Robust membrane detection based on tensor voting for electron tomography.

PubMed

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

2014-04-01

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

Moment inference from tomograms

USGS Publications Warehouse

Day-Lewis, F. D.; Chen, Y.; Singha, K.

2007-01-01

Time-lapse geophysical tomography can provide valuable qualitative insights into hydrologic transport phenomena associated with aquifer dynamics, tracer experiments, and engineered remediation. Increasingly, tomograms are used to infer the spatial and/or temporal moments of solute plumes; these moments provide quantitative information about transport processes (e.g., advection, dispersion, and rate-limited mass transfer) and controlling parameters (e.g., permeability, dispersivity, and rate coefficients). The reliability of moments calculated from tomograms is, however, poorly understood because classic approaches to image appraisal (e.g., the model resolution matrix) are not directly applicable to moment inference. Here, we present a semi-analytical approach to construct a moment resolution matrix based on (1) the classic model resolution matrix and (2) image reconstruction from orthogonal moments. Numerical results for radar and electrical-resistivity imaging of solute plumes demonstrate that moment values calculated from tomograms depend strongly on plume location within the tomogram, survey geometry, regularization criteria, and measurement error. Copyright 2007 by the American Geophysical Union.

Moment inference from tomograms

USGS Publications Warehouse

Day-Lewis, Frederick D.; Chen, Yongping; Singha, Kamini

2007-01-01

Time-lapse geophysical tomography can provide valuable qualitative insights into hydrologic transport phenomena associated with aquifer dynamics, tracer experiments, and engineered remediation. Increasingly, tomograms are used to infer the spatial and/or temporal moments of solute plumes; these moments provide quantitative information about transport processes (e.g., advection, dispersion, and rate-limited mass transfer) and controlling parameters (e.g., permeability, dispersivity, and rate coefficients). The reliability of moments calculated from tomograms is, however, poorly understood because classic approaches to image appraisal (e.g., the model resolution matrix) are not directly applicable to moment inference. Here, we present a semi-analytical approach to construct a moment resolution matrix based on (1) the classic model resolution matrix and (2) image reconstruction from orthogonal moments. Numerical results for radar and electrical-resistivity imaging of solute plumes demonstrate that moment values calculated from tomograms depend strongly on plume location within the tomogram, survey geometry, regularization criteria, and measurement error.

Morphologic changes of the nasal cavity induced by rapid maxillary expansion: a study on 3-dimensional computed tomography models.

PubMed

Haralambidis, Adam; Ari-Demirkaya, Arzu; Acar, Ahu; Küçükkeleş, Nazan; Ateş, Mustafa; Ozkaya, Selin

2009-12-01

The aim of this study was to evaluate the effect of rapid maxillary expansion on the volume of the nasal cavity by using computed tomography. The sample consisted of 24 patients (10 boys, 14 girls) in the permanent dentition who had maxillary constriction and bilateral posterior crossbite. Ten patients had skeletal Class I and 14 had Class II relationships. Skeletal maturity was assessed with the modified cervical vertebral maturation method. Computed tomograms were taken before expansion and at the end of the 3-month retention period, after active expansion. The tomograms were analyzed by Mimics software (version 10.11, Materialise Medical Co, Leuven, Belgium) to reconstruct 3-dimensional images and calculate the volume of the nasal cavities before and after expansion. A significant (P = 0.000) average increase of 11.3% in nasal volume was found. Sex, growth, and skeletal relationship did not influence measurements or response to treatment. A significant difference was found in the volume increase between the Class I and Class II patients, but it was attributed to the longer expansion period of the latter. Therefore, rapid maxillary expansion induces a significant average increase of the nasal volume and consequently can increase nasal permeability and establish a predominant nasal respiration pattern.

Radiology case of the month. Abnormally dilated arteries in an asymptomatic male. RADIOLOGIC DIAGNOSIS: Aortic coarctation. There is narrowing in the region of the aortic isthmus (arrows, Figures 2 and 4). The extent of collateral arterial dilation (arrows, Figures 1 and 3) suggests this to be a hemodynamically significant finding.

PubMed

Mabry, Christian; Yandle, Gretchen; Erbil, Jen; Happel, Kyle; Neitzschman, Harold R

2014-01-01

A 61-year-old male with a past medical history of chronic, uncontrolled hypertension received a non-contrasted computed tomogram (CT) of the chest and abdomen to investigate for possible Conn syndrome. This noncontrast study showed some areas of nodularity around the vertebral bodies bilaterally and extending into the posterior mediastinal region. A CT of the chest with intravenous contrast, and 3D reconstruction were then obtained.

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

PubMed

Houben, L; Bar Sadan, M

2011-01-01

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

Medical ultrasonic tomographic system

NASA Technical Reports Server (NTRS)

Heyser, R. C.; Lecroissette, D. H.; Nathan, R.; Wilson, R. L.

1977-01-01

An electro-mechanical scanning assembly was designed and fabricated for the purpose of generating an ultrasound tomogram. A low cost modality was demonstrated in which analog instrumentation methods formed a tomogram on photographic film. Successful tomogram reconstructions were obtained on in vitro test objects by using the attenuation of the fist path ultrasound signal as it passed through the test object. The nearly half century tomographic methods of X-ray analysis were verified as being useful for ultrasound imaging.

Hydrologic Process Regularization for Improved Geoelectrical Monitoring of a Lab-Scale Saline Tracer Experiment

NASA Astrophysics Data System (ADS)

Oware, E. K.; Moysey, S. M.

2016-12-01

Regularization stabilizes the geophysical imaging problem resulting from sparse and noisy measurements that render solutions unstable and non-unique. Conventional regularization constraints are, however, independent of the physics of the underlying process and often produce smoothed-out tomograms with mass underestimation. Cascaded time-lapse (CTL) is a widely used reconstruction technique for monitoring wherein a tomogram obtained from the background dataset is employed as starting model for the inversion of subsequent time-lapse datasets. In contrast, a proper orthogonal decomposition (POD)-constrained inversion framework enforces physics-based regularization based upon prior understanding of the expected evolution of state variables. The physics-based constraints are represented in the form of POD basis vectors. The basis vectors are constructed from numerically generated training images (TIs) that mimic the desired process. The target can be reconstructed from a small number of selected basis vectors, hence, there is a reduction in the number of inversion parameters compared to the full dimensional space. The inversion involves finding the optimal combination of the selected basis vectors conditioned on the geophysical measurements. We apply the algorithm to 2-D lab-scale saline transport experiments with electrical resistivity (ER) monitoring. We consider two transport scenarios with one and two mass injection points evolving into unimodal and bimodal plume morphologies, respectively. The unimodal plume is consistent with the assumptions underlying the generation of the TIs, whereas bimodality in plume morphology was not conceptualized. We compare difference tomograms retrieved from POD with those obtained from CTL. Qualitative comparisons of the difference tomograms with images of their corresponding dye plumes suggest that POD recovered more compact plumes in contrast to those of CTL. While mass recovery generally deteriorated with increasing number of time-steps, POD outperformed CTL in terms of mass recovery accuracy rates. POD is computationally superior requiring only 2.5 mins to complete each inversion compared to 3 hours for CTL to do the same.

The Dynamo package for tomography and subtomogram averaging: components for MATLAB, GPU computing and EC2 Amazon Web Services

PubMed Central

Castaño-Díez, Daniel

2017-01-01

Dynamo is a package for the processing of tomographic data. As a tool for subtomogram averaging, it includes different alignment and classification strategies. Furthermore, its data-management module allows experiments to be organized in groups of tomograms, while offering specialized three-dimensional tomographic browsers that facilitate visualization, location of regions of interest, modelling and particle extraction in complex geometries. Here, a technical description of the package is presented, focusing on its diverse strategies for optimizing computing performance. Dynamo is built upon mbtools (middle layer toolbox), a general-purpose MATLAB library for object-oriented scientific programming specifically developed to underpin Dynamo but usable as an independent tool. Its structure intertwines a flexible MATLAB codebase with precompiled C++ functions that carry the burden of numerically intensive operations. The package can be delivered as a precompiled standalone ready for execution without a MATLAB license. Multicore parallelization on a single node is directly inherited from the high-level parallelization engine provided for MATLAB, automatically imparting a balanced workload among the threads in computationally intense tasks such as alignment and classification, but also in logistic-oriented tasks such as tomogram binning and particle extraction. Dynamo supports the use of graphical processing units (GPUs), yielding considerable speedup factors both for native Dynamo procedures (such as the numerically intensive subtomogram alignment) and procedures defined by the user through its MATLAB-based GPU library for three-dimensional operations. Cloud-based virtual computing environments supplied with a pre-installed version of Dynamo can be publicly accessed through the Amazon Elastic Compute Cloud (EC2), enabling users to rent GPU computing time on a pay-as-you-go basis, thus avoiding upfront investments in hardware and longterm software maintenance. PMID:28580909

The Dynamo package for tomography and subtomogram averaging: components for MATLAB, GPU computing and EC2 Amazon Web Services.

PubMed

Castaño-Díez, Daniel

2017-06-01

Dynamo is a package for the processing of tomographic data. As a tool for subtomogram averaging, it includes different alignment and classification strategies. Furthermore, its data-management module allows experiments to be organized in groups of tomograms, while offering specialized three-dimensional tomographic browsers that facilitate visualization, location of regions of interest, modelling and particle extraction in complex geometries. Here, a technical description of the package is presented, focusing on its diverse strategies for optimizing computing performance. Dynamo is built upon mbtools (middle layer toolbox), a general-purpose MATLAB library for object-oriented scientific programming specifically developed to underpin Dynamo but usable as an independent tool. Its structure intertwines a flexible MATLAB codebase with precompiled C++ functions that carry the burden of numerically intensive operations. The package can be delivered as a precompiled standalone ready for execution without a MATLAB license. Multicore parallelization on a single node is directly inherited from the high-level parallelization engine provided for MATLAB, automatically imparting a balanced workload among the threads in computationally intense tasks such as alignment and classification, but also in logistic-oriented tasks such as tomogram binning and particle extraction. Dynamo supports the use of graphical processing units (GPUs), yielding considerable speedup factors both for native Dynamo procedures (such as the numerically intensive subtomogram alignment) and procedures defined by the user through its MATLAB-based GPU library for three-dimensional operations. Cloud-based virtual computing environments supplied with a pre-installed version of Dynamo can be publicly accessed through the Amazon Elastic Compute Cloud (EC2), enabling users to rent GPU computing time on a pay-as-you-go basis, thus avoiding upfront investments in hardware and longterm software maintenance.

Guide-star-based computational adaptive optics for broadband interferometric tomography

PubMed Central

Adie, Steven G.; Shemonski, Nathan D.; Graf, Benedikt W.; Ahmad, Adeel; Scott Carney, P.; Boppart, Stephen A.

2012-01-01

We present a method for the numerical correction of optical aberrations based on indirect sensing of the scattered wavefront from point-like scatterers (“guide stars”) within a three-dimensional broadband interferometric tomogram. This method enables the correction of high-order monochromatic and chromatic aberrations utilizing guide stars that are revealed after numerical compensation of defocus and low-order aberrations of the optical system. Guide-star-based aberration correction in a silicone phantom with sparse sub-resolution-sized scatterers demonstrates improvement of resolution and signal-to-noise ratio over a large isotome. Results in highly scattering muscle tissue showed improved resolution of fine structure over an extended volume. Guide-star-based computational adaptive optics expands upon the use of image metrics for numerically optimizing the aberration correction in broadband interferometric tomography, and is analogous to phase-conjugation and time-reversal methods for focusing in turbid media. PMID:23284179

An orthodontic technique for minimally invasive extraction of impacted lower third molar.

PubMed

Ma, Zhi-Gui; Xie, Qian-Yang; Yang, Chi; Xu, Guang-Zhou; Cai, Xie-Yi; Li, Jie-Yan

2013-08-01

To present a novel orthodontic approach for minimally invasive extraction of impacted mandibular third molars (M3s) close to the inferior alveolar nerve (IAN). Eight patients (8 M3s) requiring extraction of M3s were included in this study; there were 2 cases of horizontal impaction, 4 of mesioangular impaction, and 2 of vertical impaction. Cone-beam computed tomogram showed that the roots of impacted M3s in 2 cases interrupted the cortices of the mandibular canal, and those in the other 6 cases were very close to the IAN. Orthodontic treatment was performed in this study. The crowns of 5 impacted teeth were surgically exposed before the application of the orthodontic device, whereas bonding was performed directly to the occlusal surface of the other 3 M3s, which had partially erupted. The opposing maxillary M3s were removed in 3 cases. One-step orthodontic extraction was applied to vertically impacted M3s and 2-step treatment was applied to horizontally or mesioangularly impacted M3s. Success was defined as the separation of the impacted tooth from the IAN as visualized on cone-beam computed tomogram. After orthodontic treatment, all impacted M3s were extruded and separated from the IAN (mean, 6.6 months; range, 4 to 10 months), without any neurologic consequences. The average time of extraction was 5 minutes. In all 8 cases, new bone formation occurred distal to the adjacent second molar. This orthodontic technique may be a minimally invasive approach for the extraction of impacted M3s adjacent to the IAN, with a decreased risk of paresthesias and with osteoperiodontal advantages. Copyright © 2013 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

Optimal and fast rotational alignment of volumes with missing data in Fourier space.

PubMed

Shatsky, Maxim; Arbelaez, Pablo; Glaeser, Robert M; Brenner, Steven E

2013-11-01

Electron tomography of intact cells has the potential to reveal the entire cellular content at a resolution corresponding to individual macromolecular complexes. Characterization of macromolecular complexes in tomograms is nevertheless an extremely challenging task due to the high level of noise, and due to the limited tilt angle that results in missing data in Fourier space. By identifying particles of the same type and averaging their 3D volumes, it is possible to obtain a structure at a more useful resolution for biological interpretation. Currently, classification and averaging of sub-tomograms is limited by the speed of computational methods that optimize alignment between two sub-tomographic volumes. The alignment optimization is hampered by the fact that the missing data in Fourier space has to be taken into account during the rotational search. A similar problem appears in single particle electron microscopy where the random conical tilt procedure may require averaging of volumes with a missing cone in Fourier space. We present a fast implementation of a method guaranteed to find an optimal rotational alignment that maximizes the constrained cross-correlation function (cCCF) computed over the actual overlap of data in Fourier space. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Assessing the resolution-dependent utility of tomograms for geostatistics

USGS Publications Warehouse

Day-Lewis, F. D.; Lane, J.W.

2004-01-01

Geophysical tomograms are used increasingly as auxiliary data for geostatistical modeling of aquifer and reservoir properties. The correlation between tomographic estimates and hydrogeologic properties is commonly based on laboratory measurements, co-located measurements at boreholes, or petrophysical models. The inferred correlation is assumed uniform throughout the interwell region; however, tomographic resolution varies spatially due to acquisition geometry, regularization, data error, and the physics underlying the geophysical measurements. Blurring and inversion artifacts are expected in regions traversed by few or only low-angle raypaths. In the context of radar traveltime tomography, we derive analytical models for (1) the variance of tomographic estimates, (2) the spatially variable correlation with a hydrologic parameter of interest, and (3) the spatial covariance of tomographic estimates. Synthetic examples demonstrate that tomograms of qualitative value may have limited utility for geostatistics; moreover, the imprint of regularization may preclude inference of meaningful spatial statistics from tomograms.

Applying petrophysical models to radar travel time and electrical resistivity tomograms: Resolution-dependent limitations

USGS Publications Warehouse

Day-Lewis, F. D.; Singha, K.; Binley, A.M.

2005-01-01

Geophysical imaging has traditionally provided qualitative information about geologic structure; however, there is increasing interest in using petrophysical models to convert tomograms to quantitative estimates of hydrogeologic, mechanical, or geochemical parameters of interest (e.g., permeability, porosity, water content, and salinity). Unfortunately, petrophysical estimation based on tomograms is complicated by limited and variable image resolution, which depends on (1) measurement physics (e.g., electrical conduction or electromagnetic wave propagation), (2) parameterization and regularization, (3) measurement error, and (4) spatial variability. We present a framework to predict how core-scale relations between geophysical properties and hydrologic parameters are altered by the inversion, which produces smoothly varying pixel-scale estimates. We refer to this loss of information as "correlation loss." Our approach upscales the core-scale relation to the pixel scale using the model resolution matrix from the inversion, random field averaging, and spatial statistics of the geophysical property. Synthetic examples evaluate the utility of radar travel time tomography (RTT) and electrical-resistivity tomography (ERT) for estimating water content. This work provides (1) a framework to assess tomograms for geologic parameter estimation and (2) insights into the different patterns of correlation loss for ERT and RTT. Whereas ERT generally performs better near boreholes, RTT performs better in the interwell region. Application of petrophysical models to the tomograms in our examples would yield misleading estimates of water content. Although the examples presented illustrate the problem of correlation loss in the context of near-surface geophysical imaging, our results have clear implications for quantitative analysis of tomograms for diverse geoscience applications. Copyright 2005 by the American Geophysical Union.

[Recurrent pulmonary infarction associated with familial protein S deficiency type III].

PubMed

Ide, K; Chida, K; Suda, T; Imokawa, S; Tsukamoto, K; Todate, A; Sato, J; Yonekawa, O; Nakamura, H

1999-05-01

A 38-year-old woman was admitted to our hospital because of recurrent chest pain and fever. Chest X-ray films and computed tomograms showed subpleural consolidation containing small cavity-like opacities. Open lung biopsy revealed non-infectious abscess and vessels with organizing thrombus. The patient was given a diagnosis of pulmonary infarction due to the existence of deep venous thrombosis. Coagulation studies demonstrated that she had decreased plasma protein S activity, whereas her free and total protein S antigen levels were normal. Because her mother and maternal uncle and aunt also demonstrated decreased protein S activity with normal plasma protein S antigen levels, the patient was considered to be affected by familial protein S deficiency type III.

Digital Longitudinal Tomosynthesis

NASA Astrophysics Data System (ADS)

Rimkus, Daniel Steven

1985-12-01

The purpose of this dissertation was to investigate the clinical utility of digital longitudinal tomosynthesis in radiology. By acquiring a finite group of digital images during a longitudinal tomographic exposure, and processing these images, tomographic planes, other than the fulcrum plane, can be reconstructed. This process is now termed "tomosynthesis". A prototype system utilizing this technique was developed. Both phantom and patient studies were done with this system. The phantom studies were evaluated by subjective, visual criterion and by quantitative analysis of edge sharpness and noise in the reconstructions. Two groups of patients and one volunteer were studied. The first patient group consisted of 8 patients undergoing intravenous urography (IVU). These patients had digital tomography and film tomography of the abdomen. The second patient group consisted of 4 patients with lung cancer admitted to the hospital for laser resection of endobronchial tumor. These patients had mediastinal digital tomograms to evaluate the trachea and mainstem bronchi. The knee of one volunteer was imaged by film tomography and digital tomography. The results of the phantom studies showed that the digital reconstructions accurately produced images of the desired planes. The edge sharpness of the reconstructions approached that of the acquired images. Adequate reconstructions were achieved with as few as 5 images acquired during the exposure, with the quality of the reconstructions improving as the number of images acquired increased. The IVU patients' digital studies had less contrast and spatial resolution than the film tomograms. The single renal lesion visible on the film tomograms was also visible in the digital images. The digital mediastinal studies were felt by several radiologists to be superior to a standard chest xray in evaluating the airways. The digital images of the volunteer's knee showed many of the same anatomic features as the film tomogram, but the digital images had less spatial and contrast resolution. With the equipment improvements discussed in the thesis, digital tomography may have an important role in radiology.

Derivation of site-specific relationships between hydraulic parameters and p-wave velocities based on hydraulic and seismic tomography

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

Brauchler, R.; Doetsch, J.; Dietrich, P.

2012-01-10

In this study, hydraulic and seismic tomographic measurements were used to derive a site-specific relationship between the geophysical parameter p-wave velocity and the hydraulic parameters, diffusivity and specific storage. Our field study includes diffusivity tomograms derived from hydraulic travel time tomography, specific storage tomograms, derived from hydraulic attenuation tomography, and p-wave velocity tomograms, derived from seismic tomography. The tomographic inversion was performed in all three cases with the SIRT (Simultaneous Iterative Reconstruction Technique) algorithm, using a ray tracing technique with curved trajectories. The experimental set-up was designed such that the p-wave velocity tomogram overlaps the hydraulic tomograms by half. Themore » experiments were performed at a wellcharacterized sand and gravel aquifer, located in the Leine River valley near Göttingen, Germany. Access to the shallow subsurface was provided by direct-push technology. The high spatial resolution of hydraulic and seismic tomography was exploited to derive representative site-specific relationships between the hydraulic and geophysical parameters, based on the area where geophysical and hydraulic tests were performed. The transformation of the p-wave velocities into hydraulic properties was undertaken using a k-means cluster analysis. Results demonstrate that the combination of hydraulic and geophysical tomographic data is a promising approach to improve hydrogeophysical site characterization.« less

Near‐surface void detection using a seismic landstreamer and horizontal velocity and attenuation tomography

USGS Publications Warehouse

Buckley, Sean F.; Lane, John W.

2012-01-01

The detection and characterization of subsurface voids plays an important role in the study of karst formations and clandestine tunnels. Horizontal velocity and attenuation tomography (HVAT) using offset‐fan shooting and a towed seismic land streamer is a simple, rapid, minimally invasive method that shows promise for detecting near‐surface voids and providing information on the orientation of linear voids. HVAT surveys were conducted over a known subsurface steam tunnel on the University of Connecticut Depot Campus, Storrs, Connecticut. First‐arrival travel‐time and amplitude data were used to produce two‐dimensional (2D) horizontal (map view) velocity and attenuation tomograms. In addition, attenuation tomograms were produced based on normalized total trace energy (TTE). Both the velocity and TTE attenuation tomograms depict an anomaly consistent with the location and orientation of the known tunnel; the TTE method, however, requires significantly less processing time, and therefore may provide a path forward to semi‐automated, near real‐time detection of near‐surface voids. Further study is needed to assess the utility of the HVAT method to detect deeper voids and the effects of a more complex geology on HVAT results.

Automated tilt series alignment and tomographic reconstruction in IMOD.

PubMed

Mastronarde, David N; Held, Susannah R

2017-02-01

Automated tomographic reconstruction is now possible in the IMOD software package, including the merging of tomograms taken around two orthogonal axes. Several developments enable the production of high-quality tomograms. When using fiducial markers for alignment, the markers to be tracked through the series are chosen automatically; if there is an excess of markers available, a well-distributed subset is selected that is most likely to track well. Marker positions are refined by applying an edge-enhancing Sobel filter, which results in a 20% improvement in alignment error for plastic-embedded samples and 10% for frozen-hydrated samples. Robust fitting, in which outlying points are given less or no weight in computing the fitting error, is used to obtain an alignment solution, so that aberrant points from the automated tracking can have little effect on the alignment. When merging two dual-axis tomograms, the alignment between them is refined from correlations between local patches; a measure of structure was developed so that patches with insufficient structure to give accurate correlations can now be excluded automatically. We have also developed a script for running all steps in the reconstruction process with a flexible mechanism for setting parameters, and we have added a user interface for batch processing of tilt series to the Etomo program in IMOD. Batch processing is fully compatible with interactive processing and can increase efficiency even when the automation is not fully successful, because users can focus their effort on the steps that require manual intervention. Copyright © 2016 Elsevier Inc. All rights reserved.

An Energy-Based Three-Dimensional Segmentation Approach for the Quantitative Interpretation of Electron Tomograms

PubMed Central

Bartesaghi, Alberto; Sapiro, Guillermo; Subramaniam, Sriram

2006-01-01

Electron tomography allows for the determination of the three-dimensional structures of cells and tissues at resolutions significantly higher than that which is possible with optical microscopy. Electron tomograms contain, in principle, vast amounts of information on the locations and architectures of large numbers of subcellular assemblies and organelles. The development of reliable quantitative approaches for the analysis of features in tomograms is an important problem, and a challenging prospect due to the low signal-to-noise ratios that are inherent to biological electron microscopic images. This is, in part, a consequence of the tremendous complexity of biological specimens. We report on a new method for the automated segmentation of HIV particles and selected cellular compartments in electron tomograms recorded from fixed, plastic-embedded sections derived from HIV-infected human macrophages. Individual features in the tomogram are segmented using a novel robust algorithm that finds their boundaries as global minimal surfaces in a metric space defined by image features. The optimization is carried out in a transformed spherical domain with the center an interior point of the particle of interest, providing a proper setting for the fast and accurate minimization of the segmentation energy. This method provides tools for the semi-automated detection and statistical evaluation of HIV particles at different stages of assembly in the cells and presents opportunities for correlation with biochemical markers of HIV infection. The segmentation algorithm developed here forms the basis of the automated analysis of electron tomograms and will be especially useful given the rapid increases in the rate of data acquisition. It could also enable studies of much larger data sets, such as those which might be obtained from the tomographic analysis of HIV-infected cells from studies of large populations. PMID:16190467

Non-destructive measurement of soil liquefaction density change by crosshole radar tomography, Treasure Island, California

USGS Publications Warehouse

Kayen, Robert E.; Barnhardt, Walter A.; Ashford, Scott; Rollins, Kyle

2000-01-01

A ground penetrating radar (GPR) experiment at the Treasure Island Test Site [TILT] was performed to non-destructively image the soil column for changes in density prior to, and following, a liquefaction event. The intervening liquefaction was achieved by controlled blasting. A geotechnical borehole radar technique was used to acquire high-resolution 2-D radar velocity data. This method of non-destructive site characterization uses radar trans-illumination surveys through the soil column and tomographic data manipulation techniques to construct radar velocity tomograms, from which averaged void ratios can be derived at 0.25 - 0.5m pixel footprints. Tomograms of void ratio were constructed through the relation between soil porosity and dielectric constant. Both pre- and post-blast tomograms were collected and indicate that liquefaction related densification occurred at the site. Volumetric strains estimated from the tomograms correlate well with the observed settlement at the site. The 2-D imagery of void ratio can serve as high-resolution data layers for numerical site response analysis.

Center-of-Mass Tomography and Wigner Function for Multimode Photon States

NASA Astrophysics Data System (ADS)

Dudinets, Ivan V.; Man'ko, Vladimir I.

2018-06-01

Tomographic probability representation of multimode electromagnetic field states in the scheme of center-of-mass tomography is reviewed. Both connection of the field state Wigner function and observable Weyl symbols with the center-of-mass tomograms as well as connection of the Grönewold kernel with the center-of-mass tomographic kernel determining the noncommutative product of the tomograms are obtained. The dual center-of-mass tomogram of the photon states are constructed and the dual tomographic kernel is obtained. The models of other generalized center-of-mass tomographies are discussed. Example of two-mode even and odd Schrödinger cat states is presented in details.

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

Richards, Mercedes T.; Agafonov, Michail I.; Sharova, Olga I., E-mail: mrichards@astro.psu.edu, E-mail: agfn@nirfi.sci-nnov.ru, E-mail: shol@nirfi.sci-nnov.ru

Time-resolved H{alpha} spectra of magnetically active interacting binaries have been used to create three-dimensional (3D) Doppler tomograms by means of the Radioastronomical Approach. This is the first 3D reconstruction of {beta} Per, with RS Vul for comparison. These 3D tomograms have revealed evidence of the mass transfer process (gas stream, circumprimary emission, localized region, absorption zone), as well as loop prominences and coronal mass ejections (CMEs) in {beta} Per and RS Vul that could not be discovered from two-dimensional tomograms alone. The gas stream in both binaries may have been deflected beyond the central plane by the donor star's magneticmore » field. The stream was more elongated along the predicted trajectory in RS Vul than in {beta} Per, but not as pronounced as in U CrB (stream state). The loop prominence reached maximum V{sub z} velocities of {+-}155 km s{sup -1} in RS Vul compared to {+-}120 km s{sup -1} in {beta} Per, while the CME reached a maximum V{sub z} velocity of +150 km s{sup -1} in RS Vul and +100 km s{sup -1} in {beta} Per. The 3D tomograms show that the gas flows are not symmetric relative to the central plane and are not confined to that plane, a result confirmed by recent 15 GHz VLBI radio images of {beta} Per. Both the 3D H{alpha} tomography and the VLBI radio images support an earlier prediction of the superhump phenomenon in {beta} Per: that the gas between the stars is threaded with a magnetic field even though the hot B8V mass-gaining star is not known to have a magnetic field.« less

Electron cryotomography of vitrified cells with a Volta phase plate.

PubMed

Fukuda, Yoshiyuki; Laugks, Ulrike; Lučić, Vladan; Baumeister, Wolfgang; Danev, Radostin

2015-05-01

Electron cryotomography provides a means of studying the three dimensional structure of pleomorphic objects, such as organelles or cells, with a resolution of 1-3nm. A limitation in the study of radiation sensitive biological samples is the low signal-to-noise ratio of the tomograms which may obscure fine details. To overcome this limitation, the recently developed Volta phase plate (VPP) was applied in electron cryotomographic studies of a wide range of cellular structures, from magnetotactic bacteria to primary cultured neurons. The results show that the VPP improves contrast significantly and consequently the signal-to-noise ratio of the tomograms, moreover it avoids disturbing fringing artifacts typical for Zernike phase plates. The contrast improvement provided by the VPP was also confirmed in projection images of relatively thick (∼400nm) samples. In order to investigate the respective contributions of the VPP and the energy filter, images acquired with different combinations of the two were compared. Zero-loss energy filtering reduced the background noise in thicker areas of the sample and improved the contrast of features such as poly-β-hydroxybutyrate granules in magnetotactic bacteria, whereas the VPP provided an overall contrast improvement for all sample areas. After 3D reconstruction, tomograms acquired with the combination of a VPP and an energy filter showed structural features in neuronal processes with outstanding clarity. We also show that the VPP can be combined with focused ion beam milling to examine structures embedded deeply inside cells. Thus, we expect that VPP will become a standard element of the electron cryotomography workflow. Copyright © 2015 Elsevier Inc. All rights reserved.

Processing system of jaws tomograms for pathology identification and surgical guide modeling

NASA Astrophysics Data System (ADS)

Putrik, M. B.; Lavrentyeva, Yu. E.; Ivanov, V. Yu.

2015-11-01

The aim of the study is to create an image processing system, which allows dentists to find pathological resorption and to build surgical guide surface automatically. X-rays images of jaws from cone beam tomography or spiral computed tomography are the initial data for processing. One patient's examination always includes up to 600 images (or tomograms), that's why the development of processing system for fast automation search of pathologies is necessary. X-rays images can be useful not for only illness diagnostic but for treatment planning too. We have studied the case of dental implantation - for successful surgical manipulations surgical guides are used. We have created a processing system that automatically builds jaw and teeth boundaries on the x-ray image. After this step, obtained teeth boundaries used for surgical guide surface modeling and jaw boundaries limit the area for further pathologies search. Criterion for the presence of pathological resorption zones inside the limited area is based on statistical investigation. After described actions, it is possible to manufacture surgical guide using 3D printer and apply it in surgical operation.

Ossification of transverse ligament of atlas causing cervical myelopathy: a case report and review of the literature.

PubMed

Sasaji, Tatsuro; Kawahara, Chikashi; Matsumoto, Fujio

2011-01-01

A case of ossification of transverse ligament of atlas (TLA) is reported. A 76-year-old female suffered from a transverse type myelopathy was successfully treated by posterior decompression. Dynamic lateral plain radiographs showed irreducible atlantoaxial subluxation (AAS). A computed tomogram revealed ossified mass compatible to ossification of TLA. Coalition of the atlantooccipital joints and osteoarthritis of the atlantoaxial joints with degenerated dens was also revealed. Magnetic resonance imaging showed compressed spinal cord at C1 level by the ossification of TLA and AAS. We suggest a mechanism of ossification of TLA as follows: hypertrophied dens and stress to the atlantoaxial joints caused by coalition of atlantooccipital joints could make forward shift of atlas leading to irreducible AAS, and continuous tension given to TLA from irreducible AAS would result in hypertrophied and ossification of TLA.

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

PubMed

Kang, Byung-Ho

2016-01-01

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

Orthodontic Residents' Indications for Use of the Lateral TMJ Tomogram and the Posteroanterior Cephalogram.

ERIC Educational Resources Information Center

Luke, Larry S.; And Others

1997-01-01

A study of 144 patients assigned to eight orthodontic residents over two years found residents requested lateral tomograms of the temporomandibular joint (TMJ) 28% of the time, commonly citing TMJ clicking, pain, and medico-legal protection. Posteroanterior cephalograms were ordered 26% of the time, commonly for facial asymmetry and maxillary…

High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography

NASA Astrophysics Data System (ADS)

Kim, Kyoohyun; Yoon, HyeOk; Diez-Silva, Monica; Dao, Ming; Dasari, Ramachandra R.; Park, YongKeun

2014-01-01

We present high-resolution optical tomographic images of human red blood cells (RBC) parasitized by malaria-inducing Plasmodium falciparum (Pf)-RBCs. Three-dimensional (3-D) refractive index (RI) tomograms are reconstructed by recourse to a diffraction algorithm from multiple two-dimensional holograms with various angles of illumination. These 3-D RI tomograms of Pf-RBCs show cellular and subcellular structures of host RBCs and invaded parasites in fine detail. Full asexual intraerythrocytic stages of parasite maturation (ring to trophozoite to schizont stages) are then systematically investigated using optical diffraction tomography algorithms. These analyses provide quantitative information on the structural and chemical characteristics of individual host Pf-RBCs, parasitophorous vacuole, and cytoplasm. The in situ structural evolution and chemical characteristics of subcellular hemozoin crystals are also elucidated.

High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography

PubMed Central

Kim, Kyoohyun; Yoon, HyeOk; Diez-Silva, Monica; Dao, Ming; Dasari, Ramachandra R.

2013-01-01

Abstract. We present high-resolution optical tomographic images of human red blood cells (RBC) parasitized by malaria-inducing Plasmodium falciparum (Pf)-RBCs. Three-dimensional (3-D) refractive index (RI) tomograms are reconstructed by recourse to a diffraction algorithm from multiple two-dimensional holograms with various angles of illumination. These 3-D RI tomograms of Pf-RBCs show cellular and subcellular structures of host RBCs and invaded parasites in fine detail. Full asexual intraerythrocytic stages of parasite maturation (ring to trophozoite to schizont stages) are then systematically investigated using optical diffraction tomography algorithms. These analyses provide quantitative information on the structural and chemical characteristics of individual host Pf-RBCs, parasitophorous vacuole, and cytoplasm. The in situ structural evolution and chemical characteristics of subcellular hemozoin crystals are also elucidated. PMID:23797986

Three-dimensional reconstruction of teeth and jaws based on segmentation of CT images using watershed transformation.

PubMed

Naumovich, S S; Naumovich, S A; Goncharenko, V G

2015-01-01

The objective of the present study was the development and clinical testing of a three-dimensional (3D) reconstruction method of teeth and a bone tissue of the jaw on the basis of CT images of the maxillofacial region. 3D reconstruction was performed using the specially designed original software based on watershed transformation. Computed tomograms in digital imaging and communications in medicine format obtained on multispiral CT and CBCT scanners were used for creation of 3D models of teeth and the jaws. The processing algorithm is realized in the stepwise threshold image segmentation with the placement of markers in the mode of a multiplanar projection in areas relating to the teeth and a bone tissue. The developed software initially creates coarse 3D models of the entire dentition and the jaw. Then, certain procedures specify the model of the jaw and cut the dentition into separate teeth. The proper selection of the segmentation threshold is very important for CBCT images having a low contrast and high noise level. The developed semi-automatic algorithm of multispiral and cone beam computed tomogram processing allows 3D models of teeth to be created separating them from a bone tissue of the jaws. The software is easy to install in a dentist's workplace, has an intuitive interface and takes little time in processing. The obtained 3D models can be used for solving a wide range of scientific and clinical tasks.

Single-photon tomographic determination of regional cerebral blood flow in epilepsy

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

Bonte, F.J.; Devous, M.D. Sr.; Stokely, E.M.

Using a single-photon emission computed tomographic scanner (SPECT) the authors determined regional cerebral blood flow (rCBF) with inhaled xenon-133, a noninvasive procedure. Studies were performed in 40 normal individuals, and these were compared with rCBF determinations in 51 patients with seizure disorders. Although positive results were obtained in 15 of 16 patients with mass lesions, the group of principal interest comprised 25 patients suffering from ''temporal lobe'' epilepsy. Only one of these had a positive x-ray computed tomogram, but 16 had positive findings on rCBF study. These findings included increased local blood flow in the ictal state and reduced flowmore » interictally.« less

Cerebral blood flow tomography with xenon-133

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

Lassen, N.A.

1985-10-01

Cerebral blood flow (CBF) can be measured tomographically by inhalation of Xenon-/sup 133/. The calculation is based on taking a sequence of tomograms during the wash-in and wash-out phase of the tracer. Due to the dynamic nature of the process, a highly sensitive and fast moving single photon emission computed tomograph (SPECT) is required. Two brain-dedicated SPECT systems designed for this purpose are mentioned, and the method is described with special reference to the limitations inherent in the soft energy of the 133Xe primary photons. CBF tomography can be used for a multitude of clinical and investigative purposes. This articlemore » discusses in particular its use for the selection of patients with carotid occlusion for extracranial/intracranial bypass surgery, for detection of severe arterial spasm after aneurysm bleeding, and for detection of low flow areas during severe migraine attacks. The use of other tracers for CBF tomography using SPECT is summarized with emphasis on the /sup 99m/Tc chelates that freely pass the intact blood-brain barrier. The highly sensitive brain-dedicated SPECT systems described are a prerequisite for achieving high resolution tomograms with such tracers.« less

Processing system of jaws tomograms for pathology identification and surgical guide modeling

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

Putrik, M. B., E-mail: pmb-88@mail.ru; Ivanov, V. Yu.; Lavrentyeva, Yu. E.

The aim of the study is to create an image processing system, which allows dentists to find pathological resorption and to build surgical guide surface automatically. X-rays images of jaws from cone beam tomography or spiral computed tomography are the initial data for processing. One patient’s examination always includes up to 600 images (or tomograms), that’s why the development of processing system for fast automation search of pathologies is necessary. X-rays images can be useful not for only illness diagnostic but for treatment planning too. We have studied the case of dental implantation – for successful surgical manipulations surgical guidesmore » are used. We have created a processing system that automatically builds jaw and teeth boundaries on the x-ray image. After this step, obtained teeth boundaries used for surgical guide surface modeling and jaw boundaries limit the area for further pathologies search. Criterion for the presence of pathological resorption zones inside the limited area is based on statistical investigation. After described actions, it is possible to manufacture surgical guide using 3D printer and apply it in surgical operation.« less

Parsimonious surface wave interferometry

NASA Astrophysics Data System (ADS)

Li, Jing; Hanafy, Sherif; Schuster, Gerard T.

2018-03-01

To decrease the recording time of a 2-D seismic survey from a few days to one hour or less, we present a parsimonious surface wave interferometry method. Interferometry allows for the creation of a large number of virtual shot gathers from just two reciprocal shot gathers by crosscoherence of trace pairs. Then, the virtual surface waves can be inverted for the S-wave velocity model by wave-equation dispersion inversion (WD). Synthetic and field data tests suggest that parsimonious WD (PWD) gives S-velocity tomograms that are comparable to those obtained from a conventional survey with a shot at each receiver. The limitation of PWD is that the virtual data lose some information so that the resolution of the S-velocity tomogram can be modestly lower than that of the S-velocity tomogram inverted from a conventional survey.

Zernike ultrasonic tomography for fluid velocity imaging based on pipeline intrusive time-of-flight measurements.

PubMed

Besic, Nikola; Vasile, Gabriel; Anghel, Andrei; Petrut, Teodor-Ion; Ioana, Cornel; Stankovic, Srdjan; Girard, Alexandre; d'Urso, Guy

2014-11-01

In this paper, we propose a novel ultrasonic tomography method for pipeline flow field imaging, based on the Zernike polynomial series. Having intrusive multipath time-offlight ultrasonic measurements (difference in flight time and speed of ultrasound) at the input, we provide at the output tomograms of the fluid velocity components (axial, radial, and orthoradial velocity). Principally, by representing these velocities as Zernike polynomial series, we reduce the tomography problem to an ill-posed problem of finding the coefficients of the series, relying on the acquired ultrasonic measurements. Thereupon, this problem is treated by applying and comparing Tikhonov regularization and quadratically constrained ℓ1 minimization. To enhance the comparative analysis, we additionally introduce sparsity, by employing SVD-based filtering in selecting Zernike polynomials which are to be included in the series. The first approach-Tikhonov regularization without filtering, is used because it is the most suitable method. The performances are quantitatively tested by considering a residual norm and by estimating the flow using the axial velocity tomogram. Finally, the obtained results show the relative residual norm and the error in flow estimation, respectively, ~0.3% and ~1.6% for the less turbulent flow and ~0.5% and ~1.8% for the turbulent flow. Additionally, a qualitative validation is performed by proximate matching of the derived tomograms with a flow physical model.

Regional brain hematocrit in stroke by single photon emission computed tomography imaging

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

Loutfi, I.; Frackowiak, R.S.; Myers, M.J.

1987-01-01

Nineteen studies on 18 subjects were performed by single photon emission computed tomography (SPECT) of the head after the successive intravenous administration of a plasma label (/sup 99m/Tc-human serum albumin (HSA)) and /sup 99m/Tc-labeled autologous red blood cells (RBC). Two sets of cerebral tomographic sections were generated: for cerebral /sup 99m/Tc-HSA alone and for combined /sup 99m/Tc-HSA and /sup 99m/Tc-RBC. By relating counts in regions of interest from the cerebral tomograms to counts from blood samples obtained during each tomographic acquisition, regional cerebral haematocrit (Hct) was calculated by the application of a simple formula. Results show 1) lower cerebral Hctmore » than venous Hct (ratio of HCT brain/Hct venous 0.65-0.90) in all subjects, and 2) comparison between right and left hemisphere Hct in 3/3 normal subjects, 6/6 patients with transient ischaemic attacks and 3/8 patients with stroke showed no significant difference. However, in 3/8 patients with stroke (most recent strokes) significant differences were found, the higher Hct value corresponding to the affected side.« less

Osteoid osteoma of the foot: presentation following trauma.

PubMed

Ambrosia, J M; Kernek, C B

1985-05-01

A 15 year old black boy presented with a seven-month history of apparent post traumatic foot pain. Radiologic workup including bone scan, tomograms, and CT scan showed osteoid osteoma, which was treated by surgical excision. This treatment resulted in complete pain relief and return to full activities.

Improving image quality in laboratory x-ray phase-contrast imaging

NASA Astrophysics Data System (ADS)

De Marco, F.; Marschner, M.; Birnbacher, L.; Viermetz, M.; Noël, P.; Herzen, J.; Pfeiffer, F.

2017-03-01

Grating-based X-ray phase-contrast (gbPC) is known to provide significant benefits for biomedical imaging. To investigate these benefits, a high-sensitivity gbPC micro-CT setup for small (≍ 5 cm) biological samples has been constructed. Unfortunately, high differential-phase sensitivity leads to an increased magnitude of data processing artifacts, limiting the quality of tomographic reconstructions. Most importantly, processing of phase-stepping data with incorrect stepping positions can introduce artifacts resembling Moiré fringes to the projections. Additionally, the focal spot size of the X-ray source limits resolution of tomograms. Here we present a set of algorithms to minimize artifacts, increase resolution and improve visual impression of projections and tomograms from the examined setup. We assessed two algorithms for artifact reduction: Firstly, a correction algorithm exploiting correlations of the artifacts and differential-phase data was developed and tested. Artifacts were reliably removed without compromising image data. Secondly, we implemented a new algorithm for flatfield selection, which was shown to exclude flat-fields with strong artifacts. Both procedures successfully improved image quality of projections and tomograms. Deconvolution of all projections of a CT scan can minimize blurring introduced by the finite size of the X-ray source focal spot. Application of the Richardson-Lucy deconvolution algorithm to gbPC-CT projections resulted in an improved resolution of phase-contrast tomograms. Additionally, we found that nearest-neighbor interpolation of projections can improve the visual impression of very small features in phase-contrast tomograms. In conclusion, we achieved an increase in image resolution and quality for the investigated setup, which may lead to an improved detection of very small sample features, thereby maximizing the setup's utility.

