix, Mathieu; Veron, Emmanuel; Deschamps, Michael; Montouillout, Valérie; Suchomel, Matthew R; Suard, Emmanuelle; Barre, Maud; Ocaña, Manuel; Sadoc, Aymeric; Boucher, Florent; Bessada, Catherine; Massiot, Dominique; Fayon, Franck

2012-02-20

The synthesis and structure resolution of RbLaF(4) are described. RbLaF(4) is synthesized by solid-state reaction between RbF and LaF(3) at 425 °C under a nonoxidizing atmosphere. Its crystal structure has been resolved by combining neutron and synchrotron powder diffraction data refinements (Pnma,a = 6.46281(2) Å, b = 3.86498(1) Å, c = 16.17629(4) Å, Z = 4). One-dimensional (87)Rb, (139)La, and (19)F MAS NMR spectra have been recorded and are in agreement with the proposed structural model. Assignment of the (19)F resonances is performed on the basis of both (19)F-(139)La J-coupling multiplet patterns observed in a heteronuclear DQ-filtered J-resolved spectrum and (19)F-(87)Rb HMQC MAS experiments. DFT calculations of both the (19)F isotropic chemical shieldings and the (87)Rb, (139)La electric field gradient tensors using the GIPAW and PAW methods implemented in the CASTEP code are in good agreement with the experimental values and support the proposed structural model. Finally, the conductivity of RbLaF(4) and luminescence properties of Eu-doped LaRbF(4) are investigated.

Super-resolution structured illumination in optically thick specimens without fluorescent tagging

NASA Astrophysics Data System (ADS)

Hoffman, Zachary R.; DiMarzio, Charles A.

2017-11-01

This research extends the work of Hoffman et al. to provide both sectioning and super-resolution using random patterns within thick specimens. Two methods of processing structured illumination in reflectance have been developed without the need for a priori knowledge of either the optical system or the modulation patterns. We explore the use of two deconvolution algorithms that assume either Gaussian or sparse priors. This paper will show that while both methods accomplish their intended objective, the sparse priors method provides superior resolution and contrast against all tested targets, providing anywhere from ˜1.6× to ˜2× resolution enhancement. The methods developed here can reasonably be implemented to work without a priori knowledge about the patterns or point spread function. Further, all experiments are run using an incoherent light source, unknown random modulation patterns, and without the use of fluorescent tagging. These additional modifications are challenging, but the generalization of these methods makes them prime candidates for clinical application, providing super-resolved noninvasive sectioning in vivo.

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

Laser ablated hydantoin: A high resolution rotational study.

PubMed

Alonso, Elena R; Kolesniková, Lucie; Alonso, José L

2017-09-28

Laser ablation techniques coupled with broadband and narrowband Fourier transform microwave spectroscopies have allowed the high resolution rotational study of solid hydantoin, an important target in astrochemistry as a possible precursor of glycine. The complicated hyperfine structure arising from the presence of two 14 N nuclei in non-equivalent positions has been resolved and interpreted in terms of the nuclear quadrupole coupling interactions. The results reported in this work provide a solid base for the interstellar searches of hydantoin in the astrophysical surveys. The values of the nuclear quadrupole coupling constants have been also discussed in terms of the electronic environment around the respective nitrogen atom.

Subnanometre-resolution structure of the doublet microtubule reveals new classes of microtubule-associated proteins

PubMed Central

Ichikawa, Muneyoshi; Liu, Dinan; Kastritis, Panagiotis L.; Basu, Kaustuv; Hsu, Tzu Chin; Yang, Shunkai; Bui, Khanh Huy

2017-01-01

Cilia are ubiquitous, hair-like appendages found in eukaryotic cells that carry out functions of cell motility and sensory reception. Cilia contain an intriguing cytoskeletal structure, termed the axoneme that consists of nine doublet microtubules radially interlinked and longitudinally organized in multiple specific repeat units. Little is known, however, about how the axoneme allows cilia to be both actively bendable and sturdy or how it is assembled. To answer these questions, we used cryo-electron microscopy to structurally analyse several of the repeating units of the doublet at sub-nanometre resolution. This structural detail enables us to unambiguously assign α- and β-tubulins in the doublet microtubule lattice. Our study demonstrates the existence of an inner sheath composed of different kinds of microtubule inner proteins inside the doublet that likely stabilizes the structure and facilitates the specific building of the B-tubule. PMID:28462916

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.

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.

X-ray structure of imidazolonepropionase from Agrobacterium tumefaciens at 1.87 Å resolution

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

Tyagi, Rajiv; Kumaran, Desigan; Burley, Stephen K.