[The application of the computer technologies for the mathematical simulation of the ethmoidal labyrinth].

PubMed

Markeeva, M V; Mareev, O V; Nikolenko, V N; Mareev, G O; Danilova, T V; Fadeeva, E A; Fedorov, R V

The objective of the present work was to study the relationship between the dimensions of the ethmoidal labyrinth and the skull in the subjects differing in the nose shape by means of the factorial and correlation analysis with the application of the modern computer-assisted methods for the three-dimensional reconstruction of the skull. We developed an original method for computed craniometry with the use the original program that made it possible to determine the standard intravital craniometrics characteristics of the human skull with a high degree of accuracy based on the results of analysis of 200 computed tomograms of the head. It was shown that the length of the inferior turbinated bones and the posterior edge of the orbital plate is of special relevance for practically all parameters of the ethmoidal labyrinth. Also, the width of the choanae positively relates to the height of the ethmoidal labyrinth.

NDE application of ultrasonic tomography to a full-scale concrete structure.

PubMed

Choi, Hajin; Popovics, John S

2015-06-01

Newly developed ultrasonic imaging technology for large concrete elements, based on tomographic reconstruction, is presented. The developed 3-D internal images (velocity tomograms) are used to detect internal defects (polystyrene foam and pre-cracked concrete prisms) that represent structural damage within a large steel reinforced concrete element. A hybrid air-coupled/contact transducer system is deployed. Electrostatic air-coupled transducers are used to generate ultrasonic energy and contact accelerometers are attached on the opposing side of the concrete element to detect the ultrasonic pulses. The developed hybrid testing setup enables collection of a large amount of high-quality, through-thickness ultrasonic data without surface preparation to the concrete. The algebraic reconstruction technique is used to reconstruct p-wave velocity tomograms from the obtained time signal data. A comparison with a one-sided ultrasonic imaging method is presented for the same specimen. Through-thickness tomography shows some benefit over one-sided imaging for highly reinforced concrete elements. The results demonstrate that the proposed through-thickness ultrasonic technique shows great potential for evaluation of full-scale concrete structures in the field.

Refractive index tomograms and dynamic membrane fluctuations of red blood cells from patients with diabetes mellitus.

PubMed

Lee, SangYun; Park, HyunJoo; Kim, Kyoohyun; Sohn, YongHak; Jang, Seongsoo; Park, YongKeun

2017-04-21

In this paper, we present the optical characterisations of diabetic red blood cells (RBCs) in a non-invasive manner employing three-dimensional (3-D) quantitative phase imaging. By measuring 3-D refractive index tomograms and 2-D time-series phase images, the morphological (volume, surface area and sphericity), biochemical (haemoglobin concentration and content) and mechanical (membrane fluctuation) parameters were quantitatively retrieved at the individual cell level. With simultaneous measurements of individual cell properties, systematic correlative analyses on retrieved RBC parameters were also performed. Our measurements show there exist no statistically significant alterations in morphological and biochemical parameters of diabetic RBCs, compared to those of healthy (non-diabetic) RBCs. In contrast, membrane deformability of diabetic RBCs is significantly lower than that of healthy, non-diabetic RBCs. Interestingly, non-diabetic RBCs exhibit strong correlations between the elevated glycated haemoglobin in RBC cytoplasm and decreased cell deformability, whereas diabetic RBCs do not show correlations. Our observations strongly support the idea that slow and irreversible glycation of haemoglobin and membrane proteins of RBCs by hyperglycaemia significantly compromises RBC deformability in diabetic patients.

iPhone-based teleradiology for the diagnosis of acute cervico-dorsal spine trauma.

PubMed

Modi, Jayesh; Sharma, Pranshu; Earl, Alex; Simpson, Mark; Mitchell, J Ross; Goyal, Mayank

2010-11-01

To assess the feasibility of iPhone-based teleradiology as a potential solution for the diagnosis of acute cervico-dorsal spine trauma. We have developed a solution that allows visualization of images on the iPhone. Our system allows rapid, remote, secure, visualization of medical images without storing patient data on the iPhone. This retrospective study is comprised of cervico-dorsal computed tomogram (CT) scan examination of 75 consecutive patients having clinically suspected cervico-dorsal spine fracture. Two radiologists reviewed CT scan images on the iPhone. Computed tomogram spine scans were analyzed for vertebral body fracture and posterior elements fractures, any associated subluxation-dislocation and cord lesion. The total time taken from the launch of viewing application on the iPhone until interpretation was recorded. The results were compared with that of a diagnostic workstation monitor. Inter-rater agreement was assessed. The sensitivity and accuracy of detecting vertebral body fractures was 80% and 97% by both readers using the iPhone system with a perfect inter-rater agreement (kappa:1). The sensitivity and accuracy of detecting posterior elements fracture was 75% and 98% for Reader 1 and 50% and 97% for Reader 2 using the iPhone. There was good inter-rater agreement (kappa: 0.66) between both readers. No statistically significant difference was noted between time on the workstation and the iPhone system. iPhone-based teleradiology system is accurate in the diagnosis of acute cervicodorsal spinal trauma. It allows rapid, remote, secure, visualization of medical images without storing patient data on the iPhone.

Tarsal navicular stress fractures: radiographic evaluation

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

Pavlov, H.; Torg, J.S.; Freiberger, R.H.

1983-09-01

Tarsal navicular stress fractures are a potential source of disabling foot pain in physically active individuals. The diagnosis of tarsal navicular stress fracture requires a high index of clinical and radiographic suspicion because the fracture is only rarely evident on routine radiographs or standard tomograms. The radiographic diagnosis of a tarsal navicular stress fracture may require anatomic anteroposterior tomograms or a radionuclide bone scan with plantar views. Radiographic examinations of 23 fractures in 21 patients are evaluated.

Unimpeded permeation of water through biocidal graphene oxide sheets anchored on to 3D porous polyolefinic membranes

NASA Astrophysics Data System (ADS)

Mural, Prasanna Kumar S.; Jain, Shubham; Kumar, Sachin; Madras, Giridhar; Bose, Suryasarathi

2016-04-01

3D porous membranes were developed by etching one of the phases (here PEO, polyethylene oxide) from melt-mixed PE/PEO binary blends. Herein, we have systematically discussed the development of these membranes using X-ray micro-computed tomography. The 3D tomograms of the extruded strands and hot-pressed samples revealed a clear picture as to how the morphology develops and coarsens over a function of time during post-processing operations like compression molding. The coarsening of PE/PEO blends was traced using X-ray micro-computed tomography and scanning electron microscopy (SEM) of annealed blends at different times. It is now understood from X-ray micro-computed tomography that by the addition of a compatibilizer (here lightly maleated PE), a stable morphology can be visualized in 3D. In order to anchor biocidal graphene oxide sheets onto these 3D porous membranes, the PE membranes were chemically modified with acid/ethylene diamine treatment to anchor the GO sheets which were further confirmed by Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS) and surface Raman mapping. The transport properties through the membrane clearly reveal unimpeded permeation of water which suggests that anchoring GO on to the membranes does not clog the pores. Antibacterial studies through the direct contact of bacteria with GO anchored PE membranes resulted in 99% of bacterial inactivation. The possible bacterial inactivation through physical disruption of the bacterial cell wall and/or reactive oxygen species (ROS) is discussed herein. Thus this study opens new avenues in designing polyolefin based antibacterial 3D porous membranes for water purification.3D porous membranes were developed by etching one of the phases (here PEO, polyethylene oxide) from melt-mixed PE/PEO binary blends. Herein, we have systematically discussed the development of these membranes using X-ray micro-computed tomography. The 3D tomograms of the extruded strands and hot-pressed samples revealed a clear picture as to how the morphology develops and coarsens over a function of time during post-processing operations like compression molding. The coarsening of PE/PEO blends was traced using X-ray micro-computed tomography and scanning electron microscopy (SEM) of annealed blends at different times. It is now understood from X-ray micro-computed tomography that by the addition of a compatibilizer (here lightly maleated PE), a stable morphology can be visualized in 3D. In order to anchor biocidal graphene oxide sheets onto these 3D porous membranes, the PE membranes were chemically modified with acid/ethylene diamine treatment to anchor the GO sheets which were further confirmed by Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS) and surface Raman mapping. The transport properties through the membrane clearly reveal unimpeded permeation of water which suggests that anchoring GO on to the membranes does not clog the pores. Antibacterial studies through the direct contact of bacteria with GO anchored PE membranes resulted in 99% of bacterial inactivation. The possible bacterial inactivation through physical disruption of the bacterial cell wall and/or reactive oxygen species (ROS) is discussed herein. Thus this study opens new avenues in designing polyolefin based antibacterial 3D porous membranes for water purification. Electronic supplementary information (ESI) available: SEM micrographs of porous PE with and without maleated PE, X-ray micro-computed tomogram of porous extruded PE, FTIR spectra of GO, XPS wide spectra of untreated and GO immobilized PE and Raman spectra of PE and GO. See DOI: 10.1039/c6nr01356b

Balamuthia mandrillaris meningoencephalitis: the first case in southeast Asia.

PubMed

Intalapaporn, Poj; Suankratay, Chusana; Shuangshoti, Shanop; Phantumchinda, Kammant; Keelawat, Somboon; Wilde, Henry

2004-06-01

We present a case of 23-year-old man with acute meningoencephalitis, accompanied by inflammation of a nasal ulcer. He had been healthy until six months prior to admission to the hospital when he had a motorcycle accident. A star-shaped wound at his nose was incurred after falling into a swamp. A computed tomogram of the brain showed two nonenhancing hypodense lesions at the left caudate nucleus and the right parietal lobe, ependymitis and leptomeningeal enhancement. A skin biopsy showed chronic noncaseous granulomatous inflammation without demonstrated microorganisms. The patient did not respond to the empirical treatment with cloxacillin, ceftriaxone, and amphotericin B, and eventually died on the thirteenth day of hospitalization. At autopsy, hematoxylin and eosin-stained brain sections showed a chronic necrotizing inflammation with numerous amebic trophozoites and rare cysts. Definitive identification of Balamuthia mandrillaris was made by fluorescent immunohistochemical analysis. There were 10 Naegleria fowleri primary amebic meningoencephalitis, eight Acanthamoeba granulomatous amebic encephalitis, and three Acanthamoeba meningitis in Thailand. To our knowledge, this case is the first reported case of B. mandrillaris in Southeast Asia.

Cryo-Electron Tomography for Structural Characterization of Macromolecular Complexes

PubMed Central

Cope, Julia; Heumann, John; Hoenger, Andreas

2011-01-01

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

Vectorization with SIMD extensions speeds up reconstruction in electron tomography.

PubMed

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

2010-06-01

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

Analysis of sublethal arsenic toxicity to Ceratophyllum demersum: subcellular distribution of arsenic and inhibition of chlorophyll biosynthesis

PubMed Central

Mishra, Seema; Alfeld, Matthias; Sobotka, Roman; Andresen, Elisa; Falkenberg, Gerald; Küpper, Hendrik

2016-01-01

Arsenic (As) pollution is a serious concern worldwide. Recent studies under environmentally relevant conditions revealed that, in the aquatic plant Ceratophyllum demersum, pigments are the first observable target of toxicity, prior to any effect on photosynthetic parameters or to oxidative stress. Lethal toxicity was initiated by a change of As species and their distribution pattern in various tissues. Here, the localization of As was investigated at the subcellular level through X-ray fluorescence using a submicron beam and a Maia detector. Further, it was possible to obtain useful tissue structural information from the ratio of the tomogram of photon flux behind the sample to the tomogram of Compton scattering. The micro-X-ray fluorescence tomograms showed that As predominantly accumulated in the nucleus of the epidermal cells in young mature leaves exposed to sublethal 1 µM As. This suggests that As may exert toxic effects in the nucleus, for example, by interfering with nucleic acid synthesis by replacing phosphorous with As. At higher cellular concentrations, As was mainly stored in the vacuole, particularly in mature leaves. An analysis of precursors of chlorophyll and degradation metabolites revealed that the observed decrease in chlorophyll concentration was associated with hindered biosynthesis, and was not due to degradation. Coproporphyrinogen III could not be detected after exposure to only 0.5 µM As. Levels of subsequent precursors, for example, protoporphyrin IX, Mg-protoporphyrin, Mg-protoporphyrin methyl ester, and divinyl protochlorophyllide, were significantly decreased at this concentration as well, indicating that the pathway was blocked upstream of tetrapyrrole synthesis. PMID:27340233

Risks to the Superior Gluteal Neurovascular Bundle During Iliosacral and Transsacral Screw Fixation: A Computed Tomogram Arteriography Study.

PubMed

Maslow, Jed; Collinge, Cory A

2017-12-01

Iliosacral (IS) and transsacral (TS) screws are popular techniques to repair complicated injuries to the pelvis. The anatomy of the superior gluteal neurovasculature (SG NV bundle) is well described as running along the posterior ilium, providing innervation and perfusion to important abductor muscles. The method of pelvis fixation least likely to injure the SG NV bundle is unknown. Twenty uninjured patients with a contrasted computed tomogram of the pelvis and lower extremities (CTA) were evaluated. Starting points for an S1 IS screw and S1 and S2 TS screws were estimated on the "ghost" lateral CTA image for those pelvi with safe corridors (>9 mm diameter). The distance from the projected screw to the SG artery was measured. A distance of <3.65 mm (half of a 7.3-mm screw's diameter) was considered likely for NV bundle injury. Of 40 pelvi CTAs (single sides), 10 pelvi (25%) were determined to be inappropriate for an S1 TS screw. The average distances from the screw starting point and the artery were 25.3 mm (±9.2) for S1 IS, 12.4 mm (±9.0) for S1 TS, and 23.5 mm (±10.7) for S2 TS screws, respectively. Ten S1 TS screws (25%) and no S1 IS or S2 TS screws were projected to have caused injury to the SG NV bundle (P < 0.001). Inserting S1 IS and S2 TS screws put the SG NV anatomy at significantly less risk than S1 TS screws. This information may aid in choosing the "best" fixation option for patients with pelvic ring trauma requiring surgery.

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

NASA Astrophysics Data System (ADS)

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

2010-03-01

Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS2 or MoS2 fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties.Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS2 or MoS2 fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties. Electronic supplementary information (ESI) available: Figs. S1 and S2 and movies S1-S6. See DOI: 10.1039/b9nr00251k

Efficient determination of the uncertainty for the optimization of SPECT system design: a subsampled fisher information matrix.

PubMed

Fuin, Niccolo; Pedemonte, Stefano; Arridge, Simon; Ourselin, Sebastien; Hutton, Brian F

2014-03-01

System designs in single photon emission tomography (SPECT) can be evaluated based on the fundamental trade-off between bias and variance that can be achieved in the reconstruction of emission tomograms. This trade off can be derived analytically using the Cramer-Rao type bounds, which imply the calculation and the inversion of the Fisher information matrix (FIM). The inverse of the FIM expresses the uncertainty associated to the tomogram, enabling the comparison of system designs. However, computing, storing and inverting the FIM is not practical with 3-D imaging systems. In order to tackle the problem of the computational load in calculating the inverse of the FIM, a method based on the calculation of the local impulse response and the variance, in a single point, from a single row of the FIM, has been previously proposed for system design. However this approximation (circulant approximation) does not capture the global interdependence between the variables in shift-variant systems such as SPECT, and cannot account e.g., for data truncation or missing data. Our new formulation relies on subsampling the FIM. The FIM is calculated over a subset of voxels arranged in a grid that covers the whole volume. Every element of the FIM at the grid points is calculated exactly, accounting for the acquisition geometry and for the object. This new formulation reduces the computational complexity in estimating the uncertainty, but nevertheless accounts for the global interdependence between the variables, enabling the exploration of design spaces hindered by the circulant approximation. The graphics processing unit accelerated implementation of the algorithm reduces further the computation times, making the algorithm a good candidate for real-time optimization of adaptive imaging systems. This paper describes the subsampled FIM formulation and implementation details. The advantages and limitations of the new approximation are explored, in comparison with the circulant approximation, in the context of design optimization of a parallel-hole collimator SPECT system and of an adaptive imaging system (similar to the commercially available D-SPECT).

Comparative study of transient hydraulic tomography with varying parameterizations and zonations: Laboratory sandbox investigation

NASA Astrophysics Data System (ADS)

Luo, Ning; Zhao, Zhanfeng; Illman, Walter A.; Berg, Steven J.

2017-11-01

Transient hydraulic tomography (THT) is a robust method of aquifer characterization to estimate the spatial distributions (or tomograms) of both hydraulic conductivity (K) and specific storage (Ss). However, the highly-parameterized nature of the geostatistical inversion approach renders it computationally intensive for large-scale investigations. In addition, geostatistics-based THT may produce overly smooth tomograms when head data used to constrain the inversion is limited. Therefore, alternative model conceptualizations for THT need to be examined. To investigate this, we simultaneously calibrated different groundwater models with varying parameterizations and zonations using two cases of different pumping and monitoring data densities from a laboratory sandbox. Specifically, one effective parameter model, four geology-based zonation models with varying accuracy and resolution, and five geostatistical models with different prior information are calibrated. Model performance is quantitatively assessed by examining the calibration and validation results. Our study reveals that highly parameterized geostatistical models perform the best among the models compared, while the zonation model with excellent knowledge of stratigraphy also yields comparable results. When few pumping tests with sparse monitoring intervals are available, the incorporation of accurate or simplified geological information into geostatistical models reveals more details in heterogeneity and yields more robust validation results. However, results deteriorate when inaccurate geological information are incorporated. Finally, our study reveals that transient inversions are necessary to obtain reliable K and Ss estimates for making accurate predictions of transient drawdown events.

Analysis of sublethal arsenic toxicity to Ceratophyllum demersum: subcellular distribution of arsenic and inhibition of chlorophyll biosynthesis.

PubMed

Mishra, Seema; Alfeld, Matthias; Sobotka, Roman; Andresen, Elisa; Falkenberg, Gerald; Küpper, Hendrik

2016-08-01

Arsenic (As) pollution is a serious concern worldwide. Recent studies under environmentally relevant conditions revealed that, in the aquatic plant Ceratophyllum demersum, pigments are the first observable target of toxicity, prior to any effect on photosynthetic parameters or to oxidative stress. Lethal toxicity was initiated by a change of As species and their distribution pattern in various tissues. Here, the localization of As was investigated at the subcellular level through X-ray fluorescence using a submicron beam and a Maia detector. Further, it was possible to obtain useful tissue structural information from the ratio of the tomogram of photon flux behind the sample to the tomogram of Compton scattering. The micro-X-ray fluorescence tomograms showed that As predominantly accumulated in the nucleus of the epidermal cells in young mature leaves exposed to sublethal 1 µM As. This suggests that As may exert toxic effects in the nucleus, for example, by interfering with nucleic acid synthesis by replacing phosphorous with As. At higher cellular concentrations, As was mainly stored in the vacuole, particularly in mature leaves. An analysis of precursors of chlorophyll and degradation metabolites revealed that the observed decrease in chlorophyll concentration was associated with hindered biosynthesis, and was not due to degradation. Coproporphyrinogen III could not be detected after exposure to only 0.5 µM As. Levels of subsequent precursors, for example, protoporphyrin IX, Mg-protoporphyrin, Mg-protoporphyrin methyl ester, and divinyl protochlorophyllide, were significantly decreased at this concentration as well, indicating that the pathway was blocked upstream of tetrapyrrole synthesis. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

A Method for 3D-Reconstruction of a Muscle Thick Filament Using the Tilt Series Images of a Single Filament Electron Tomogram

PubMed Central

Márquez, G.; Pinto, A.; Alamo, L.; Baumann, B.; Ye, F.; Winkler, H.; Taylor, K.; Padrón, R.

2014-01-01

Summary Myosin interacting-heads (MIH) motifs are visualized in 3D-reconstructions of thick filaments from striated muscle. These reconstructions are calculated by averaging methods using images from electron micrographs of grids prepared using numerous filament preparations. Here we propose an alternative method to calculate the 3D-reconstruction of a single thick filament using only a tilt series images recorded by electron tomography. Relaxed thick filaments, prepared from tarantula leg muscle homogenates, were negatively stained. Single-axis tilt series of single isolated thick filaments were obtained with the electron microscope at a low electron dose, and recorded on a CCD camera by electron tomography. An IHRSR 3D-recontruction was calculated from the tilt series images of a single thick filament. The reconstruction was enhanced by including in the search stage dual tilt image segments while only single tilt along the filament axis is usually used, as well as applying a band pass filter just before the back projection. The reconstruction from a single filament has a 40 Å resolution and clearly shows the presence of MIH motifs. In contrast, the electron tomogram 3D-reconstruction of the same thick filament –calculated without any image averaging and/or imposition of helical symmetry- only reveals MIH motifs infrequently. This is –to our knowledge- the first application of the IHRSR method to calculate a 3D reconstruction from tilt series images. This single filament IHRSR reconstruction method (SF-IHRSR) should provide a new tool to assess structural differences between well-ordered thick (or thin) filaments in a grid by recording separately their electron tomograms. PMID:24727133

A method for 3D-reconstruction of a muscle thick filament using the tilt series images of a single filament electron tomogram.

PubMed

Márquez, G; Pinto, A; Alamo, L; Baumann, B; Ye, F; Winkler, H; Taylor, K; Padrón, R

2014-05-01

Myosin interacting-heads (MIH) motifs are visualized in 3D-reconstructions of thick filaments from striated muscle. These reconstructions are calculated by averaging methods using images from electron micrographs of grids prepared using numerous filament preparations. Here we propose an alternative method to calculate the 3D-reconstruction of a single thick filament using only a tilt series images recorded by electron tomography. Relaxed thick filaments, prepared from tarantula leg muscle homogenates, were negatively stained. Single-axis tilt series of single isolated thick filaments were obtained with the electron microscope at a low electron dose, and recorded on a CCD camera by electron tomography. An IHRSR 3D-recontruction was calculated from the tilt series images of a single thick filament. The reconstruction was enhanced by including in the search stage dual tilt image segments while only single tilt along the filament axis is usually used, as well as applying a band pass filter just before the back projection. The reconstruction from a single filament has a 40 Å resolution and clearly shows the presence of MIH motifs. In contrast, the electron tomogram 3D-reconstruction of the same thick filament - calculated without any image averaging and/or imposition of helical symmetry - only reveals MIH motifs infrequently. This is - to our knowledge - the first application of the IHRSR method to calculate a 3D reconstruction from tilt series images. This single filament IHRSR reconstruction method (SF-IHRSR) should provide a new tool to assess structural differences between well-ordered thick (or thin) filaments in a grid by recording separately their electron tomograms. Copyright © 2014 Elsevier Inc. All rights reserved.

Cardiac phase-synchronized myocardial thallium-201 single-photon emission tomography using list mode data acquisition and iterative tomographic reconstruction.

PubMed

Vemmer, T; Steinbüchel, C; Bertram, J; Eschner, W; Kögler, A; Luig, H

1997-03-01

The purpose of this study was to determine whether data acquisition in the list mode and iterative tomographic reconstruction would render feasible cardiac phase-synchronized thallium-201 single-photon emission tomography (SPET) of the myocardium under routine conditions without modifications in tracer dose, acquisition time, or number of steps of the a gamma camera. Seventy non-selected patients underwent 201T1 SPET imaging according to a routine protocol (74 MBq/2 mCi 201T1, 180 degrees rotation of the gamma camera, 32 steps, 30 min). Gamma camera data, ECG, and a time signal were recorded in list mode. The cardiac cycle was divided into eight phases, the end-diastolic phase encompassing the QRS complex, and the end-systolic phase the T wave. Both phase- and non-phase-synchronized tomograms based on the same list mode data were reconstructed iteratively. Phase-synchronized and non-synchronized images were compared. Patients were divided into two groups depending on whether or not coronary artery disease had been definitely diagnosed prior to SPET imaging. The numbers of patients in both groups demonstrating defects visible on the phase-synchronized but not on the non-synchronized images were compared. It was found that both postexercise and redistribution phase tomograms were suited for interpretation. The changes from end-diastolic to end-systolic images allowed a comparative assessment of regional wall motility and tracer uptake. End-diastolic tomograms provided the best definition of defects. Additional defects not apparent on non-synchronized images were visible in 40 patients, six of whom did not show any defect on the non-synchronized images. Of 42 patients in whom coronary artery disease had been definitely diagnosed, 19 had additional defects not visible on the non-synchronized images, in comparison to 21 of 28 in whom coronary artery disease was suspected (P < 0.02; chi 2). It is concluded that cardiac phase-synchronized 201T1 SPET of the myocardium was made feasible by list mode data acquisition and iterative reconstruction. The additional findings on the phase-synchronized tomograms, not visible on the non-synchronized ones, represented genuine defects. Cardiac phase-synchronized 201T1 SPET is advantageous in allowing simultaneous assessment of regional wall motion and tracer uptake, and in visualizing smaller defects.

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

PubMed

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

2010-03-01

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

A 3D Image Filter for Parameter-Free Segmentation of Macromolecular Structures from Electron Tomograms

PubMed Central

Ali, Rubbiya A.; Landsberg, Michael J.; Knauth, Emily; Morgan, Garry P.; Marsh, Brad J.; Hankamer, Ben

2012-01-01

3D image reconstruction of large cellular volumes by electron tomography (ET) at high (≤5 nm) resolution can now routinely resolve organellar and compartmental membrane structures, protein coats, cytoskeletal filaments, and macromolecules. However, current image analysis methods for identifying in situ macromolecular structures within the crowded 3D ultrastructural landscape of a cell remain labor-intensive, time-consuming, and prone to user-bias and/or error. This paper demonstrates the development and application of a parameter-free, 3D implementation of the bilateral edge-detection (BLE) algorithm for the rapid and accurate segmentation of cellular tomograms. The performance of the 3D BLE filter has been tested on a range of synthetic and real biological data sets and validated against current leading filters—the pseudo 3D recursive and Canny filters. The performance of the 3D BLE filter was found to be comparable to or better than that of both the 3D recursive and Canny filters while offering the significant advantage that it requires no parameter input or optimisation. Edge widths as little as 2 pixels are reproducibly detected with signal intensity and grey scale values as low as 0.72% above the mean of the background noise. The 3D BLE thus provides an efficient method for the automated segmentation of complex cellular structures across multiple scales for further downstream processing, such as cellular annotation and sub-tomogram averaging, and provides a valuable tool for the accurate and high-throughput identification and annotation of 3D structural complexity at the subcellular level, as well as for mapping the spatial and temporal rearrangement of macromolecular assemblies in situ within cellular tomograms. PMID:22479430

Eckert and Davis Grade 3 Superior Peroneal Retinaculum Injury: Treated by Endoscopic Peroneal Retinaculum Reconstruction and Complicated by Malposition of the Suture Anchors.

PubMed

Lui, T H

2015-01-01

Eckert and Davis grade 3 superior peroneal retinaculum injury is rare and the optimal treatment is not yet determined. A 57 year-old lady sprained her left ankle resulting in grade 3 injury of the superior peroneal retinaculum and was treated by endoscopic retinaculum reconstruction. The fracture healed and the peroneal tendons were stabilized. However, it was complicated by protusion of the suture anchors into the posterolateral ankle gutter. The implants were successfully removed endoscopically. Proper selection of the size and dimension of the suture anchor and preoperative planning with computed tomogram is important for usage of suture anchors in the lateral malleolus.

Seismic Tomography of the Arabian-Eurasian Collision Zone and Surrounding Areas

DTIC Science & Technology

2010-05-20

zone. The crustal models correlate well with geologic and tectonic features. The upper mantle tomograms show the images of the subducted Neotethys...We first obtain Pn and Sn velocities using local and regional arrival time data. Second, we obtain the 3-D crustal P and S velocity models...teleseismic tomography provides a high-resolution, 3-D P-wave velocity model for the crust, upper mantle, and the transition zone. The crustal models

Morphological Characterisation of Unstained and Intact Tissue Micro-architecture by X-ray Computed Micro- and Nano-Tomography

NASA Astrophysics Data System (ADS)

Walton, Lucy A.; Bradley, Robert S.; Withers, Philip J.; Newton, Victoria L.; Watson, Rachel E. B.; Austin, Clare; Sherratt, Michael J.

2015-05-01

Characterisation and quantification of tissue structures is limited by sectioning-induced artefacts and by the difficulties of visualising and segmenting 3D volumes. Here we demonstrate that, even in the absence of X-ray contrast agents, X-ray computed microtomography (microCT) and nanotomography (nanoCT) can circumvent these problems by rapidly resolving compositionally discrete 3D tissue regions (such as the collagen-rich adventitia and elastin-rich lamellae in intact rat arteries) which in turn can be segmented due to their different X-ray opacities and morphologies. We then establish, using X-ray tomograms of both unpressurised and pressurised arteries that intra-luminal pressure not only increases lumen cross-sectional area and straightens medial elastic lamellae but also induces profound remodelling of the adventitial layer. Finally we apply microCT to another human organ (skin) to visualise the cell-rich epidermis and extracellular matrix-rich dermis and to show that conventional histological and immunohistochemical staining protocols are compatible with prior X-ray exposure. As a consequence we suggest that microCT could be combined with optical microscopy to characterise the 3D structure and composition of archival paraffin embedded biological materials and of mechanically stressed dynamic tissues such as the heart, lungs and tendons.

Morphological Characterisation of Unstained and Intact Tissue Micro-architecture by X-ray Computed Micro- and Nano-Tomography

PubMed Central

Walton, Lucy A.; Bradley, Robert S.; Withers, Philip J.; Newton, Victoria L.; Watson, Rachel E. B.; Austin, Clare; Sherratt, Michael J.

2015-01-01

Characterisation and quantification of tissue structures is limited by sectioning-induced artefacts and by the difficulties of visualising and segmenting 3D volumes. Here we demonstrate that, even in the absence of X-ray contrast agents, X-ray computed microtomography (microCT) and nanotomography (nanoCT) can circumvent these problems by rapidly resolving compositionally discrete 3D tissue regions (such as the collagen-rich adventitia and elastin-rich lamellae in intact rat arteries) which in turn can be segmented due to their different X-ray opacities and morphologies. We then establish, using X-ray tomograms of both unpressurised and pressurised arteries that intra-luminal pressure not only increases lumen cross-sectional area and straightens medial elastic lamellae but also induces profound remodelling of the adventitial layer. Finally we apply microCT to another human organ (skin) to visualise the cell-rich epidermis and extracellular matrix-rich dermis and to show that conventional histological and immunohistochemical staining protocols are compatible with prior X-ray exposure. As a consequence we suggest that microCT could be combined with optical microscopy to characterise the 3D structure and composition of archival paraffin embedded biological materials and of mechanically stressed dynamic tissues such as the heart, lungs and tendons. PMID:25975937

PCA Tomography: how to extract information from data cubes

NASA Astrophysics Data System (ADS)

Steiner, J. E.; Menezes, R. B.; Ricci, T. V.; Oliveira, A. S.

2009-05-01

Astronomy has evolved almost exclusively by the use of spectroscopic and imaging techniques, operated separately. With the development of modern technologies, it is possible to obtain data cubes in which one combines both techniques simultaneously, producing images with spectral resolution. To extract information from them can be quite complex, and hence the development of new methods of data analysis is desirable. We present a method of analysis of data cube (data from single field observations, containing two spatial and one spectral dimension) that uses Principal Component Analysis (PCA) to express the data in the form of reduced dimensionality, facilitating efficient information extraction from very large data sets. PCA transforms the system of correlated coordinates into a system of uncorrelated coordinates ordered by principal components of decreasing variance. The new coordinates are referred to as eigenvectors, and the projections of the data on to these coordinates produce images we will call tomograms. The association of the tomograms (images) to eigenvectors (spectra) is important for the interpretation of both. The eigenvectors are mutually orthogonal, and this information is fundamental for their handling and interpretation. When the data cube shows objects that present uncorrelated physical phenomena, the eigenvector's orthogonality may be instrumental in separating and identifying them. By handling eigenvectors and tomograms, one can enhance features, extract noise, compress data, extract spectra, etc. We applied the method, for illustration purpose only, to the central region of the low ionization nuclear emission region (LINER) galaxy NGC 4736, and demonstrate that it has a type 1 active nucleus, not known before. Furthermore, we show that it is displaced from the centre of its stellar bulge. Based on observations obtained at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the National Science Foundation on behalf of the Gemini partnership: the National Science Foundation (United States), the Science and Technology Facilities Council (United Kingdom), the National Research Council (Canada), CONICYT (Chile), the Australian Research Council (Australia), Ministério da Ciência e Tecnologia (Brazil) and SECYT (Argentina). E-mail: steiner@astro.iag.usp.br

Spectral optical coherence tomography: a novel technique for cornea imaging.

PubMed

Kaluzny, Bartłomiej J; Kaluzy, Bartłomiej J; Kałuzny, Jakub J; Szkulmowska, Anna; Gorczyńska, Iwona; Szkulmowski, Maciej; Bajraszewski, Tomasz; Wojtkowski, Maciej; Targowski, Piotr

2006-09-01

Spectral optical coherence tomography (SOCT) is a new, noninvasive, noncontact, high-resolution technique that provides cross-sectional images of the objects that weakly absorb and scatter light. SOCT, because of very short acquisition time and high sensitivity, is capable of providing tomograms of substantially better quality than the conventional OCT. The aim of this paper is to show the application of the SOCT to cross-sectional imaging of the cornea and its pathologies. Eleven eyes with different corneal pathologies were examined with a slit lamp and the use of a prototype SOCT instrument constructed in the Institute of Physics, Nicolaus Copernicus University, Toruń, Poland. Our SOCT system provides high-resolution (4 microm axial, 10 microm transversal) tomograms composed of 3000-5000 A-scans with an acquisition time of 120-200 ms. The quality of the images is adequate for detailed cross-sectional evaluation of various corneal pathologies. Objective assessment of the localization, size, shape, and light-scattering properties of the changed tissue is possible. Corneal and epithelial thickness and the depth and width of lesions can be estimated. SOCT technique allows acquiring clinically valuable cross-sectional optical biopsy of the cornea and its pathologies.

Rotator cuff tear measurement by arthropneumotomography

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

Kilcoyne, R.F.; Matsen, F.A. III

1983-02-01

Five years of experience with a method of shoulder arthrography using upright tomography in cases of suspected or known rotator cuff tears has demonstrated its effectiveness. The value of the procedure lies in its ability to demonstrate the size of the cuff tear and the thickness of the remaining cuff tissue. This information provides the surgeon with a preoperative estimate of the difficulty of the repair and the prognosis for a good functional recovery. In 33 cases, there was good correlation between the upright thin-section tomogram findings and the surgical results. The tomograms provided better information about the size ofmore » the tear and the quality of the remaining cuff than did plain arthrograms.« less

Sub-10-ms X-ray tomography using a grating interferometer

NASA Astrophysics Data System (ADS)

Yashiro, Wataru; Noda, Daiji; Kajiwara, Kentaro

2017-05-01

An X-ray phase tomogram was successfully obtained with an exposure time of less than 10 ms by X-ray grating interferometry, an X-ray phase imaging technique that enables high-sensitivity X-ray imaging even of materials consisting of light elements. This high-speed X-ray imaging experiment was performed at BL28B2, SPring-8, where a white X-ray beam is available, and the tomogram was reconstructed from projection images recorded at a frame rate of 100,000 fps. The setup of the experiment will make it possible to realize three-dimensional observation of unrepeatable high-speed phenomena with a time resolution of less than 10 ms.

Detection of an embolized central venous catheter fragment with endobronchial ultrasound.

PubMed

Dhillon, Samjot Singh; Harris, Kassem; Alraiyes, Abdul H; Picone, Anthony L

2018-01-01

An 84-year-old woman underwent Convex-probe Endobronchial Ultrasound (CP-EBUS) for 18 F-fluorodeoxyglucose avid subcarinal lymphadenopathy on Positron Emission Tomogram (PET) scan. Endobronchial ultrasound-guided transbronchial needle aspiration of the subcarinal lymph node revealed squamous cell lung carcinoma. A small hyperechoic rounded density was noted inside the lumen of the azygous vein. Based on chest computed tomography findings and her clinical history, this was felt to be a broken fragment of a peripherally inserted central catheter, which was placed for intravenous antibiotics, a few months prior to this presentation. To the best of our knowledge, this is the first ever CP-EBUS description of a broken fragment of central venous catheter. © 2016 John Wiley & Sons Ltd.

Saccular aortic aneurysm that resembled a mediastinal neoplasm

PubMed Central

Nose, Naohiro; Kataoka, Hiroumi; Hamada, Masakatsu; Kosako, Yukio; Matsuno, Yasuji; Ishii, Takahiro

2012-01-01

INTRODUCTION Saccular aortic arch aneurysms in unusual sites may be misdiagnosed as a neoplasm. We present the case of a rare saccular aortic arch aneurysm between trachea and esophagus that resembled a mediastinal neoplasm in the preoperative findings. PRESENTATION OF CASE A 63-year-old male with an abnormal mediastinal shadow on chest X-ray was referred to the hospital. An axial plain computed tomogram of the chest revealed mediastinal soft tissue next to the right side of the aortic arch resembling a neoplasm originating from the gap between the trachea and the esophagus. The coronal view constructed by enhanced 64-row multi detector computed tomography revealed the soft tissue was an aneurysm arising from the inner side of the aortic arch. An aortic arch replacement was performed via a median sternotomy. DISCUSSION A thoracic aortic aneurysm sometimes behaves like a mediastinal neoplasm. The multiple cross-sectional image from multidetector computed tomography was useful for the correct diagnosis of such an aneurysm. CONCLUSION The possibility of an aneurysm should be considered whenever a mass in contact with the aortic wall is identified. PMID:22995656

15Mcps photon-counting X-ray computed tomography system using a ZnO-MPPC detector and its application to gadolinium imaging.

PubMed

Sato, Eiichi; Sugimura, Shigeaki; Endo, Haruyuki; Oda, Yasuyuki; Abudurexiti, Abulajiang; Hagiwara, Osahiko; Osawa, Akihiro; Matsukiyo, Hiroshi; Enomoto, Toshiyuki; Watanabe, Manabu; Kusachi, Shinya; Sato, Shigehiro; Ogawa, Akira; Onagawa, Jun

2012-01-01

15Mcps photon-counting X-ray computed tomography (CT) system is a first-generation type and consists of an X-ray generator, a turntable, a translation stage, a two-stage controller, a detector consisting of a 2mm-thick zinc-oxide (ZnO) single-crystal scintillator and an MPPC (multipixel photon counter) module, a counter card (CC), and a personal computer (PC). High-speed photon counting was carried out using the detector in the X-ray CT system. The maximum count rate was 15Mcps (mega counts per second) at a tube voltage of 100kV and a tube current of 1.95mA. Tomography is accomplished by repeated translations and rotations of an object, and projection curves of the object are obtained by the translation. The pulses of the event signal from the module are counted by the CC in conjunction with the PC. The minimum exposure time for obtaining a tomogram was 15min, and photon-counting CT was accomplished using gadolinium-based contrast media. Copyright © 2011 Elsevier Ltd. All rights reserved.

Robust identification and localization of intramedullary nail holes for distal locking using CBCT: a simulation study.

PubMed

Kamarianakis, Z; Buliev, I; Pallikarakis, N

2011-05-01

Closed intramedullary nailing is a common technique for treatment of femur and tibia fractures. The most challenging step in this procedure is the precise placement of the lateral screws that stabilize the fragmented bone. The present work concerns the development and the evaluation of a method to accurately identify in the 3D space the axes of the nail hole canals. A limited number of projection images are acquired around the leg with the help of a C-arm. On two of them, the locking hole entries are interactively selected and a rough localization of the hole axes is performed. Perpendicularly to one of them, cone-beam computed tomography (CBCT) reconstructions are produced. The accurate identification and localization of the hole axes are done by an identification of the centers of the nail holes on the tomograms and a further 3D linear regression through principal component analysis (PCA). Various feature-based approaches (RANSAC, least-square fitting, Hough transform) have been compared for best matching the contours and the centers of the holes on the tomograms. The robustness of the suggested method was investigated using simulations. Programming is done in Matlab and C++. Results obtained on synthetic data confirm very good localization accuracy - mean translational error of 0.14 mm (std=0.08 mm) and mean angular error of 0.84° (std=0.35°) at no radiation excess. Successful localization can be further used to guide a surgeon or a robot for correct drilling the bone along the nail openings. Copyright © 2010 IPEM. Published by Elsevier Ltd. All rights reserved.

Simultaneous determination of sample thickness, tilt, and electron mean free path using tomographic tilt images based on Beer-Lambert law

PubMed Central

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

2015-01-01

Cryo-electron tomography (cryo-ET) is an emerging technique that can elucidate the architecture of macromolecular complexes and cellular ultrastructure in a near-native state. Some important sample parameters, such as thickness and tilt, are needed for 3-D reconstruction. However, these parameters can currently only be determined using trial 3-D reconstructions. Accurate electron mean free path plays a significant role in modeling image formation process essential for simulation of electron microscopy images and model-based iterative 3-D reconstruction methods; however, their values are voltage and sample dependent and have only been experimentally measured for a limited number of sample conditions. Here, we report a computational method, tomoThickness, based on the Beer-Lambert law, to simultaneously determine the sample thickness, tilt and electron inelastic mean free path by solving an overdetermined nonlinear least square optimization problem utilizing the strong constraints of tilt relationships. The method has been extensively tested with both stained and cryo datasets. The fitted electron mean free paths are consistent with reported experimental measurements. The accurate thickness estimation eliminates the need for a generous assignment of Z-dimension size of the tomogram. Interestingly, we have also found that nearly all samples are a few degrees tilted relative to the electron beam. Compensation of the intrinsic sample tilt can result in horizontal structure and reduced Z-dimension of tomograms. Our fast, pre-reconstruction method can thus provide important sample parameters that can help improve performance of tomographic reconstruction of a wide range of samples. PMID:26433027

Simultaneous determination of sample thickness, tilt, and electron mean free path using tomographic tilt images based on Beer-Lambert law.

PubMed

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

2015-11-01

Cryo-electron tomography (cryo-ET) is an emerging technique that can elucidate the architecture of macromolecular complexes and cellular ultrastructure in a near-native state. Some important sample parameters, such as thickness and tilt, are needed for 3-D reconstruction. However, these parameters can currently only be determined using trial 3-D reconstructions. Accurate electron mean free path plays a significant role in modeling image formation process essential for simulation of electron microscopy images and model-based iterative 3-D reconstruction methods; however, their values are voltage and sample dependent and have only been experimentally measured for a limited number of sample conditions. Here, we report a computational method, tomoThickness, based on the Beer-Lambert law, to simultaneously determine the sample thickness, tilt and electron inelastic mean free path by solving an overdetermined nonlinear least square optimization problem utilizing the strong constraints of tilt relationships. The method has been extensively tested with both stained and cryo datasets. The fitted electron mean free paths are consistent with reported experimental measurements. The accurate thickness estimation eliminates the need for a generous assignment of Z-dimension size of the tomogram. Interestingly, we have also found that nearly all samples are a few degrees tilted relative to the electron beam. Compensation of the intrinsic sample tilt can result in horizontal structure and reduced Z-dimension of tomograms. Our fast, pre-reconstruction method can thus provide important sample parameters that can help improve performance of tomographic reconstruction of a wide range of samples. Copyright © 2015 Elsevier Inc. All rights reserved.

Permeability Changes of Integrin-Containing Multivesicular Structures Triggered by Picornavirus Entry

PubMed Central

Soonsawad, Pan; Weerachatyanukul, Wattana; Rintanen, Nina; Espinoza, Juan; McNerney, Gregory; Marjomäki, Varpu; Cheng, R. Holland

2014-01-01

Cellular uptake of clustered α2β1-integrin induces the formation of membrane compartments that subsequently mature into a multivesicular body (MVB). Enhanced internalization mediated by clustered integrins was observed upon infection by the picornavirus echovirus 1 (EVI). We elucidated the structural features of virus-induced MVBs (vMVBs) in comparison to antibody-induced control MVBs (mock infection) by means of high-pressure cryo fixation of cells followed by immuno electron tomography during early entry of the virus. Three-dimensional tomograms revealed a marked increase in the size and complexity of these vMVBs and the intraluminal vesicles (ILVs) at 2 and 3.5 hours post infection (p.i.), in contrast to the control MVBs without virus. Breakages in the membranes of vMVBs were detected from tomograms after 2 and especially after 3.5 h suggesting that these breakages could facilitate the genome release to the cytoplasm. The in situ neutral-red labeling of viral genome showed that virus uncoating starts as early as 30 min p.i., while an increase of permeability was detected in the vMVBs between 1 and 3 hours p.i., based on a confocal microscopy assay. Altogether, the data show marked morphological changes in size and permeability of the endosomes in the infectious entry pathway of this non-enveloped enterovirus and suggest that the formed breakages facilitate the transfer of the genome to the cytoplasm for replication. PMID:25299706

Computer-assisted learning in anatomy at the international medical school in Debrecen, Hungary: a preliminary report.

PubMed

Kish, Gary; Cook, Samuel A; Kis, Gréta

2013-01-01

The University of Debrecen's Faculty of Medicine has an international, multilingual student population with anatomy courses taught in English to all but Hungarian students. An elective computer-assisted gross anatomy course, the Computer Human Anatomy (CHA), has been taught in English at the Anatomy Department since 2008. This course focuses on an introduction to anatomical digital images along with clinical cases. This low-budget course has a large visual component using images from magnetic resonance imaging and computer axial tomogram scans, ultrasound clinical studies, and readily available anatomy software that presents topics which run in parallel to the university's core anatomy curriculum. From the combined computer images and CHA lecture information, students are asked to solve computer-based clinical anatomy problems in the CHA computer laboratory. A statistical comparison was undertaken of core anatomy oral examination performances of English program first-year medical students who took the elective CHA course and those who did not in the three academic years 2007-2008, 2008-2009, and 2009-2010. The results of this study indicate that the CHA-enrolled students improved their performance on required anatomy core curriculum oral examinations (P < 0.001), suggesting that computer-assisted learning may play an active role in anatomy curriculum improvement. These preliminary results have prompted ongoing evaluation of what specific aspects of CHA are valuable and which students benefit from computer-assisted learning in a multilingual and diverse cultural environment. Copyright © 2012 American Association of Anatomists.

Multi-method characterization of a landslide in Champagne vineyards: the case study of the Jacotines landslide (Marne, France)

NASA Astrophysics Data System (ADS)

Nicolas, Bollot; Guillaume, Pierre; Gilles, Grandjean

2014-05-01

Key words : landslide, Champagne vineyards , geomorphology, geophysical data, superficial structure The Champagne region is strongly impacted by landslides. Usually inactive, these landslides suffer from partial reactivations leading to important damages, especially when they occur in the vineyards. In the Marne valley, and particularly in the center of Champagne vineyards area (Reuil), the Jacotines site is representative of such landslides since it presents typical surface characteristics widely observed in the region. However, its size, and especially its internal structure, can't be deduced from the surface analysis only. The aim of this work is to combine surface patterns analysis, geophysical data and borehole data to produce an interpretative model of the landslide. Preliminary geomorphological cartography was used for determining the influence of the landslide. From this information, geophysical investigations were carried out to image the internal structure of the landslide. Geophysical data fusion (combination of seismic and geoelectrical tomograms) was used to estimate the mechanical behavior and the fissuring pattern of the slope. Three transverse and longitudinal tomograms were used to define an heterogeneous area between 20 and 50 meters depth and a weathered zone from 0 to 10-20 meters depth. A 60 meters depth borehole on the main transverse tomogram found the shear plane and clarified the structure of the heterogeneous area as well as the uppermost weathered layer composed by debris flows resulting from partial reactivations processes.

Nocardiosis in a patient with rheumatoid athritis treated with rituximab and a summary of reported cases

PubMed Central

Ngiu, C S; Said, M S Mohamed; Periyasamy, P; Low, S F

2010-01-01

Rituximab is a B-cell-depleting monoclonal anti-CD20 antibody. It is widely used in haematology and rheumatology. However, usage of rituximab in immunosupressed patient has been associated with various opportunistic infections. The authors reported a case of refractory rheumatoid arthritis treated with rituximab, which later presented with non-resolving pneumonia with pulmonary nodule. Percutaneous computer tomogram guided lung biopsy was arranged to confirm the suspicion of tuberculosis, but did not yield conclusive results. Later, she presented left-chest abscess and underwent incision and drainage. The pus culture and sensitivity confirmed pulmonary nocardiosis with chest wall dissemination. She was treated with 2-week course of trimethoprim sulfamethoxazole and responded. The authors also reviewed published cases of nocardiosis post-rituximab. PMID:22778377

ICON-MIC: Implementing a CPU/MIC Collaboration Parallel Framework for ICON on Tianhe-2 Supercomputer.

PubMed

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

2018-03-01

Electron tomography (ET) is an important technique for studying the three-dimensional structures of the biological ultrastructure. Recently, ET has reached sub-nanometer resolution for investigating the native and conformational dynamics of macromolecular complexes by combining with the sub-tomogram averaging approach. Due to the limited sampling angles, ET reconstruction typically suffers from the "missing wedge" problem. Using a validation procedure, iterative compressed-sensing optimized nonuniform fast Fourier transform (NUFFT) reconstruction (ICON) demonstrates its power in restoring validated missing information for a low-signal-to-noise ratio biological ET dataset. However, the huge computational demand has become a bottleneck for the application of ICON. In this work, we implemented a parallel acceleration technology ICON-many integrated core (MIC) on Xeon Phi cards to address the huge computational demand of ICON. During this step, we parallelize the element-wise matrix operations and use the efficient summation of a matrix to reduce the cost of matrix computation. We also developed parallel versions of NUFFT on MIC to achieve a high acceleration of ICON by using more efficient fast Fourier transform (FFT) calculation. We then proposed a hybrid task allocation strategy (two-level load balancing) to improve the overall performance of ICON-MIC by making full use of the idle resources on Tianhe-2 supercomputer. Experimental results using two different datasets show that ICON-MIC has high accuracy in biological specimens under different noise levels and a significant acceleration, up to 13.3 × , compared with the CPU version. Further, ICON-MIC has good scalability efficiency and overall performance on Tianhe-2 supercomputer.

A comparative study of accuracy of linear measurements using cone beam and multi-slice computed tomographies for evaluation of mandibular canal location in dry mandibles.

PubMed

Naser, Asieh Zamani; Mehr, Bahar Behdad

2013-01-01

Cross- sectional tomograms have been used for optimal pre-operative planning of dental implant placement. The aim of the present study was to assess the accuracy of Cone Beam Computed Tomography (CBCT) measurements of specific distances around the mandibular canal by comparing them to those obtained from Multi-Slice Computed Tomography (MSCT) images. Ten hemi-mandible specimens were examined using CBCT and MSCT. Before imaging, wires were placed at 7 locations between the anterior margin of the third molar and the anterior margin of the second premolar as reference points. Following distances were measured by two observers on each cross-sectional CBCT and MSCT image: Mandibular Width (W), Length (L), Upper Distance (UD), Lower Distance (LD), Buccal Distance (BD), and Lingual Distance (LID). The obtained data were evaluated using SPSS software, applying paired t-test and intra-class correlation coefficient (ICC). There was a significant difference between the values obtained by MSCT and CBCT measurement for all areas such as H, W, UD, LD, BD, and LID, (P < 0.001), with a difference less than 1 mm. The ICC for all distances by both techniques, measured by a single observer with a one week interval and between 2 observers was 99% and 98%, respectively. Comparing the obtained data of both techniques indicates that the difference between two techniques is 2.17% relative to MSCT. The results of this study showed that there is significant difference between measurements obtained by CBCT and MSCT. However, the difference is not clinically significant.

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

PubMed

Stewart, Phoebe L

2017-03-01

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

Osmotic blood-brain barrier disruption. Computerized tomographic monitoring of chemotherapeutic agent delivery.

PubMed Central

Neuwelt, E A; Maravilla, K R; Frenkel, E P; Rapaport, S I; Hill, S A; Barnett, P A

1979-01-01

The present study describes a canine model of transient reversible blood-brain barrier disruption with hyperosmolar mannitol infusion into the internal carotid artery. Studies in this model show that osmotic blood-brain barrier disruption before intracarotid infusion of methotrexate results in markedly elevated (therapeutic) levels of drug in the ipsilateral cerebral hemisphere. Levels in the cerebrospinal fluid correlate poorly and inconsistently with brain levels. Computerized tomograms in this canine model provide a noninvasive monitor of the degree, time-course, and localization of osmotic blood-brain barrier disruption. Images PMID:457877

Inter- and intraobserver reliability of the vertebral, local and segmental kyphosis in 120 traumatic lumbar and thoracic burst fractures: evaluation in lateral X-rays and sagittal computed tomographies

PubMed Central

Brunner, Alexander; Gühring, Markus; Schmälzle, Traude; Weise, Kuno; Badke, Andreas

2009-01-01

Evaluation of the kyphosis angle in thoracic and lumbar burst fractures is often used to indicate surgical procedures. The kyphosis angle could be measured as vertebral, segmental and local kyphosis according to the method of Cobb. The vertebral, segmental and local kyphosis according to the method of Cobb were measured at 120 lateral X-rays and sagittal computed tomographies of 60 thoracic and 60 lumbar burst fractures by 3 independent observers on 2 separate occasions. Osteoporotic fractures were excluded. The intra- and interobserver reliability of these angles in X-ray and computed tomogram, using the intra class correlation coefficient (ICC) were evaluated. Highest reproducibility showed the segmental kyphosis followed by the vertebral kyphosis. For thoracic fractures segmental kyphosis shows in X-ray “excellent” inter- and intraobserver reliabilities (ICC 0.826, 0.802) and for lumbar fractures “good” to “excellent” inter- and intraobserver reliabilities (ICC = 0.790, 0.803). In computed tomography, the segmental kyphosis showed “excellent” inter- and intraobserver reliabilities (ICC = 0.824, 0.801) for thoracic and “excellent” inter- and intraobserver reliabilities (ICC = 0.874, 0.835) for the lumbar fractures. Regarding both diagnostic work ups (X-ray and computed tomography), significant differences were evaluated in interobserver reliabilities for vertebral kyphosis measured in lumbar fracture X-rays (p = 0.035) and interobserver reliabilities for local kyphosis, measured in thoracic fracture X-rays (p = 0.010). Regarding both fracture localizations (thoracic and lumbar fractures), significant differences could only be evaluated in interobserver reliabilities for the local kyphosis measured in computed tomographies (p = 0.045) and in intraobserver reliabilities for the vertebral kyphosis measured in X-rays (p = 0.024). “Good” to “excellent” inter- and intraobserver reliabilities for vertebral, segmental and local kyphosis in X-ray make these angles to a helpful tool, indicating surgical procedures. For the practical use in lateral X-ray, we emphasize the determination of the segmental kyphosis, because of the highest reproducibility of this angle. “Good” to “excellent” inter- and intraobserver reliabilities for these three angles could also be evaluated in computed tomographies. Therefore, also in computed tomography, the use of these three angles seems to be generally possible. For a direct correlation of the results in lateral X-ray and in computed tomography, further studies should be needed. PMID:19953277

Computer-assisted individual osteotomy design for mandibular reconstruction

NASA Astrophysics Data System (ADS)

Zeilhofer, Hans-Florian U.; Sader, Robert; Horch, Hans-Henning; Wunderlich, Arthur P.; Kirsten, Rainer; Gerhardt, H. C. P.

1994-04-01

The complex structure and functional capacity of the mandible places high demands on the design for mandibular reconstructions for graft or transplant purposes. When using the crista iliac as a basis for grafts to bridge large defects, the graft is empirically shaped by the operator according to this experience, whereby it is often necessary to dissect and reconstruct it numerous times. A 3-D computer tomogram of the lower jaw and ilium is carried out on patients undergoing a planned mandible reconstruction. The 3-D CT data are processed in a workstation using a medical image analysis system. The ala of the ilium is superimposed over the region of the lower jaw which is to be replaced. This enables a coincidence of the structure of the lower jaw and the structure of the ilium crest to be formed to within an accuracy of one voxel - despite the complex three dimensional structure and distortions in all three spatial planes. In accordance with the computer simulation, the applicably shaped ilium crest is placed on the individually calculated donor site and transplanted in the resected section of the lower jaw. An exact reconstruction of the lower jaw bone is made possible using computer assisted individual osteotomy design, resulting in complete restoration regarding shape and functionality.

Mcps-range photon-counting x-ray computed tomography system

NASA Astrophysics Data System (ADS)

Sato, Eiichi; Oda, Yasuyuki; Abudurexiti, Abulajiang; Hagiwara, Osahiko; Enomoto, Toshiyuki; Sugimura, Shigeaki; Endo, Haruyuki; Sato, Shigehiro; Ogawa, Akira; Onagawa, Jun

2011-10-01

10 Mcps photon counting was carried out using a detector consisting of a 2.0 mm-thick ZnO (zinc oxide) single-crystal scintillator and an MPPC (multipixel photon counter) module in an X-ray computed tomography (CT) system. The maximum count rate was 10 Mcps (mega counts per second) at a tube voltage of 70 kV and a tube current of 2.0 mA. Next, a photon-counting X-ray CT system consists of an X-ray generator, a turntable, a scan stage, a two-stage controller, the ZnO-MPPC detector, a counter card (CC), and a personal computer (PC). Tomography is accomplished by repeated linear scans and rotations of an object, and projection curves of the object are obtained by the linear scan with a scan velocity of 25 mm/s. The pulses of the event signal from the module are counted by the CC in conjunction with the PC. The exposure time for obtaining a tomogram was 600 s at a scan step of 0.5 mm and a rotation step of 1.0°, and photon-counting CT was accomplished using iodine-based contrast media.

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

PubMed Central

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

2018-01-01

As key functional units in neural circuits, different types of neuronal synapses play distinct roles in brain information processing, learning, and memory. Synaptic abnormalities are believed to underlie various neurological and psychiatric disorders. Here, by combining cryo-electron tomography and cryo-correlative light and electron microscopy, we distinguished intact excitatory and inhibitory synapses of cultured hippocampal neurons, and visualized the in situ 3D organization of synaptic organelles and macromolecules in their native state. Quantitative analyses of >100 synaptic tomograms reveal that excitatory synapses contain a mesh-like postsynaptic density (PSD) with thickness ranging from 20 to 50 nm. In contrast, the PSD in inhibitory synapses assumes a thin sheet-like structure ∼12 nm from the postsynaptic membrane. On the presynaptic side, spherical synaptic vesicles (SVs) of 25–60 nm diameter and discus-shaped ellipsoidal SVs of various sizes coexist in both synaptic types, with more ellipsoidal ones in inhibitory synapses. High-resolution tomograms obtained using a Volta phase plate and electron filtering and counting reveal glutamate receptor-like and GABAA receptor-like structures that interact with putative scaffolding and adhesion molecules, reflecting details of receptor anchoring and PSD organization. These results provide an updated view of the ultrastructure of excitatory and inhibitory synapses, and demonstrate the potential of our approach to gain insight into the organizational principles of cellular architecture underlying distinct synaptic functions. SIGNIFICANCE STATEMENT To understand functional properties of neuronal synapses, it is desirable to analyze their structure at molecular resolution. We have developed an integrative approach combining cryo-electron tomography and correlative fluorescence microscopy to visualize 3D ultrastructural features of intact excitatory and inhibitory synapses in their native state. Our approach shows that inhibitory synapses contain uniform thin sheet-like postsynaptic densities (PSDs), while excitatory synapses contain previously known mesh-like PSDs. We discovered “discus-shaped” ellipsoidal synaptic vesicles, and their distributions along with regular spherical vesicles in synaptic types are characterized. High-resolution tomograms further allowed identification of putative neurotransmitter receptors and their heterogeneous interaction with synaptic scaffolding proteins. The specificity and resolution of our approach enables precise in situ analysis of ultrastructural organization underlying distinct synaptic functions. PMID:29311144

Rapid structural analysis of nanomaterials in aqueous solutions

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Active illumination using a digital micromirror device for quantitative phase imaging.

PubMed

Shin, Seungwoo; Kim, Kyoohyun; Yoon, Jonghee; Park, YongKeun

2015-11-15

We present a powerful and cost-effective method for active illumination using a digital micromirror device (DMD) for quantitative phase-imaging techniques. Displaying binary illumination patterns on a DMD with appropriate spatial filtering, plane waves with various illumination angles are generated and impinged onto a sample. Complex optical fields of the sample obtained with various incident angles are then measured via Mach-Zehnder interferometry, from which a high-resolution 2D synthetic aperture phase image and a 3D refractive index tomogram of the sample are reconstructed. We demonstrate the fast and stable illumination-control capability of the proposed method by imaging colloidal spheres and biological cells. The capability of high-speed optical diffraction tomography is also demonstrated by measuring 3D Brownian motion of colloidal particles with the tomogram acquisition rate of 100 Hz.

4D electron tomography.

PubMed

Kwon, Oh-Hoon; Zewail, Ahmed H

2010-06-25

Electron tomography provides three-dimensional (3D) imaging of noncrystalline and crystalline equilibrium structures, as well as elemental volume composition, of materials and biological specimens, including those of viruses and cells. We report the development of 4D electron tomography by integrating the fourth dimension (time resolution) with the 3D spatial resolution obtained from a complete tilt series of 2D projections of an object. The different time frames of tomograms constitute a movie of the object in motion, thus enabling studies of nonequilibrium structures and transient processes. The method was demonstrated using carbon nanotubes of a bracelet-like ring structure for which 4D tomograms display different modes of motion, such as breathing and wiggling, with resonance frequencies up to 30 megahertz. Applications can now make use of the full space-time range with the nanometer-femtosecond resolution of ultrafast electron tomography.

4D Electron Tomography

NASA Astrophysics Data System (ADS)

Kwon, Oh-Hoon; Zewail, Ahmed H.

2010-06-01

Electron tomography provides three-dimensional (3D) imaging of noncrystalline and crystalline equilibrium structures, as well as elemental volume composition, of materials and biological specimens, including those of viruses and cells. We report the development of 4D electron tomography by integrating the fourth dimension (time resolution) with the 3D spatial resolution obtained from a complete tilt series of 2D projections of an object. The different time frames of tomograms constitute a movie of the object in motion, thus enabling studies of nonequilibrium structures and transient processes. The method was demonstrated using carbon nanotubes of a bracelet-like ring structure for which 4D tomograms display different modes of motion, such as breathing and wiggling, with resonance frequencies up to 30 megahertz. Applications can now make use of the full space-time range with the nanometer-femtosecond resolution of ultrafast electron tomography.

Cryo-tomography Tilt-series Alignment with Consideration of the Beam-induced Sample Motion

PubMed Central

Fernandez, Jose-Jesus; Li, Sam; Bharat, Tanmay A. M.; Agard, David A.

2018-01-01

Recent evidence suggests that the beam-induced motion of the sample during tilt-series acquisition is a major resolution-limiting factor in electron cryo-tomography (cryoET). It causes suboptimal tilt-series alignment and thus deterioration of the reconstruction quality. Here we present a novel approach to tilt-series alignment and tomographic reconstruction that considers the beam-induced sample motion through the tilt-series. It extends the standard fiducial-based alignment approach in cryoET by introducing quadratic polynomials to model the sample motion. The model can be used during reconstruction to yield a motion-compensated tomogram. We evaluated our method on various datasets with different sample sizes. The results demonstrate that our method could be a useful tool to improve the quality of tomograms and the resolution in cryoET. PMID:29410148

Phase-Resolved Spectroscopy of the Low-Mass X-ray Binary V801 Ara

NASA Astrophysics Data System (ADS)

Brauer, Kaley; Vrtilek, Saeqa Dil; Peris, Charith; McCollough, Michael

2018-06-01

We present phase-resolved optical spectra of the low mass X-ray binary system V801 Ara. The spectra, obtained in 2014 with IMACS on the Magellan/Baade telescope at Las Campanas Observatory, cover the full binary orbit of 3.8 hours. They contain strong emission features allowing us to map the emission of Hα, Hβ, He II λ4686, and the Bowen blend at λ4640. The radial velocity curves of the Bowen blend shows significantly stronger modulation at the orbital period than Hα as expected for the former originating on the secondary with the latter consistent with emission dominated by the disk. Our tomograms of Hα and Hβ are the most detailed studies of these lines for V801 to date and they clearly detect the accretion disk. The Hβ emission extends to higher velocities than Hα, suggesting emission from closer to the neutron star and differentiating temperature variance in the accretion disk for the first time. The center of the accretion disk appears offset from the center-of-mass of the neutron star as has been seen in several other X-ray binaries. This is often interpreted to imply disk eccentricity. Our tomograms do not show strong evidence for a hot spot at the point where the accretion stream hits the disk. This could imply a reduced accretion rate or could be due to the spot being drowned out by bright accretion flow around it. There is enhanced emission further along the disk, however, which implies gas stream interaction downstream of the hot spot.

Nonclassicality and decoherence of photon-added squeezed coherent Schrödinger kitten states in a Kerr medium

NASA Astrophysics Data System (ADS)

Chakrabarti, R.; Yogesh, V.

2018-01-01

We study the nonclassicality of the evolution of a superposition of an arbitrary number of photon-added squeezed coherent Schrödinger cat states in a nonlinear Kerr medium. The nonlinearity of the medium gives rise to the periodicities of the quantities such as the Wehrl entropy SQ and the negativity δW of the W-distribution, and a series of local minima of these quantities arise at the rational submultiples of the said period. At these local minima the evolving state coincides with the transient Yurke-Stoler type of photon-added squeezed kitten states, which, for the choice of the phase space variables reflecting their macroscopic nature, show extremely short-lived behavior. Proceeding further we provide the closed form tomograms, which furnish the alternate description of these short-lived states. The increasing complexity in the kitten formations induces more number of interference terms that trigger more quantumness of the corresponding states. The nonclassical depth of the photon-added squeezed kitten states are observed to be of maximum possible value. Employing the Lindblad master equation approach we study the amplitude and the phase damping models for the initial state considered here. In the phase damping model the nonclassicality is not completely erased even in the long time limit when the dynamical quantities, such as the negativity δW and the tomogram, assume nontrivial asymptotic values.

Three-dimensional holographic display of ultrasound computed tomograms

NASA Astrophysics Data System (ADS)

Andre, Michael P.; Janee, Helmar S.; Ysrael, Mariana Z.; Hodler, Jeurg; Olson, Linda K.; Leopold, George R.; Schulz, Raymond

1997-05-01

Breast ultrasound is a valuable adjunct to mammography but is limited by a very small field of view, particularly with high-resolution transducers necessary for breast diagnosis. We have been developing an ultrasound system based on a diffraction tomography method that provides slices through the breast on a large 20-cm diameter circular field of view. Eight to fifteen images are typically produced in sequential coronal planes from the nipple to the chest wall with either 0.25 or 0.5 mm pixels. As a means to simplify the interpretation of this large set of images, we report experience with 3D life-sized displays of the entire breast of human volunteers using a digital holographic technique. The compound 3D holographic images are produced from the digital image matrix, recorded on 14 X 17 inch transparency and projected on a special white-light viewbox. Holographic visualization of the entire breast has proved to be the preferred method for 3D display of ultrasound computed tomography images. It provides a unique perspective on breast anatomy and may prove useful for biopsy guidance and surgical planning.

Characteristics of a ceramic-substrate x-ray diode and its application to computed tomography

NASA Astrophysics Data System (ADS)

Watanabe, Manabu; Sato, Eiichi; Kodama, Hajime; Hagiwara, Osahiko; Matsukiyo, Hiroshi; Osawa, Akihiro; Enomoto, Toshiyuki; Kusachi, Shinya; Sato, Shigehiro; Ogawa, Akira

2013-09-01

X-ray photon counting was performed using a silicon X-ray diode (Si-XD) at a tube current of 2.0 mA and tube voltages ranging from 50 to 70 kV. The Si-XD is a high-sensitivity Si photodiode selected for detecting X-ray photons, and Xray photons are directly detected using the Si-XD without a scintillator. Photocurrent from the diode is amplified using charge-sensitive and shaping amplifiers. To investigate the X-ray-electric conversion, we performed the event-pulseheight (EPH) analysis using a multichannel analyzer. Photon-counting computed tomography (PC-CT) is accomplished by repeated linear scans and rotations of an object, and projection curves of the object are obtained by the linear scan. The exposure time for obtaining a tomogram was 10 min at a scan step of 0.5 mm and a rotation step of 1.0°. In PC-CT at a tube voltage of 70 kV, the image contrast of iodine media fell with increasing lower-level voltage of the event pulse using a comparator.

Computed Tomographic Pattern of Physiological Intracranial Calcifications in a City in Central Africa

PubMed Central

Uduma, Uduma Felix; Pius, Fokam; Mathieu, Motah

2012-01-01

Objective: Intracranial calcifications underlie certain brain diseases which may be de novo or systemic. But calclfications un-connected to pathologies are classified physiological. Aim: To evaluate physiological intracranial calcifications in Douala with establishment of earliest age range of detection. Materials and Methods: Prospective study of brain computed tomograms was done from April to October 2009 using Schumadzu CT Scan machine. Axial, reconstructed and bone window images as well Hounsfield unit measurements were used for final evaluations. Results were analysed with SSPS 3. Results: 132 patients with 75 males and 57 females were studied and 163 separate calcifications were identified due to co-existent calcifications. The highest calcification was in choroid plexi, constituiting 56.82% of the studied population. This was followed by pineal gland. Both were commonly co-existent with advancing age. These calcifications were first seen at 10-19years. No type of physiological intracranial calcification was seen below age 10. The least calcification of 0.76% of population was in dentate nucleus. Conclusion: No intra-cranial physiological calcifications started earlier than 9years in Douala, a city in Cameroon, Central Africa. PMID:22980109

Computed tomographic pattern of physiological intracranial calcifications in a city in central Africa.

PubMed

Uduma, Felix Uduma; Pius, Fokam; Mathieu, Motah

2011-12-29

Intracranial calcifications underlie certain brain diseases which may be de novo or systemic. But calcifications un-connected to pathologies are classified physiological. To evaluate physiological intracranial calcifications in Douala with establishment of earliest age range of detection. Prospective study of brain computed tomograms was done from April to October 2009 using Schumadzu CT Scan machine. Axial, reconstructed and bone window images as well Hounsfield unit measurements were used for final evaluations. RESULTS were analysed with SSPS 3. 132 patients with 75 males and 57 females were studied and 163 separate calcifications were identified due to co-existent calcifications. The highest calcification was in choroid plexi, constituting 56.82% of the studied population. This was followed by pineal gland. Both were commonly co-existent with advancing age. These calcifications were first seen at 10-19 years. No type of physiological intracranial calcification was seen below age 10. The least calcification of 0.76% of population was in dentate nucleus. No intra-cranial physiological calcifications started earlier than 9 years in Douala, a city in Cameroon, Central Africa.

Internal Carotid Artery Hypoplasia: Role of Color-Coded Carotid Duplex Sonography.

PubMed

Chen, Pei-Ya; Liu, Hung-Yu; Lim, Kun-Eng; Lin, Shinn-Kuang

2015-10-01

The purpose of this study was to determine the role of color-coded carotid duplex sonography for diagnosis of internal carotid artery hypoplasia. We retrospectively reviewed 25,000 color-coded carotid duplex sonograms in our neurosonographic database to establish more diagnostic criteria for internal carotid artery hypoplasia. A definitive diagnosis of internal carotid artery hypoplasia was made in 9 patients. Diagnostic findings on color-coded carotid duplex imaging include a long segmental small-caliber lumen (52% diameter) with markedly decreased flow (13% flow volume) in the affected internal carotid artery relative to the contralateral side but without intraluminal lesions. Indirect findings included markedly increased total flow volume (an increase of 133%) in both vertebral arteries, antegrade ipsilateral ophthalmic arterial flow, and a reduced vessel diameter with increased flow resistance in the ipsilateral common carotid artery. Ten patients with distal internal carotid artery dissection showed a similar color-coded duplex pattern, but the reductions in the internal and common carotid artery diameters and increase in collateral flow from the vertebral artery were less prominent than those in hypoplasia. The ipsilateral ophthalmic arterial flow was retrograde in 40% of patients with distal internal carotid artery dissection. In addition, thin-section axial and sagittal computed tomograms of the skull base could show the small diameter of the carotid canal in internal carotid artery hypoplasia and help distinguish hypoplasia from distal internal carotid artery dissection. Color-coded carotid duplex sonography provides important clues for establishing a diagnosis of internal carotid artery hypoplasia. A hypoplastic carotid canal can be shown by thin-section axial and sagittal skull base computed tomography to confirm the final diagnosis. © 2015 by the American Institute of Ultrasound in Medicine.

Quantitative wood–adhesive penetration with X-ray computed tomography

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

Paris, Jesse L.; Kamke, Frederick A.

Micro X-ray computed tomography (XCT) was used to analyze the 3D adhesive penetration behavior of different wood–adhesive bondlines. Three adhesives, a phenol formaldehyde (PF), a polymeric diphenylmethane diisocyanate (pMDI), and a hybrid polyvinyl acetate (PVA), all tagged with iodine for enhanced X-ray attenuation, were used to prepare single-bondline laminates in two softwoods, Douglas-fir and loblolly pine, and one hardwood, a hybrid polar. Adhesive penetration depth was measured with two separate calculations, and results were compared with 2D fluorescent micrographs. A total of 54 XCT scans were collected, representing six replicates of each treatment type; each replicate, however, consisted of approximatelymore » 1500 individual, cross-section slices stacked along the specimen length. As these adhesives were highly modified, the presented results do not indicate typical behavior for their broader adhesive classes. Still, clear penetration differences were observed between each adhesive type, and between wood species bonded with both the PF and pMDI adhesives. Furthermore, penetration results depended on the calculation method used. Two adhesive types with noticeably different resin distributions in the cured bondline, showed relatively similar penetration depths when calculated with a traditional effective penetration equation. However, when the same data was calculated with a weighted penetration calculation, which accounts for both adhesive area and depth, the results appeared to better represent the different distributions depicted in the photomicrographs and tomograms. Additionally, individual replicate comparisons showed variation due to specimen anatomy, not easily observed or interpreted from 2D images. Finally, 3D views of segmented 3D adhesive phases offered unique, in-situ views of the cured adhesive structures. In particular, voids formed by CO 2 bubbles generated during pMDI cure were clearly visible in penetrated columns of the solidified adhesive.« less

Fresnel-propagated imaging for the study of human tooth dentin by partially coherent x-ray tomography

NASA Astrophysics Data System (ADS)

Zabler, S.; Riesemeier, H.; Fratzl, P.; Zaslansky, P.

2006-09-01

Recent methods of phase imaging in x-ray tomography allow the visualization of features that are not resolved in conventional absorption microtomography. Of these, the relatively simple setup needed to produce Fresnel-propagated tomograms appears to be well suited to probe tooth-dentin where composition as well as microstructure vary in a graded manner. By adapting analytical propagation approximations we provide predictions of the form of the interference patterns in the 3D images, which we compare to numerical simulations as well as data obtained from measurements of water immersed samples. Our observations reveal details of the tubular structure of dentin, and may be evaluated similarly to conventional absorption tomograms. We believe this exemplifies the power of Fresnel-propagated imaging as a form of 3D microscopy, well suited to quantify gradual microstructural-variations in teeth and similar tissues.

Visco-acoustic wave-equation traveltime inversion and its sensitivity to attenuation errors

NASA Astrophysics Data System (ADS)

Yu, Han; Chen, Yuqing; Hanafy, Sherif M.; Huang, Jiangping

2018-04-01

A visco-acoustic wave-equation traveltime inversion method is presented that inverts for the shallow subsurface velocity distribution. Similar to the classical wave equation traveltime inversion, this method finds the velocity model that minimizes the squared sum of the traveltime residuals. Even though, wave-equation traveltime inversion can partly avoid the cycle skipping problem, a good initial velocity model is required for the inversion to converge to a reasonable tomogram with different attenuation profiles. When Q model is far away from the real model, the final tomogram is very sensitive to the starting velocity model. Nevertheless, a minor or moderate perturbation of the Q model from the true one does not strongly affect the inversion if the low wavenumber information of the initial velocity model is mostly correct. These claims are validated with numerical tests on both the synthetic and field data sets.

Comparative Analysis of Cervical Spine Management in a Subset of Severe Traumatic Brain Injury Cases Using Computer Simulation

PubMed Central

Carter, Kimbroe J.; Dunham, C. Michael; Castro, Frank; Erickson, Barbara

2011-01-01

Background No randomized control trial to date has studied the use of cervical spine management strategies in cases of severe traumatic brain injury (TBI) at risk for cervical spine instability solely due to damaged ligaments. A computer algorithm is used to decide between four cervical spine management strategies. A model assumption is that the emergency room evaluation shows no spinal deficit and a computerized tomogram of the cervical spine excludes the possibility of fracture of cervical vertebrae. The study's goal is to determine cervical spine management strategies that maximize brain injury functional survival while minimizing quadriplegia. Methods/Findings The severity of TBI is categorized as unstable, high risk and stable based on intracranial hypertension, hypoxemia, hypotension, early ventilator associated pneumonia, admission Glasgow Coma Scale (GCS) and age. Complications resulting from cervical spine management are simulated using three decision trees. Each case starts with an amount of primary and secondary brain injury and ends as a functional survivor, severely brain injured, quadriplegic or dead. Cervical spine instability is studied with one-way and two-way sensitivity analyses providing rankings of cervical spine management strategies for probabilities of management complications based on QALYs. Early collar removal received more QALYs than the alternative strategies in most arrangements of these comparisons. A limitation of the model is the absence of testing against an independent data set. Conclusions When clinical logic and components of cervical spine management are systematically altered, changes that improve health outcomes are identified. In the absence of controlled clinical studies, the results of this comparative computer assessment show that early collar removal is preferred over a wide range of realistic inputs for this subset of traumatic brain injury. Future research is needed on identifying factors in projecting awakening from coma and the role of delirium in these cases. PMID:21544239

Method for evaluation of predictive models of microwave ablation via post-procedural clinical imaging

NASA Astrophysics Data System (ADS)

Collins, Jarrod A.; Brown, Daniel; Kingham, T. Peter; Jarnagin, William R.; Miga, Michael I.; Clements, Logan W.

2015-03-01

Development of a clinically accurate predictive model of microwave ablation (MWA) procedures would represent a significant advancement and facilitate an implementation of patient-specific treatment planning to achieve optimal probe placement and ablation outcomes. While studies have been performed to evaluate predictive models of MWA, the ability to quantify the performance of predictive models via clinical data has been limited to comparing geometric measurements of the predicted and actual ablation zones. The accuracy of placement, as determined by the degree of spatial overlap between ablation zones, has not been achieved. In order to overcome this limitation, a method of evaluation is proposed where the actual location of the MWA antenna is tracked and recorded during the procedure via a surgical navigation system. Predictive models of the MWA are then computed using the known position of the antenna within the preoperative image space. Two different predictive MWA models were used for the preliminary evaluation of the proposed method: (1) a geometric model based on the labeling associated with the ablation antenna and (2) a 3-D finite element method based computational model of MWA using COMSOL. Given the follow-up tomographic images that are acquired at approximately 30 days after the procedure, a 3-D surface model of the necrotic zone was generated to represent the true ablation zone. A quantification of the overlap between the predicted ablation zones and the true ablation zone was performed after a rigid registration was computed between the pre- and post-procedural tomograms. While both model show significant overlap with the true ablation zone, these preliminary results suggest a slightly higher degree of overlap with the geometric model.

Introduction of a hybrid treatment delivery system used for quality assurance in multi-catheter interstitial brachytherapy

NASA Astrophysics Data System (ADS)

Kallis, Karoline; Kreppner, Stephan; Lotter, Michael; Fietkau, Rainer; Strnad, Vratislav; Bert, Christoph

2018-05-01

Multi-catheter interstitial brachytherapy (iBT) is a treatment option for breast cancer patients after breast conserving surgery. Typically, only a few additional quality interventions after the first irradiation have been introduced to ensure the planned treatment delivery. Therefore, the purpose of this study is to show the possibilities of an electromagnetic tracking (EMT) system integrated into the afterloader for quality assurance (QA) in high-dose rate (HDR) iBT of patients with breast cancer. The hybrid afterloader system equipped with an electromagnetic sensor was used for all phantom and patient measurements. Phantom measurements were conducted to estimate the quality of different evaluation schemes. After a coherent point drift registration of the EMT traces to the reconstructed catheters based on computed tomograms the dwell positions (DP) were defined. Different fitting and interpolation methods were analyzed for the reconstruction of DPs. All estimated DPs were compared to the DPs defined in treatment planning. Until now, the implant geometry of 20 patients treated with HDR brachytherapy was acquired and explored. Regarding the reconstruction techniques, both fitting and interpolation were able to detect manually introduced shifts and swaps. Nonetheless, interpolation showed superior results (RMSE  =  1.27 mm), whereas fitting seemed to be more stable to distortion and motion. The EMT system proved to be beneficial for QA in brachytherapy and furthermore, clinical feasibility was proven.

The Nature and Subsurface Geometry of Late Holocene Coquina Rocks, Karaburun-Istanbul, NW Turkey

NASA Astrophysics Data System (ADS)

Ekinci, Y. L.; Demirci, A.; Erginal, A. E.; Kaya, H.; Ekinci, R.

2012-04-01

The so-called coquina defines moderately to hardly amalgamated shell debris by calcium carbonate cement. Even though its some depositional features are similar to intertidal beachrocks and carbonate-cemented dune rocks or eolianites, coquina occurs in shoal environments and is, in some cases, representative of tectonically uplifted coasts when it exposes remarkably above sea-level. In this study (supported financially by the Research Foundation of Çanakkale Onsekiz Mart University under project number COMUBAP: 2011/41), we discuss diagenetic features, radiocarbon age and subsurface geometry of coquina on Black Sea coast of Istanbul, NW Turkey, where such a Late Holocene occurrence has not been recorded so far. Having a visible thickness of 1 m, the coquina beds crop out on a slightly inclined wide beach formed mostly of shell fragments less than 5 cm in size. It contains calcite and aragonite as connective cement and broken or unbroken shells of Donacilla sp., Pecten glaucum and Ostrea edulis together with various foraminifera such as Elphidium macellum Ammonia compacta and coccolithophore Emiliania huxleyi. Radiocarbon ages from four bulk samples yielded calibrated ages ranging between 3.7 and 2.8 ka BP. Electrical resistivity tomography survey along three distinct transects perpendicular to the coastline were carried out in order to understand the thickness of coquina and its subsurface extensions along the beach. The apparent resistivity data were acquired along the survey lines of 21 electrodes with electrode spacing of 2 m, to give a total length of the line of 40 m. Dipole-dipole electrode configuration was used for 9 data levels. Topographic changes at the locations of each electrode points were determined by means of optical leveling technique for a more accurate calculation and interpretation. Apparent resistivity data were inverted by using 2D smoothness-constrained least squares algorithm. Similar electrical resistivity tomograms were obtained for three lines after the inversion process. The 2D resistivity images displayed a depth range of ~ 4.5 m and showed a strong resistivity contrast between coquina beach material (composed of shell fragments) and coquina rocks. Low resistivity values located at the northern lowermost part of tomograms point to seawater saturated material whilst the highest resistivity values indicate coquina beach material, having larger pore spaces between the grains. The northern uppermost parts of the tomograms, having a moderate resistivity range, mark the coquina rocks with a thickness of ~ 1-1.5 m. Additionally, the images also showed that the landward extension of the coquina rocks reaches ~ 22 m. Keywords: Coquina rocks, diagenetic features, radiocarbon age, subsurface geometry, İstanbul-Turkey

Correction of scatter in megavoltage cone-beam CT

NASA Astrophysics Data System (ADS)

Spies, L.; Ebert, M.; Groh, B. A.; Hesse, B. M.; Bortfeld, T.

2001-03-01

The role of scatter in a cone-beam computed tomography system using the therapeutic beam of a medical linear accelerator and a commercial electronic portal imaging device (EPID) is investigated. A scatter correction method is presented which is based on a superposition of Monte Carlo generated scatter kernels. The kernels are adapted to both the spectral response of the EPID and the dimensions of the phantom being scanned. The method is part of a calibration procedure which converts the measured transmission data acquired for each projection angle into water-equivalent thicknesses. Tomographic reconstruction of the projections then yields an estimate of the electron density distribution of the phantom. It is found that scatter produces cupping artefacts in the reconstructed tomograms. Furthermore, reconstructed electron densities deviate greatly (by about 30%) from their expected values. The scatter correction method removes the cupping artefacts and decreases the deviations from 30% down to about 8%.

Minimally invasive sinus augmentation using ultrasonic piezoelectric vibration and hydraulic pressure: a multicenter retrospective study.

PubMed

Kim, Ji-Min; Sohn, Dong-Seok; Heo, Jeong-Uk; Park, Jun-Sub; Jung, Heui-Seung; Moon, Jee-Won; Lee, Ju-Hyoung; Park, In-Sook

2012-12-01

The purpose of this study was to evaluate the success rate of implants and vertical bone gain of edentulous posterior maxilla using ultrasonic piezoelectric vibration and hydraulic pressure, namely the hydrodynamic piezoelectric internal sinus elevation (HPISE) technique through a crestal approach. A total of 250 maxillary sinuses were augmented using HPISE and 353 implants (averaging 11.8 mm in length and 4.5 mm in diameter), with 12 different systems, were placed simultaneously with or without additional bone grafting. Plain radiograms and cone beam computed tomograms were taken in all patients to evaluate sinus augmentation. Membrane perforation was recorded at 10 of the 353 implant sites. The perforation rate was 2.83%. The total success rate of implantation was 97.2% after an average of 69.3 weeks of loading. The crestally approached sinus augmentation using ultrasonic piezoelectric vibration and hydraulic pressure is an additional method of maxillary sinus augmentation.

6 Mcps photon-counting X-ray computed tomography system using a 25 mm/s-scan linear LSO-MPPC detector and its application to gadolinium imaging

NASA Astrophysics Data System (ADS)

Sato, Eiichi; Oda, Yasuyuki; Abudurexiti, Abulajiang; Hagiwara, Osahiko; Matsukiyo, Hiroshi; Osawa, Akihiro; Enomoto, Toshiyuki; Watanabe, Manabu; Kusachi, Shinya; Sugimura, Shigeaki; Endo, Haruyuki; Sato, Shigehiro; Ogawa, Akira; Onagawa, Jun

2011-12-01

6 Mcps photon counting was carried out using a detector consisting of a 1.0 mm-thick LSO [Lu 2(SiO 4)O] single-crystal scintillator and an MPPC (multipixel photon counter) module in an X-ray computed tomography (CT) system. The maximum count rate was 6 Mcps (mega counts per second) at a tube voltage of 100 kV and a tube current of 0.91 mA. Next, a photon-counting X-ray CT system consists of an X-ray generator, a turntable, a scan stage, a two-stage controller, the LSO-MPPC detector, a counter card (CC), and a personal computer (PC). Tomography is accomplished by repeated linear scans and rotations of an object, and projection curves of the object are obtained by the linear scan with a scan velocity of 25 mm/s. The pulses of the event signal from the module are counted by the CC in conjunction with the PC. The exposure time for obtaining a tomogram was 600 s at a scan step of 0.5 mm and a rotation step of 1.0°, and photon-counting CT was accomplished using gadolinium-based contrast media.