2010-01-12

Histidine degradation in Agrobacterium tumefaciens involves four enzymes, including histidase (EC 4.3.1.3), urocanase (EC 4.2.1.49), imidazolonepropionase (EC 3.5.2.7), and N-formylglutamate amidohydrolase (EC 3.5.3.8). The third enzyme of the pathway, imidazolone-propionase, a 45.6 kDa protein, catalyzes conversion of imidazolone-5-propanoate to N-forminio-L-glutamate. Initial studies of the role of imidazolonepropionase in histidine degradation were published in 1953. Subsequent publications have been limited to enzyme kinetics, crystallization, and a recently reported structure determination. The imidazolonepropionases are members of metallodepenent-hydrolases (or amidohydroase) superfamily, which includs ureases, adenosine deaminases, phosphotriesterases, dihydroorotases, allantoinases, hydantoinases, adenine and cytosine deaminases, imidazolonepropionases, aryldial-kylphosphatases, chlorohydrolases, and formylmethanofuran dehydroases. Proteins belonging tomore » this large group share a common three-dimensional structural motif (an eightfold {alpha}/{beta} or TIM barrel) with similar active sites. Most superfamily members also share a conserved metal binding site, involving four histidine residues and one aspartic acid. Imidazolonepropionase is one of the targets selected for X-ray crystallpgrahpic structure determination by the New York Structural GenomiX Research Consortium (NYSGXRC) Target ID: 9252b to correlate the structure function relationship of poorly studied by important enzyme. Here they report the crystal structure of imidazolonepropionase from Agrobacterium tumefaciens determined at 1.87 {angstrom} resolution.« less

High-resolution TEM Studies of Carbon Nanotubes and Catalyst Nanoparticles Produced During CVD from Metal Multilayer Films

NASA Astrophysics Data System (ADS)

Howe, Jane Y.; Puretzky, Alex A.; Geohegan, David B.; Cui, Hongtao; Eres, Varela; Maria, Alex A.; Lowndes, Douglas H.

2003-03-01

The structure of single-wall and multiwall carbon nanotubes and associated metal catalyst nanoparticles produced during chemical vapor deposition from multilayered metal films deposited on Si and Mo substrates were studied by high-resolution TEM and EDS. Electron beam-evaporated metal multilayer films (e.g. Al-Fe-Mo, typically 11-50 nm total thickness) roughen upon heat treatment to form a variety of catalyst particle sizes suitable for carbon nanotube growth by chemical vapor deposition using acetylene, hydrogen, and argon flow gases. This study investigates these nanoparticles, the type of nanotubes grown, their wall, tip, and basal structures, as well as the associated amounts of amorphous carbon deposited on their walls in different temperature and pressure ranges. Mixtures of SWNT and MWNT are found even for low growth temperatures (650-700 C), while rapid growth of vertically-aligned multiwall nanotubes (VA-MWNTs) predominate in a narrow temperature range at a given pressure. Arrested growth experiments were performed to determine the time periods for SWNT vs. MWNT growth. The nature of the catalyst nanoparticles, their support structure, and insights on the mechanisms of growth will be discussed.

The Structure of Carbonic Anhydrase IX Is Adapted for Low-pH Catalysis.

PubMed

Mahon, Brian P; Bhatt, Avni; Socorro, Lilien; Driscoll, Jenna M; Okoh, Cynthia; Lomelino, Carrie L; Mboge, Mam Y; Kurian, Justin J; Tu, Chingkuang; Agbandje-McKenna, Mavis; Frost, Susan C; McKenna, Robert

2016-08-23

Human carbonic anhydrase IX (hCA IX) expression in many cancers is associated with hypoxic tumors and poor patient outcome. Inhibitors of hCA IX have been used as anticancer agents with some entering Phase I clinical trials. hCA IX is transmembrane protein whose catalytic domain faces the extracellular tumor milieu, which is typically associated with an acidic microenvironment. Here, we show that the catalytic domain of hCA IX (hCA IX-c) exhibits the necessary biochemical and biophysical properties that allow for low pH stability and activity. Furthermore, the unfolding process of hCA IX-c appears to be reversible, and its catalytic efficiency is thought to be correlated directly with its stability between pH 3.0 and 8.0 but not above pH 8.0. To rationalize this, we determined the X-ray crystal structure of hCA IX-c to 1.6 Å resolution. Insights from this study suggest an understanding of hCA IX-c stability and activity in low-pH tumor microenvironments and may be applicable to determining pH-related effects on enzymes.

Probing long-range structural order in SnPc/Ag(111) by umklapp process assisted low-energy angle-resolved photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Jauernik, Stephan; Hein, Petra; Gurgel, Max; Falke, Julian; Bauer, Michael

2018-03-01

Laser-based angle-resolved photoelectron spectroscopy is performed on tin-phthalocyanine (SnPc) adsorbed on silver Ag(111). Upon adsorption of SnPc, strongly dispersing bands are observed which are identified as secondary Mahan cones formed by surface umklapp processes acting on photoelectrons from the silver substrate as they transit through the ordered adsorbate layer. We show that the photoemission data carry quantitative structural information on the adsorbate layer similar to what can be obtained from a conventional low-energy electron diffraction (LEED) study. More specifically, we compare photoemission data and LEED data probing an incommensurate-to-commensurate structural phase transition of the adsorbate layer. Based on our results we propose that Mahan-cone spectroscopy operated in a pump-probe configuration can be used in the future to probe structural dynamics at surfaces with a temporal resolution in the sub-100-fs regime.

A Virtual Study of Grid Resolution on Experiments of a Highly-Resolved Turbulent Plume

NASA Astrophysics Data System (ADS)

Maisto, Pietro M. F.; Marshall, Andre W.; Gollner, Michael J.; Fire Protection Engineering Department Collaboration