PubMed Central

DI NARDO, W.; GIANNANTONIO, S.; DI GIUDA, D.; DE CORSO, E.; SCHINAIA, L.; PALUDETTI, G.

2013-01-01

SUMMARY Pre-surgery evaluation, indications for cochlear implantation and expectations in terms of post-operative functional results remain challenging topics in pre-lingually deaf adults. Our study has the purpose of determining the benefits of Single Photon Emission Tomography (SPECT) assessment in pre-surgical evaluation of pre-lingually deaf adults who are candidates for cochlear implantation. In 7 pre-lingually profoundly deaf patients, brain SPECT was performed at baseline conditions and in bilateral simultaneous multi-frequency acoustic stimulation. Six sagittal tomograms of both temporal cortices were used for semi-quantitative analysis in each patient. Percentage increases in cortical perfusion resulting from auditory stimulation were calculated. The results showed an inter-hemispherical asymmetry of the activation extension and intensity in the stimulated temporal areas. Consistent with the obtained brain activation data, patients were implanted preferring the side that showed higher activation after acoustic stimulus. Considering the increment in auditory perception performances, it was possible to point out a relationship between cortical brain activity shown by SPECT and hearing performances, and, even more significant, a correlation between post-operative functional performances and the activation of the most medial part of the sagittal temporal tomograms, corresponding to medium-high frequencies. In light of these findings, we believe that brain SPECT could be considered in the evaluation of deaf patients candidate for cochlear implantation, and that it plays a major role in functional assessment of the auditory cortex of pre-lingually deaf subjects, even if further studies are necessary to conclusively establish its utility. Further developments of this technique are possible by using trans-tympanic electrical stimulation of the cochlear promontory, which could give the opportunity to study completely deaf patients, whose evaluation is objectively difficult with current audiological methods. PMID:23620636

Regional Characterization of Tokyo Metoropolitan area using a highly-dense seismic netwok(MeSO-net)

NASA Astrophysics Data System (ADS)

Hirata, N.; Nakagawa, S.; Sakai, S.; Panayotopoulos, Y.; Ishikawa, M.; Ishibe, T.; Kimura, H.; Honda, R.

2014-12-01

We have developed　a dense seismic network, MeSO-net (Metropolitan Seismic Observation network), since 2007 in the greater Tokyo urban region　under the Special Project for Earthquake Disaster Mitigation in Tokyo Metropolitan Area (FY2007-FY2011) and Special Project for Reducing Vulnerability for Urban Mega Earthquake Disasters (FY2012-FY2016)( Hirata et al., 2009). So far we have acquired more than 120TB continuous seismic data form MeSO-net which consists of about 300 seismic stations. Using MeSO-net data, we obtain clear P- and S- wave velocity tomograms (Nakagawa et al., 2010) and Qp, Qs tomograms (Panayotopoulos et al., 2014) which show a clear image of Philippine Sea Plate (PSP) and PAcific Plate (PAP). A depth to the top of PSP, 20 to 30 km beneath northern part of Tokyo bay, is about 10 km shallower than previous estimates based on the distribution of seismicity (Ishida, 1992). This shallower plate geometry changes estimations of strong ground motion for seismic hazards analysis within the Tokyo region. Based on elastic wave velocities of rocks and minerals, we interpreted the tomographic images as petrologic images. Tomographic images revealed the presence of two stepwise velocity increase of the top layer of the subducting PSP slab. Because strength of the serpentinized peridotite is not large enough for brittle fracture, if the area is smaller than previously estimated, a possible area of the large thrust fault on the upper surface of PSP can be larger than previously thought. Change of seismicity rate after the 2011 Tohoku-oki earthquake suggests change of stressing rate in greater Tokyo. Quantitative analysis of MeSO-net data shows significant increase of rate of earthquakes that have a fault orientation favorable to increasing Coulomb stress after the Tohoku-oki event.

Lithostratigraphic and Hydrogeologic Characteristics of the Ordovician Sinnipee Group in the Vicinity of Waupun, Fond du Lac County, Wisconsin, 1995-96

USGS Publications Warehouse

Dunning, Charles P.; Yeskis, Douglas J.

2007-01-01

Three boreholes were drilled at a farm site near Waupun, Wis., to improve the understanding of regional hydrogeology of the Ordovician Sinnipee Group. At the site the Sinnipee Group is the uppermost bedrock unit and is found to be about 183 ft thick. On the basis of core descriptions by the Illinois State Geological Survey, the Sinnipee Group at the site comprises (stratigraphically lowest to highest) the Platteville Formation (about 51 ft thick), the Decorah Formation (about 14 ft thick), and the Galena Dolomite (about 119 ft thick). The Illinois State Geological Survey noted that hardgrounds were common in the rock core, some having stratigraphic significance. Four very well developed hardgrounds were identified, three of which were used as formation or member contacts. The hardground at about 797 ft NGVD 29 represents the top of the Platteville Formation, the hardground at about 754 ft represents the top of the Pecatonica Member of the Platteville Formation, and the hardground at about 746 ft represents the top of the Glenwood Formation. On the basis of samples collected from one borehole, the ground water at the site is of the calcium-magnesium bicarbonate type. Trichloroethene was detected in one sample at a concentration of 1 ?g/L, and the concentration of antimony in one sample exceeded the U.S. Environmental Protection Agency (USEPA) Primary Drinking Water Standard. Other water samples contained aluminum and sodium in concentrations that exceeded the USEPA Secondary Drinking Water Standard and the USEPA Drinking Water Equivalent Level, respectively. Samples from various depths contained concentrations of iron, manganese, or dissolved manganese that were near or exceeded the USEPA Secondary Drinking Water Standard. The cross-borehole radar tomography data show differences in velocity and attenuation among the three major units in the Sinnipee Group. Matrix porosity measured in rock-core samples correlates well with these velocity and attenuation tomograms. The Galena Dolomite has the lowest mean porosity at 2.4 percent (7 samples) and is represented in the tomograms as generally having the lowest attenuation and greatest velocity. Below the Galena Dolomite is a transition to a zone with the greatest attenuation and lowest velocity on the tomograms. The rock core shows this interval to be the shaley dolomite of the Decorah Formation which has a mean porosity of 8.3 percent (2 samples). Below the Decorah Formation, the Platteville Formation has a mean porosity of 3.6 percent (6 samples) and is represented in the tomograms as having velocity and attenuation generally intermediate between the Galena Dolomite and the Decorah Formation. The evaluation of the single-hole directional ground-penetrating radar reflection survey in FL-800 identified 15 reflectors (secondary permeability features). Some of the reflectors do correlate with fractures and partings noted on geophysical logs and rock core; however, many additional fractures and partings identified by the televiewer log and/or core description were not measured by the borehole radar survey. Horizontal or sub-horizontal reflectors (bedding-plane partings) which do correlate with indications of bedding-plane partings on the acoustic televiewer intersect the borehole at about 917 ft, 907 ft, 870 ft, 805 ft, and 797 ft. The flowmeter profiles indicate that water entering and exiting the boreholes at seven bedding-plane partings accounts for most of the total borehole transmissivity. The flowmeter profiles in all three boreholes show that more than 90 percent of the total borehole transmissivity is provided by bedding-plane partings found at 870 ft and higher stratigraphically within the Galena Dolomite. Static water levels were measured in selected intervals of the three boreholes, and vertical hydraulic gradients were estimated by comparing levels in adjacent intervals. Gradients were found to be almost uniformly downward, ranging from -0.040 to -1.251 ft/ft. On th

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

PubMed

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

2018-02-07

As key functional units in neural circuits, different types of neuronal synapses play distinct roles in brain information processing, learning, and memory. Synaptic abnormalities are believed to underlie various neurological and psychiatric disorders. Here, by combining cryo-electron tomography and cryo-correlative light and electron microscopy, we distinguished intact excitatory and inhibitory synapses of cultured hippocampal neurons, and visualized the in situ 3D organization of synaptic organelles and macromolecules in their native state. Quantitative analyses of >100 synaptic tomograms reveal that excitatory synapses contain a mesh-like postsynaptic density (PSD) with thickness ranging from 20 to 50 nm. In contrast, the PSD in inhibitory synapses assumes a thin sheet-like structure ∼12 nm from the postsynaptic membrane. On the presynaptic side, spherical synaptic vesicles (SVs) of 25-60 nm diameter and discus-shaped ellipsoidal SVs of various sizes coexist in both synaptic types, with more ellipsoidal ones in inhibitory synapses. High-resolution tomograms obtained using a Volta phase plate and electron filtering and counting reveal glutamate receptor-like and GABA A receptor-like structures that interact with putative scaffolding and adhesion molecules, reflecting details of receptor anchoring and PSD organization. These results provide an updated view of the ultrastructure of excitatory and inhibitory synapses, and demonstrate the potential of our approach to gain insight into the organizational principles of cellular architecture underlying distinct synaptic functions. SIGNIFICANCE STATEMENT To understand functional properties of neuronal synapses, it is desirable to analyze their structure at molecular resolution. We have developed an integrative approach combining cryo-electron tomography and correlative fluorescence microscopy to visualize 3D ultrastructural features of intact excitatory and inhibitory synapses in their native state. Our approach shows that inhibitory synapses contain uniform thin sheet-like postsynaptic densities (PSDs), while excitatory synapses contain previously known mesh-like PSDs. We discovered "discus-shaped" ellipsoidal synaptic vesicles, and their distributions along with regular spherical vesicles in synaptic types are characterized. High-resolution tomograms further allowed identification of putative neurotransmitter receptors and their heterogeneous interaction with synaptic scaffolding proteins. The specificity and resolution of our approach enables precise in situ analysis of ultrastructural organization underlying distinct synaptic functions. Copyright © 2018 Tao, Liu et al.

Improved specimen reconstruction by Hilbert phase contrast tomography.

PubMed

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

2008-11-01

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

Maxillary growth in a congenital cleft palate canine model for surgical research.

PubMed

Paradas-Lara, Irene; Casado-Gómez, Inmaculada; Martín, Conchita; Martínez-Sanz, Elena; López-Gordillo, Yamila; González, Pablo; Rodríguez-Bobada, Cruz; Chamorro, Manuel; Arias, Pablo; Maldonado, Estela; Ortega, Ricardo; Berenguer, Beatriz; Martínez-Álvarez, Concepción

2014-01-01

We have recently presented the Old Spanish Pointer dog, with a 15-20% spontaneous congenital cleft palate rate, as a unique experimental model of this disease. This study aimed to describe the cleft palate of these dogs for surgical research purposes and to determine whether congenital cleft palate influences maxillofacial growth. Seven newborn Old Spanish Pointer dogs of both sexes, comprising a cleft palate group (n = 4) and a normal palate group (n = 3), were fed using the same technique. Macroscopic photographs and plaster casts from the palate, lateral radiographs and computer tomograms of the skull were taken sequentially over 41 weeks, starting at week 5. The cleft morphology, the size and the tissue characteristics in these dogs resembled the human cleft better than current available animal models. During growth, the cleft width varies. Most of the transverse and longitudinal measures of the palate were statistically lower in the cleft palate group. The cleft palate group showed hypoplasia of the naso-maxillary complex. This model of congenital cleft palate seems suitable for surgical research purposes. A reduced maxillofacial pre- and post-natal development is associated to the congenital cleft palate in the Old Spanish Pointer dog. Copyright © 2013 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

EDITORIAL The 17th Central European Workshop on Quantum Optics

NASA Astrophysics Data System (ADS)

Man'ko, Margarita A.

2011-02-01

Although the origin of quantum optics can be traced back to the beginning of the 20th century, when the fundamental ideas about the quantum nature of the interaction between light and matter were put forward, the splendid blossoming of this part of physics began half a century later, after the invention of masers and lasers. It is remarkable that after another half a century the tree of quantum optics is not only very strong and spreading, but all its branches continue to grow, showing new beautiful blossoms and giving very useful fruits. A reflection of this progress has been the origin and development of the series of annual events called the Central European Workshops on Quantum Optics (CEWQO). They started at the beginning of the 1990s as rather small meetings of physicists from a few countries in central-eastern Europe, but in less than two decades they have transformed into important events, gathering 100 to 200 participants from practically all European countries. Moreover, many specialists from other continents like to attend these meetings, since they provide an excellent chance to hear about the latest results and new directions of research. Regarding this, it seems worth mentioning at least some of the most interesting and important areas of quantum optics that have attracted the attention of researchers for the past two decades. One of these areas is quantum information, which over the course of time has become an almost independent area of quantum physics. But it still maintains very close ties with quantum optics. The specific parts of this area are, in particular, quantum computing, quantum communication and quantum cryptography, and the problem of quantitative description of such genuine quantum phenomena as entanglement is one of the central items in the current stream of publications. Theory and experiment related to quantum tomography have also become important to contemporary quantum optics. They are closely related to the subject of so-called quantum-state engineering. Different schemes proposed within the framework of this new area enabled the creation in laboratories of various superpositions of quantum states which had previously existed only as beautiful mathematical constructions by theoreticians. Connected to this, recent experiments related to such old problems as decoherence and quantum-classical transition are quite impressive. The same can be said about the interrelations between quantum optics and physics of ultracold atoms and Bose-Einstein condensates. Great progress has been made in cavity quantum electrodynamics, and the past decade gave rise to the new area of circuit quantum electrodynamics. Nowadays, we are very close to the observation of the quantum behavior of macroscopic bodies (mirrors), and the methods used in quantum optics help to achieve this goal. Quantum optics over the past two decades has resulted in such impressive discoveries as the slowing down of light to extremely low velocities and the creation of photonic crystals. The new methods of achieving very strong coupling coefficients between quantized field modes and atomic degrees of freedom open new possibilities for storing and retrieving quantum information transmitted by light. New areas of terahertz, femto- and atto-second optics were born or were significantly developed during the past two decades. In addition, the tomographic-probability representation of photon-quantum states has created new possibilities both in theoretical and experimental aspects of quantum optics. Traditionally, measured optical tomograms of photon states were considered as a technical tool for reconstructing the Wigner functions of quantum states. It became clear that these measured tomograms are primary objects; one does not need to reconstruct the Wigner function to extract information on physical properties of the state, for example, on the state purity. Purity is experimentally obtained directly from measured optical tomograms of photon states. The uncertainty relations for photon quadratures were also checked for the thermal photon state using experimental values of optical tomograms and avoiding the reconstruction procedure of the Wigner function and its associated precision constrains. In the tomographic-probability representation of quantum mechanics and quantum optics, tomograms are used for the description of quantum states as an alternative to the wave function and density matrix. The purity, fidelity, entropy and photon temperature associated with quantum states are expressed in terms of tomograms. This provides the possibility of measuring these characteristics directly by taking optical tomograms and checking basic inequalities like entropic uncertainty relations, temperature-dependent quadrature uncertainty relations, etc. The better understanding that quantum states can be identified with measurable probability distributions like optical tomograms opens new prospects in quantum optics, for example, to check experimentally the uncertainty relations for higher quadrature momenta and to control the precision with which the fundamental inequalities of quantum mechanics are experimentally confirmed. This Topical Issue is a collection of papers presented at the 17th Central European Workshops on Quantum Optics (CEWQO10) held at the University of St Andrews, Scotland, UK, 6-11 June 2010. The other collaborators from different scientific centers who could not, due to different reasons, come to St Andrews but participated in the previous CEWQOs and plan to participate in future CEWQOs also contributed to this issue. The paper by Ulf Leonhardt and Natalia Korolkova, the CEWQO10 Organizers, opens this issue. The order of the following papers corresponds to the alphabetical order of the first author of the paper. The history of CEWQOs can be found in the Preface to the Proceedings of the 15th CEWQO (2009 Phys. Scr. T135 011005). The Proceedings of the 16th Central European Workshop on Quantum Optics (CEWQO09), held at the University of Turku, are also available (2010 Phys. Scr. T140). The 18th Central European Workshop on Quantum Optics (CEWQO11) will be held in Madrid, Spain on 30 May--3 June 2011. It will be chaired by Professor Luis Lorenzo Sanchez Soto from the Complutense University of Madrid. List of Papers The 17th Central European Workshop on Quantum Optics in St Andrews, Scotland Ulf Leonhardt and Natalia Korolkova Double self-Kerr scheme for optical Schrödinger-cat state preparation P Adam, Z Darázs, T Kiss and M Mechler Relations between scaling transformed Husimi functions, Wigner functions and symplectic tomograms describing corresponding physical states V A Andreev, D M Davidović, L D Davidović and M D Davidović Entanglement dynamics of two independent cavity-embedded quantum dots B Bellomo, G Compagno, R Lo Franco, A Ridolfo and S Savasta Dynamical stabilization of spin systems in time-dependent magnetic fields Yu V Bezvershenko, P I Holod and A Messina Entanglement dynamics of a bipartite system in squeezed vacuum reservoirs Smail Bougouffa and Awatif Hindi On Wheeler's delayed-choice Gedankenexperiment and its laboratory realization M Božić, L Vušković, M Davidović and Á S Sanz A smooth, holographically generated ring trap for the investigation of superfluidity in ultracold atoms Graham D Bruce, James Mayoh, Giuseppe Smirne, Lara Torralbo-Campo and Donatella Cassettari Parametric amplification of the classical field in cavities with photoexcited semiconductors V V Dodonov Mutually unbiased bases: tomography of spin states and the star-product scheme S N Filippov and V I Man'ko Quantum trajectory model for photon detectors and optoelectronic devices Teppo Häyrynen, Jani Oksanen and Jukka Tulkki Entanglement in two-mode continuous variable open quantum systems Aurelian Isar A classical field comeback? The classical field viewpoint on triparticle entanglement Andrei Khrennikov Experimental investigation of the enhancement factor and the cross-correlation function for graphs with and without time-reversal symmetry: the open system case Michał Ławniczak, Szymon Bauch, Oleh Hul and Leszek Sirko Independent nonclassical tests for states and measurements in the same experiment Alfredo Luis and Ángel Rivas On the classical capacity of quantum Gaussian channels Cosmo Lupo, Stefano Pirandola, Paolo Aniello and Stefano Mancini Entropic inequalities for center-of-mass tomograms Margarita A Man'ko Semiclassical dynamics for an ion confined within a nonlinear electromagnetic trap Bogdan M Mihalcea Zeno-like phenomena in STIRAP processes B Militello, M Scala, A Messina and N V Vitanov A beam splitter with second-order nonlinearity modeled as a nonlinear coupler V Peřinová, A Lukš and J Křepelka Energy-level shifts of a uniformly accelerated atom between two reflecting plates L Rizzuto and S Spagnolo Cross-Kerr nonlinearities in an optically dressed periodic medium K Słowik, A Raczyński, J Zaremba, S Zielińska-Kaniasty, M Artoni and G C La Rocca An approximate effective beamsplitter interaction between light and atomic ensembles Richard Tatham, David Menzies and Natalia Korolkova Stochastic simulation of long-time nonadiabatic dynamics Daniel A Uken, Alessandro Sergi and Francesco Petruccione

Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility

PubMed Central

Pancera, Marie; Majeed, Shahzad; Ban, Yih-En Andrew; Chen, Lei; Huang, Chih-chin; Kong, Leopold; Stuckey, Jonathan; Zhou, Tongqing; Robinson, James E.; Schief, William R.; Sodroski, Joseph; Wyatt, Richard; Kwong, Peter D.

2009-01-01

The viral spike of HIV-1 is composed of three gp120 envelope glycoproteins attached noncovalently to three gp41 transmembrane molecules. Viral entry is initiated by binding to the CD4 receptor on the cell surface, which induces large conformational changes in gp120. These changes not only provide a model for receptor-triggered entry, but affect spike sensitivity to drug- and antibody-mediated neutralization. Although some of the details of the CD4-induced conformational change have been visualized by crystal structures and cryoelectron tomograms, the critical gp41-interactive region of gp120 was missing from previous atomic-level characterizations. Here we determine the crystal structure of an HIV-1 gp120 core with intact gp41-interactive region in its CD4-bound state, compare this structure to unliganded and antibody-bound forms to identify structurally invariant and plastic components, and use ligand-oriented cryoelectron tomograms to define component mobility in the viral spike context. Newly defined gp120 elements proximal to the gp41 interface complete a 7-stranded β-sandwich, which appeared invariant in conformation. Loop excursions emanating from the sandwich form three topologically separate—and structurally plastic—layers, topped off by the highly glycosylated gp120 outer domain. Crystal structures, cryoelectron tomograms, and interlayer chemistry were consistent with a mechanism in which the layers act as a shape-changing spacer, facilitating movement between outer domain and gp41-associated β-sandwich and providing for conformational diversity used in immune evasion. A “layered” gp120 architecture thus allows movement among alternative glycoprotein conformations required for virus entry and immune evasion, whereas a β-sandwich clamp maintains gp120–gp41 interaction and regulates gp41 transitions. PMID:20080564

Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility.

PubMed

Pancera, Marie; Majeed, Shahzad; Ban, Yih-En Andrew; Chen, Lei; Huang, Chih-chin; Kong, Leopold; Kwon, Young Do; Stuckey, Jonathan; Zhou, Tongqing; Robinson, James E; Schief, William R; Sodroski, Joseph; Wyatt, Richard; Kwong, Peter D

2010-01-19

The viral spike of HIV-1 is composed of three gp120 envelope glycoproteins attached noncovalently to three gp41 transmembrane molecules. Viral entry is initiated by binding to the CD4 receptor on the cell surface, which induces large conformational changes in gp120. These changes not only provide a model for receptor-triggered entry, but affect spike sensitivity to drug- and antibody-mediated neutralization. Although some of the details of the CD4-induced conformational change have been visualized by crystal structures and cryoelectron tomograms, the critical gp41-interactive region of gp120 was missing from previous atomic-level characterizations. Here we determine the crystal structure of an HIV-1 gp120 core with intact gp41-interactive region in its CD4-bound state, compare this structure to unliganded and antibody-bound forms to identify structurally invariant and plastic components, and use ligand-oriented cryoelectron tomograms to define component mobility in the viral spike context. Newly defined gp120 elements proximal to the gp41 interface complete a 7-stranded beta-sandwich, which appeared invariant in conformation. Loop excursions emanating from the sandwich form three topologically separate--and structurally plastic--layers, topped off by the highly glycosylated gp120 outer domain. Crystal structures, cryoelectron tomograms, and interlayer chemistry were consistent with a mechanism in which the layers act as a shape-changing spacer, facilitating movement between outer domain and gp41-associated beta-sandwich and providing for conformational diversity used in immune evasion. A "layered" gp120 architecture thus allows movement among alternative glycoprotein conformations required for virus entry and immune evasion, whereas a beta-sandwich clamp maintains gp120-gp41 interaction and regulates gp41 transitions.

Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms

PubMed Central

Xu, Min; Chai, Xiaoqi; Muthakana, Hariank; Liang, Xiaodan; Yang, Ge; Zeev-Ben-Mordehai, Tzviya; Xing, Eric P.

2017-01-01

Abstract Motivation: Cellular Electron CryoTomography (CECT) enables 3D visualization of cellular organization at near-native state and in sub-molecular resolution, making it a powerful tool for analyzing structures of macromolecular complexes and their spatial organizations inside single cells. However, high degree of structural complexity together with practical imaging limitations makes the systematic de novo discovery of structures within cells challenging. It would likely require averaging and classifying millions of subtomograms potentially containing hundreds of highly heterogeneous structural classes. Although it is no longer difficult to acquire CECT data containing such amount of subtomograms due to advances in data acquisition automation, existing computational approaches have very limited scalability or discrimination ability, making them incapable of processing such amount of data. Results: To complement existing approaches, in this article we propose a new approach for subdividing subtomograms into smaller but relatively homogeneous subsets. The structures in these subsets can then be separately recovered using existing computation intensive methods. Our approach is based on supervised structural feature extraction using deep learning, in combination with unsupervised clustering and reference-free classification. Our experiments show that, compared with existing unsupervised rotation invariant feature and pose-normalization based approaches, our new approach achieves significant improvements in both discrimination ability and scalability. More importantly, our new approach is able to discover new structural classes and recover structures that do not exist in training data. Availability and Implementation: Source code freely available at http://www.cs.cmu.edu/∼mxu1/software. Contact: mxu1@cs.cmu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28881965

Human-machine interface for a VR-based medical imaging environment

NASA Astrophysics Data System (ADS)

Krapichler, Christian; Haubner, Michael; Loesch, Andreas; Lang, Manfred K.; Englmeier, Karl-Hans

1997-05-01

Modern 3D scanning techniques like magnetic resonance imaging (MRI) or computed tomography (CT) produce high- quality images of the human anatomy. Virtual environments open new ways to display and to analyze those tomograms. Compared with today's inspection of 2D image sequences, physicians are empowered to recognize spatial coherencies and examine pathological regions more facile, diagnosis and therapy planning can be accelerated. For that purpose a powerful human-machine interface is required, which offers a variety of tools and features to enable both exploration and manipulation of the 3D data. Man-machine communication has to be intuitive and efficacious to avoid long accustoming times and to enhance familiarity with and acceptance of the interface. Hence, interaction capabilities in virtual worlds should be comparable to those in the real work to allow utilization of our natural experiences. In this paper the integration of hand gestures and visual focus, two important aspects in modern human-computer interaction, into a medical imaging environment is shown. With the presented human- machine interface, including virtual reality displaying and interaction techniques, radiologists can be supported in their work. Further, virtual environments can even alleviate communication between specialists from different fields or in educational and training applications.

The role of the lateral pterygoid muscle in the sagittal fracture of mandibular condyle (SFMC) healing process.

PubMed

Liu, Chng-Kui; Liu, Ping; Meng, Fan-Wen; Deng, Bang-Lian; Xue, Yang; Mao, Tian-Qiu; Hu, Kai-Jin

2012-06-01

The aim of this study was to examine the role of the lateral peterygoid muscle in the reconstruction of the shape of the condyle during healing of a sagittal fracture of the mandibular condyle. Twenty adult sheep were divided into 2 groups: all had a unilateral operation on the right side when the anterior and posterior attachments of the discs were cut, and an oblique vertical osteotomy was made from the lateral pole of the condyle to the medial side of the condylar neck. Ten sheep had the lateral pterygoid muscle cut, and the other 10 sheep did not. Sheep were killed at 4 weeks (n=2 from each group), 12 weeks (n=4), and 24 weeks (n=4) postoperatively. Computed tomograms (CT) were taken before and after operations. We dissected the joints, and recorded with the naked eye the shape, degree of erosion, and amount of calcification of the temporomandibular joint (TMJ). In the group in which the lateral peterygoid muscle had not been cut the joints showed overgrowth of new bone and more advanced ankylosis. Our results show that the lateral pterygoid muscle plays an important part in reconstructing the shape of the condyle during the healing of a sagittal fracture of the mandibular condyle, and combined with the dislocated and damaged disc is an important factor in the aetiology of traumatic ankylosis of the TMJ. Copyright © 2011. Published by Elsevier Ltd.

Computational adaptive optics for broadband optical interferometric tomography of biological tissue

NASA Astrophysics Data System (ADS)

Boppart, Stephen A.

2015-03-01

High-resolution real-time tomography of biological tissues is important for many areas of biological investigations and medical applications. Cellular level optical tomography, however, has been challenging because of the compromise between transverse imaging resolution and depth-of-field, the system and sample aberrations that may be present, and the low imaging sensitivity deep in scattering tissues. The use of computed optical imaging techniques has the potential to address several of these long-standing limitations and challenges. Two related techniques are interferometric synthetic aperture microscopy (ISAM) and computational adaptive optics (CAO). Through three-dimensional Fourierdomain resampling, in combination with high-speed OCT, ISAM can be used to achieve high-resolution in vivo tomography with enhanced depth sensitivity over a depth-of-field extended by more than an order-of-magnitude, in realtime. Subsequently, aberration correction with CAO can be performed in a tomogram, rather than to the optical beam of a broadband optical interferometry system. Based on principles of Fourier optics, aberration correction with CAO is performed on a virtual pupil using Zernike polynomials, offering the potential to augment or even replace the more complicated and expensive adaptive optics hardware with algorithms implemented on a standard desktop computer. Interferometric tomographic reconstructions are characterized with tissue phantoms containing sub-resolution scattering particles, and in both ex vivo and in vivo biological tissue. This review will collectively establish the foundation for high-speed volumetric cellular-level optical interferometric tomography in living tissues.

Computational adaptive optics for broadband optical interferometric tomography of biological tissue.

PubMed

Adie, Steven G; Graf, Benedikt W; Ahmad, Adeel; Carney, P Scott; Boppart, Stephen A

2012-05-08

Aberrations in optical microscopy reduce image resolution and contrast, and can limit imaging depth when focusing into biological samples. Static correction of aberrations may be achieved through appropriate lens design, but this approach does not offer the flexibility of simultaneously correcting aberrations for all imaging depths, nor the adaptability to correct for sample-specific aberrations for high-quality tomographic optical imaging. Incorporation of adaptive optics (AO) methods have demonstrated considerable improvement in optical image contrast and resolution in noninterferometric microscopy techniques, as well as in optical coherence tomography. Here we present a method to correct aberrations in a tomogram rather than the beam of a broadband optical interferometry system. Based on Fourier optics principles, we correct aberrations of a virtual pupil using Zernike polynomials. When used in conjunction with the computed imaging method interferometric synthetic aperture microscopy, this computational AO enables object reconstruction (within the single scattering limit) with ideal focal-plane resolution at all depths. Tomographic reconstructions of tissue phantoms containing subresolution titanium-dioxide particles and of ex vivo rat lung tissue demonstrate aberration correction in datasets acquired with a highly astigmatic illumination beam. These results also demonstrate that imaging with an aberrated astigmatic beam provides the advantage of a more uniform depth-dependent signal compared to imaging with a standard gaussian beam. With further work, computational AO could enable the replacement of complicated and expensive optical hardware components with algorithms implemented on a standard desktop computer, making high-resolution 3D interferometric tomography accessible to a wider group of users and nonspecialists.

Patients who reattend after head injury: a high risk group.

PubMed Central

Voss, M.; Knottenbelt, J. D.; Peden, M. M.

1995-01-01

OBJECTIVE--To assess risk factors for important neurosurgical effects in patients who reattend after head injury. DESIGN--Retrospective study. SUBJECTS--606 patients who reattended a trauma unit after minor head injury. MAIN OUTCOME MEASURES--Intracranial abnormality detected on computed tomography or the need for neurosurgical intervention. RESULTS--Five patients died: two from unrelated causes and three from raised intracranial pressure. On multiple regression analysis the only significant predictor for both abnormality on computed tomography (14.4% of reattenders) and the need for operation (5% of reattenders) was vault fracture seen on the skull radiograph (P < 10(-6)); predictors for abnormal computed tomogram were a Glasgow coma scale score < 15 at either first or second attendance (P < 0.0001) and convulsion at second attendance (P < 0.05); predictive for operation only was penetrating injury of the skull (P < 10(-6)). On contingency table analysis these associations were confirmed. In addition significant associations with both abnormality on computed tomography and operation were focal neurological abnormality, weakness, or speech disturbance. Amnesia or loss of consciousness at the time of initial injury, personality change, and seizures were significantly associated only with abnormality on computed tomography. Headache, dizziness, nausea, and vomiting were common in reattenders but were found to have no independent significance. CONCLUSIONS--All patients who reattend after head injury should undergo computed tomography as at least 14% of scans can be expected to yield positive results. Where this facility is not available patients with predictors for operation should be urgently referred for neurosurgical opinion. Other patients can be readmitted and need referral only if symptoms persist despite symptomatic treatment or there is neurological deterioration while under observation. These patients are a high risk group and should be treated seriously. PMID:8520273

Image calibration and registration in cone-beam computed tomogram for measuring the accuracy of computer-aided implant surgery

NASA Astrophysics Data System (ADS)

Lam, Walter Y. H.; Ngan, Henry Y. T.; Wat, Peter Y. P.; Luk, Henry W. K.; Goto, Tazuko K.; Pow, Edmond H. N.

2015-02-01

Medical radiography is the use of radiation to "see through" a human body without breaching its integrity (surface). With computed tomography (CT)/cone beam computed tomography (CBCT), three-dimensional (3D) imaging can be produced. These imagings not only facilitate disease diagnosis but also enable computer-aided surgical planning/navigation. In dentistry, the common method for transfer of the virtual surgical planning to the patient (reality) is the use of surgical stent either with a preloaded planning (static) like a channel or a real time surgical navigation (dynamic) after registration with fiducial markers (RF). This paper describes using the corner of a cube as a radiopaque fiducial marker on an acrylic (plastic) stent, this RF allows robust calibration and registration of Cartesian (x, y, z)- coordinates for linking up the patient (reality) and the imaging (virtuality) and hence the surgical planning can be transferred in either static or dynamic way. The accuracy of computer-aided implant surgery was measured with reference to coordinates. In our preliminary model surgery, a dental implant was planned virtually and placed with preloaded surgical guide. The deviation of the placed implant apex from the planning was x=+0.56mm [more right], y=- 0.05mm [deeper], z=-0.26mm [more lingual]) which was within clinically 2mm safety range. For comparison with the virtual planning, the physically placed implant was CT/CBCT scanned and errors may be introduced. The difference of the actual implant apex to the virtual apex was x=0.00mm, y=+0.21mm [shallower], z=-1.35mm [more lingual] and this should be brought in mind when interpret the results.

A novel approach for planning orthognathic surgery: the integration of dental casts into three-dimensional printed mandibular models.

PubMed

Ayoub, A F; Rehab, M; O'Neil, M; Khambay, B; Ju, X; Barbenel, J; Naudi, K

2014-04-01

A method of producing a composite model consisting of a three-dimensional printed mandible bearing plaster teeth is presented. Printed models were obtained from cone beam computed tomograms (CBCT) of dry human mandibles. The plaster casts of the teeth were obtained from impressions of the teeth of the dry mandibles. The distorted teeth of the printed models were removed and replaced by the plaster casts of the teeth using a simple transfer jig. The accuracy of the composite models obtained from six mandibles was assessed from laser scans. The scans of the dry mandibles and the composite models were superimposed and the magnitude of the discrepancies at six points on the dentition and six on the mandible were obtained. It was concluded that the errors of the method were small enough to be clinically significant. The use of the composite models is illustrated in two clinical cases. Copyright © 2013 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Replacing Heavily Damaged Teeth by Third Molar Autotransplantation With the Use of Cone-Beam Computed Tomography and Rapid Prototyping.

PubMed

Verweij, Jop P; Anssari Moin, David; Wismeijer, Daniel; van Merkesteyn, J P Richard

2017-09-01

This article describes the autotransplantation of third molars to replace heavily damaged premolars and molars. Specifically, this article reports on the use of preoperative cone-beam computed tomographic planning and 3-dimensional (3D) printed replicas of donor teeth to prepare artificial tooth sockets. In the present case, an 18-year-old patient underwent autotransplantation of 3 third molars to replace 1 premolar and 2 molars that were heavily damaged after trauma. Approximately 1 year after the traumatic incident, autotransplantation with the help of 3D planning and rapid prototyping was performed. The right maxillary third molar replaced the right maxillary first premolar. The 2 mandibular wisdom teeth replaced the left mandibular first and second molars. During the surgical procedure, artificial tooth sockets were prepared with the help of 3D printed donor tooth copies to prevent iatrogenic damage to the actual donor teeth. These replicas of the donor teeth were designed based on the preoperative cone-beam computed tomogram and manufactured with the help of 3D printing techniques. The use of a replica of the donor tooth resulted in a predictable and straightforward procedure, with extra-alveolar times shorter than 2 minutes for all transplantations. The transplanted teeth were placed in infraocclusion and fixed with a suture splint. Postoperative follow-up showed physiologic integration of the transplanted teeth and a successful outcome for all transplants. In conclusion, this technique facilitates a straightforward and predictable procedure for autotransplantation of third molars. The use of printed analogues of the donor teeth decreases the risk of iatrogenic damage and the extra-alveolar time of the transplanted tooth is minimized. This facilitates a successful outcome. Copyright © 2017 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms.

PubMed

Xu, Min; Chai, Xiaoqi; Muthakana, Hariank; Liang, Xiaodan; Yang, Ge; Zeev-Ben-Mordehai, Tzviya; Xing, Eric P

2017-07-15

Cellular Electron CryoTomography (CECT) enables 3D visualization of cellular organization at near-native state and in sub-molecular resolution, making it a powerful tool for analyzing structures of macromolecular complexes and their spatial organizations inside single cells. However, high degree of structural complexity together with practical imaging limitations makes the systematic de novo discovery of structures within cells challenging. It would likely require averaging and classifying millions of subtomograms potentially containing hundreds of highly heterogeneous structural classes. Although it is no longer difficult to acquire CECT data containing such amount of subtomograms due to advances in data acquisition automation, existing computational approaches have very limited scalability or discrimination ability, making them incapable of processing such amount of data. To complement existing approaches, in this article we propose a new approach for subdividing subtomograms into smaller but relatively homogeneous subsets. The structures in these subsets can then be separately recovered using existing computation intensive methods. Our approach is based on supervised structural feature extraction using deep learning, in combination with unsupervised clustering and reference-free classification. Our experiments show that, compared with existing unsupervised rotation invariant feature and pose-normalization based approaches, our new approach achieves significant improvements in both discrimination ability and scalability. More importantly, our new approach is able to discover new structural classes and recover structures that do not exist in training data. Source code freely available at http://www.cs.cmu.edu/∼mxu1/software . mxu1@cs.cmu.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

A cylindrical specimen holder for electron cryo-tomography

PubMed Central

Palmer, Colin M.; Löwe, Jan

2014-01-01

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

Effect of occlusal appliances and clenching on the internally deranged TMJ space.

PubMed

Kuboki, T; Takenami, Y; Orsini, M G; Maekawa, K; Yamashita, A; Azuma, Y; Clark, G T

1999-01-01

Stabilization appliances and mandibular anterior repositioning appliances have been used to treat patients with internal derangement of the temporomandibular joint (TMJ) based on the assumption that these appliances work by decompressing the TMJ. The purpose of this study was to indirectly test this assumption. Bilateral TMJ tomograms of 7 subjects with unilateral anterior disc displacement without reduction (ADDwor) were taken during comfortable closure and during maximum clenching in maximum intercuspation; tomograms were also taken with the 2 types of occlusal appliances in use. Outlines of the condyle and the temporal fossa were automatically determined by an edge-detection protocol, and the minimum joint space dimension of the joints with and without ADDwor was automatically measured for each experimental condition as the outcome variable. Upon comfortable closure and maximum clenching, the minimum joint space dimensions of the ipsilateral and contralateral joints with the use of stabilization appliances and mandibular anterior repositioning appliances were not significantly different from those seen in maximum intercuspation. These findings do not indicate that these appliances induce an increase in joint space during closing and clenching in joints with ADDwor.

Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.

PubMed

Lagerstedt, Ingvar; Moore, William J; Patwardhan, Ardan; Sanz-García, Eduardo; Best, Christoph; Swedlow, Jason R; Kleywegt, Gerard J

2013-11-01

The Protein Data Bank in Europe (PDBe) has developed web-based tools for the visualisation and analysis of 3D electron microscopy (3DEM) structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB). The tools include: (1) a volume viewer for 3D visualisation of maps, tomograms and models, (2) a slice viewer for inspecting 2D slices of tomographic reconstructions, and (3) visual analysis pages to facilitate analysis and validation of maps, tomograms and models. These tools were designed to help non-experts and experts alike to get some insight into the content and assess the quality of 3DEM structures in EMDB and PDB without the need to install specialised software or to download large amounts of data from these archives. The technical challenges encountered in developing these tools, as well as the more general considerations when making archived data available to the user community through a web interface, are discussed. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Optimized x-ray source scanning trajectories for iterative reconstruction in high cone-angle tomography

NASA Astrophysics Data System (ADS)

Kingston, Andrew M.; Myers, Glenn R.; Latham, Shane J.; Li, Heyang; Veldkamp, Jan P.; Sheppard, Adrian P.

2016-10-01

With the GPU computing becoming main-stream, iterative tomographic reconstruction (IR) is becoming a com- putationally viable alternative to traditional single-shot analytical methods such as filtered back-projection. IR liberates one from the continuous X-ray source trajectories required for analytical reconstruction. We present a family of novel X-ray source trajectories for large-angle CBCT. These discrete (sparsely sampled) trajectories optimally fill the space of possible source locations by maximising the degree of mutually independent information. They satisfy a discrete equivalent of Tuy's sufficiency condition and allow high cone-angle (high-flux) tomog- raphy. The highly isotropic nature of the trajectory has several advantages: (1) The average source distance is approximately constant throughout the reconstruction volume, thus avoiding the differential-magnification artefacts that plague high cone-angle helical computed tomography; (2) Reduced streaking artifacts due to e.g. X-ray beam-hardening; (3) Misalignment and component motion manifests as blur in the tomogram rather than double-edges, which is easier to automatically correct; (4) An approximately shift-invariant point-spread-function which enables filtering as a pre-conditioner to speed IR convergence. We describe these space-filling trajectories and demonstrate their above-mentioned properties compared with a traditional helical trajectories.

X-ray Photon Counting Using 100 MHz Ready-Made Silicon P-Intrinsic-N X-ray Diode and Its Application to Energy-Dispersive Computed Tomography

NASA Astrophysics Data System (ADS)

Kodama, Hajime; Watanabe, Manabu; Sato, Eiichi; Oda, Yasuyuki; Hagiwara, Osahiko; Matsukiyo, Hiroshi; Osawa, Akihiro; Enomoto, Toshiyuki; Kusachi, Shinya; Sato, Shigehiro; Ogawa, Akira

2013-07-01

X-ray photons are directly detected using a 100 MHz ready-made silicon P-intrinsic-N X-ray diode (Si-PIN-XD). The Si-PIN-XD is shielded using an aluminum case with a 25-µm-thick aluminum window and a BNC connector. The photocurrent from the Si-PIN-XD is amplified by charge sensitive and shaping amplifiers, and the event pulses are sent to a multichannel analyzer (MCA) to measure X-ray spectra. At a tube voltage of 90 kV, we observe K-series characteristic X-rays of tungsten. Photon-counting computed tomography (PC-CT) is accomplished by repeated linear scans and rotations of an object, and projection curves of the object are obtained by linear scanning at a tube current of 2.0 mA. The exposure time for obtaining a tomogram is 10 min with scan steps of 0.5 mm and rotation steps of 1.0°. At a tube voltage of 90 kV, the maximum count rate is 150 kcps. We carry out PC-CT using gadolinium media and confirm the energy-dispersive effect with changes in the lower level voltage of the event pulse using a comparator.

An experimental study of arch perimeter and arch width increase with mandibular expansion: a finite element method.

PubMed

Baswaraj; Hemanth, M; Jayasudha; Patil, Chandrashekhargouda; Sunilkumar, P; Raghuveer, H P; Chandralekha, B

2013-01-01

The objective of this study was to estimate the increase in arch perimeter associated with mandibular lateral expansion, To estimate the increase in intermolar width with mandibular lateral expansion and to find out the changes of tooth inclination with mandibular expansion. The mandibular bone with dentition of indian skeletal specimen was obtained. The computer tomogram (CT) slices of the mandible were taken. Finite element model (FEM): Numerical representation of the geometry was created by dividing the geometry into finite number of elements and the elements were connected together with nodes at the junction. The result of the study showed when 10° of lateral expansion was applied to the lower buccal segment at the center of rotation found at 4.3 mm below the root apex of first molar, a space of 1.3 mm between the canine and first premolar, and thus an increase in arch perimeter of 2.6 mm. The tip of the mesiolingual cusp of the first molar moved 4.2 mm laterally, resulting in a change in intermolar width by 8.4 mm. Three-dimensional simulation showed that 1 mm of intermolar expansion increased the arch perimeter by 0.30 mm. As the finite element method evolves and scientists are able to more clearly define physical properties of biological tissues, more accurate information can be generated at the level that other analytical methods cannot fully provide data.This result would be of value clinically for prediction of the effects of mandibular expansion.

FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms

PubMed Central

Kaltdorf, Kristin Verena; Schulze, Katja; Helmprobst, Frederik; Kollmannsberger, Philip; Stigloher, Christian

2017-01-01

Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation. Both automatic and semi-automatic modes are explained including a tutorial. PMID:28056033

Zernike phase contrast cryo-electron tomography of whole bacterial cells

PubMed Central

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

2014-01-01

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

The use of seismic tomograms for the identification of internal problems with earthen dams and levees

USDA-ARS?s Scientific Manuscript database

According to the National Inventory of dams (NID, 2009), out of the 84,134 dams in the US, more than 87% (73,423) are earthen dams. The majority of these earthen dams are past or approaching their design life expectancy of 50 years. According to the National committee on Levee Safety (NCLS, 2009),...

A cylindrical specimen holder for electron cryo-tomography.

PubMed

Palmer, Colin M; Löwe, Jan

2014-02-01

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

Dynamics of quantum tomography in an open system

NASA Astrophysics Data System (ADS)

Uchiyama, Chikako

2015-06-01

In this study, we provide a way to describe the dynamics of quantum tomography in an open system with a generalized master equation, considering a case where the relevant system under tomographic measurement is influenced by the environment. We apply this to spin tomography because such situations typically occur in μSR (muon spin rotation/relaxation/resonance) experiments where microscopic features of the material are investigated by injecting muons as probes. As a typical example to describe the interaction between muons and a sample material, we use a spin-boson model where the relevant spin interacts with a bosonic environment. We describe the dynamics of a spin tomogram using a time-convolutionless type of generalized master equation that enables us to describe short time scales and/or low-temperature regions. Through numerical evaluation for the case of Ohmic spectral density with an exponential cutoff, a clear interdependency is found between the time evolution of elements of the density operator and a spin tomogram. The formulation in this paper may provide important fundamental information for the analysis of results from, for example, μSR experiments on short time scales and/or in low-temperature regions using spin tomography.

Results From YOUTHSAT - Indian experiment in earths thermosphere-ionosphere region.

NASA Astrophysics Data System (ADS)

Tarun Kumar, Pant

It is known that the characterization and modeling of the ionosphere/thermosphere necessitates a comprehensive understanding of the various processes prevailing therein. India’s first, indigenous and dedicated aeronomy satellite 'YOUTHSAT' carrying two Indian payloads - RaBIT (Radio Beacon for Ionospheric Tomography), and LiVHySI (Limb Viewing Hyper Spectral Imager) and one Russian payload SOLRAD, was conceived primarily to address to this aspect and launched on April 20, 2011 in an 818 Km polar orbit from SHAR on ISRO launch vehicle PSLV. The payloads RaBIT and LiVHySI were designed specifically to observe the ionised and neutral components of the upper atmosphere respectively. YOUTHSAT is a small satellite quiet advanced in its class having all the functionalities which are normally associated with a bigger satellite. The rising phase of the 23rd solar cycle was considered to be the best window for various observations from onboard YOUTHSAT. As an Indo Russian endeavour, it was launched with an objective of investigating the terrestrial upper atmosphere vis-a-vis the activity on the sun. RaBIT, an ISRO venture, is a radio beacon emitting coherent radio signal at 150 and 400 MHz frequencies. These are received using a chain of five receivers deployed along the ~76oE meridian at Trivandrum, Bangalore, Hyderabad, Bhopal and Delhi. The receivers estimate the Total Electron Content (TEC) of the ionosphere through the relative phase change of the received radio signals. The TECs thus estimated near simultaneously, are used to generate a tomogram, which gives an Altitude-Latitude distribution of the ionospheric electron density. For YOUTHSAT configuration, the tomogram covers the ionosphere from a few degrees (5-6o) south of Trivandrum to about 3-4o north of Delhi depending upon the satellite elevation. The RaBIT tomography network is by far the longest network existing anywhere in the world, and is unique therefore. Through RaBIT, a unique dataset leading to ionospheric tomograms representing altitude-latitude variation of electron density over the 77oE meridian over the Indian region has been generated around specific times (~10:30 AM/PM). These tomograms have provided, among others: (a) First ever images of the ionospheric nighttime ESF irregularities (b) Quantification of the topside F3 ionospheric layers using Tomography (c) Evidence of wavelike modulations in the overall low and equatorial ionospheric region using tomography (d) Day and night differences in the electron density distribution, (e) Evidence of the presence of the ionospheric top-side layer (f) Modulations in the ionosphere due to space weather activity and (g) Direct evidence of the presence of Travelling Atmospheric Disturbance (TAD). YOUTHSAT recently completed its mission life time of about two years, after having generated a comprehensive set of data on terrestrial upper atmosphere. The YOUTHSAT data are being analysed by various researchers and more results providing a new insight into the upper atmospheric processes are in offing. Some of the important outcomes mentioned above will be discussed in detail.

New method to analyze internal disruptions with tomographic reconstructions

NASA Astrophysics Data System (ADS)

Tanzi, C. P.; de Blank, H. J.

1997-03-01

Sawtooth crashes have been investigated on the Rijnhuizen Tokamak Project (RTP) [N. J. Lopes Cardozo et al., Proceedings of the 14th International Conference on Plasma Physics and Controlled Nuclear Fusion Research, Würzburg, 1992 (International Atomic Energy Agency, Vienna, 1993), Vol. 1, p. 271]. Internal disruptions in tokamak plasmas often exhibit an m=1 poloidal mode structure prior to the collapse which can be clearly identified by means of multicamera soft x-ray diagnostics. In this paper tomographic reconstructions of such m=1 modes are analyzed with a new method, based on magnetohydrodynamic (MHD) invariants computed from the two-dimensional emissivity profiles, which quantifies the amount of profile flattening not only after the crash but also during the precursor oscillations. The results are interpreted by comparing them with two models which simulate the measurements of the m=1 redistribution of soft x-ray emissivity prior to the sawtooth crash. One model is based on the magnetic reconnection model of Kadomtsev. The other involves ideal MHD motion only. In cases where differences in magnetic topology between the two models cannot be seen in the tomograms, the analysis of profile flattening has an advantage. The analysis shows that in RTP the clearly observed m=1 displacement of some sawteeth requires the presence of convective ideal MHD motion, whereas other precursors are consistent with magnetic reconnection of up to 75% of the magnetic flux within the q=1 surface. The possibility of ideal interchange combined with enhanced cross-field transport is not excluded.

Bilateral pheochromocytoma associated with paraganglioma and papillary thyroid carcinoma: report of an unusual case.

PubMed

Yang, Jeong Hoon; Bae, Sung Jin; Park, Sanghui; Park, Hyun-Kyung; Jung, Hye Seung; Chung, Jae Hoon; Min, Yong-Ki; Lee, Myung-Shik; Kim, Kwang-Won; Lee, Moon-Kyu

2007-04-01

A 42-year old woman presented with headache, palpitation and facial flushing. Ultrasonograms and computed tomograms revealed tumors in both of the adrenal glands, anterior aspect of the inferior vena cava, and the right lobe of the thyroid gland. Fine needle aspiration biopsy of the thyroid nodule revealed papillary thyroid carcinoma. Serum calcitonin, CEA, intact PTH and calcium levels were within normal limits. Markedly elevated levels of urinary normetanephrine and vanillylmandelic acid, and the result of 131I-metaiodobenzylguanidine (131I-MIBG) scintigraphy indicated that both adrenal masses were pheochromocytoma. Bilateral adrenalectomy, paracaval mass removal and total thyroidectomy together with central lymph node dissection were performed. The final pathological diagnosis was bilateral adrenal pheochromocytoma, paraganglioma, papillary thyroid carcinoma and either parathyroid adenoma or hyperplasia. Analysis of the RET proto-oncogene mutation, von Hippel Lindau mutation, succinate dehydrogenase subunit B mutation, and succinate dehydrogenase subunit D mutation yielded negative results. The relationship of these lesions could not be determined. This is the first report of a combination of bilateral pheochromocytoma, abdominal paraganglioma, papillary thyroid carcinoma and either parathyroid adenoma or hyperplasia without hyperparathyroidism.

Neocondyle distraction osteogenesis in the management of temporomandibular joint ankylosis: Report of five cases with review of literature.

PubMed

Sharma, Ravi; Manikandhan, R; Sneha, P; Parameswaran, Anantanarayanan; Kumar, J Naveen; Sailer, Hermann F

2017-01-01

Management of temporomandibular joint (TMJ) ankylosis is a challenging and rather daunting task owing to complex abnormal anatomy and its sequel to craniofacial structures. Various autogenous grafts and alloplastic materials have been tried with variable success for creation of a near-normal joint. In recent years, neocondyle distraction has added a new dimension to the management of TMJ ankylosis. The aim of this paper is to describe the role of neocondyle distraction in TMJ ankylosis. Neocondyle distraction was carried out in five patients with TMJ ankylosis following gap arthroplasty. Computed tomogram scans were taken before surgery and 1-year postdistraction for surgical planning and postoperative assessment, respectively. The intraoral distractors (KLS Martin, Jacksonville, FL, USA) were used in this study. All five patients reported with adequate mouth opening and functional jaw movements. The procedure was well tolerated by all the patients. None of the patients underwent reankylosis following neocondyle distraction. With proper surgical planning and distraction protocol, neocondyle distraction is an effective and safe technique for TMJ reconstruction and preventing reankylosis.

The Palatal Approach to Distraction Osteogenesis of the Anterior Maxillary Alveolus.

PubMed

Bell, Robert E

2015-07-01

This report describes the palatal approach to gain access for osteodistraction of the anterior maxilla to improve the vector of force during distraction. This case report illustrates a novel approach to anterior maxillary osteodistraction. The palatal approach allows the maxillary segment to be moved anteriorly and inferiorly. This is in contrast to the buccal approach, in which the palatal tissue creates a vector of force toward the palate. The vascular pedicle for the transport segment is the labial mucosa and musculature. In the present case, the alveolar segment was advanced 3.6 mm anteriorly and 12.2 mm inferiorly as measured by pre- and postoperative computed tomograms. This patient with a large vertical alveolar defect and high smile line had successful restoration with dental implants. The result has been stable for 14 months. In this case, the palatal approach to the anterior maxillary osteotomy was shown to be an effective method of reconstructing a large vertical anterior defect. Copyright © 2015 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

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

PubMed

Guerrero-Ferreira, Ricardo C; Wright, Elizabeth R

2014-01-01

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

2D phase tomography of biotissues: IV. Wavelet processing of phase tomograms of the background and precancerous endometrial states

NASA Astrophysics Data System (ADS)

Peresunko, A. P.; Zavadovskya, I. G.

2004-06-01

The paper deals with the studying of prognostic possibilities of determining the orientation structure of endometrial strome in the normal state and hiperplasia. The laser diagnostic of endometrial state is based on the principles of optical changes of laser radiation during its passing through the histological sample with the following investigation of its wavelet coefficients.

Delineation of fractures, foliation, and groundwater-flow zones of the bedrock at the Harlem River Tunnel in northern New York County, New York

USGS Publications Warehouse

Stumm, Frederick; Chu, Anthony; Joesten, Peter K.; Noll, Michael L.; Como, Michael D.

2013-01-01

Advanced borehole-geophysical methods were used to investigate the hydrogeology of the crystalline bedrock in 36 boreholes on the northernmost part of New York County, New York, for the construction of a utilities tunnel beneath the Harlem River. The borehole-logging techniques were used to delineate bedrock fractures, foliation, and groundwater-flow zones in test boreholes at the site. Fracture indexes of the deep boreholes ranged from 0.65 to 0.76 per foot. Most of the fracture populations had either northwest to southwest or east to southeast dip azimuths with moderate dip angles. The mean foliation dip azimuth ranged from 100º to 124º southeast with dip angles of 52º to 60º. Groundwater appears to flow through an interconnected network of fractures that are affected by tidal variations from the nearby Harlem River and tunnel construction dewatering operations. The transmissivities of the 3 boreholes tested (USGS-1, USGS-3, and USGS-4), calculated from specific capacity data, were 2, 48, and 30 feet squared per day (ft2/d), respectively. The highest transmissivities were observed in wells north and west of the secant ring. Three borehole-radar velocity tomograms were collected. In the USGS-1 and USGS-4 velocity tomogram there are two areas of low radar velocity. The first is at the top of the tomogram and runs from 105 ft below land surface (BLS) at USGS-4 and extends to 125 ft BLS at USGS-1, the second area is centered at a depth of 150 ft BLS at USGS-1 and 135 to 150 ft BLS at USGS-4. Field measurements of specific conductance of 14 boreholes under ambient conditions at the site indicate an increase in conductivity toward the southwest part of the site (nearest the Harlem River). Specific conductance ranged from 107 microsiemens per centimeter (μS/cm) (borehole 63C) to 11,000 μS/cm (borehole 79B). The secant boreholes had the highest specific conductance.

About probabilistic integration of ill-posed geophysical tomography and logging data: A knowledge discovery approach versus petrophysical transfer function concepts illustrated using cross-borehole radar-, P- and S-wave traveltime tomography in combination with cone penetration and dielectric logging data

NASA Astrophysics Data System (ADS)

Paasche, Hendrik

2018-01-01

Site characterization requires detailed and ideally spatially continuous information about the subsurface. Geophysical tomographic experiments allow for spatially continuous imaging of physical parameter variations, e.g., seismic wave propagation velocities. Such physical parameters are often related to typical geotechnical or hydrological target parameters, e.g. as achieved from 1D direct push or borehole logging. Here, the probabilistic inference of 2D tip resistance, sleeve friction, and relative dielectric permittivity distributions in near-surface sediments is constrained by ill-posed cross-borehole seismic P- and S-wave and radar wave traveltime tomography. In doing so, we follow a discovery science strategy employing a fully data-driven approach capable of accounting for tomographic ambiguity and differences in spatial resolution between the geophysical tomograms and the geotechnical logging data used for calibration. We compare the outcome to results achieved employing classical hypothesis-driven approaches, i.e., deterministic transfer functions derived empirically for the inference of 2D sleeve friction from S-wave velocity tomograms and theoretically for the inference of 2D dielectric permittivity from radar wave velocity tomograms. The data-driven approach offers maximal flexibility in combination with very relaxed considerations about the character of the expected links. This makes it a versatile tool applicable to almost any combination of data sets. However, error propagation may be critical and justify thinking about a hypothesis-driven pre-selection of an optimal database going along with the risk of excluding relevant information from the analyses. Results achieved by transfer function rely on information about the nature of the link and optimal calibration settings drawn as retrospective hypothesis by other authors. Applying such transfer functions at other sites turns them into a priori valid hypothesis, which can, particularly for empirically derived transfer functions, result in poor predictions. However, a mindful utilization and critical evaluation of the consequences of turning a retrospectively drawn hypothesis into an a priori valid hypothesis can also result in good results for inference and prediction problems when using classical transfer function concepts.

Effectiveness of Physiotherapy and GaAlAs Laser in the Management of Temporomandibular Joint Disorders

PubMed Central

Hlinakova, Petra; Kasparova, Magdalena; Rehacek, Adam; Vavrickova, Lenka; Navrátil, Leoš

2012-01-01

Abstract Objective: Low-level laser therapy (LLLT) is a treatment method commonly used in physiotherapy for musculoskeletal disorders. The aim of this study was to monitor the function of temporomandibular joint (TMJ) and surrounding tissues and compare the objective measurements of the effect of LLLT. Background data: LLLT has been considered effective in reducing pain and muscular tension; thus improving the quality of patients' lives. Materials and Methods: TMJ function was evaluated by cephalometric tracing analysis, orthopantomogram, TMJ tomogram, and computer face-bow record. Interalveolar space between central incisors before and after therapy was measured. Patients evaluated pain on the Visual Analog Scale. LLLT was performed in five treatment sessions (energy density of 15.4 J/cm2) by semiconductive GaAlAs laser with an output of 280 mW, emitting radiation wavelength of 830 mm. The laser supplied a spot of∼0.2 cm2. Results: Baseline comparisons between the healthy patients and patients with low-level laser application show that TMJ pain during function is based on anatomical and function changes in TMJ areas. Significant differences were seen in the posterior and anterior face height. The results comparing healthy and impaired TMJ sagittal condyle paths showed that patients with TMJ pain during function had significantly flatter nonanatomical movement during function. After therapy, the unpleasant feeling was reduced from 27.5 to 4.16 on the pain Visual Analog Scale. The pain had reduced the ability to open the mouth from 34 to 42 mm. Conclusions: The laser therapy was effective in the improvement of the range of temporomandibular disorders (TMD) and promoted a significant reduction of pain symptoms. PMID:22551049

The relationship between skull morphology, masticatory muscle force and cranial skeletal deformation during biting.

PubMed

Toro-Ibacache, Viviana; Zapata Muñoz, Víctor; O'Higgins, Paul

2016-01-01

The human skull is gracile when compared to many Middle Pleistocene hominins. It has been argued that it is less able to generate and withstand high masticatory forces, and that the morphology of the lower portion of the modern human face correlates most strongly with dietary characteristics. This study uses geometric morphometrics and finite element analysis (FEA) to assess the relationship between skull morphology, muscle force and cranial deformations arising from biting, which is relevant in understanding how skull morphology relates to mastication. The three-dimensional skull anatomies of 20 individuals were reconstructed from medical computed tomograms. Maximal contractile muscle forces were estimated from muscular anatomical cross-sectional areas (CSAs). Fifty-nine landmarks were used to represent skull morphology. A partial least squares analysis was performed to assess the association between skull shape and muscle force, and FEA was used to compare the deformation (strains) generated during incisor and molar bites in two individuals representing extremes of morphological variation in the sample. The results showed that only the proportion of total muscle CSA accounted for by the temporalis appears associated with skull morphology, albeit weekly. However, individuals with a large temporalis tend to possess a relatively wider face, a narrower, more vertically oriented maxilla and a lower positioning of the coronoid process. The FEAs showed that, despite differences in morphology, biting results in similar modes of deformation for both crania, but with localised lower magnitudes of strains arising in the individual with the narrowest, most vertically oriented maxilla. Our results suggest that the morphology of the maxilla modulates the transmission of forces generated during mastication to the rest of the cranium by deforming less in individuals with the ability to generate proportionately larger temporalis muscle forces. Copyright © 2015 Elsevier GmbH. All rights reserved.

CBF tomograms with (/sup 99m/Tc-HM-PAO in patients with dementia (Alzheimer type and HIV) and Parkinson's disease--initial results

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

Costa, D.C.; Ell, P.J.; Burns, A.

1988-12-01

We present preliminary data on the utility of functional brain imaging with (99mTc)-d,l-HM-PAO and single photon emission computed tomography (SPECT) in the study of patients with dementia of the Alzheimer type (DAT), HIV-related dementia syndrome, and the on-off syndrome of Parkinson's disease. In comparison with a group of age-matched controls, the DAT patients revealed distinctive bilateral temporal and posterior parietal deficits, which correlate with detailed psychometric evaluation. Patients with amnesia as the main symptom (group A) showed bilateral mesial temporal lobe perfusion deficits (p less than 0.02). More severely affected patients (group B) with significant apraxia, aphasia, or agnosia exhibitedmore » patterns compatible with bilateral reduced perfusion in the posterior parietal cortex, as well as reduced perfusion to both temporal lobes, different from the patients of the control group (p less than 0.05). SPECT studies of HIV patients with no evidence of intracraneal space occupying pathology showed marked perfusion deficits. Patients with Parkinson's disease and the on-off syndrome studied during an on phase (under levodopa therapy) and on another occasion after withdrawal of levodopa (off) demonstrated a significant change in the uptake of (99mTc)-d,l-HM-PAO in the caudate nucleus (lower on off) and thalamus (higher on off). These findings justify the present interest in the functional evaluation of the brain of patients with dementia. (99mTc)-d,l-HM-PAO and regional cerebral blood flow (rCBF)/SPECT appear useful and highlight individual disorders of flow in a variety of neuropsychiatric conditions.« less

Mirror-Imaged Rapid Prototype Skull Model and Pre-Molded Synthetic Scaffold to Achieve Optimal Orbital Cavity Reconstruction.

PubMed

Park, Sung Woo; Choi, Jong Woo; Koh, Kyung S; Oh, Tae Suk

2015-08-01

Reconstruction of traumatic orbital wall defects has evolved to restore the original complex anatomy with the rapidly growing use of computer-aided design and prototyping. This study evaluated a mirror-imaged rapid prototype skull model and a pre-molded synthetic scaffold for traumatic orbital wall reconstruction. A single-center retrospective review was performed of patients who underwent orbital wall reconstruction after trauma from 2012 to 2014. Patients were included by admission through the emergency department after facial trauma or by a tertiary referral for post-traumatic orbital deformity. Three-dimensional (3D) computed tomogram-based mirror-imaged reconstruction images of the orbit and an individually manufactured rapid prototype skull model by a 3D printing technique were obtained for each case. Synthetic scaffolds were anatomically pre-molded using the skull model as guide and inserted at the individual orbital defect. Postoperative complications were assessed and 3D volumetric measurements of the orbital cavity were performed. Paired samples t test was used for statistical analysis. One hundred four patients with immediate orbital defect reconstructions and 23 post-traumatic orbital deformity reconstructions were included in this study. All reconstructions were successful without immediate postoperative complications, although there were 10 cases with mild enophthalmos and 2 cases with persistent diplopia. Reoperations were performed for 2 cases of persistent diplopia and secondary touchup procedures were performed to contour soft tissue in 4 cases. Postoperative volumetric measurement of the orbital cavity showed nonsignificant volume differences between the damaged orbit and the reconstructed orbit (21.35 ± 1.93 vs 20.93 ± 2.07 cm(2); P = .98). This protocol was extended to severe cases in which more than 40% of the orbital frame was lost and combined with extensive soft tissue defects. Traumatic orbital reconstruction can be optimized and successful using an individually manufactured rapid prototype skull model and a pre-molded synthetic scaffold by computer-aid design and manufacturing. Copyright © 2015 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

Panoramic radiographic predictors of mandibular third molar eruption.

PubMed

Niedzielska, Iwona Anna; Drugacz, Jan; Kus, Nina; Kreska, Joanna

2006-08-01

Third molar (M3) eruption can be problematic. According to some orthodontic surgeons, the teeth are capable of aggravating the average crowding level in the dental arch. The question is whether it might be possible to give a prognosis for ultimate M3 position in the arch and make an early decision to extract or retain them. The purpose of the study was to determine which measurements made on panoramic tomograms might facilitate prognosis for M3 position in the dental arch over the years. The investigation involved 64 patients who had been enrolled to the study group 10 years earlier, ie, in 1993, when an analysis had been carried out regarding M3 effect on dental arch crowding. At that time panoramic tomograms had been taken, and dental casts made. The procedures were repeated in 2003. The following measurements were taken at baseline (1993) and at the end of the study (2003): (1)/the retromolar space to lower third molar crown width, (2) third molar angulation to the base of the mandible, and (3) third molar to second molar inclination. At some defined values of the Ganss ratio, and M3 inclination to mandibular base and second molar, it is possible to predict potential lower third molar alignment in the dental arch using a panoramic radiograph.

Marine electrical resistivity imaging of submarine groundwater discharge: Sensitivity analysis and application in Waquoit Bay, Massachusetts, USA

USGS Publications Warehouse

Henderson, Rory; Day-Lewis, Frederick D.; Abarca, Elena; Harvey, Charles F.; Karam, Hanan N.; Liu, Lanbo; Lane, John W.

2010-01-01

Electrical resistivity imaging has been used in coastal settings to characterize fresh submarine groundwater discharge and the position of the freshwater/salt-water interface because of the relation of bulk electrical conductivity to pore-fluid conductivity, which in turn is a function of salinity. Interpretation of tomograms for hydrologic processes is complicated by inversion artifacts, uncertainty associated with survey geometry limitations, measurement errors, and choice of regularization method. Variation of seawater over tidal cycles poses unique challenges for inversion. The capabilities and limitations of resistivity imaging are presented for characterizing the distribution of freshwater and saltwater beneath a beach. The experimental results provide new insight into fresh submarine groundwater discharge at Waquoit Bay National Estuarine Research Reserve, East Falmouth, Massachusetts (USA). Tomograms from the experimental data indicate that fresh submarine groundwater discharge may shut down at high tide, whereas temperature data indicate that the discharge continues throughout the tidal cycle. Sensitivity analysis and synthetic modeling provide insight into resolving power in the presence of a time-varying saline water layer. In general, vertical electrodes and cross-hole measurements improve the inversion results regardless of the tidal level, whereas the resolution of surface arrays is more sensitive to time-varying saline water layer.

Image reconstruction of x-ray tomography by using image J platform

NASA Astrophysics Data System (ADS)

Zain, R. M.; Razali, A. M.; Salleh, K. A. M.; Yahya, R.

2017-01-01

A tomogram is a technical term for a CT image. It is also called a slice because it corresponds to what the object being scanned would look like if it were sliced open along a plane. A CT slice corresponds to a certain thickness of the object being scanned. So, while a typical digital image is composed of pixels, a CT slice image is composed of voxels (volume elements). In the case of x-ray tomography, similar to x-ray Radiography, the quantity being imaged is the distribution of the attenuation coefficient μ(x) within the object of interest. The different is only on the technique to produce the tomogram. The image of x-ray radiography can be produced straight foward after exposed to x-ray, while the image of tomography produces by combination of radiography images in every angle of projection. A number of image reconstruction methods by converting x-ray attenuation data into a tomography image have been produced by researchers. In this work, Ramp filter in "filtered back projection" has been applied. The linear data acquired at each angular orientation are convolved with a specially designed filter and then back projected across a pixel field at the same angle. This paper describe the step of using Image J software to produce image reconstruction of x-ray tomography.

Simultaneous Impacted Third Molar Extraction and Lateral Ramus Block Graft Harvest for Horizontal Ridge Augmentation: A Case Series.

PubMed

Deeb, George R; Laskin, Daniel M; Deeb, Janina Golob

2017-03-01

The purpose of this study was to confirm the efficiency of using a lateral ramus block graft taken at the time of impacted mandibular third molar removal for horizontal ridge augmentation and implant placement. Ten patients had grafts obtained from the lateral aspect of the mandible during impacted third molar removal and placed in areas of horizontal ridge deficiency. Measurements made on cone-beam computerized tomograms after 4 months showed gains of 2.7 to 3.5 mm and 16 implants were placed successfully. In patients with impacted third molars requiring dental implants, simultaneous harvest of a lateral block bone graft is an efficient way of obtaining bone for horizontal ridge augmentation. Copyright © 2016 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

Influence of DNA sequence on the structure of minicircles under torsional stress

PubMed Central

Wang, Qian; Irobalieva, Rossitza N.; Chiu, Wah; Schmid, Michael F.; Fogg, Jonathan M.; Zechiedrich, Lynn

2017-01-01

Abstract The sequence dependence of the conformational distribution of DNA under various levels of torsional stress is an important unsolved problem. Combining theory and coarse-grained simulations shows that the DNA sequence and a structural correlation due to topology constraints of a circle are the main factors that dictate the 3D structure of a 336 bp DNA minicircle under torsional stress. We found that DNA minicircle topoisomers can have multiple bend locations under high torsional stress and that the positions of these sharp bends are determined by the sequence, and by a positive mechanical correlation along the sequence. We showed that simulations and theory are able to provide sequence-specific information about individual DNA minicircles observed by cryo-electron tomography (cryo-ET). We provided a sequence-specific cryo-ET tomogram fitting of DNA minicircles, registering the sequence within the geometric features. Our results indicate that the conformational distribution of minicircles under torsional stress can be designed, which has important implications for using minicircle DNA for gene therapy. PMID:28609782

Spatiotemporal observation of transport in fractured rocks

NASA Astrophysics Data System (ADS)

Kulenkampff, Johannes; Enzmann, Frieder; Gründig, Marion; Mittmann, Hellmuth; Wolf, Martin

2010-05-01

A number of injection experiments in different rocks types have been conducted with positron emission-process-tomography using a high-resolution "small-animal" PET-scanner (ClearPET by Raytest, Straubenhardt) for the monitoring of transport processes. The fluids are labelled with positron-emitting isotopes like e.g. 18F-, 124I- or dissolvable complexes like K3[58Co(CN)6], without affecting their physico-chemical properties. The annihilation radiation from individual decaying tracer atoms is detected with high sensitivity, and the tomographic reconstruction of the recorded events yields quantitative 3D-images of the tracer distribution. Sequential tomograms during and after tracer injection are used for the spatiotemporal observation of the fluid transport. Raw data is corrected with respect to background radiation (randoms) and Compton scattering, which turns out to be much more significant in rocks than in common biomedical applications. Although in principle these effects are exactly known, we developed and apply simplified and fast correction methods. Deficiencies of these correction algorithms generate some artefacts, that cause the lower limit of the tracer concentration in the order of 1 kBq/?l or about 107 atoms/?l, still outranging other methods (e.g. NMR or resistivity tomography) by many orders of magnitude. New 3D-visualizations of the process-tomograms in fractured rocks show strongly localized and complex flow paths and in parts unexpected deviations from the fracture structures as deduced from ?CT-images. Such results demonstrate the potential of large discrepancies between ?CT-derived parameters like pore volume and specific surface area and the hydraulic effective parameters as derived by means of the PET-process-tomography. We conclude that such discrepancies and the complexity of the transport process in natural heterogeneous porous media illustrates the limits of parameter determination methods from model simulations based on structural pore-space models - in particular as long as the simulations are not verified by experimental data.

Entropy-Bayesian Inversion of Time-Lapse Tomographic GPR data for Monitoring Dielectric Permittivity and Soil Moisture Variations

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

Hou, Z; Terry, N; Hubbard, S S

2013-02-12

In this study, we evaluate the possibility of monitoring soil moisture variation using tomographic ground penetrating radar travel time data through Bayesian inversion, which is integrated with entropy memory function and pilot point concepts, as well as efficient sampling approaches. It is critical to accurately estimate soil moisture content and variations in vadose zone studies. Many studies have illustrated the promise and value of GPR tomographic data for estimating soil moisture and associated changes, however, challenges still exist in the inversion of GPR tomographic data in a manner that quantifies input and predictive uncertainty, incorporates multiple data types, handles non-uniquenessmore » and nonlinearity, and honors time-lapse tomograms collected in a series. To address these challenges, we develop a minimum relative entropy (MRE)-Bayesian based inverse modeling framework that non-subjectively defines prior probabilities, incorporates information from multiple sources, and quantifies uncertainty. The framework enables us to estimate dielectric permittivity at pilot point locations distributed within the tomogram, as well as the spatial correlation range. In the inversion framework, MRE is first used to derive prior probability distribution functions (pdfs) of dielectric permittivity based on prior information obtained from a straight-ray GPR inversion. The probability distributions are then sampled using a Quasi-Monte Carlo (QMC) approach, and the sample sets provide inputs to a sequential Gaussian simulation (SGSim) algorithm that constructs a highly resolved permittivity/velocity field for evaluation with a curved-ray GPR forward model. The likelihood functions are computed as a function of misfits, and posterior pdfs are constructed using a Gaussian kernel. Inversion of subsequent time-lapse datasets combines the Bayesian estimates from the previous inversion (as a memory function) with new data. The memory function and pilot point design takes advantage of the spatial-temporal correlation of the state variables. We first apply the inversion framework to a static synthetic example and then to a time-lapse GPR tomographic dataset collected during a dynamic experiment conducted at the Hanford Site in Richland, WA. We demonstrate that the MRE-Bayesian inversion enables us to merge various data types, quantify uncertainty, evaluate nonlinear models, and produce more detailed and better resolved estimates than straight-ray based inversion; therefore, it has the potential to improve estimates of inter-wellbore dielectric permittivity and soil moisture content and to monitor their temporal dynamics more accurately.« less

Entropy-Bayesian Inversion of Time-Lapse Tomographic GPR data for Monitoring Dielectric Permittivity and Soil Moisture Variations

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

Hou, Zhangshuan; Terry, Neil C.; Hubbard, Susan S.

2013-02-22

In this study, we evaluate the possibility of monitoring soil moisture variation using tomographic ground penetrating radar travel time data through Bayesian inversion, which is integrated with entropy memory function and pilot point concepts, as well as efficient sampling approaches. It is critical to accurately estimate soil moisture content and variations in vadose zone studies. Many studies have illustrated the promise and value of GPR tomographic data for estimating soil moisture and associated changes, however, challenges still exist in the inversion of GPR tomographic data in a manner that quantifies input and predictive uncertainty, incorporates multiple data types, handles non-uniquenessmore » and nonlinearity, and honors time-lapse tomograms collected in a series. To address these challenges, we develop a minimum relative entropy (MRE)-Bayesian based inverse modeling framework that non-subjectively defines prior probabilities, incorporates information from multiple sources, and quantifies uncertainty. The framework enables us to estimate dielectric permittivity at pilot point locations distributed within the tomogram, as well as the spatial correlation range. In the inversion framework, MRE is first used to derive prior probability density functions (pdfs) of dielectric permittivity based on prior information obtained from a straight-ray GPR inversion. The probability distributions are then sampled using a Quasi-Monte Carlo (QMC) approach, and the sample sets provide inputs to a sequential Gaussian simulation (SGSIM) algorithm that constructs a highly resolved permittivity/velocity field for evaluation with a curved-ray GPR forward model. The likelihood functions are computed as a function of misfits, and posterior pdfs are constructed using a Gaussian kernel. Inversion of subsequent time-lapse datasets combines the Bayesian estimates from the previous inversion (as a memory function) with new data. The memory function and pilot point design takes advantage of the spatial-temporal correlation of the state variables. We first apply the inversion framework to a static synthetic example and then to a time-lapse GPR tomographic dataset collected during a dynamic experiment conducted at the Hanford Site in Richland, WA. We demonstrate that the MRE-Bayesian inversion enables us to merge various data types, quantify uncertainty, evaluate nonlinear models, and produce more detailed and better resolved estimates than straight-ray based inversion; therefore, it has the potential to improve estimates of inter-wellbore dielectric permittivity and soil moisture content and to monitor their temporal dynamics more accurately.« less

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

Doug Blankenship

PDFs of seismic reflection profiles 101,110, 111 local to the West Flank FORGE site. 45 line kilometers of seismic reflection data are processed data collected in 2001 through the use of vibroseis trucks. The initial analysis and interpretation of these data was performed by Unruh et al. (2001). Optim processed these data by inverting the P-wave first arrivals to create a 2-D velocity structure. Kirchhoff images were then created for each line using velocity tomograms (Unruh et al., 2001).

Unimpeded permeation of water through biocidal graphene oxide sheets anchored on to 3D porous polyolefinic membranes.

PubMed

Mural, Prasanna Kumar S; Jain, Shubham; Kumar, Sachin; Madras, Giridhar; Bose, Suryasarathi

2016-04-21

3D porous membranes were developed by etching one of the phases (here PEO, polyethylene oxide) from melt-mixed PE/PEO binary blends. Herein, we have systematically discussed the development of these membranes using X-ray micro-computed tomography. The 3D tomograms of the extruded strands and hot-pressed samples revealed a clear picture as to how the morphology develops and coarsens over a function of time during post-processing operations like compression molding. The coarsening of PE/PEO blends was traced using X-ray micro-computed tomography and scanning electron microscopy (SEM) of annealed blends at different times. It is now understood from X-ray micro-computed tomography that by the addition of a compatibilizer (here lightly maleated PE), a stable morphology can be visualized in 3D. In order to anchor biocidal graphene oxide sheets onto these 3D porous membranes, the PE membranes were chemically modified with acid/ethylene diamine treatment to anchor the GO sheets which were further confirmed by Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS) and surface Raman mapping. The transport properties through the membrane clearly reveal unimpeded permeation of water which suggests that anchoring GO on to the membranes does not clog the pores. Antibacterial studies through the direct contact of bacteria with GO anchored PE membranes resulted in 99% of bacterial inactivation. The possible bacterial inactivation through physical disruption of the bacterial cell wall and/or reactive oxygen species (ROS) is discussed herein. Thus this study opens new avenues in designing polyolefin based antibacterial 3D porous membranes for water purification.

A splenic artery aneurysm presenting with multiple episodes of upper gastrointestinal bleeding: a case report.

PubMed

De Silva, W S L; Gamlaksha, D S; Jayasekara, D P; Rajamanthri, S D

2017-05-03

Splenic artery aneurysm is rare and its diagnosis is challenging due to the nonspecific nature of the clinical presentation. We report a case of a splenic artery aneurysm in which the patient presented with chronic dyspepsia and multiple episodes of minor intragastric bleeding. A 60-year-old, previously healthy Sri Lankan man presented with four episodes of hematemesis and severe dyspeptic symptoms over a period of 6 months. The results of two initial upper gastrointestinal endoscopies and an abdominal ultrasound scan were unremarkable. A third upper gastrointestinal endoscopy detected a pulsatile bulge at the posterior wall of the gastric antrum. A contrast-enhanced computed tomogram of his abdomen detected a splenic artery aneurysm measuring 3 × 3 × 2.5 cm. While awaiting routine surgery, he developed a torrential upper gastrointestinal bleeding and shock, leading to emergency laparotomy. Splenectomy and en bloc resection of the aneurysm with the posterior stomach wall were performed. Histology revealed evidence for a true aneurysm without overt, acute, or chronic inflammation of the surrounding gastric mucosa. He became completely asymptomatic 2 weeks after the surgery. Splenic artery aneurysms can result in recurrent upper gastrointestinal bleeding. The possibility of impending catastrophic bleeding should be remembered when managing patients with splenic artery aneurysms after a minor bleeding. Negative endoscopy and ultrasonography should require contrast-enhanced computed tomography to look for the cause of recurrent upper gastrointestinal bleeding.

High-sensitive computed tomography system using a silicon-PIN x-ray diode

NASA Astrophysics Data System (ADS)

Sato, Eiichi; Sato, Yuich; Abudurexiti, Abulajiang; Hagiwara, Osahiko; Matsukiyo, Hiroshi; Osawa, Akihiro; Enomoto, Toshiyuki; Watanabe, Manabu; Kusachi, Shinya; Sato, Shigehiro; Ogawa, Akira; Onagawa, Jun

2012-10-01

A low-dose-rate X-ray computed tomography (CT) system is useful for reducing absorbed dose for patients. The CT system with a tube current of 1.91 mA was developed using a silicon-PIN X-ray diode (Si-PIN-XD). The Si-PIN-XD is a selected high-sensitive Si-PIN photodiode (PD) for detecting X-ray photons. X-ray photons are detected directly using the Si-PIN-XD without a scintillator, and the photocurrent from the diode is amplified using current-voltage and voltage-voltage amplifiers. The output voltage is converted into logical pulses using a voltage-frequency converter with maximum frequency of 500 kHz, and the frequency is proportional to the voltage. The pulses from the converter are sent to differentiator with a time constant of 1 μs to generate short positive pulses for counting, and the pulses are counted using a counter card. Tomography is accomplished by repeated linear scans and rotations of an object, and projection curves of the object are obtained by the linear scan. The exposure time for obtaining a tomogram was 5 min at a scan step of 0.5 mm and a rotation step of 3.0°. The tube current and voltage were 1.91 mA and 100 kV, respectively, and gadolinium K-edge CT was carried out using filtered X-ray spectra with a peak energy of 52 keV.

Platform for intraoperative analysis of video streams

NASA Astrophysics Data System (ADS)

Clements, Logan; Galloway, Robert L., Jr.

2004-05-01

Interactive, image-guided surgery (IIGS) has proven to increase the specificity of a variety of surgical procedures. However, current IIGS systems do not compensate for changes that occur intraoperatively and are not reflected in preoperative tomograms. Endoscopes and intraoperative ultrasound, used in minimally invasive surgery, provide real-time (RT) information in a surgical setting. Combining the information from RT imaging modalities with traditional IIGS techniques will further increase surgical specificity by providing enhanced anatomical information. In order to merge these techniques and obtain quantitative data from RT imaging modalities, a platform was developed to allow both the display and processing of video streams in RT. Using a Bandit-II CV frame grabber board (Coreco Imaging, St. Laurent, Quebec) and the associated library API, a dynamic link library was created in Microsoft Visual C++ 6.0 such that the platform could be incorporated into the IIGS system developed at Vanderbilt University. Performance characterization, using two relatively inexpensive host computers, has shown the platform capable of performing simple image processing operations on frames captured from a CCD camera and displaying the processed video data at near RT rates both independent of and while running the IIGS system.

[Effective combination therapy using radiation and a daily low dose of cis-platinum for advanced oropharyngeal carcinoma in an elderly patient--report of a case].

PubMed

Tamura, M; Miyashita, T; Ogiso, A; Kotani, A; Oguchi, M; Izuno, I

1994-01-01

An 83-year-old male with advanced oropharyngeal carcinoma was treated with combined radiotherapy and a daily low dose of cis-platinum with excellent results. In the early part of the treatment, radiotherapy was delivered in fractions of 1.8 Gy/day (5 days/week) to a cumulative dose of 20 Gy, concomitantly with UFT (400 mg/day po), but the response was not adequate. Then, instead of UFT, a single intravenous injection of cis-platinum (5 mg) was administered within 30 min after each radiation session without intravenous hydration. The total dose of cis-platinum was 140 mg and that of radiation was 70 Gy. Moderate leukocytopenia and moderate mucositis/dermatitis were observed as side effects, but despite the lack of intravenous hydration no signs of renal toxicity were observed. Partial remission was attained by the end of the therapy, remnant lesions progressively diminished in size, and 4 months later all of them had completely disappeared on the computed tomogram. The prognosis is favorable, and neither recurrence nor metastasis has been found in the 14-month follow-up period since the lesions disappeared.

Genetics and Early Detection in Idiopathic Pulmonary Fibrosis

PubMed Central

Putman, Rachel K.; Rosas, Ivan O.

2014-01-01

Genetic studies hold promise in helping to identify patients with early idiopathic pulmonary fibrosis (IPF). Recent studies using chest computed tomograms (CTs) in smokers and in the general population have demonstrated that imaging abnormalities suggestive of an early stage of pulmonary fibrosis are not uncommon and are associated with respiratory symptoms, physical examination abnormalities, and physiologic decrements expected, but less severe than those noted in patients with IPF. Similarly, recent genetic studies have demonstrated strong and replicable associations between a common promoter polymorphism in the mucin 5B gene (MUC5B) and both IPF and the presence of abnormal imaging findings in the general population. Despite these findings, it is important to note that the definition of early-stage IPF remains unclear, limited data exist to definitively connect abnormal imaging findings to IPF, and genetic studies assessing early-stage pulmonary fibrosis remain in their infancy. In this perspective we provide updated information on interstitial lung abnormalities and their connection to IPF. We summarize information on the genetics of pulmonary fibrosis by focusing on the recent genetic findings of MUC5B. Finally, we discuss the implications of these findings and suggest a roadmap for the use of genetics in the detection of early IPF. PMID:24547893

Reliability of implant surgical guides based on soft-tissue models.

PubMed

Maney, Pooja; Simmons, David E; Palaiologou, Archontia; Kee, Edwin

2012-12-01

The purpose of this study was to determine the accuracy of implant surgical guides fabricated on diagnostic casts. Guides were fabricated with radiopaque rods representing implant positions. Cone beam computerized tomograms were taken with guides in place. Accuracy was evaluated using software to simulate implant placement. Twenty-two sites (47%) were considered accurate (13 of 24 maxillary and 9 of 23 mandibular sites). Soft-tissue models do not always provide sufficient accuracy for fabricating implant surgical guides.

Composition and structure of aggregates from compacted soil horizons in the southern steppe zone of European Russia

NASA Astrophysics Data System (ADS)

Sorokin, A. S.; Abrosimov, K. N.; Lebedeva, M. P.; Kust, G. S.

2016-03-01

The composition and structure of aggregates from different agrogenic soils in the southern steppe zone of European Russia have been studied. It is shown that the multi-level study (from the macro- to microlevel) of these horizons makes it possible to identify soil compaction caused by different elementary soil processes: solonetz-forming, vertisol-forming, and mechanical (wheel) compaction in the rainfed and irrigated soils. The understanding of the genesis of the compaction of soil horizons (natural or anthropogenic) is important for the economic evaluation of soil degradation. It should enable us to make more exact predictions of the rates of degradation processes and undertake adequate mitigation measures. The combined tomographic and micromorphological studies of aggregates of 1-2 and 3-5 mm in diameter from compacted horizons of different soils have been performed for the first time. Additional diagnostic features of negative solonetz- forming processes (low open porosity of aggregates seen on tomograms and filling of a considerable part of the intraped pores with mobile substance) and the vertisol-forming processes (large amount of fine intraaggregate pores seen on tomograms and a virtual absence of humus-clay plasma in the intraped zone)—have been identified. It is shown that the combination of microtomographic and micromorphological methods is helpful for studying the pore space of compacted horizons in cultivated soils.

A novel ultrasonic method for measuring breast density and breast cancer risk

NASA Astrophysics Data System (ADS)

Glide-Hurst, Carri K.; Duric, Neb; Littrup, Peter J.

2008-03-01

Women with high mammographic breast density are at 4- to 6-fold increased risk of developing breast cancer compared to women with fatty breasts. However, current breast density estimations rely on mammography, which cannot provide accurate volumetric breast representation. Therefore, we explored two techniques of breast density evaluation via ultrasound tomography. A sample of 93 patients was imaged with our clinical prototype; each dataset contained 45-75 tomograms ranging from near the chest wall through the nipple. Whole breast acoustic velocity was determined by creating image stacks and evaluating the sound speed frequency distribution. Ultrasound percent density (USPD) was determined by segmenting high sound speed areas from each tomogram using k-means clustering, integrating over the entire breast, and dividing by total breast area. Both techniques were independently evaluated using two mammographic density measures: (1) qualitative, determined by a radiologist's visual assessment using BI-RADS Categories, and (2) quantitative, via semi-automatic segmentation to calculate mammographic percent density (MPD) for craniocaudal and medio-lateral oblique mammograms. ~140 m/s difference in acoustic velocity was observed between fatty and dense BI-RADS Categories. Increased sound speed was found with increased BI-RADS Category and quantitative MPD. Furthermore, strong positive associations between USPD, BI-RADS Category, and calculated MPD were observed. These results confirm that utilizing sound speed, both for whole-breast evaluation and segmenting locally, can be implemented to evaluate breast density.

Three-dimensional refractive index and fluorescence tomography using structured illumination (Conference Presentation)

NASA Astrophysics Data System (ADS)

Park, GwangSik; Shin, SeungWoo; Kim, Kyoohyun; Park, YongKeun

2017-02-01

Optical diffraction tomography (ODT) has been an emerging optical technique for label-free imaging of three-dimensional (3-D) refractive index (RI) distribution of biological samples. ODT employs interferometric microscopy for measuring multiple holograms of samples with various incident angles, from which the Fourier diffraction theorem reconstructs the 3-D RI distribution of samples from retrieved complex optical fields. Since the RI value is linearly proportional to the protein concentration of biological samples where the proportional coefficient is called as refractive index increment (RII), reconstructed 3-D RI tomograms provide precise structural and biochemical information of individual biological samples. Because most proteins have similar RII value, however, ODT has limited molecular specificity, especially for imaging eukaryotic cells having various types of proteins and subcellular organelles. Here, we present an ODT system combined with structured illumination microscopy which can measure the 3-D RI distribution of biological samples as well as 3-D super-resolution fluorescent images in the same optical setup. A digital micromirror device (DMD) controls the incident angle of the illumination beam for tomogram reconstruction, and the same DMD modulates the structured illumination pattern of the excitation beam for super-resolution fluorescent imaging. We first validate the proposed method for simultaneous optical diffraction tomographic imaging and super-resolution fluorescent imaging of fluorescent beads. The proposed method is also exploited for various biological samples.

Phantom experiments to improve parathyroid lesion detection

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

Nichols, Kenneth J.; Tronco, Gene G.; Tomas, Maria B.

2007-12-15

This investigation tested the hypothesis that visual analysis of iteratively reconstructed tomograms by ordered subset expectation maximization (OSEM) provides the highest accuracy for localizing parathyroid lesions using {sup 99m}Tc-sestamibi SPECT data. From an Institutional Review Board approved retrospective review of 531 patients evaluated for parathyroid localization, image characteristics were determined for 85 {sup 99m}Tc-sestamibi SPECT studies originally read as equivocal (EQ). Seventy-two plexiglas phantoms using cylindrical simulated lesions were acquired for a clinically realistic range of counts (mean simulated lesion counts of 75{+-}50 counts/pixel) and target-to-background (T:B) ratios (range=2.0 to 8.0) to determine an optimal filter for OSEM. Two experiencedmore » nuclear physicians graded simulated lesions, blinded to whether chambers contained radioactivity or plain water, and two observers used the same scale to read all phantom and clinical SPECT studies, blinded to pathology findings and clinical information. For phantom data and all clinical data, T:B analyses were not statistically different for OSEM versus FB, but visual readings were significantly more accurate than T:B (88{+-}6% versus 68{+-}6%, p=0.001) for OSEM processing, and OSEM was significantly more accurate than FB for visual readings (88{+-}6% versus 58{+-}6%, p<0.0001). These data suggest that visual analysis of iteratively reconstructed MIBI tomograms should be incorporated into imaging protocols performed to localize parathyroid lesions.« less

Dual host specificity of phage SP6 is facilitated by tailspike rotation

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

Tu, Jiagang

Bacteriophage SP6 exhibits dual-host adsorption specificity. The SP6 tailspikes are recognized as important in host range determination but the mechanisms underlying dual host specificity are unknown. Cryo-electron tomography and sub-tomogram classification were used to analyze the SP6 virion with a particular focus on the interaction of tailspikes with host membranes. The SP6 tail is surrounded by six V-shaped structures that interconnect in forming a hand-over-hand hexameric garland. Each V-shaped structure consists of two trimeric tailspike proteins: gp46 and gp47, connected through the adaptor protein gp37. SP6 infection of Salmonella enterica serovars Typhimurium and Newport results in distinguishable changes in tailspikemore » orientation, providing the first direct demonstration how tailspikes can confer dual host adsorption specificity. SP6 also infects S. Typhimurium strains lacking O antigen; in these infections tailspikes have no apparent specific role and the phage tail must therefore interact with a distinct host receptor to allow infection. - Highlights: •Cryo-electron tomography reveals the structural basis for dual host specificity. •Sub-tomogram classification reveals distinct orientations of the tailspikes during infection of different hosts. •Tailspike-adaptor modules rotate as they bind different O antigens. •In the absence of any O antigen, tailspikes bind weakly and without specificity to LPS. •Interaction of the phage tail with LPS is essential for infection.« less

Time‐lapse imaging of saline‐tracer transport in fractured rock using difference‐attenuation radar tomography

USGS Publications Warehouse

Day-Lewis, Frederick D.; Lane, John W.; Harris, Jerry M.; Gorelick, Steven M.

2003-01-01

Accurate characterization of fractured‐rock aquifer heterogeneity remains one of the most challenging and important problems in groundwater hydrology. We demonstrate a promising strategy to identify preferential flow paths in fractured rock using a combination of geophysical monitoring and conventional hydrogeologic tests. Cross‐well difference‐attenuation ground‐penetrating radar was used to monitor saline‐tracer migration in an experiment at the U.S. Geological Survey Fractured Rock Hydrology Research Site in Grafton County, New Hampshire. Radar data sets were collected every 10 min in three adjoining planes for 5 hours during each of 12 tracer tests. An innovative inversion method accounts for data acquisition times and temporal changes in attenuation during data collection. The inverse algorithm minimizes a combination of two functions. The first is the sum of weighted squared data residuals. Second is a measure of solution complexity based on an a priori space‐time covariance function, subject to constraints that limit radar‐attenuation changes to regions of the tomograms traversed by high difference‐attenuation ray paths. The time series of tomograms indicate relative tracer concentrations and tracer arrival times in the image planes; from these we infer the presence and location of a preferential flow path within a previously identified zone of transmissive fractures. These results provide new insights into solute channeling and the nature of aquifer heterogeneity at the site.

Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus

PubMed Central

Mangala Prasad, Vidya

2017-01-01

Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway. PMID:28575072

Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus.

PubMed

Mangala Prasad, Vidya; Klose, Thomas; Rossmann, Michael G

2017-06-01

Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway.

Routine single particle CryoEM sample and grid characterization by tomography

PubMed Central

Noble, Alex J; Brasch, Julia; Chase, Jillian; Acharya, Priyamvada; Tan, Yong Zi; Zhang, Zhening; Kim, Laura Y; Scapin, Giovanna; Rapp, Micah; Eng, Edward T; Rice, William J; Cheng, Anchi; Negro, Carl J; Shapiro, Lawrence; Kwong, Peter D; Jeruzalmi, David; des Georges, Amedee; Potter, Clinton S

2018-01-01

Single particle cryo-electron microscopy (cryoEM) is often performed under the assumption that particles are not adsorbed to the air-water interfaces and in thin, vitreous ice. In this study, we performed fiducial-less tomography on over 50 different cryoEM grid/sample preparations to determine the particle distribution within the ice and the overall geometry of the ice in grid holes. Surprisingly, by studying particles in holes in 3D from over 1000 tomograms, we have determined that the vast majority of particles (approximately 90%) are adsorbed to an air-water interface. The implications of this observation are wide-ranging, with potential ramifications regarding protein denaturation, conformational change, and preferred orientation. We also show that fiducial-less cryo-electron tomography on single particle grids may be used to determine ice thickness, optimal single particle collection areas and strategies, particle heterogeneity, and de novo models for template picking and single particle alignment. PMID:29809143

Delayed rupture of gallbladder following blunt abdominal trauma.

PubMed

Mohanty, Debajyoti; Agarwal, Himanshu; Aggarwal, Krittika; Garg, Pankaj Kumar

2014-09-01

A 29-year-old gentleman presented to surgery emergency with severe upper abdominal pain and vomiting. He reported to had been hit in his abdomen by a ball during a cricket match. Computerized tomogram of the abdomen revealed hematoma within the gallbladder lumen, laceration of segment six of liver, and hemoperitoneum. The patient did not agree for laparotomy advised to him, and so, managed conservatively. The patient reported back to us with high grade fever, jaundice, and painful abdominal distension after seven days of discharge from the hospital. His abdominal examination showed features of generalized peritonitis. Surgical abdominal exploration revealed a single perforation in the fundus of gallbladder with frozen calot'striangle. Subtotal cholecystectomy was done. Histopathology of excised gallbladder revealed xanthogranulomatous inflammation. The present case report highlights that early exploration and cholecystectomy should be considered in patients with gallbladder injury to obviate the risk of delayed perforation.

Label-free tomographic reconstruction of optically thick structures using GLIM (Conference Presentation)

NASA Astrophysics Data System (ADS)

Kandel, Mikhail E.; Kouzehgarani, Ghazal N.; Ngyuen, Tan H.; Gillette, Martha U.; Popescu, Gabriel

2017-02-01

Although the contrast generated in transmitted light microscopy is due to the elastic scattering of light, multiple scattering scrambles the image and reduces overall visibility. To image both thin and thick samples, we turn to gradient light interference microscopy (GLIM) to simultaneously measure morphological parameters such as cell mass, volume, and surfaces as they change through time. Because GLIM combines multiple intensity images corresponding to controlled phase offsets between laterally sheared beams, incoherent contributions from multiple scattering are implicitly cancelled during the phase reconstruction procedure. As the interfering beams traverse near identical paths, they remain comparable in power and interfere with optimal contrast. This key property lets us obtain tomographic parameters from wide field z-scans after simple numerical processing. Here we show our results on reconstructing tomograms of bovine embryos, characterizing the time-lapse growth of HeLa cells in 3D, and preliminary results on imaging much larger specimen such as brain slices.

Monitoring an artificial tracer test within streambed sediments with time lapse underwater 3D ERT

NASA Astrophysics Data System (ADS)

Clémence, Houzé; Marc, Pessel; Véronique, Durand; Toihir, Ali

2017-04-01

The stream-aquifer interface is considered a hotspot for environmental and ecological issues. Due to their complexity, the exchange mechanisms occurring between groundwater and surface water at this interface are not yet fully understood. Many studies have focused on the characterization of the two-dimensional distribution of an artificial tracer (generally injected into the stream) within and outside the streambed, but there is insufficient information about the 3D spatial distribution of the tracer fluxes and their temporal variations. We monitored the transport of an artificial solute tracer transport with 3D electrical resistivity tomography (ERT) in order to improve the 3D spatial resolution in the imaging of the first tens of centimeters of streambed sediments and propose an innovative approach of the three-dimensional and temporal observation of the water fluxes. The hydro-geophysical field measurements were made on a small stream located within the Orgeval watershed (Seine et Marne, France). Using a resistivimeter connected to 180 electrodes, 3D electrical resistivity tomograms were made on a riverbed section, as a brine tracer was injected directly into the hyporheic zone. Before the tracer monitoring, the static 3D resistivity tomograms were consistent with the lithological heterogeneities identified at the site. However, this study defines some prerequisites to high-resolution 3D underwater resistivity measurements: for instance, a precise knowledge of an eventual weak electrode contact and a spatial resolution identical in every spatial direction. First results show a rapid development and persistence of a conductive plume around the injection point which disappears progressively after the injection. Within the sediments top layer, preferential flowpaths were highlighted due to the highly heterogeneous medium and hydraulic conductivity. The riverbed topography showed some pool-riffle sequences which conduct the formation of local entering and exiting zones. It seems clear that riverbed heterogeneities drive some local exchanges between surface water and pore water, despite the gaining condition of the stream. Moreover, inversion and data processing appear very sensitive to the boundary condition variations, such as the thickness and the resistivity of the water layer. This makes a quantitative interpretation of tracer fluxes within the hyporheic zone difficult. We demonstrate that for this type of study, knowledge of these conditions and precise monitoring of their fluctuations in time are required.

Optical studies of the X-ray transient XTE J2123-058 - II. Phase-resolved spectroscopy

NASA Astrophysics Data System (ADS)

Hynes, R. I.; Charles, P. A.; Haswell, C. A.; Casares, J.; Zurita, C.; Serra-Ricart, M.

2001-06-01

We present time-resolved spectroscopy of the soft X-ray transient XTEJ2123-058 in outburst. A useful spectral coverage of 3700-6700Å was achieved spanning two orbits of the binary, with single-epoch coverage extending to ~9000Å. The optical spectrum approximates a steep blue power law, consistent with emission on the Rayleigh-Jeans tail of a hot blackbody spectrum. The strongest spectral lines are Heii 4686Å and Ciii/Niii 4640Å (Bowen blend) in emission. Their relative strengths suggest that XTEJ2123-058 was formed in the Galactic plane, not in the halo. Other weak emission lines of Heii and Civ are present, and Balmer lines show a complex structure, blended with Heii. Heii 4686-Å profiles show a complex multiple S-wave structure, with the strongest component appearing at low velocities in the lower-left quadrant of a Doppler tomogram. Hα shows transient absorption between phases 0.35 and 0.55. Both of these effects appear to be analogous to similar behaviour in SW Sex type cataclysmic variables. We therefore consider whether the spectral line behaviour of XTEJ2123-058 can be explained by the same models invoked for those systems.

Dynamo Catalogue: Geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms.

PubMed

Castaño-Díez, Daniel; Kudryashev, Mikhail; Stahlberg, Henning

2017-02-01

Cryo electron tomography allows macromolecular complexes within vitrified, intact, thin cells or sections thereof to be visualized, and structural analysis to be performed in situ by averaging over multiple copies of the same molecules. Image processing for subtomogram averaging is specific and cumbersome, due to the large amount of data and its three dimensional nature and anisotropic resolution. Here, we streamline data processing for subtomogram averaging by introducing an archiving system, Dynamo Catalogue. This system manages tomographic data from multiple tomograms and allows visual feedback during all processing steps, including particle picking, extraction, alignment and classification. The file structure of a processing project file structure includes logfiles of performed operations, and can be backed up and shared between users. Command line commands, database queries and a set of GUIs give the user versatile control over the process. Here, we introduce a set of geometric tools that streamline particle picking from simple (filaments, spheres, tubes, vesicles) and complex geometries (arbitrary 2D surfaces, rare instances on proteins with geometric restrictions, and 2D and 3D crystals). Advanced functionality, such as manual alignment and subboxing, is useful when initial templates are generated for alignment and for project customization. Dynamo Catalogue is part of the open source package Dynamo and includes tools to ensure format compatibility with the subtomogram averaging functionalities of other packages, such as Jsubtomo, PyTom, PEET, EMAN2, XMIPP and Relion. Copyright © 2016. Published by Elsevier Inc.

Capture, Release and Culture of Circulating Tumor Cells from Pancreatic Cancer Patients using an Enhanced Mixing Chip

PubMed Central

Sheng, Weian; Ogunwobi, Olorunseun O.; Chen, Tao; Zhang, Jinling; George, Thomas J.; Liu, Chen; Fan, Z. Hugh

2013-01-01

Circulating tumor cells (CTCs) from peripheral blood hold important information for cancer diagnosis and disease monitoring. Analysis of this “liquid biopsy” holds the promise to usher in a new era of personalized therapeutic treatments and real-time monitoring for cancer patients. But the extreme rarity of CTCs in blood makes their isolation and characterization technologically challenging. This paper reports the development of a geometrically enhanced mixing (GEM) chip for high-efficiency and high-purity tumor cell capture. We also successfully demonstrated the release and culture of the captured tumor cells, as well as the isolation of CTCs from cancer patients. The high-performance microchip is based on geometrically optimized micromixer structures, which enhance the transverse flow and flow folding, maximizing the interaction between CTCs and antibody-coated surfaces. With the optimized channel geometry and flow rate, the capture efficiency reached >90% with a purity of >84% when capturing spiked tumor cells in buffer. The system was further validated by isolating a wide range of spiked tumor cells (50–50,000) in 1 mL of lysed blood and whole blood. With the combination of trypsinization and high flow rate washing, captured tumor cells were efficiently released. The released cells were viable and able to proliferate, and showed no difference compared with intact cells that were not subjected to the capture and release process. Furthermore, we applied the device for detecting CTCs from metastatic pancreatic cancer patients’ blood; and CTCs were found from 17 out of 18 samples (>94%). We also tested the potential utility of the device in monitoring the response to anti-cancer drug treatment in pancreatic cancer patients, and the CTC numbers correlated with the clinical computed tomograms (CT scans) of tumors. The presented technology shows great promise for accurate CTC enumeration, biological studies of CTCs and cancer metastasis, as well as for cancer diagnosis and treatment monitoring. PMID:24220648

Translating Computer-Aided Design and Surgical Planning Into Successful Mandibular Reconstruction Using a Vascularized Iliac-Crest Flap.

PubMed

Zheng, Lei; Lv, Xiaoming; Zhang, Jie; Liu, Shuming; Zhang, Jianguo; Zhang, Yi

2018-04-01

This study evaluated the computer-aided approach to the reconstruction of mandibular defects using a vascularized iliac-crest flap. From December 2015 to October 2016, 14 patients (8 men and 6 women) 18 to 64 years old (median age, 29 yr) were treated at the Peking University School and Stomatology Hospital (Beijing, China). Biopsy specimens from all patients were subjected to histologic examination before segmental mandibulectomy. Computer-based surgical techniques, including virtual surgical planning, computer-aided design and manufacturing, rapid prototyping, and intraoperative navigation, were used to restore the anatomic continuity and configuration of the mandible using a vascularized iliac-crest flap. Two transverse dimensions and 1 anteroposterior (A-P) dimension were evaluated based on the virtual plan and postoperative computed tomogram. Lines from condylar head to condylar head and from gonial angle to gonial angle were defined as the transverse dimensions. A perpendicular line drawn from the mandibular midline to the center point on the condylar head to condylar head measurement was defined as the A-P dimension. Complications were evaluated during follow-up. The flap success rate was 92.9% (13 of 14), with 1 flap failure. After the operation, there were no other serious complications in 13 of the 14 patients, who exhibited a good mandibular configuration with good occlusion. Furthermore, the height of bone graft was sufficient for implants. Healing of the recipient and donor sites with no serious complication was uneventful. The average surgical errors in the A-P dimension and transverse dimensions were 1.8 ± 1.0 mm (range, 0.2 to 3.7 mm), 2.2 ± 1.1 mm (range, 0.9 to 5.0 mm), and 2.6 ± 1.6 mm (range, 0.3 to 7.2 mm), respectively. The use of these digital techniques was found to be a viable option for reconstruction of mandibular defects, but the results should be interpreted cautiously because of the small number of patients and the relatively short follow-up. Copyright © 2017. Published by Elsevier Inc.

4D Optimization of Scanned Ion Beam Tracking Therapy for Moving Tumors

PubMed Central

Eley, John Gordon; Newhauser, Wayne David; Lüchtenborg, Robert; Graeff, Christian; Bert, Christoph

2014-01-01

Motion mitigation strategies are needed to fully realize the theoretical advantages of scanned ion beam therapy for patients with moving tumors. The purpose of this study was to determine whether a new four-dimensional (4D) optimization approach for scanned-ion-beam tracking could reduce dose to avoidance volumes near a moving target while maintaining target dose coverage, compared to an existing 3D-optimized beam tracking approach. We tested these approaches computationally using a simple 4D geometrical phantom and a complex anatomic phantom, that is, a 4D computed tomogram of the thorax of a lung cancer patient. We also validated our findings using measurements of carbon-ion beams with a motorized film phantom. Relative to 3D-optimized beam tracking, 4D-optimized beam tracking reduced the maximum predicted dose to avoidance volumes by 53% in the simple phantom and by 13% in the thorax phantom. 4D-optimized beam tracking provided similar target dose homogeneity in the simple phantom (standard deviation of target dose was 0.4% versus 0.3%) and dramatically superior homogeneity in the thorax phantom (D5-D95 was 1.9% versus 38.7%). Measurements demonstrated that delivery of 4D-optimized beam tracking was technically feasible and confirmed a 42% decrease in maximum film exposure in the avoidance region compared with 3D-optimized beam tracking. In conclusion, we found that 4D-optimized beam tracking can reduce the maximum dose to avoidance volumes near a moving target while maintaining target dose coverage, compared with 3D-optimized beam tracking. PMID:24889215

Validation of model-based deformation correction in image-guided liver surgery via tracked intraoperative ultrasound: preliminary method and results

NASA Astrophysics Data System (ADS)

Clements, Logan W.; Collins, Jarrod A.; Wu, Yifei; Simpson, Amber L.; Jarnagin, William R.; Miga, Michael I.

2015-03-01

Soft tissue deformation represents a significant error source in current surgical navigation systems used for open hepatic procedures. While numerous algorithms have been proposed to rectify the tissue deformation that is encountered during open liver surgery, clinical validation of the proposed methods has been limited to surface based metrics and sub-surface validation has largely been performed via phantom experiments. Tracked intraoperative ultrasound (iUS) provides a means to digitize sub-surface anatomical landmarks during clinical procedures. The proposed method involves the validation of a deformation correction algorithm for open hepatic image-guided surgery systems via sub-surface targets digitized with tracked iUS. Intraoperative surface digitizations were acquired via a laser range scanner and an optically tracked stylus for the purposes of computing the physical-to-image space registration within the guidance system and for use in retrospective deformation correction. Upon completion of surface digitization, the organ was interrogated with a tracked iUS transducer where the iUS images and corresponding tracked locations were recorded. After the procedure, the clinician reviewed the iUS images to delineate contours of anatomical target features for use in the validation procedure. Mean closest point distances between the feature contours delineated in the iUS images and corresponding 3-D anatomical model generated from the preoperative tomograms were computed to quantify the extent to which the deformation correction algorithm improved registration accuracy. The preliminary results for two patients indicate that the deformation correction method resulted in a reduction in target error of approximately 50%.

Mantle circulation models with variational data assimilation: Inferring past mantle flow and structure from plate motion histories and seismic tomography

NASA Astrophysics Data System (ADS)

Bunge, Hans-Peter

2002-08-01

Earth's mantle overturns itself about once every 200 Million years (myrs). Prima facie evidence for this overturn is the motion of tectonic plates at the surface of the Earth driving the geologic activity of our planet. Supporting evidence also comes from seismic tomograms of the Earth's interior that reveal the convective currents in remarkable clarity. Much has been learned about the physics of solid state mantle convection over the past two decades aided primarily by sophisticated computer simulations. Such simulations are reaching the threshold of fully resolving the convective system globally. In this talk we will review recent progress in mantle dynamics studies. We will then turn our attention to the fundamental question of whether it is possible to explicitly reconstruct mantle flow back in time. This is a classic problem of history matching, amenable to control theory and data assimilation. The technical advances that make such approach feasible are dramatically increasing compute resources, represented for example through Beowulf clusters, and new observational initiatives, represented for example through the US-Array effort that should lead to an order-of-magnitude improvement in our ability to resolve Earth structure seismically below North America. In fact, new observational constraints on deep Earth structure illustrate the growing importance of of improving our data assimilation skills in deep Earth models. We will explore data assimilation through high resolution global adjoint models of mantle circulation and conclude that it is feasible to reconstruct mantle flow back in time for at least the past 100 myrs.

4D optimization of scanned ion beam tracking therapy for moving tumors

NASA Astrophysics Data System (ADS)

Eley, John Gordon; Newhauser, Wayne David; Lüchtenborg, Robert; Graeff, Christian; Bert, Christoph

2014-07-01

Motion mitigation strategies are needed to fully realize the theoretical advantages of scanned ion beam therapy for patients with moving tumors. The purpose of this study was to determine whether a new four-dimensional (4D) optimization approach for scanned-ion-beam tracking could reduce dose to avoidance volumes near a moving target while maintaining target dose coverage, compared to an existing 3D-optimized beam tracking approach. We tested these approaches computationally using a simple 4D geometrical phantom and a complex anatomic phantom, that is, a 4D computed tomogram of the thorax of a lung cancer patient. We also validated our findings using measurements of carbon-ion beams with a motorized film phantom. Relative to 3D-optimized beam tracking, 4D-optimized beam tracking reduced the maximum predicted dose to avoidance volumes by 53% in the simple phantom and by 13% in the thorax phantom. 4D-optimized beam tracking provided similar target dose homogeneity in the simple phantom (standard deviation of target dose was 0.4% versus 0.3%) and dramatically superior homogeneity in the thorax phantom (D5-D95 was 1.9% versus 38.7%). Measurements demonstrated that delivery of 4D-optimized beam tracking was technically feasible and confirmed a 42% decrease in maximum film exposure in the avoidance region compared with 3D-optimized beam tracking. In conclusion, we found that 4D-optimized beam tracking can reduce the maximum dose to avoidance volumes near a moving target while maintaining target dose coverage, compared with 3D-optimized beam tracking.

Seasonal Response and Characterization of a Scree Slope and Active Debris Flow Catchment Using Multiple Geophysical Techniques: The case of the Meretschibach Catchment, Switzerland

NASA Astrophysics Data System (ADS)

Fankhauser, Kerstin; Guzman, Daisy R. Lucas; Oggier, Nicole; Maurer, Hansruedi; Springman, Sarah M.

2015-04-01

Various types of mass movements cause extensive natural hazards in populated mountain regions. They need to be quantified, and possibly predicted, for implementing effective mitigation and protection measures. The Meretschibach catchment in the Valais area, Switzerland, is a source region for such events. Various forms of instabilities occur on the steep slopes. They manifest themselves in form of smaller rock falls and rock slides on the open scree slopes. Moreover, large sediment volumes of channelized stream deposits can evolve into debris flows, with a substantial run-out along the Meretschibach. Geophysical methods, such as electrical resistivity tomography (ERT) and ground-penetrating-radar (GPR) have been proven to be powerful tools for characterizing mass movements and slope instabilities. They complement other remote sensing techniques and in-situ geotechnical experiments. Ground-based and helicopter-borne GPR measurements were carried out at the Meretschibach test site, to determine the depth to the bedrock. The results indicate that the bedrock is generally shallow, ranging from a few centimetres to about 5 metres vertically below the surface. A particularly interesting aspect of the GPR investigations was the observation that bedrock depth could be resolved by both, ground-based and helicopter-borne GPR data. Ground-based GPR surveying proved to be extremely challenging on the steep slopes, and some areas were even inaccessible due to safety concerns. It is therefore encouraging for future projects that helicopter-borne GPR acquisition offers a promising alternative. The spatial distribution of the soil moisture content and the temporal variations were determined with repeated ERT measurements. The resulting tomograms allowed a conductive soil layer and more resistive bedrock to be distinguished clearly. The ERT results were in good agreement with in-situ geotechnical measurements in a nearby test pit, and the depth of the soil-bedrock interface was broadly consistent with the GPR results. A comparison of tomograms obtained during the relatively dry month of June 2014, with those acquired after heavy rainfall in July 2014, showed significant changes of the shallow subsurface resistivities. These changes could be attributed in a quantitative fashion to variations of the soil water Saturation.

Comparison of aquifer characterization approaches through steady state groundwater model validation: A controlled laboratory sandbox study

USGS Publications Warehouse

Illman, W.A.; Zhu, J.; Craig, A.J.; Yin, D.

2010-01-01

Groundwater modeling has become a vital component to water supply and contaminant transport investigations. An important component of groundwater modeling under steady state conditions is selecting a representative hydraulic conductivity (K) estimate or set of estimates which defines the K field of the studied region. Currently, there are a number of characterization approaches to obtain K at various scales and in varying degrees of detail, but there is a paucity of information in terms of which characterization approach best predicts flow through aquifers or drawdowns caused by some drawdown inducing events. The main objective of this paper is to assess K estimates obtained by various approaches by predicting drawdowns from independent cross-hole pumping tests and total flow rates through a synthetic heterogeneous aquifer from flow-through tests. Specifically, we (1) characterize a synthetic heterogeneous aquifer built in the sandbox through various techniques (permeameter analyses of core samples, single-hole, cross-hole, and flow-through testing), (2) obtain mean K fields through traditional analysis of test data by treating the medium to be homogeneous, (3) obtain heterogeneous K fields through kriging and steady state hydraulic tomography, and (4) conduct forward simulations of 16 independent pumping tests and six flowthrough tests using these homogeneous and heterogeneous K fields and comparing them to actual data. Results show that the mean K and heterogeneous K fields estimated through kriging of small-scale K data (core and single-hole tests) yield biased predictions of drawdowns and flow rates in this synthetic heterogeneous aquifer. In contrast, the heterogeneous K distribution or ?K tomogram? estimated via steady state hydraulic tomography yields excellent predictions of drawdowns of pumping tests not used in the construction of the tomogram and very good estimates of total flow rates from the flowthrough tests. These results suggest that steady state groundwater model validation is possible in this laboratory sandbox aquifer if the heterogeneous K distribution and forcing functions (boundary conditions and source/sink terms) are characterized sufficiently. ?? 2010 by the American Geophysical Union.

Rationale for the development and the mechanism of action of endoscopic thermal vapor ablation (InterVapor) for the treatment of emphysema.

PubMed

Kesten, Steven; Anderson, Joseph C; Tuck, Stephanie A

2012-07-01

Emphysema remains a disabling disease despite current treatment. Novel approaches to the underlying physiological abnormalities responsible for symptom generation are warranted. A review of current hypotheses and preclinical and clinical data on the utility of endoscopic thermal vapor ablation (InterVapor) in the treatment of emphysema. In animal studies, thermal energy in the form of heated water vapor both in healthy and in papain-induced emphysema in dogs and sheep leads to an inflammatory response followed by healing with airway and parenchymal fibrosis. The fibrosis and associated distal atelectasis result in volume reduction. The amount of thermal energy delivered has been based on the amount of target tissue mass determined from a high-resolution computed tomogram. Early human studies indicated the feasibility of InterVapor with 5 cal/g tissue; however, the dose appeared insufficient to induce lobar volume reduction. A study using 10 cal/g to 1 upper lobe (n=44) induced a mean of 46% lobar volume reduction at 12 months along with significant improvements in the physiology and health outcomes. InterVapor induces lung volume reduction in patients with emphysema. The mechanism of action is through a thermally induced inflammatory response followed by healing with subsequent remodeling of tissue (fibrosis and distal atelectasis).

4D nano-tomography of electrochemical energy devices using lab-based X-ray imaging

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

Heenan, T. M. M.; Finegan, D. P.; Tjaden, B.

Electrochemical energy devices offer a variety of alternate means for low-carbon, multi-scale energy conversion and storage. Reactions in these devices are supported by electrodes with characteristically complex microstructures. To meet the increasing capacity and lifetime demands across a range of applications, it is essential to understand microstructural evolutions at a cell and electrode level which are thought to be critical aspects influencing material and device lifetime and performance. X-ray computed tomography (CT) has become a highly employed method for non-destructive characterisation of such microstructures with high spatial resolution. However, sub-micron resolutions present significant challenges for sample preparation and handling particularlymore » in 4D studies, (three spatial dimensions plus time). Here, microstructural information is collected from the same region of interest within two electrode materials: a solid oxide fuel cell and the positive electrode from a lithium-ion battery. Using a lab-based X-ray instrument, tomograms with sub-micron resolutions were obtained between thermal cycling. The intricate microstructural evolutions captured within these two materials provide model examples of 4D X-ray nano-CT capabilities in tracking challenging degradation mechanisms. This technique is valuable in the advancement of electrochemical research as well as broader applications for materials characterisation.« less

Universal in vivo Textural Model for Human Skin based on Optical Coherence Tomograms.

PubMed

Adabi, Saba; Hosseinzadeh, Matin; Noei, Shahryar; Conforto, Silvia; Daveluy, Steven; Clayton, Anne; Mehregan, Darius; Nasiriavanaki, Mohammadreza

2017-12-20

Currently, diagnosis of skin diseases is based primarily on the visual pattern recognition skills and expertise of the physician observing the lesion. Even though dermatologists are trained to recognize patterns of morphology, it is still a subjective visual assessment. Tools for automated pattern recognition can provide objective information to support clinical decision-making. Noninvasive skin imaging techniques provide complementary information to the clinician. In recent years, optical coherence tomography (OCT) has become a powerful skin imaging technique. According to specific functional needs, skin architecture varies across different parts of the body, as do the textural characteristics in OCT images. There is, therefore, a critical need to systematically analyze OCT images from different body sites, to identify their significant qualitative and quantitative differences. Sixty-three optical and textural features extracted from OCT images of healthy and diseased skin are analyzed and, in conjunction with decision-theoretic approaches, used to create computational models of the diseases. We demonstrate that these models provide objective information to the clinician to assist in the diagnosis of abnormalities of cutaneous microstructure, and hence, aid in the determination of treatment. Specifically, we demonstrate the performance of this methodology on differentiating basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) from healthy tissue.

Cyclic reconstruction of 4D retinal blood flow with pulse synchronization

NASA Astrophysics Data System (ADS)

Schmoll, Tilman; Lasser, Theo; Leitgeb, Rainer A.

2009-02-01

Doppler OCT systems allow nowadays to visualize quantitative and qualitative angiographic maps of retinal tissue. We equipped the instrument with a pulse oximeter and recorded the pulse synchronously with the resonant Doppler flow data. Recombination of tomograms according to the heart beat cycles yields full volumes for each cycle instant. We believe such multi-dimensional functional information and the ability to monitor dynamic processes over time to open exciting perspectives that ultimately contribute to a better understanding of retinal physiology and patho-physiology in-vivo.

UWB tomosynthesis of objects in mediums with metal inclusions

NASA Astrophysics Data System (ADS)

Yakubov, V. P.; Shipilov, S. E.; Sukhanov, D. Ya; Minin, I. V.; Minin, O. V.

2017-08-01

Radiowave tomography of dielectric objects containing metal inclusions is a rather complex problem, since the scattering of waves by dielectric inhomogeneities occurs against the background of substantially stronger reflections from metal parts, even if they are geometrically small. The arising features of obtaining a tomogram in such conditions, including overcoming of disguising by reinforcing ribbons and the appearance of locational shadows at different depths, are discussed in the paper. Herewith principled importance to achieve high focusing of UWB radiation by tomosynthesis is noted on the basis of direct experimental data.

Three-dimensional Stochastic Estimation of Porosity Distribution: Benefits of Using Ground-penetrating Radar Velocity Tomograms in Simulated-annealing-based or Bayesian Sequential Simulation Approaches

DTIC Science & Technology

2012-05-30

annealing-based or Bayesian sequential simulation approaches B. Dafflon1,2 and W. Barrash1 Received 13 May 2011; revised 12 March 2012; accepted 17 April 2012...the withheld porosity log are also withheld for this estimation process. For both cases we do this for two wells having locally variable stratigraphy ...borehole location is given at the bottom of each log comparison panel. For comparison with stratigraphy at the BHRS, contacts between Units 1 to 4

Tomographic brain imaging with nucleolar detail and automatic cell counting

NASA Astrophysics Data System (ADS)

Hieber, Simone E.; Bikis, Christos; Khimchenko, Anna; Schweighauser, Gabriel; Hench, Jürgen; Chicherova, Natalia; Schulz, Georg; Müller, Bert

2016-09-01

Brain tissue evaluation is essential for gaining in-depth insight into its diseases and disorders. Imaging the human brain in three dimensions has always been a challenge on the cell level. In vivo methods lack spatial resolution, and optical microscopy has a limited penetration depth. Herein, we show that hard X-ray phase tomography can visualise a volume of up to 43 mm3 of human post mortem or biopsy brain samples, by demonstrating the method on the cerebellum. We automatically identified 5,000 Purkinje cells with an error of less than 5% at their layer and determined the local surface density to 165 cells per mm2 on average. Moreover, we highlight that three-dimensional data allows for the segmentation of sub-cellular structures, including dendritic tree and Purkinje cell nucleoli, without dedicated staining. The method suggests that automatic cell feature quantification of human tissues is feasible in phase tomograms obtained with isotropic resolution in a label-free manner.

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

Ono, Kenji; Fuma, Kazuya; Tabata, Kaori

Magnetic resonance imaging (MRI) is a minimally invasive way to provide high spatial resolution tomograms. However, MRI has been considered to be useless for gene expression imaging compared to optical imaging. In this study, we used a ferritin reporter, binding with biogenic iron, to make it a powerful tool for gene expression imaging in MRI studies. GL261 mouse glioma cells were over-expressed with dual-reporter ferritin-DsRed under {beta}-actin promoter, then gene expression was observed by optical imaging and MRI in a brain tumor model. GL261 cells expressing ferritin-DsRed fusion protein showed enhanced visualizing effect by reducing T2-weighted signal intensity for inmore » vitro and in vivo MRI studies, as well as DsRed fluorescence for optical imaging. Furthermore, a higher contrast was achieved on T2-weighted images when permeating the plasma membrane of ferritin-DsRed-expressing GL261. Thus, a ferritin expression vector can be used as an MRI reporter to monitor in vivo gene expression.« less

Noninvasive characterisation of foot reflexology areas by swept source-optical coherence tomography in patients with low back pain.

PubMed

Dalal, Krishna; Elanchezhiyan, D; Das, Raunak; Dalal, Devjyoti; Pandey, Ravindra Mohan; Chatterjee, Subhamoy; Upadhyay, Ashish Datt; Maran, V Bharathi; Chatterjee, Jyotirmoy

2013-01-01

Objective. When exploring the scientific basis of reflexology techniques, elucidation of the surface and subsurface features of reflexology areas (RAs) is crucial. In this study, the subcutaneous features of RAs related to the lumbar vertebrae were evaluated by swept source-optical coherence tomography (SS-OCT) in subjects with and without low back pain (LBP). Methods. Volunteers without LBP (n = 6 (male : female = 1 : 1)) and subjects with LBP (n = 15 (male : female = 2 : 3)) were clinically examined in terms of skin colour (visual perception), localised tenderness (visual analogue scale) and structural as well as optical attributes as per SS-OCT. From each subject, 6 optical tomograms were recorded from equidistant transverse planes along the longitudinal axis of the RAs, and from each tomogram, 25 different spatial locations were considered for recording SS-OCT image attributes. The images were analysed with respect to the optical intensity distributions and thicknesses of different skin layers by using AxioVision Rel. 4.8.2 software. The SS-OCT images could be categorised into 4 pathological grades (i.e., 0, 1, 2, and 3) according to distinctness in the visible skin layers. Results. Three specific grades for abnormalities in SS-OCT images were identified considering gradual loss of distinctness and increase in luminosity of skin layers. Almost 90.05% subjects were of mixed type having predominance in certain grades. Conclusion. The skin SS-OCT system demonstrated a definite association of the surface features of healthy/unhealthy RAs with cutaneous features and the clinical status of the lumbar vertebrae.

Noninvasive Characterisation of Foot Reflexology Areas by Swept Source-Optical Coherence Tomography in Patients with Low Back Pain

PubMed Central

Dalal, Krishna; Elanchezhiyan, D.; Das, Raunak; Dalal, Devjyoti; Pandey, Ravindra Mohan; Chatterjee, Subhamoy; Upadhyay, Ashish Datt; Maran, V. Bharathi; Chatterjee, Jyotirmoy

2013-01-01

Objective. When exploring the scientific basis of reflexology techniques, elucidation of the surface and subsurface features of reflexology areas (RAs) is crucial. In this study, the subcutaneous features of RAs related to the lumbar vertebrae were evaluated by swept source-optical coherence tomography (SS-OCT) in subjects with and without low back pain (LBP). Methods. Volunteers without LBP (n = 6 (male : female = 1 : 1)) and subjects with LBP (n = 15 (male : female = 2 : 3)) were clinically examined in terms of skin colour (visual perception), localised tenderness (visual analogue scale) and structural as well as optical attributes as per SS-OCT. From each subject, 6 optical tomograms were recorded from equidistant transverse planes along the longitudinal axis of the RAs, and from each tomogram, 25 different spatial locations were considered for recording SS-OCT image attributes. The images were analysed with respect to the optical intensity distributions and thicknesses of different skin layers by using AxioVision Rel. 4.8.2 software. The SS-OCT images could be categorised into 4 pathological grades (i.e., 0, 1, 2, and 3) according to distinctness in the visible skin layers. Results. Three specific grades for abnormalities in SS-OCT images were identified considering gradual loss of distinctness and increase in luminosity of skin layers. Almost 90.05% subjects were of mixed type having predominance in certain grades. Conclusion. The skin SS-OCT system demonstrated a definite association of the surface features of healthy/unhealthy RAs with cutaneous features and the clinical status of the lumbar vertebrae. PMID:23662156

Geophysical monitoring of a field-scale biostimulation pilot project

USGS Publications Warehouse

Lane, J.W.; Day-Lewis, F. D.; Casey, C.C.

2006-01-01

The USGS conducted a geophysical investigation in support of a U.S. Naval Facilities Engineering Command, Southern Division field-scale biostimulation pilot project at Anoka County Riverfront Park (ACP), downgradient of the Naval Industrial Reserve Ordnance Plant, Fridley, Minnesota. The goal of the pilot project is to evaluate subsurface injection of vegetable oil emulsion (VOE) to stimulate microbial degradation of chlorinated hydrocarbons. To monitor the emplacement and movement of the VOE and changes in water chemistry resulting from VOE dissolution and/or enhanced biological activity, the USGS acquired cross-hole radar zero-offset profiles, traveltime tomograms, and borehole geophysical logs during five site visits over 1.5 years. Analysis of pre- and postinjection data sets using petrophysical models developed to estimate VOE saturation and changes in total dissolved solids provides insights into the spatial and temporal distribution of VOE and ground water with altered chemistry. Radar slowness-difference tomograms and zero-offset slowness profiles indicate that the VOE remained close to the injection wells, whereas radar attenuation profiles and electromagnetic induction logs indicate that bulk electrical conductivity increased downgradient of the injection zone, diagnostic of changing water chemistry. Geophysical logs indicate that some screened intervals were located above or below zones of elevated dissolved solids; hence, the geophysical data provide a broader context for interpretation of water samples and evaluation of the biostimulation effort. Our results include (1) demonstration of field and data analysis methods for geophysical monitoring of VOE biostimulation and (2) site-specific insights into the spatial and temporal distributions of VOE at the ACP. ?? 2006 National Ground Water Association.

Geophysical monitoring of a field-scale biostimulation pilot project.

PubMed

Lane, John W; Day-Lewis, Frederick D; Casey, Clifton C

2006-01-01

The USGS conducted a geophysical investigation in support of a U.S. Naval Facilities Engineering Command, Southern Division field-scale biostimulation pilot project at Anoka County Riverfront Park (ACP), down-gradient of the Naval Industrial Reserve Ordnance Plant, Fridley, Minnesota. The goal of the pilot project is to evaluate subsurface injection of vegetable oil emulsion (VOE) to stimulate microbial degradation of chlorinated hydrocarbons. To monitor the emplacement and movement of the VOE and changes in water chemistry resulting from VOE dissolution and/or enhanced biological activity, the USGS acquired cross-hole radar zero-offset profiles, travel-time tomograms, and borehole geophysical logs during five site visits over 1.5 years. Analysis of pre- and postinjection data sets using petrophysical models developed to estimate VOE saturation and changes in total dissolved solids provides insights into the spatial and temporal distribution of VOE and ground water with altered chemistry. Radar slowness-difference tomograms and zero-offset slowness profiles indicate that the VOE remained close to the injection wells, whereas radar attenuation profiles and electromagnetic induction logs indicate that bulk electrical conductivity increased down-gradient of the injection zone, diagnostic of changing water chemistry. Geophysical logs indicate that some screened intervals were located above or below zones of elevated dissolved solids; hence, the geophysical data provide a broader context for interpretation of water samples and evaluation of the biostimulation effort. Our results include (1) demonstration of field and data analysis methods for geophysical monitoring of VOE biostimulation and (2) site-specific insights into the spatial and temporal distributions of VOE at the ACP.

Hydraulic tomography offers improved imaging of heterogeneity in fractured rocks.

PubMed

Illman, Walter A

2014-01-01

Fractured rocks have presented formidable challenges for accurately predicting groundwater flow and contaminant transport. This is mainly due to our difficulty in mapping the fracture-rock matrix system, their hydraulic properties and connectivity at resolutions that are meaningful for groundwater modeling. Over the last several decades, considerable effort has gone into creating maps of subsurface heterogeneity in hydraulic conductivity (K) and specific storage (Ss ) of fractured rocks. Developed methods include kriging, stochastic simulation, stochastic inverse modeling, and hydraulic tomography. In this article, I review the evolution of various heterogeneity mapping approaches and contend that hydraulic tomography, a recently developed aquifer characterization technique for unconsolidated deposits, is also a promising approach in yielding robust maps (or tomograms) of K and Ss heterogeneity for fractured rocks. While hydraulic tomography has recently been shown to be a robust technique, the resolution of the K and Ss tomograms mainly depends on the density of pumping and monitoring locations and the quality of data. The resolution will be improved through the development of new devices for higher density monitoring of pressure responses at discrete intervals in boreholes and potentially through the integration of other data from single-hole tests, borehole flowmeter profiling, and tracer tests. Other data from temperature and geophysical surveys as well as geological investigations may improve the accuracy of the maps, but more research is needed. Technological advances will undoubtedly lead to more accurate maps. However, more effort should go into evaluating these maps so that one can gain more confidence in their reliability. © 2013, National Ground Water Association.

Hydraulic tomography offers improved imaging of heterogeneity in fractured rocks

NASA Astrophysics Data System (ADS)

Illman, W. A.

2013-12-01

Fractured rocks have presented formidable challenges for accurately predicting groundwater flow and contaminant transport. This is mainly due to our difficulty in mapping the fracture-rock matrix system, their hydraulic properties and connectivity at resolutions that are meaningful for groundwater flow and especially transport modeling. Over the last several decades, considerable effort has gone into creating maps of subsurface heterogeneity in hydraulic conductivity (K) and specific storage (Ss) of fractured rocks. Developed methods include kriging, stochastic simulation, stochastic inverse modeling, and hydraulic tomography. In this presentation, I review the evolution of various heterogeneity mapping approaches and contend that hydraulic tomography, a recently developed aquifer characterization technique for unconsolidated deposits, is also a promising approach in yielding robust maps (or tomograms) of K and Ss heterogeneity for fractured rocks. While hydraulic tomography has recently been shown to be a robust technique, the resolution of the K and Ss tomograms mainly depends on the density of pumping and monitoring locations and the quality of data. The resolution will be improved through the development of new devices for higher density monitoring of pressure responses at discrete intervals in boreholes and potentially through the integration of other data from single-hole tests, borehole flowmeter profiling and tracer tests. Other data from temperature and geophysical surveys as well as geological investigations may improve the accuracy of the maps, but more research is needed. Technological advances will undoubtedly lead to more accurate maps. However, more effort should go into evaluating these maps so that one can gain more confidence in their reliability.

Saline tracer visualized with three-dimensional electrical resistivity tomography: Field-scale spatial moment analysis

USGS Publications Warehouse

Singha, Kamini; Gorelick, Steven M.

2005-01-01

Cross-well electrical resistivity tomography (ERT) was used to monitor the migration of a saline tracer in a two-well pumping-injection experiment conducted at the Massachusetts Military Reservation in Cape Cod, Massachusetts. After injecting 2200 mg/L of sodium chloride for 9 hours, ERT data sets were collected from four wells every 6 hours for 20 days. More than 180,000 resistance measurements were collected during the tracer test. Each ERT data set was inverted to produce a sequence of 3-D snapshot maps that track the plume. In addition to the ERT experiment a pumping test and an infiltration test were conducted to estimate horizontal and vertical hydraulic conductivity values. Using modified moment analysis of the electrical conductivity tomograms, the mass, center of mass, and spatial variance of the imaged tracer plume were estimated. Although the tomograms provide valuable insights into field-scale tracer migration behavior and aquifer heterogeneity, standard tomographic inversion and application of Archie's law to convert electrical conductivities to solute concentration results in underestimation of tracer mass. Such underestimation is attributed to (1) reduced measurement sensitivity to electrical conductivity values with distance from the electrodes and (2) spatial smoothing (regularization) from tomographic inversion. The center of mass estimated from the ERT inversions coincided with that given by migration of the tracer plume using 3-D advective-dispersion simulation. The 3-D plumes seen using ERT exhibit greater apparent dispersion than the simulated plumes and greater temporal spreading than observed in field data of concentration breakthrough at the pumping well.

Uses of megavoltage digital tomosynthesis in radiotherapy

NASA Astrophysics Data System (ADS)

Sarkar, Vikren

With the advent of intensity modulated radiotherapy, radiation treatment plans are becoming more conformal to the tumor with the decreasing margins. It is therefore of prime importance that the patient be positioned correctly prior to treatment. Therefore, image guided treatment is necessary for intensity modulated radiotherapy plans to be implemented successfully. Current advanced imaging devices require costly hardware and software upgrade, and radiation imaging solutions, such as cone beam computed tomography, may introduce extra radiation dose to the patient in order to acquire better quality images. Thus, there is a need to extend current existing imaging device ability and functions while reducing cost and radiation dose. Existing electronic portal imaging devices can be used to generate computed tomography-like tomograms through projection images acquired over a small angle using the technique of cone-beam digital tomosynthesis. Since it uses a fraction of the images required for computed tomography reconstruction, use of this technique correspondingly delivers only a fraction of the imaging dose to the patient. Furthermore, cone-beam digital tomosynthesis can be offered as a software-only solution as long as a portal imaging device is available. In this study, the feasibility of performing digital tomosynthesis using individually-acquired megavoltage images from a charge coupled device-based electronic portal imaging device was investigated. Three digital tomosynthesis reconstruction algorithms, the shift-and-add, filtered back-projection, and simultaneous algebraic reconstruction technique, were compared considering the final image quality and radiation dose during imaging. A software platform, DART, was created using a combination of the Matlab and C++ languages. The platform allows for the registration of a reference Cone Beam Digital Tomosynthesis (CBDT) image against a daily acquired set to determine how to shift the patient prior to treatment. Finally, the software was extended to investigate if the digital tomosynthesis dataset could be used in an adaptive radiotherapy regimen through the use of the Pinnacle treatment planning software to recalculate dose delivered. The feasibility study showed that the megavoltage CBDT visually agreed with corresponding megavoltage computed tomography images. The comparative study showed that the best compromise between imaging quality and imaging dose is obtained when 11 projection images, acquired over an imaging angle of 40°, are used with the filtered back-projection algorithm. DART was successfully used to register reference and daily image sets to within 1 mm in-plane and 2.5 mm out of plane. The DART platform was also effectively used to generate updated files that the Pinnacle treatment planning system used to calculate updated dose in a rigidly shifted patient. These doses were then used to calculate a cumulative dose distribution that could be used by a physician as reference to decide when the treatment plan should be updated. In conclusion, this study showed that a software solution is possible to extend existing electronic portal imaging devices to function as cone-beam digital tomosynthesis devices and achieve daily requirement for image guided intensity modulated radiotherapy treatments. The DART platform also has the potential to be used as a part of adaptive radiotherapy solution.

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

Stevens, Andrew; Browning, Nigel D.

Traditionally, microscopists have worked with the Nyquist-Shannon theory of sampling, which states that to be able to reconstruct the image fully it needs to be sampled at a rate of at least twice the highest spatial frequency in the image. This sampling rate assumes that the image is sampled at regular intervals and that every pixel contains information that is crucial for the image (it even assumes that noise is important). Images in general, and especially low dose S/TEM images, contain significantly less information than can be encoded by a grid of pixels (which is why image compression works). Mathematicallymore » speaking, the image data has a low dimensional or sparse representation. Through the application of compressive sensing methods [1,2,3] this representation can be found using pre-designed measurements that are usually random for implementation simplicity. These measurements and the compressive sensing reconstruction algorithms have the added benefit of reducing noise. This reconstruction approach can be extended into higher dimensions, whereby the random sampling in each 2-D image can be extended into: a sequence of tomographic projections (i.e. tilt images); a sequence of video frames (i.e. incorporating temporal resolution and dynamics); spectral resolution (i.e. energy filtering an image to see the distribution of elements); and ptychography (i.e. sampling a full diffraction image at each location in a 2-D grid across the sample). This approach has been employed experimentally for materials science samples requiring low-dose imaging [2], and can be readily applied to biological samples. Figure 1 shows the resolution possible in a complex biological system, mouse pancreatic islet beta cells [4], when tomogram slices are reconstructed using subsampling. Reducing the number of pixels (1/6 pix and 1/3*1/3) shows minimal degradation compared to the reconstructions using all pixels (all data and 1/3 tilt). Although subsampling 1/6 of the tilts (1/6 of overall dose) degrades the reconstruction to the point that the cellular structures cannot be identified. Using 1/3 of both the pixels and the tilts provides a high quality image at 1/9 the overall dose even for this most basic and rapid demonstration of the CS methods. Figure 2 demonstrates the theoretical tomogram reconstruction quality (vertical axis) as undersampling (horizontal axis) is increased; we examined subsampling pixels and tilt-angles individually and a combined approach in which both pixels and tilts are sub-sampled. Note that subsampling pixels maintains high quality reconstructions (solid lines). Using the inpainting algorithm to obtain tomograms can automatically reduce the dose applied to the system by an order of magnitude. Perhaps the best way to understand the impact is to consider that by using inpainting (and with minimal hardware changes), a sample that can normally withstand a dose of ~10 e/Å2 can potentially be imaged with an “equivalent quality” to a dose level of 103 e/Å2. To put this in perspective, this is approaching the dose level used for the most advanced images, in terms of spatial resolution, for inorganic systems. While there are issues for biological specimens beyond dose (structural complexity being the most important one), this sampling approach allows the methods that are traditionally used for materials science to be applied to biological systems [5]. References: [1] A Stevens, H Yang, L Carin et al. Microscopy 63(1), (2014), pp. 41. [2] L Kovarik, A Stevens, A Liyu et al. Appl. Phys. Lett. 109, 164102 (2016) [3] A Stevens, L Kovarik, P Abellan et al. Adv. Structural and Chemical Imaging 1(10), (2015), pp. 1. [4] MD Guay, W Czaja, MA Aronova et al. Scientific Reports 6, 27614 (2016) [5] Supported by the Chemical Imaging, Signature Discovery, and Analytics in Motion Initiatives at PNNL. PNNL is operated by Battelle Memorial Inst. for the US DOE; contract DE-AC05-76RL01830.« less

Mineral density volume gradients in normal and diseased human tissues

DOE PAGES

Djomehri, Sabra I.; Candell, Susan; Case, Thomas; ...

2015-04-09

Clinical computed tomography provides a single mineral density (MD) value for heterogeneous calcified tissues containing early and late stage pathologic formations. The novel aspect of this study is that, it extends current quantitative methods of mapping mineral density gradients to three dimensions, discretizes early and late mineralized stages, identifies elemental distribution in discretized volumes, and correlates measured MD with respective calcium (Ca) to phosphorus (P) and Ca to zinc (Zn) elemental ratios. To accomplish this, MD variations identified using polychromatic radiation from a high resolution micro-computed tomography (micro-CT) benchtop unit were correlated with elemental mapping obtained from a microprobe X-raymore » fluorescence (XRF) using synchrotron monochromatic radiation. Digital segmentation of tomograms from normal and diseased tissues (N=5 per group; 40-60 year old males) contained significant mineral density variations (enamel: 2820-3095mg/cc, bone: 570-1415mg/cc, cementum: 1240-1340mg/cc, dentin: 1480-1590mg/cc, cementum affected by periodontitis: 1100-1220mg/cc, hypomineralized carious dentin: 345-1450mg/cc, hypermineralized carious dentin: 1815-2740mg/cc, and dental calculus: 1290-1770mg/cc). A plausible linear correlation between segmented MD volumes and elemental ratios within these volumes was established, and Ca/P ratios for dentin (1.49), hypomineralized dentin (0.32-0.46), cementum (1.51), and bone (1.68) were observed. Furthermore, varying Ca/Zn ratios were distinguished in adapted compared to normal tissues, such as in bone (855-2765) and in cementum (595-990), highlighting Zn as an influential element in prompting observed adaptive properties. Hence, results provide insights on mineral density gradients with elemental concentrations and elemental footprints that in turn could aid in elucidating mechanistic processes for pathologic formations.« less

Mineral density volume gradients in normal and diseased human tissues

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

Djomehri, Sabra I.; Candell, Susan; Case, Thomas

Clinical computed tomography provides a single mineral density (MD) value for heterogeneous calcified tissues containing early and late stage pathologic formations. The novel aspect of this study is that, it extends current quantitative methods of mapping mineral density gradients to three dimensions, discretizes early and late mineralized stages, identifies elemental distribution in discretized volumes, and correlates measured MD with respective calcium (Ca) to phosphorus (P) and Ca to zinc (Zn) elemental ratios. To accomplish this, MD variations identified using polychromatic radiation from a high resolution micro-computed tomography (micro-CT) benchtop unit were correlated with elemental mapping obtained from a microprobe X-raymore » fluorescence (XRF) using synchrotron monochromatic radiation. Digital segmentation of tomograms from normal and diseased tissues (N=5 per group; 40-60 year old males) contained significant mineral density variations (enamel: 2820-3095mg/cc, bone: 570-1415mg/cc, cementum: 1240-1340mg/cc, dentin: 1480-1590mg/cc, cementum affected by periodontitis: 1100-1220mg/cc, hypomineralized carious dentin: 345-1450mg/cc, hypermineralized carious dentin: 1815-2740mg/cc, and dental calculus: 1290-1770mg/cc). A plausible linear correlation between segmented MD volumes and elemental ratios within these volumes was established, and Ca/P ratios for dentin (1.49), hypomineralized dentin (0.32-0.46), cementum (1.51), and bone (1.68) were observed. Furthermore, varying Ca/Zn ratios were distinguished in adapted compared to normal tissues, such as in bone (855-2765) and in cementum (595-990), highlighting Zn as an influential element in prompting observed adaptive properties. Hence, results provide insights on mineral density gradients with elemental concentrations and elemental footprints that in turn could aid in elucidating mechanistic processes for pathologic formations.« less

Mineral density volume gradients in normal and diseased human tissues.

PubMed

Djomehri, Sabra I; Candell, Susan; Case, Thomas; Browning, Alyssa; Marshall, Grayson W; Yun, Wenbing; Lau, S H; Webb, Samuel; Ho, Sunita P

2015-01-01

Clinical computed tomography provides a single mineral density (MD) value for heterogeneous calcified tissues containing early and late stage pathologic formations. The novel aspect of this study is that, it extends current quantitative methods of mapping mineral density gradients to three dimensions, discretizes early and late mineralized stages, identifies elemental distribution in discretized volumes, and correlates measured MD with respective calcium (Ca) to phosphorus (P) and Ca to zinc (Zn) elemental ratios. To accomplish this, MD variations identified using polychromatic radiation from a high resolution micro-computed tomography (micro-CT) benchtop unit were correlated with elemental mapping obtained from a microprobe X-ray fluorescence (XRF) using synchrotron monochromatic radiation. Digital segmentation of tomograms from normal and diseased tissues (N=5 per group; 40-60 year old males) contained significant mineral density variations (enamel: 2820-3095 mg/cc, bone: 570-1415 mg/cc, cementum: 1240-1340 mg/cc, dentin: 1480-1590 mg/cc, cementum affected by periodontitis: 1100-1220 mg/cc, hypomineralized carious dentin: 345-1450 mg/cc, hypermineralized carious dentin: 1815-2740 mg/cc, and dental calculus: 1290-1770 mg/cc). A plausible linear correlation between segmented MD volumes and elemental ratios within these volumes was established, and Ca/P ratios for dentin (1.49), hypomineralized dentin (0.32-0.46), cementum (1.51), and bone (1.68) were observed. Furthermore, varying Ca/Zn ratios were distinguished in adapted compared to normal tissues, such as in bone (855-2765) and in cementum (595-990), highlighting Zn as an influential element in prompting observed adaptive properties. Hence, results provide insights on mineral density gradients with elemental concentrations and elemental footprints that in turn could aid in elucidating mechanistic processes for pathologic formations.

The Role of a Coronary Artery Calcium Scan in Type 1 Diabetes

PubMed Central

Eaton, R. Philip; Schade, David S.

2016-01-01

Abstract The coronary artery calcium (CAC) scan has recently emerged as a reproducible noninvasive test to detect asymptomatic atherosclerotic coronary artery disease. It has several advantages over the traditional cardiac stress testing modalities, including lower cost, greater sensitivity for nonobstructing coronary artery lesions, and excellent prognostic value when combined with the Framingham risk parameters. Its chief disadvantage is that it does not identify obstructing coronary artery lesions or noncalcified coronary artery plaque. A CAC scan utilizes a chest computed tomogram and computer software to calculate the amount of calcium in the four main coronary vessels. Calcium is deposited in coronary plaques so that the greater the calcium score, the greater the plaque burden. This, in turn, is the basis for predicting a 10–15-year risk of a cardiovascular event. Individuals with a zero calcium score have a very low 10-year risk of a cardiovascular event. Obtaining a calcium score in a diabetic patient permits rational decisions for prescribing statin therapy. In patients with a zero score, the initiation of statin therapy is not recommended because the 5-year incidence of atherosclerotic cardiovascular disease is so low. In patients with diabetes, it is recommended to repeat the calcium scan in 4–5 years to permit timely therapy in the event that the score becomes positive. Since statins mildly increase coronary calcium as part of the stabilization of plaque, a reduction in the calcium score should not be anticipated. However, progression of the calcium score by more than 15%/year (calculated from a repeat CAC scan) provides additional prognostic information of an indication of progression of atherosclerosis. In summary, the coronary calcium score is a major clinical advance for noninvasively detecting coronary artery disease and managing antiatherosclerotic therapy in type 1 diabetes. PMID:27585206

Mineral Density Volume Gradients in Normal and Diseased Human Tissues

PubMed Central

Djomehri, Sabra I.; Candell, Susan; Case, Thomas; Browning, Alyssa; Marshall, Grayson W.; Yun, Wenbing; Lau, S. H.; Webb, Samuel; Ho, Sunita P.

2015-01-01

Clinical computed tomography provides a single mineral density (MD) value for heterogeneous calcified tissues containing early and late stage pathologic formations. The novel aspect of this study is that, it extends current quantitative methods of mapping mineral density gradients to three dimensions, discretizes early and late mineralized stages, identifies elemental distribution in discretized volumes, and correlates measured MD with respective calcium (Ca) to phosphorus (P) and Ca to zinc (Zn) elemental ratios. To accomplish this, MD variations identified using polychromatic radiation from a high resolution micro-computed tomography (micro-CT) benchtop unit were correlated with elemental mapping obtained from a microprobe X-ray fluorescence (XRF) using synchrotron monochromatic radiation. Digital segmentation of tomograms from normal and diseased tissues (N=5 per group; 40-60 year old males) contained significant mineral density variations (enamel: 2820-3095mg/cc, bone: 570-1415mg/cc, cementum: 1240-1340mg/cc, dentin: 1480-1590mg/cc, cementum affected by periodontitis: 1100-1220mg/cc, hypomineralized carious dentin: 345-1450mg/cc, hypermineralized carious dentin: 1815-2740mg/cc, and dental calculus: 1290-1770mg/cc). A plausible linear correlation between segmented MD volumes and elemental ratios within these volumes was established, and Ca/P ratios for dentin (1.49), hypomineralized dentin (0.32-0.46), cementum (1.51), and bone (1.68) were observed. Furthermore, varying Ca/Zn ratios were distinguished in adapted compared to normal tissues, such as in bone (855-2765) and in cementum (595-990), highlighting Zn as an influential element in prompting observed adaptive properties. Hence, results provide insights on mineral density gradients with elemental concentrations and elemental footprints that in turn could aid in elucidating mechanistic processes for pathologic formations. PMID:25856386

Low-Dose-Rate Computed Tomography System Utilizing 25 mm/s-Scan Silicon X-ray Diode and Its Application to Iodine K-Edge Imaging Using Filtered Bremsstrahlung Photons

NASA Astrophysics Data System (ADS)

Matsushita, Ryo; Sato, Eiichi; Yanbe, Yutaka; Chiba, Hiraku; Maeda, Tomoko; Hagiwara, Osahiko; Matsukiyo, Hiroshi; Osawa, Akihiro; Enomoto, Toshiyuki; Watanabe, Manabu; Kusachi, Shinya; Sato, Shigehiro; Ogawa, Akira; Onagawa, Jun

2013-03-01

A low-dose-rate X-ray computed tomography (CT) system is useful for reducing absorbed dose for patients. The CT system with a tube current of sub-mA was developed using a silicon X-ray diode (Si-XD). The Si-XD is a high-sensitivity Si photodiode (PD) selected for detecting X-ray photons, and the X-ray sensitivity of the Si-XD was twice as high as that of Si-PD cerium-doped yttrium aluminum perovskite [YAP(Ce)]. X-ray photons are directly detected using the Si-XD without a scintillator, and the photocurrent from the diode is amplified using current-voltage and voltage-voltage amplifiers. The output voltage is converted into logical pulses using a voltage-frequency converter with a maximum frequency of 500 kHz, and the frequency is proportional to the voltage. The pulses from the converter are sent to the differentiator with a time constant of 500 ns to generate short positive pulses for counting, and the pulses are counted using a counter card. Tomography is accomplished by repeated linear scans and rotations of an object, and projection curves of the object are obtained by the linear scan. The exposure time for obtaining a tomogram was 5 min at a scan step of 0.5 mm and a rotation step of 3.0°. The tube current and voltage were 0.55 mA and 60 kV, respectively, and iodine K-edge CT was carried out using filtered bremsstrahlung X-ray spectra with a peak energy of 38 keV.

Efficiency of optical-electronic systems: methods application for the analysis of structural changes in the process of eye grounds diagnosis

NASA Astrophysics Data System (ADS)

Saldan, Yosyp R.; Pavlov, Sergii V.; Vovkotrub, Dina V.; Saldan, Yulia Y.; Vassilenko, Valentina B.; Mazur, Nadia I.; Nikolaichuk, Daria V.; Wójcik, Waldemar; Romaniuk, Ryszard; Suleimenov, Batyrbek; Bainazarov, Ulan

2017-08-01

Process of eye tomogram obtaining by means of optical coherent tomography is studied. Stages of idiopathic macula holes formation in the process of eye grounds diagnostics are considered. Main stages of retina pathology progression are determined: Fuzzy logic units for obtaining reliable conclusions regarding the result of diagnosis are developed. By the results of theoretical and practical research system and technique of retinal macular region of the eye state analysis is developed ; application of the system, based on fuzzy logic device, improves the efficiency of eye retina complex.

Fluoroscopic tomography. [for body section synthesis

NASA Technical Reports Server (NTRS)

Baily, N. A.; Crepeau, R. L.; Lasser, E. C.

1974-01-01

A fluoroscopic tomography system capable of synthesizing body sections at a number of levels within the body has been developed. The synthesized body sections may lie either in a range of planes parallel to, tilted with respect to, skewed with respect to, or both tilted and skewed with respect to the plane of motion of the X-ray tube target. In addition, body sections can be presented which are contoured to the patient's anatomy. That is to say, they may even encompass such complex surfaces as a quadratic hyperplane. In addition, tomograms of organs in motion can be imaged.

Nonlinear inversion of borehole-radar tomography data to reconstruct velocity and attenuation distribution in earth materials

USGS Publications Warehouse

Zhou, C.; Liu, L.; Lane, J.W.

2001-01-01

A nonlinear tomographic inversion method that uses first-arrival travel-time and amplitude-spectra information from cross-hole radar measurements was developed to simultaneously reconstruct electromagnetic velocity and attenuation distribution in earth materials. Inversion methods were developed to analyze single cross-hole tomography surveys and differential tomography surveys. Assuming the earth behaves as a linear system, the inversion methods do not require estimation of source radiation pattern, receiver coupling, or geometrical spreading. The data analysis and tomographic inversion algorithm were applied to synthetic test data and to cross-hole radar field data provided by the US Geological Survey (USGS). The cross-hole radar field data were acquired at the USGS fractured-rock field research site at Mirror Lake near Thornton, New Hampshire, before and after injection of a saline tracer, to monitor the transport of electrically conductive fluids in the image plane. Results from the synthetic data test demonstrate the algorithm computational efficiency and indicate that the method robustly can reconstruct electromagnetic (EM) wave velocity and attenuation distribution in earth materials. The field test results outline zones of velocity and attenuation anomalies consistent with the finding of previous investigators; however, the tomograms appear to be quite smooth. Further work is needed to effectively find the optimal smoothness criterion in applying the Tikhonov regularization in the nonlinear inversion algorithms for cross-hole radar tomography. ?? 2001 Elsevier Science B.V. All rights reserved.

Early central diabetes insipidus: An ominous sign in post-cardiac arrest patients.

PubMed

Chae, Minjung Kathy; Lee, Jeong Hoon; Lee, Tae Rim; Yoon, Hee; Hwang, Sung Yeon; Cha, Won Chul; Shin, Tae Gun; Sim, Min Seob; Jo, Ik Joon; Song, Keun Jeong; Rhee, Joong Eui; Jeong, Yeon Kwon

2016-04-01

Central diabetes insipidus (CDI) after cardiac arrest is not well described. Thus, we aim to study the occurrences, outcomes, and risk factors of CDI of survivors after out-of-hospital cardiac arrest (OHCA). We retrospectively analyzed post-OHCA patients treated at a single center. Central diabetes insipidus was retrospectively defined by diagnostic criteria. One-month cerebral performance category (CPC) scores were collected for outcomes. Of the 169 patients evaluated, 36 patients (21.3%) were diagnosed with CDI. All CDI patients had a poor neurologic outcome of either CPC 4 (13.9%) or CPC 5 (86.1%), and CDI was strongly associated with mortality. Age (odds ratio [OR], 0.96; 95% confidence interval [CI], 0.93-0.99), respiratory arrest (OR, 6.62; 95% CI, 1.23-35.44), asphyxia (OR, 9.26; 95% CI, 2.17-34.61), and gray to white matter ratio on brain computed tomogram (OR, 0.88; 95% CI, 0.81-0.95) were associated with the development of CDI. The onset of CDI was earlier (P < .001) and the maximum 24-hour urine output was larger (P = .03) in patients with worst outcomes. All patients diagnosed with CDI had poor neurologic outcomes, and occurrence of CDI was associated with mortality. Central diabetes insipidus patients with death or brain death had earlier occurrence of CDI and more maximum urine output. Copyright © 2015 Elsevier Inc. All rights reserved.

Field-portable lensfree tomographic microscope†

PubMed Central

Isikman, Serhan O.; Bishara, Waheb; Sikora, Uzair; Yaglidere, Oguzhan; Yeah, John; Ozcan, Aydogan

2011-01-01

We present a field-portable lensfree tomographic microscope, which can achieve sectional imaging of a large volume (~20 mm3) on a chip with an axial resolution of <7 μm. In this compact tomographic imaging platform (weighing only ~110 grams), 24 light-emitting diodes (LEDs) that are each butt-coupled to a fibre-optic waveguide are controlled through a cost-effective micro-processor to sequentially illuminate the sample from different angles to record lensfree holograms of the sample that is placed on the top of a digital sensor array. In order to generate pixel super-resolved (SR) lensfree holograms and hence digitally improve the achievable lateral resolution, multiple sub-pixel shifted holograms are recorded at each illumination angle by electromagnetically actuating the fibre-optic waveguides using compact coils and magnets. These SR projection holograms obtained over an angular range of ~50° are rapidly reconstructed to yield projection images of the sample, which can then be back-projected to compute tomograms of the objects on the sensor-chip. The performance of this compact and light-weight lensfree tomographic microscope is validated by imaging micro-beads of different dimensions as well as a Hymenolepis nana egg, which is an infectious parasitic flatworm. Achieving a decent three-dimensional spatial resolution, this field-portable on-chip optical tomographic microscope might provide a useful toolset for telemedicine and high-throughput imaging applications in resource-poor settings. PMID:21573311

Optic nerve head parameters of high-definition optical coherence tomography and Heidelberg retina tomogram in perimetric and preperimetric glaucoma.

PubMed

Begum, Viquar Unnisa; Addepalli, Uday Kumar; Senthil, Sirisha; Garudadri, Chandra Sekhar; Rao, Harsha Laxmana

2016-04-01

Heidelberg retina tomogram (HRT) and optical coherence tomography (OCT) are two widely used imaging modalities to evaluate the optic nerve head (ONH) in glaucoma. To compare the ONH parameters of HRT3 and high-definition OCT (HD-OCT) and evaluate their diagnostic abilities in perimetric and preperimetric glaucoma. Cross-sectional analysis. 35 control eyes (24 subjects), 21 preperimetric glaucoma eyes (15 patients), and 64 perimetric glaucoma eyes (44 patients) from the Longitudinal Glaucoma Evaluation Study underwent HRT3 and HD-OCT examinations. Agreement between the ONH parameters of HRT and HD-OCT were assessed using Bland-Altman plots. Diagnostic abilities of ONH parameters were evaluated using area under the receiver operating characteristic curves (AUCs), sensitivity at fixed specificity, and likelihood ratios (LR). Optic disc area, vertical cup to disc ratio, and cup volume with HD-OCT were larger than with HRT, while the rim area was smaller with HD-OCT (P < 0.001 for all comparisons). AUCs of all HD-OCT ONH parameters (0.90-0.97 in perimetric and 0.62-0.71 in preperimetric glaucoma) were comparable (P > 0.10) to the corresponding HRT ONH parameters (0.81-0.95 in perimetric and 0.55-0.72 in preperimetric glaucoma). LRs associated with diagnostic categorization of ONH parameters of both HD-OCT and HRT were associated with larger effects on posttest probability of perimetric compared to preperimetric glaucoma. ONH measurements of HD-OCT and HRT3 cannot be used interchangeably. Though the diagnostic abilities of ONH parameters of HD-OCT and HRT in glaucoma were comparable, the same were significantly lower in preperimetric compared to perimetric glaucoma.

Optic nerve head parameters of high-definition optical coherence tomography and Heidelberg retina tomogram in perimetric and preperimetric glaucoma

PubMed Central

Begum, Viquar Unnisa; Addepalli, Uday Kumar; Senthil, Sirisha; Garudadri, Chandra Sekhar; Rao, Harsha Laxmana

2016-01-01

Background: Heidelberg retina tomogram (HRT) and optical coherence tomography (OCT) are two widely used imaging modalities to evaluate the optic nerve head (ONH) in glaucoma. Purpose: To compare the ONH parameters of HRT3 and high-definition OCT (HD-OCT) and evaluate their diagnostic abilities in perimetric and preperimetric glaucoma. Design: Cross-sectional analysis. Methods: 35 control eyes (24 subjects), 21 preperimetric glaucoma eyes (15 patients), and 64 perimetric glaucoma eyes (44 patients) from the Longitudinal Glaucoma Evaluation Study underwent HRT3 and HD-OCT examinations. Statistical Analysis: Agreement between the ONH parameters of HRT and HD-OCT were assessed using Bland-Altman plots. Diagnostic abilities of ONH parameters were evaluated using area under the receiver operating characteristic curves (AUCs), sensitivity at fixed specificity, and likelihood ratios (LR). Results: Optic disc area, vertical cup to disc ratio, and cup volume with HD-OCT were larger than with HRT, while the rim area was smaller with HD-OCT (P < 0.001 for all comparisons). AUCs of all HD-OCT ONH parameters (0.90-0.97 in perimetric and 0.62-0.71 in preperimetric glaucoma) were comparable (P > 0.10) to the corresponding HRT ONH parameters (0.81-0.95 in perimetric and 0.55-0.72 in preperimetric glaucoma). LRs associated with diagnostic categorization of ONH parameters of both HD-OCT and HRT were associated with larger effects on posttest probability of perimetric compared to preperimetric glaucoma. Conclusions: ONH measurements of HD-OCT and HRT3 cannot be used interchangeably. Though the diagnostic abilities of ONH parameters of HD-OCT and HRT in glaucoma were comparable, the same were significantly lower in preperimetric compared to perimetric glaucoma. PMID:27221679

The Three-Dimensional Distribution of αA-Crystalline in Rat Lenses and Its Possible Relation to Transparency

PubMed Central

Zampighi, Guido A.; Zampighi, Lorenzo; Lanzavecchia, Salvatore

2011-01-01

Lens transparency depends on the accumulation of massive quantities (600–800 mg/ml) of twelve primary crystallines and two truncated crystallines in highly elongated “fiber” cells. Despite numerous studies, major unanswered questions are how this heterogeneous group of proteins becomes organized to bestow the lens with its unique optical properties and how it changes during cataract formation. Using novel methods based on conical tomography and labeling with antibody/gold conjugates, we have profiled the 3D-distribution of the αA-crystalline in rat lenses at ∼2 nm resolutions and three-dimensions. Analysis of tomograms calculated from lenses labeled with anti-αA-crystalline and gold particles (∼3 nm and ∼7 nm diameter) revealed geometric patterns shaped as lines, isosceles triangles and polyhedrons. A Gaussian distribution centered at ∼7.5 nm fitted the distances between the ∼3 nm diameter gold conjugates. A Gaussian distribution centered at ∼14 nm fitted the Euclidian distances between the smaller and the larger gold particles and another Gaussian at 21–24 nm the distances between the larger particles. Independent of their diameters, tethers of 14–17 nm in length connected files of gold particles to thin filaments or clusters to ∼15 nm diameter “beads.” We used the information gathered from tomograms of labeled lenses to determine the distribution of the αA-crystalline in unlabeled lenses. We found that αA-crystalline monomers spaced ∼7 nm or αA-crystalline dimers spaced ∼15 nm center-to-center apart decorated thin filaments of the lens cytoskeleton. It thus seems likely that lost or gain of long-range order determines the 3D-structure of the fiber cell and possible also cataract formation. PMID:21909355

Scatter sensitive microscopic techniques to identify contrasting mucosal structures in ultrahigh-resolution optical coherence tomograms of mouse colon

NASA Astrophysics Data System (ADS)

Tumlinson, Alexandre R.; Hariri, Lida P.; Drexler, Wolfgang; Barton, Jennifer K.

2008-02-01

Optical coherence tomography, optical coherence microscopy, reflectance confocal microscopy, and darkfield microscopy all derive contrast from the intensity of endogenous tissue scatter. We have imaged excised mouse colon tissue with these complimentary technologies to make conclusions about structural origins of scatter in the mouse colonic mucosa observed with endoscopic OCT. We find hyperintense scattering both from the cytoplasm of epithelial cells and from the boundary between epithelia and the lamina propria. We find almost no scatter from the portion of epithelial cells containing the nucleus. These observations substantiate explanations for the appearance of colonic crypts and the luminal surface.

Measurements of morphology and refractive indexes on human downy hairs using three-dimensional quantitative phase imaging.

PubMed

Lee, SangYun; Kim, Kyoohyun; Lee, Yuhyun; Park, Sungjin; Shin, Heejae; Yang, Jongwon; Ko, Kwanhong; Park, HyunJoo; Park, YongKeun

2015-01-01

We present optical measurements of morphology and refractive indexes (RIs) of human downy arm hairs using three-dimensional (3-D) quantitative phase imaging techniques. 3-D RI tomograms and high-resolution two-dimensional synthetic aperture images of individual downy arm hairs were measured using a Mach–Zehnder laser interferometric microscopy equipped with a two-axis galvanometer mirror. From the measured quantitative images, the RIs and morphological parameters of downy hairs were noninvasively quantified including the mean RI, volume, cylinder, and effective radius of individual hairs. In addition, the effects of hydrogen peroxide on individual downy hairs were investigated.

Case Report: A giant but silent adrenal pheochromocytoma – a rare entity

PubMed Central

Munakomi, Sunil; Rajbanshi, Saroj; Adhikary, Prof Shailesh

2016-01-01

Herein we report a rare entity of a giant adrenal pheochromocytoma in a fifty-year-old male presenting with a vague abdominal pain. A computerised tomogram of the abdomen revealed a well-defined  left supraadrenal giant lesion with no evidence of invasion to surrounding structures.The patient underwent surgical excision without any untoward postoperative events. Histopathological study revealed a benign pheochromocytoma. This report highlights the importance of acknowledging the fact that sometimes a giant adrenal pheochromocytoma can present with paucity of clinical  signs and symptoms.Thorough investigations and a multidisciplinary team approach may lead  to a better outcome in these patients. PMID:27785358

Real-Time Laser Ultrasound Tomography for Profilometry of Solids

NASA Astrophysics Data System (ADS)

Zarubin, V. P.; Bychkov, A. S.; Karabutov, A. A.; Simonova, V. A.; Kudinov, I. A.; Cherepetskaya, E. B.

2018-01-01

We studied the possibility of applying laser ultrasound tomography for profilometry of solids. The proposed approach provides high spatial resolution and efficiency, as well as profilometry of contaminated objects or objects submerged in liquids. The algorithms for the construction of tomograms and recognition of the profiles of studied objects using the parallel programming technology NDIVIA CUDA are proposed. A prototype of the real-time laser ultrasound profilometer was used to obtain the profiles of solid surfaces of revolution. The proposed method allows the real-time determination of the surface position for cylindrical objects with an approximation accuracy of up to 16 μm.

Three-dimensional ophthalmic optical coherence tomography with a refraction correction algorithm

NASA Astrophysics Data System (ADS)

Zawadzki, Robert J.; Leisser, Christoph; Leitgeb, Rainer; Pircher, Michael; Fercher, Adolf F.

2003-10-01

We built an optical coherence tomography (OCT) system with a rapid scanning optical delay (RSOD) line, which allows probing full axial eye length. The system produces Three-dimensional (3D) data sets that are used to generate 3D tomograms of the model eye. The raw tomographic data were processed by an algorithm, which is based on Snell"s law to correct the interface positions. The Zernike polynomials representation of the interfaces allows quantitative wave aberration measurements. 3D images of our results are presented to illustrate the capabilities of the system and the algorithm performance. The system allows us to measure intra-ocular distances.

Monitoring the excavation damaged zone by three-dimensional reconstruction of electrical resistivity

NASA Astrophysics Data System (ADS)

Lesparre, Nolwenn; Gibert, Dominique; Nicollin, Florence; Nussbaum, Christophe; Adler, Andy

2013-11-01

A damaged zone is formed during the excavation of underground galleries, altering the rock properties. From a perspective of nuclear waste storage in deep geological sites, there is a clear interest to monitor the rock properties in such zones. We constructed electrical resistivity tomograms as a function of time to monitor the damaged area in gallery 04 of the Mont Terri underground rock laboratory (Switzerland). Measurements were performed using electrode rings surrounding the gallery. The experience showed a heterogeneous distribution of damages around the gallery and their fast formation after the excavation. Two main areas were concerned by damage formation, located in regions where the bedding was tangential to the excavated gallery. Such regions represented an extension of about 2 m along the gallery walls and reached a depth of 1.5 m. Main damages were created during the next months following the excavation process. Slight variations were still observed 3 yr after the excavation that may be related to the gallery environmental condition fluctuation. The method applied here demonstrates the interest to monitor the whole region surrounding excavated galleries dedicated to host nuclear wastes.

3D electrical conductivity tomography of volcanoes

NASA Astrophysics Data System (ADS)

Soueid Ahmed, A.; Revil, A.; Byrdina, S.; Coperey, A.; Gailler, L.; Grobbe, N.; Viveiros, F.; Silva, C.; Jougnot, D.; Ghorbani, A.; Hogg, C.; Kiyan, D.; Rath, V.; Heap, M. J.; Grandis, H.; Humaida, H.

2018-05-01

Electrical conductivity tomography is a well-established galvanometric method for imaging the subsurface electrical conductivity distribution. We characterize the conductivity distribution of a set of volcanic structures that are different in terms of activity and morphology. For that purpose, we developed a large-scale inversion code named ECT-3D aimed at handling complex topographical effects like those encountered in volcanic areas. In addition, ECT-3D offers the possibility of using as input data the two components of the electrical field recorded at independent stations. Without prior information, a Gauss-Newton method with roughness constraints is used to solve the inverse problem. The roughening operator used to impose constraints is computed on unstructured tetrahedral elements to map complex geometries. We first benchmark ECT-3D on two synthetic tests. A first test using the topography of Mt. St Helens volcano (Washington, USA) demonstrates that we can successfully reconstruct the electrical conductivity field of an edifice marked by a strong topography and strong variations in the resistivity distribution. A second case study is used to demonstrate the versatility of the code in using the two components of the electrical field recorded on independent stations along the ground surface. Then, we apply our code to real data sets recorded at (i) a thermally active area of Yellowstone caldera (Wyoming, USA), (ii) a monogenetic dome on Furnas volcano (the Azores, Portugal), and (iii) the upper portion of the caldera of Kīlauea (Hawai'i, USA). The tomographies reveal some of the major structures of these volcanoes as well as identifying alteration associated with high surface conductivities. We also review the petrophysics underlying the interpretation of the electrical conductivity of fresh and altered volcanic rocks and molten rocks to show that electrical conductivity tomography cannot be used as a stand-alone technique due to the non-uniqueness in interpreting electrical conductivity tomograms. That said, new experimental data provide evidence regarding the strong role of alteration in the vicinity of preferential fluid flow paths including magmatic conduits and hydrothermal vents.

Specific storage and hydraulic conductivity tomography through the joint inversion of hydraulic heads and self-potential data

NASA Astrophysics Data System (ADS)

Ahmed, A. Soueid; Jardani, A.; Revil, A.; Dupont, J. P.

2016-03-01

Transient hydraulic tomography is used to image the heterogeneous hydraulic conductivity and specific storage fields of shallow aquifers using time series of hydraulic head data. Such ill-posed and non-unique inverse problem can be regularized using some spatial geostatistical characteristic of the two fields. In addition to hydraulic heads changes, the flow of water, during pumping tests, generates an electrical field of electrokinetic nature. These electrical field fluctuations can be passively recorded at the ground surface using a network of non-polarizing electrodes connected to a high impedance (> 10 MOhm) and sensitive (0.1 mV) voltmeter, a method known in geophysics as the self-potential method. We perform a joint inversion of the self-potential and hydraulic head data to image the hydraulic conductivity and specific storage fields. We work on a 3D synthetic confined aquifer and we use the adjoint state method to compute the sensitivities of the hydraulic parameters to the hydraulic head and self-potential data in both steady-state and transient conditions. The inverse problem is solved using the geostatistical quasi-linear algorithm framework of Kitanidis. When the number of piezometers is small, the record of the transient self-potential signals provides useful information to characterize the hydraulic conductivity and specific storage fields. These results show that the self-potential method reveals the heterogeneities of some areas of the aquifer, which could not been captured by the tomography based on the hydraulic heads alone. In our analysis, the improvement on the hydraulic conductivity and specific storage estimations were based on perfect knowledge of electrical resistivity field. This implies that electrical resistivity will need to be jointly inverted with the hydraulic parameters in future studies and the impact of its uncertainty assessed with respect to the final tomograms of the hydraulic parameters.

Applications of electrical resistivity imaging for characterizing groundwater-surface water interactions from local to regional scales

NASA Astrophysics Data System (ADS)

Cardenas, M. B.; Befus, K. M.; Zamora, P. B.; Ong, J.; Zlotnik, V. A.; Cook, P. L.; Tait, D. R.; Erler, D.; Santos, I. R.; Siringan, F. P.

2012-12-01

Surface water (SW) and groundwater (GW) interact across multiple spatial and temporal scales and their interaction is important for ecological and biogeochemical functions. The mixing of GW and SW has been challenging to simultaneously map with sufficient detail and coverage. Fortunately, ambient differences in salinity of waters occupying geologic formations and sediment are an ideal target for electrical resistivity imaging (ERI). We present examples of the application of ERI for mapping GW discharge and for understanding GW-SW interactions at: (1) a large regulated river, (2) neighboring lakes with differing salinity, (3) fringing coral reefs and lagoons, (4) beaches, and (5) estuaries. In all these cases, the ER tomograms were critical for improving conceptual understanding of GW-SW interactions. At the Lower Colorado River in Austin, Texas (USA), time-lapse ERI was conducted across a 12-hour dam-release cycle when the river stage varied by 0.7 m. Using temporal variability in electrical resistivity (ER) signatures, we identified a shallow well-flushed hyporheic zone, a transition zone where SW and GW mix, and a stable deep zone hosting only GW. In alkaline lakes in the Nebraska Sand Hills (Nebraska, USA), ER surveys using boat-towed cables allowed for mapping the 3D electrical structure underneath the lake. The tomograms were used to distinguish flow-through lakes, which have decreasing subsurface ER from GW inflow to outflow area, from pure GW discharge lakes, which have uniformly stratified increasing-with-depth ER profiles. Moreover, GW plumes in both discharge and recharge zones were clearly outlined underneath the lake. More than 30 km of ER profiles collected via boat-towed surveys over a fringing coral reef in the Philippines identified areas of high ER within the reef that coincide with resistive zones in the seawater. Analysis of 222Rn of bottom waters and vertical conductivity-temperature-depth measurements show the persistence of fresh GW input into the ocean where low salinity and high 222Rn areas coincided with high ER areas. In Muri Lagoon in Rarotonga Island of the Cook Islands, boat-towed ER surveys similarly showed areas underneath the lagoon that have groundwater that is fresher than seawater. Likewise, there was 222Rn high concentrations throughout the lagoon. Closer to shore, ER surveys using fixed electrodes showed complex 3D mixing processes between seawater and terrestrial-sourced fresh groundwater in beach sediment. Lastly, both boat-towed and fixed surveys across the salt wedge of Werribee Estuary west of Melbourne, Australia, outlined the estuarine salt wedge and its relationship with and effect on fresh and nutrient-laden groundwater discharging to the estuary. The examples discussed illustrate that ERI is a powerful and convenient tool for mapping GW discharge and GW-SW interactions across different scales and diverse environments.

Morphologic evaluation and classification of facial asymmetry using 3-dimensional computed tomography.

PubMed

Baek, Chaehwan; Paeng, Jun-Young; Lee, Janice S; Hong, Jongrak

2012-05-01

A systematic classification is needed for the diagnosis and surgical treatment of facial asymmetry. The purposes of this study were to analyze the skeletal structures of patients with facial asymmetry and to objectively classify these patients into groups according to these structural characteristics. Patients with facial asymmetry and recent computed tomographic images from 2005 through 2009 were included in this study, which was approved by the institutional review board. Linear measurements, angles, and reference planes on 3-dimensional computed tomograms were obtained, including maxillary (upper midline deviation, maxilla canting, and arch form discrepancy) and mandibular (menton deviation, gonion to midsagittal plane, ramus height, and frontal ramus inclination) measurements. All measurements were analyzed using paired t tests with Bonferroni correction followed by K-means cluster analysis using SPSS 13.0 to determine an objective classification of facial asymmetry in the enrolled patients. Kruskal-Wallis test was performed to verify differences among clustered groups. P < .05 was considered statistically significant. Forty-three patients (18 male, 25 female) were included in the study. They were classified into 4 groups based on cluster analysis. Their mean age was 24.3 ± 4.4 years. Group 1 included subjects (44% of patients) with asymmetry caused by a shift or lateralization of the mandibular body. Group 2 included subjects (39%) with a significant difference between the left and right ramus height with menton deviation to the short side. Group 3 included subjects (12%) with atypical asymmetry, including deviation of the menton to the short side, prominence of the angle/gonion on the larger side, and reverse maxillary canting. Group 4 included subjects (5%) with severe maxillary canting, ramus height differences, and menton deviation to the short side. In this study, patients with asymmetry were classified into 4 statistically distinct groups according to their anatomic features. This diagnostic classification method will assist in treatment planning for patients with facial asymmetry and may be used to explore the etiology of these variants of facial asymmetry. Copyright © 2012 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

Local electron tomography using angular variations of surface tangents: Stomo version 2

NASA Astrophysics Data System (ADS)

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

2012-03-01

In a recent publication, we investigated the prospect of measuring the outer three-dimensional (3D) shapes of nano-scale atom probe specimens from tilt-series of images collected in the transmission electron microscope. For this purpose alone, an algorithm and simplified reconstruction theory were developed to circumvent issues that arise in commercial "back-projection" computations in this context. In our approach, we give up the difficult task of computing the complete 3D continuum structure and instead seek only the 3D morphology of internal and external scattering interfaces. These interfaces can be described as embedded 2D surfaces projected onto each image in a tilt series. Curves and other features in the images are interpreted as inscribed sets of tangent lines, which intersect the scattering interfaces at unknown locations along the direction of the incident electron beam. Smooth angular variations of the tangent line abscissa are used to compute the surface tangent intersections and hence the 3D morphology as a "point cloud". We have published the explicit details of our alternative algorithm along with the source code entitled "stomo_version_1". For this work, we have further modified the code to efficiently handle rectangular image sets, perform much faster tangent-line "edge detection" and smoother tilt-axis image alignment using simple bi-linear interpolation. We have also adapted the algorithm to detect tangent lines as "ridges", based upon 2nd order partial derivatives of the image intensity; the magnitude and orientation of which is described by a Hessian matrix. Ridges are more appropriate descriptors for tangent-line curves in phase contrast images outlined by Fresnel fringes or absorption contrast data from fine-scale objects. Improved accuracy, efficiency and speed for "stomo_version_2" is demonstrated in this paper using both high resolution electron tomography data of a nano-sized atom probe tip and simulated absorption-contrast images. Program summaryProgram title: STOMO version 2 Catalogue identifier: AEFS_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFS_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 2854 No. of bytes in distributed program, including test data, etc.: 23 559 Distribution format: tar.gz Programming language: C/C++ Computer: PC Operating system: Windows XP RAM: Scales as the product of experimental image dimensions multiplied by the number of points chosen by the user in polynomial fitting. Typical runs require between 50 Mb and 100 Mb of RAM. Supplementary material: Sample output files, for the test run provided, are available. Classification: 7.4, 14 Catalogue identifier of previous version: AEFS_v1_0 Journal reference of previous version: Comput. Phys. Comm. 181 (2010) 676 Does the new version supersede the previous version?: Yes Nature of problem: A local electron tomography algorithm of specimens for which conventional back projection may fail and or data for which there is a limited angular range (which would otherwise cause significant 'missing-wedge' artefacts). The algorithm does not solve the tomography back projection problem but rather locally reconstructs the 3D morphology of surfaces defined by varied scattering densities. Solution method: Local reconstruction is effected using image-analysis edge and ridge detection computations on experimental tilt series to measure smooth angular variations of surface tangent-line intersections, which generate point clouds decorating the embedded and or external scattering surfaces of a specimen. Reasons for new version: The new version was coded to cater for rectangular images in experimental tilt-series, ensure smoother image rotations, provide ridge detection (suitable for sensing phase-contrast Fresnel fringes and other fine-scale structures), faster/larger kernel edge detection and also greatly reduce RAM usage. Specimen surface normals are also explicitly computed from tangent-line and edge intersections, providing new information for potential use in point cloud rendering. Hysteresis thresholding implemented in the version 1 edge-detection algorithm provided only sparse edge-linking. Version 2 now implements edge tracking using recursion to fully link the edges during hysteresis thresholding. Furthermore in version 1 the minimum number of fitted polynomial points (specified in the input file) was not correctly imposed, which has been fixed for version 2. Most of these changes increase the accuracy of 3d morphology surface-tomography reconstructions by facilitating the use of more/finer tilt angles and experimental images of increased spatial-resolution. The ridge detection was incorporated to specifically improve the reconstruction of internal specimen morphology. Summary of revisions: Included Hessian() function to compute 2nd order spatial derivatives of image intensities (operates in the same fashion as the previous and existing Sobel() function). Changed convolve_Gaussian() function to alternatively use successive 1D convolutions (rather than cumbersome 2D summations implemented in version 1), resulting in a large increase in computational speed without any loss in accuracy. The convolution kernel size was hence widened to three times the full width half maximum of the Gaussian filter to improve scale-space selection accuracy. A ridge detection option was included to compute edge maps sensitive to ridges, rather than edges, using elements from a Hessian matrix; the eigenvalues of which were used to define ridge direction for Canny-type hysteresis thresholding. Function edge_detect_Canny() was also altered to pass the gradient-direction maps (from either Hessian or Sobel based operators) in and out of scope for computation of surface normals; thereby enabling the output of both point-cloud and corresponding unstructured vector-field surface descriptors. Function rotate_imgs() was changed to incorporate basic bi-linear interpolation for improved tilt-axis alignment of the entire tilt series in exp_data.dat. Smoother and more accurate edge maps are thereby produced. Algorithm convert_point_cloud_to_tomogram() was created to output the tomogram 3d_imgs.dat in a more memory efficient manner. The function shell_sort(), adapted from numerical recipes in C, was also coded for this purpose. The new function compute_xyz() was coded to calculate point-clouds and tomogram surface normals using information from single tilt images, as opposed to the entire stack. This function is hence used iteratively throughout the reconstruction as each tilt image is analysed in succession. The new function reconstruct_local() is the heart of stomo_version_2.cpp. the main() source code in stomo_version_1.cpp has been rewritten here to process experimental images and edge maps one at a time, using a buffered 3d array of dimensions dictated solely by the number of tilt images required for the local SVD fit of the angular variations. These changes (along with similar iterative file writing) have been made to vastly reduce memory usage and hence allow higher spatial and angular resolution data sets to be analysed without recourse to high performance computing resources. The input file has been simplified by removing the 'slices' and 'channels' settings (used in version 1 for crude image binning), which are now equal to the respective numbers of image rows and columns. Every summation over image rows and columns has been checked to enable the analysis of rectangular images without error. For images of specimens with high aspect-ratios, such as narrow tips, these fixes allow significant reductions in computation time and memory usage. Some arrays in the source code were not appropriately zeroed in version 1, causing reconstruction artefacts in some cases. These problems have now been fixed. Fixed an if-statement to correctly impose the minimum number of fitted polynomial points, thereby reducing noise in the reconstructed data. Implemented proper edge linking in the hysteresis thresholding code for Canny edge detection. Restrictions: The input experimental tilt-series of images must be registered with respect to a common single tilt axis with known orientation and position. Running time: For high quality reconstruction, 2-5 min.

Method of non-destructively inspecting a curved wall portion

DOEpatents

Fong, James T.

1996-01-01

A method of non-destructively inspecting a curved wall portion of a large and thick walled vessel for a defect by computed tomography is provided. A collimated source of radiation is placed adjacent one side of the wall portion and an array of detectors for the radiation is placed on the other side adjacent the source. The radiation from the source passing through the wall portion is then detected with the detectors over a limited angle, dependent upon the curvature of the wall of the vessel, to obtain a dataset. The source and array are then coordinately moved relative to the wall portion in steps and a further dataset is obtained at each step. The plurality of datasets obtained over the limited angle is then processed to produce a tomogram of the wall portion to determine the presence of a defect therein. In a preferred embodiment, the curved wall portion has a center of curvature so that the source and the array are positioned at each step along a respective arc curved about the center. If desired, the detector array and source can be reoriented relative to a new wall portion and an inspection of the new wall portion can be easily obtained. Further, the source and detector array can be indexed in a direction perpendicular to a plane including the limited angle in a plurality of steps so that by repeating the detecting and moving steps at each index step, a three dimensional image can be created of the wall portion.

Field-portable lensfree tomographic microscope.

PubMed

Isikman, Serhan O; Bishara, Waheb; Sikora, Uzair; Yaglidere, Oguzhan; Yeah, John; Ozcan, Aydogan

2011-07-07

We present a field-portable lensfree tomographic microscope, which can achieve sectional imaging of a large volume (∼20 mm(3)) on a chip with an axial resolution of <7 μm. In this compact tomographic imaging platform (weighing only ∼110 grams), 24 light-emitting diodes (LEDs) that are each butt-coupled to a fibre-optic waveguide are controlled through a cost-effective micro-processor to sequentially illuminate the sample from different angles to record lensfree holograms of the sample that is placed on the top of a digital sensor array. In order to generate pixel super-resolved (SR) lensfree holograms and hence digitally improve the achievable lateral resolution, multiple sub-pixel shifted holograms are recorded at each illumination angle by electromagnetically actuating the fibre-optic waveguides using compact coils and magnets. These SR projection holograms obtained over an angular range of ±50° are rapidly reconstructed to yield projection images of the sample, which can then be back-projected to compute tomograms of the objects on the sensor-chip. The performance of this compact and light-weight lensfree tomographic microscope is validated by imaging micro-beads of different dimensions as well as a Hymenolepis nana egg, which is an infectious parasitic flatworm. Achieving a decent three-dimensional spatial resolution, this field-portable on-chip optical tomographic microscope might provide a useful toolset for telemedicine and high-throughput imaging applications in resource-poor settings. This journal is © The Royal Society of Chemistry 2011

Synchrotron hard X-ray imaging of shock-compressed metal powders

NASA Astrophysics Data System (ADS)

Rutherford, Michael E.; Chapman, David J.; Collinson, Mark A.; Jones, David R.; Music, Jasmina; Stafford, Samuel J. P.; Tear, Gareth R.; White, Thomas G.; Winters, John B. R.; Drakopoulos, Michael; Eakins, Daniel E.

2015-06-01

This poster will present the application of a new, high-energy (50 to 250 keV) synchrotron X-ray radiography technique to the study of shock-compressed granular materials. Following plate-impact loading, transmission radiography was used to quantitatively observe the compaction and release processes in a range of high-Z metal powders (e.g. Fe, Ni, Cu). By comparing the predictions of 3D numerical models initialized from X-ray tomograms-captured prior to loading-with experimental results, this research represents a new approach to refining mesoscopic compaction models. The authors gratefully acknowledge the ongoing support of Imperial College London, EPSRC, STFC and the Diamond Light Source, and AWE Plc.

Roche tomography of cataclysmic variables - VIII. The irradiated and spotted dwarf nova, SS Cygni

NASA Astrophysics Data System (ADS)

Hill, C. A.; Smith, Robert Connon; Hebb, L.; Szkody, P.

2017-12-01

We present the results of our spectroscopic study of the dwarf nova SS Cyg, using Roche tomography to map the stellar surface and derive the system parameters. Given that this technique takes into account the inhomogeneous brightness distribution on the surface of the secondary star, our derived parameters are (in principle) the most robust yet found for this system. Furthermore, our surface maps reveal that the secondary star is highly spotted, with strongly asymmetric irradiation on the inner hemisphere. Moreover, by constructing Doppler tomograms of several Balmer emission lines, we find strong asymmetric emission from the irradiated secondary star, and an asymmetric accretion disc that exhibits spiral structures.

DART, a platform for the creation and registration of cone beam digital tomosynthesis datasets.

PubMed

Sarkar, Vikren; Shi, Chengyu; Papanikolaou, Niko

2011-04-01

Digital tomosynthesis is an imaging modality that allows for tomographic reconstructions using only a fraction of the images needed for CT reconstruction. Since it offers the advantages of tomographic images with a smaller imaging dose delivered to the patient, the technique offers much promise for use in patient positioning prior to radiation delivery. This paper describes a software environment developed to help in the creation of digital tomosynthesis image sets from digital portal images using three different reconstruction algorithms. The software then allows for use of the tomograms for patient positioning or for dose recalculation if shifts are not applied, possibly as part of an adaptive radiotherapy regimen.

Chronic osteomyelitis of the clavicle

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

Granick, M.S.; Ramasastry, S.S.; Goodman, M.A.

1989-07-01

Osteomyelitis of the clavicle is an uncommon disease, but it should be considered in patients who present with pain, cellulitis, or drainage in the sternoclavicular area following head and neck surgery, irradiation, subclavian vein catheterization, or immunosuppression. An idiopathic presentation is possible. In contrast to primary osteomyelitis of the clavicle, which is occasionally seen in children, secondary osteomyelitis is quite rare. It is often mistaken for a fracture or a possible neoplasm on plain x-rays. Tomograms and CT scanning are confirmatory, and in early cases, technetium-99m bone scanning can be helpful. Treatment must include early, aggressive surgical debridement of allmore » affected tissues, followed by wound coverage with a well-vascularized flap and perioperative antibiotics.« less

Clinical outcomes of pediatric patients with acute abdominal pain and incidental findings of free intraperitoneal fluid on diagnostic imaging.

PubMed

Matz, Samantha; Connell, Mary; Sinha, Madhumita; Goettl, Christopher S; Patel, Palak C; Drachman, David

2013-09-01

The presence of free intraperitoneal fluid on diagnostic imaging (sonography or computed tomography [CT]) may indicate an acute inflammatory process in children with abdominal pain in a nontraumatic setting. Although clinical outcomes of pediatric trauma patients with free fluid on diagnostic examinations without evidence of solid-organ injury have been studied, similar studies in the absence of trauma are rare. Our objective was to study clinical outcomes of children with acute abdominal pain of nontraumatic etiology and free intraperitoneal fluid on diagnostic imaging (abdominal/pelvic sonography, CT, or both). We conducted a retrospective review of medical records of children aged 0 to 18 years presenting to a pediatric emergency department with acute abdominal pain (nontraumatic) between April 2008 and March 2009. Patients with intraperitoneal free fluid on imaging were divided into 2 groups: group I, imaging suggestive of an intra-abdominal surgical condition such as appendicitis; and group II, no evidence of an acute surgical condition on imaging, including patients with equivocal studies. Computed tomograms and sonograms were reviewed by a board-certified radiologist, and the free fluid volume was quantitated. Of 1613 patients who underwent diagnostic imaging, 407 were eligible for the study; 134 (33%) had free fluid detected on diagnostic imaging. In patients with both sonography and CT, there was a significant correlation in the free fluid volume (r = 0.79; P < .0005). A significantly greater number of male patients with free fluid had a surgical condition identified on imaging (57.4% versus 25%; P < .001). Children with free fluid and an associated condition on imaging were more likely to have surgery (94.4% versus 6.3%; P < .001). We found clinical outcomes (surgical versus nonsurgical) to be most correlated with a surgical diagnosis on diagnostic imaging and not with the amount of fluid present.

Implementing fluid dynamics obtained from GeoPET in reactive transport models

NASA Astrophysics Data System (ADS)

Lippmann-Pipke, Johanna; Eichelbaum, Sebastian; Kulenkampff, Johannes

2016-04-01

Flow and transport simulations in geomaterials are commonly conducted on high-resolution tomograms (μCT) of the pore structure or stochastic models that are calibrated with measured integral quantities, like break through curves (BTC). Yet, there existed virtually no method for experimental verification of the simulated velocity distribution results. Positron emission tomography (PET) has unrivaled sensitivity and robustness for non-destructive, quantitative, spatio-temporal measurement of tracer concentrations in body tissue. In the past decade, we empowered PET for its applicability in opaque/geological media - GeoPET (Kulenkampff et al.; Kulenkampff et al., 2008; Zakhnini et al., 2013) and have developed detailed correction schemes to bring the images into sharp focus. Thereby it is the appropriate method for experimental verification and calibration of computer simulations of pore-scale transport by means of the observed propagation of a tracer pulse, c_PET(x,y,z,t). In parallel, we aimed at deriving velocity and porosity distributions directly from our concentration time series of fluid flow processes in geomaterials. This would allow us to directly benefit from lab scale observations and to parameterize respective numerical transport models. For this we have developed a robust spatiotemporal (3D+t) parameter extraction algorithm. Here, we will present its functionality, and demonstrate the use of obtained velocity distributions in finite element simulations of reactive transport processes on drill core scale. Kulenkampff, J., Gruendig, M., Zakhnini, A., Gerasch, R., and Lippmann-Pipke, J.: Process tomography of diffusion with PET for evaluating anisotropy and heterogeneity, Clay Minerals, in press. Kulenkampff, J., Gründig, M., Richter, M., and Enzmann, F.: Evaluation of positron emission tomography for visualisation of migration processes in geomaterials, Physics and Chemistry of the Earth, 33, 937-942, 2008. Zakhnini, A., Kulenkampff, J., Sauerzapf, S., Pietrzyk, U., and Lippmann-Pipke, J.: Monte Carlo simulations of GeoPET experiments: 3D images of tracer distributions (18-F, 124-I and 58-Co) in Opalinus Clay, anhydrite and quartz, Computers and Geosciences, 57 183-196, 2013.

A comparison of apical root resorption after orthodontic treatment with surgical exposure and traction of maxillary impacted canines versus that without impactions.

PubMed

Lempesi, Evangelia; Pandis, Nikolaos; Fleming, Padhraig S; Mavragani, Maria

2014-12-01

Orthodontic management of maxillary canine impaction (MCI), including forced eruption, may result in significant root resorption; however, the association between MCI and orthodontically induced root resorption (OIRR) is not yet sufficiently established. The purpose of this retrospective cohort study was to comparatively evaluate the severity of OIRR of maxillary incisors in orthodontically treated patients with MCI. Additionally, impaction characteristics were associated with OIRR severity. The sample comprised 48 patients undergoing fixed-appliance treatment-24 with unilateral/bilateral MCI and 24 matched controls without impaction. OIRR was calculated using pre- and post-operative panoramic tomograms. The orientation of eruption path, height, sector location, and follicle/tooth ratio of the impacted canine were also recorded. Mann-Whitney U-test and univariate and multivariate linear mixed models were used to test for the associations of interest. Maxillary central left incisor underwent more OIRR in the impaction group (mean difference = 0.58mm, P = 0.04). Overall, the impaction group had 0.38mm more OIRR compared to the control (95% confidence interval, CI: 0.03, 0.74; P = 0.04). However, multivariate analysis demonstrated no difference in the amount of OIRR between impaction and non-impaction groups overall. A positive association between OIRR and initial root length was observed (95% CI: 0.08, 0.27; P < 0.001). The severity of canine impaction was not found to be a significant predictor of OIRR. This study was a retrospective study and used panoramic tomograms for OIRR measurements. This study indicates that MCI is a weak OIRR predictor. Interpretation of the results needs caution due to the observational nature of the present study. © The Author 2014. Published by Oxford University Press on behalf of the European Orthodontic Society. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Malnutrition-inflammation-coronary calcification in pediatric patients receiving chronic hemodialysis.

PubMed

Srivaths, Poyyapakkam R; Silverstein, Douglas M; Leung, Jocelyn; Krishnamurthy, Rajesh; Goldstein, Stuart L

2010-07-01

Malnutrition, inflammation, and renal osteodystrophy parameters with resultant coronary calcification (CC) are associated with increased cardiovascular mortality in adults. Previous pediatric studies demonstrated CC in children but none assessed for an association between inflammation, malnutrition, renal osteodystrophy, and CC. To assess CC, ultrafast computerized tomogram was obtained for 16 pediatric patients (6 females; median age 17.2 years; range 9.1-21.2 years) receiving hemodialysis for >/=2 months. Inflammation was assessed by serum IL-6, IL-8, and C-reactive protein levels on the day of the computerized tomogram scan; nutrition parameters included serum albumin, cholesterol, the body mass index standard deviation score, and normalized protein catabolic rate. Renal osteodystrophy parameters included time-averaged serum calcium, phosphorus, total PTH, and calcitriol/calcium dose. Patients received hemodialysis thrice-weekly; mean single pool Kt/V 1.48+/-0.13; and mean normalized protein catabolic rate 1.27+/-0.17 g/kg/day. Five of 16 patients had CC. Patients with CC were older (19.1+/-2.1 vs. 15.4+/-3.1 months; P=0.03), had longer dialysis vintage (49.4+/-15.3 vs. 17.2+/-10.5 months, P=0.0002), lower serum cholesterol (122+/-17.7 vs. 160.4+/-10.6 mg/dL, P=0.02), and higher phosphorus (9.05+/-1.2 vs. 6.1+/-0.96 mg/dL, P=0.0001). Mean serum albumin and normalized protein catabolic rate did not differ for patients with CC. All patients had elevated IL-6 and IL-8 levels compared with healthy norms; the mean IL-6, IL-8, and C-reactive protein levels were not different in patients with CC. Coronary calcification was prevalent in older children receiving maintenance hemodialysis with a longer dialysis vintage. Worse renal osteodystrophy control and malnutrition (low cholesterol) may contribute to CC development.

Cerebral blood-flow tomography: xenon-133 compared with isopropyl-amphetamine-iodine-123: concise communication

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

Lassen, N.A.; Henriksen, L.; Holm, S.

1983-01-01

Tomographic maps of local cerebral blood flow (CBF) were obtained with xenon-133 and with isopropyl-amphetamine-iodine-123 (IMP) in 11 subjects: one normal, two tumor cases, and eight cerebrovascular cases. A highly sensitive four-face, rapidly rotating, single-photon emission tomograph was used. The Xe-133 flow maps are essentially based on the average Xe-133 concentration over the initial 2 min during and after an inhalation of the inert gas lasting 1 min. These maps agreed very well with the early IMP maps obtained over the initial 10 min following an i.v. bolus injection. The subsequent IMP tomograms showed a slight decrease in contrast amountingmore » to appr. five percentage points in the CBF ratio between diseased and contralateral areas. It is concluded that Xe-133 is more practical: low cost, available on a 7-day basis, easily repeatable, quantifiable without the need for arterial sampling, and with low radiation exposure to patient and personnel. On the other hand, IMP gives an image of slightly higher resolution. It also introduces a new class of iodinated brain-seeking compounds allowing, perhaps, imaging of other functions more important than mere blood flow.« less

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

PubMed

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

2018-04-21

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

Signal-adapted tomography as a tool for dust devil detection

NASA Astrophysics Data System (ADS)

Aguirre, C.; Franzese, G.; Esposito, F.; Vázquez, Luis; Caro-Carretero, Raquel; Vilela-Mendes, Rui; Ramírez-Nicolás, María; Cozzolino, F.; Popa, C. I.

2017-12-01

Dust devils are important phenomena to take into account to understand the global dust circulation of a planet. On Earth, their contribution to the injection of dust into the atmosphere seems to be secondary. Elsewhere, there are many indications that the dust devil's role on other planets, in particular on Mars, could be fundamental, impacting the global climate. The ability to identify and study these vortices from the acquired meteorological measurements assumes a great importance for planetary science. Here we present a new methodology to identify dust devils from the pressure time series testing the method on the data acquired during a 2013 field campaign performed in the Tafilalt region (Morocco) of the North-Western Sahara Desert. Although the analysis of pressure is usually studied in the time domain, we prefer here to follow a different approach and perform the analysis in a time signal-adapted domain, the relation between the two being a bilinear transformation, i.e. a tomogram. The tomographic technique has already been successfully applied in other research fields like those of plasma reflectometry or the neuronal signatures. Here we show its effectiveness also in the dust devils detection. To test our results, we compare the tomography with a phase picker time domain analysis. We show the level of agreement between the two methodologies and the advantages and disadvantages of the tomographic approach.

Three-dimensional behavior of ice crystals and biological cells during freezing of cell suspensions.

PubMed

Ishiguro, H; Koike, K

1998-09-11

Behavior of ice crystals and human red blood cells during extracellular-freezing was investigated in three-dimensions using a confocal laser scanning microscope(CLSM), which noninvasively produces tomograms of biological materials. Physiological saline and physiological saline with 2.4 M glycerol were used for suspension. Various cooling rates for directional solidification were used for distinctive morphology of the ice crystals. Addition of acridine orange as a fluorescent dye into the cell suspension enabled ice crystal, cells and unfrozen solution to be distinguished by different colors. The results indicate that the microscopic structure is three-dimensional for flat, cellular, and dendritic solid-liquid interfaces and that a CLSM is very effective in studying three-dimensional structure during the freezing of cell suspensions.

Chorioretinal dysplasia, hydranencephaly, and intracranial calcifications: pseudo-TORCH or a new syndrome?

PubMed

Watts, P; Kumar, N; Ganesh, A; Sastry, P; Pilz, D; Levin, A V; Chitayat, D

2008-05-01

To report the association of severe chorioretinal dysplasia, hydranencephaly, microcephaly, and intracranial calcification in children with no evidence of intrauterine infections. Two unrelated female infants with visually inattentive behaviour, hydranencephaly, and intracranial calcification were referred for an ophthalmological opinion. The fundus examination and computerised tomograms (CT scans) of head were similar in both children. There was bilateral extensive chorioretinal dysplasia, intracranial calcifications, and hydranencephaly. Serology was negative for acquired intrauterine congenital infections. We report two cases that may represent a new syndrome or the more severe end of the spectrum of the pseudo-TORCH (toxoplasma, rubella, cytomegalovirus, and herpes simplex) syndrome. The association of chorioretinal dysplasia with the pseudo-TORCH syndrome has not been reported previously.

Fracture patterns after bilateral sagittal split osteotomy of the mandibular ramus according to the Obwegeser/Dal Pont and Hunsuck/Epker modifications.

PubMed

Möhlhenrich, Stephan Christian; Kniha, Kristian; Peters, Florian; Ayoub, Nassim; Goloborodko, Evgeny; Hölzle, Frank; Fritz, Ulrike; Modabber, Ali

2017-05-01

The aim of this study was to compare the fracture patterns after sagittal split osteotomy according to Obwegeser/Dal Pont (ODP) and Hunsuck/Epker (HE), as well as to investigate the relationship between lateral bone cut ending or angle and the incidence of unfavorable/bad splits. Postoperative cone-beam computed tomograms of 124 splits according to ODP and 60 according to HE were analyzed. ODP led to 75.8% and HE led to 60% lingual fractures with mandibular foramen contact. Horizontal fractures were found in 9.7% and 6.7%, respectively, and unfavorable/bad splits were found in 11.3% and 10%, respectively. The lateral osteotomy angle was 106.22° (SD 12.03)° for bad splits and 106.6° (SD 13.12)° for favorable splits. Correlations were found between favorable fracture patterns and split modifications and between buccal ending of the lateral bone cut and bad splits (p < 0.001). No relationship was observed between split modifications (p = 0.792) or the osteotomy angle (p = 0.937) and the incidence of unfavorable/bad splits. Split modifications had no influence on the incidence of unfavorable/bad splits, but the buccal ending of the lateral bone cut did have an influence. More lingual fractures with mandibular foramen contact are expected with the ODP modification. The osteotomy angle did not differ between favorable and bad splits. Copyright © 2017 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Predicting recurrence after chronic subdural haematoma drainage.

PubMed

Jack, Andrew; O'Kelly, Cian; McDougall, Cameron; Findlay, J Max

2015-01-01

Recurrence of chronic subdural haematomas (CSDHs) after surgical drainage is a significant problem with rates up to 20%. This study focuses on determining factors predictive of haematoma recurrence and presents a scoring system stratifying recurrence risk for individual patients. Between the years 2005 and 2009, 331 consecutive patients with CSDHs treated with surgery were included in this study. Univariate and multivariate analyses were performed searching for risk factors of increased post-operative haematoma volume and haematoma recurrence requiring repeat drainage. We found a 12% reoperation rate. CSDH septation (seen on computed tomogram scan) was found to be an independent risk factor for recurrence requiring reoperation (p=0.04). Larger post-operative subdural haematoma volume was also significantly associated with requiring a second drainage procedure (p<0.001). Independent risk factors of larger post-operative haematoma volume included septations within a CSDH (p<0.01), increased pre-operative haematoma volume (p<0.01), and a greater amount of parenchymal atrophy (p=0.04). A simple scoring system for quantifying recurrence risk was created and validated based on patient age (< or ≥ 80 years), haematoma volume (< or ≥ 160 cc), and presence of septations within the subdural collection (yes or no). Septations within CSDHs are associated with larger post-operative residual haematoma collections requiring repeat drainage. When septations are clearly visible within a CSDH, craniotomy might be more suitable as a primary procedure as it allows greater access to a septated subdural collection. Our proposed scoring system combining haematoma volume, age, and presence of septations might be useful in identifying patients at higher risk for recurrence.

Visualization of the herpes simplex virus portal in situ by cryo-electron tomography

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

Cardone, Giovanni; Winkler, Dennis C.; Trus, Benes L.

2007-05-10

Herpes simplex virus type 1 (HSV-1), the prototypical herpesvirus, has an icosahedral nucleocapsid surrounded by a proteinaceous tegument and a lipoprotein envelope. As in tailed bacteriophages, the icosahedral symmetry of the capsid is broken at one of the 12 vertices, which is occupied by a dodecameric ring of portal protein, UL6, instead of a pentamer of the capsid protein, UL19. The portal ring serves as a conduit for DNA entering and exiting the capsid. From a cryo-EM reconstruction of capsids immuno-gold-labeled with anti-UL6 antibodies, we confirmed that UL6 resides at a vertex. To visualize the portal in the context ofmore » the assembled capsid, we used cryo-electron tomography to determine the three-dimensional structures of individual A-capsids (empty, mature capsids). The similarity in size and overall shape of the portal and a UL19 pentamer - both are cylinders of {approx} 800 kDa - combined with residual noise in the tomograms, prevented us from identifying the portal vertices directly; however, this was accomplished by a computational classification procedure. Averaging the portal-containing subtomograms produced a structure that tallies with the isolated portal, as previously reconstructed by cryo-EM. The portal is mounted on the outer surface of the capsid floor layer, with its narrow end pointing outwards. This disposition differs from that of known phage portals in that the bulk of its mass lies outside, not inside, the floor. This distinction may be indicative of divergence at the level of portal-related functions other than its role as a DNA channel.« less

Iodine-123 alpha-methyl tyrosine single-photon emission tomography of cerebral gliomas: standardised evaluation of tumour uptake and extent.

PubMed

Weckesser, M; Griessmeier, M; Schmidt, D; Sonnenberg, F; Ziemons, K; Kemna, L; Holschbach, M; Langen, K; Müller-Gärtner, H

1998-02-01

Single-photon emission tomography (SPET) with the amino acid analogue l-3-[123I]iodo-alpha-methyl tyrosine (IMT) is helpful in the diagnosis and monitoring of cerebral gliomas. Radiolabelled amino acids seem to reflect tumour infiltration more specifically than conventional methods like magnetic resonance imaging and computed tomography. Automatic tumour delineation based on maximal tumour uptake may cause an overestimation of mean tumour uptake and an underestimation of tumour extension in tumours with circumscribed peaks. The aim of this study was to develop a program for tumour delineation and calculation of mean tumour uptake which takes into account the mean background activity and is thus optimised to the problem of tumour definition in IMT SPET. Using the frequency distribution of pixel intensities of the tomograms a program was developed which automatically detects a reference brain region and draws an isocontour region around the tumour taking into account mean brain radioactivity. Tumour area and tumour/brain ratios were calculated. A three-compartment phantom was simulated to test the program. The program was applied to IMT SPET studies of 20 patients with cerebral gliomas and was compared to the results of manual analysis by three different investigators. Activity ratios and chamber extension of the phantom were correctly calculated by the automatic analysis. A method based on image maxima alone failed to determine chamber extension correctly. Manual region of interest analysis in patient studies resulted in a mean inter-observer standard deviation of 8.7% +/ -6.1% (range 2.7% -25.0%). The mean value of the results of the manual analysis showed a significant correlation to the results of the automatic analysis (r = 0.91, P<0. 0001 for the uptake ratio; r = 0.87, P<0.0001 for the tumour area). We conclude that the algorithm proposed simplifies the calculation of uptake ratios and may be used for observer-independent evaluation of IMT SPET studies. Three-dimensional tumour recognition and transfer to co-registered morphological images based on this program may be useful for the planning of surgical and radiation treatment.

Correlative Fluorescence and Electron Microscopy in 3D-Scanning Electron Microscope Perspective.

PubMed

Franks, Jonathan; Wallace, Callen T; Shibata, Masateru; Suga, Mitsuo; Erdman, Natasha; Stolz, Donna B; Watkins, Simon C

2017-04-03

The ability to correlate fluorescence microscopy (FM) and electron microscopy (EM) data obtained on biological (cell and tissue) specimens is essential to bridge the resolution gap between the data obtained by these different imaging techniques. In the past such correlations were limited to either EM navigation in two dimensions to the locations previously highlighted by fluorescence markers, or subsequent high-resolution acquisition of tomographic information using a TEM. We present a novel approach whereby a sample previously investigated by FM is embedded and subjected to sequential mechanical polishing and backscatter imaging by scanning electron microscope. The resulting three dimensional EM tomogram of the sample can be directly correlated to the FM data. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Invertible propagator for plane wave illumination of forward-scattering structures.

PubMed

Samelsohn, Gregory

2017-05-10

Propagation of directed waves in forward-scattering media is considered. It is assumed that the evolution of the wave field is governed by the standard parabolic wave equation. An efficient one-step momentum-space propagator, suitable for a tilted plane wave illumination of extended objects, is derived. It is expressed in terms of a propagation operator that transforms (the complex exponential of) a linogram of the illuminated object into a set of its diffraction patterns. The invertibility of the propagator is demonstrated, which permits a multiple-shot scatter correction to be performed, and makes the solution especially attractive for either projective or tomographic imaging. As an example, high-resolution tomograms are obtained in numerical simulations implemented for a synthetic phantom, with both refractive and absorptive inclusions.

Rhizosphere biophysics and root water uptake

NASA Astrophysics Data System (ADS)

Carminati, Andrea; Zarebanadkouki, Mohsen; Ahmed, Mutez A.; Passioura, John

2016-04-01

The flow of water into the roots and the (putative) presence of a large resistance at the root-soil interface have attracted the attention of plant and soil scientists for decades. Such resistance has been attributed to a partial contact between roots and soil, large gradients in soil matric potential around the roots, or accumulation of solutes at the root surface creating a negative osmotic potential. Our hypothesis is that roots are capable of altering the biophysical properties of the soil around the roots, the rhizosphere, facilitating root water uptake in dry soils. In particular, we expect that root hairs and mucilage optimally connect the roots to the soil maintaining the hydraulic continuity across the rhizosphere. Using a pressure chamber apparatus we measured the relation between transpiration rate and the water potential difference between soil and leaf xylem during drying cycles in barley mutants with and without root hairs. The samples were grown in well structured soils. At low soil moistures and high transpiration rates, large drops in water potential developed around the roots. These drops in water potential recovered very slowly, even after transpiration was severely decreased. The drops in water potential were much bigger in barley mutants without root hairs. These mutants failed to sustain high transpiration rates in dry conditions. To explain the nature of such drops in water potential across the rhizosphere we performed high resolution neutron tomography of the rhizosphere of the barleys with and without root hairs growing in the same soil described above. The tomograms suggested that the hydraulic contact between the soil structures was the highest resistance for the water flow in dry conditions. The tomograms also indicate that root hairs and mucilage improved the hydraulic contact between roots and soil structures. At high transpiration rates and low water contents, roots extracted water from the rhizosphere, while the bulk soil, due its low unsaturated conductivity, failed to compensate root water uptake. We conclude that root hairs are functional to increase the contact area between the roots and the soil structures and mucilage maintains wet the soil region between root hairs. These observations demonstrate the importance of the biophysical processes in the rhizosphere in modulating root water uptake.

Anatomic Distribution of Fluorodeoxyglucose-Avid Para-aortic Lymph Nodes in Patients With Cervical Cancer

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

Takiar, Vinita; Fontanilla, Hiral P.; Eifel, Patricia J.

Purpose: Conformal treatment of para-aortic lymph nodes (PAN) in cervical cancer allows dose escalation and reduces normal tissue toxicity. Currently, data documenting the precise location of involved PAN are lacking. We define the spatial distribution of this high-risk nodal volume by analyzing fluorodeoxyglucose (FDG)-avid lymph nodes (LNs) on positron emission tomography/computed tomography (PET/CT) scans in patients with cervical cancer. Methods and Materials: We identified 72 PANs on pretreatment PET/CT of 30 patients with newly diagnosed stage IB-IVA cervical cancer treated with definitive chemoradiation. LNs were classified as left-lateral para-aortic (LPA), aortocaval (AC), or right paracaval (RPC). Distances from the LNmore » center to the closest vessel and adjacent vertebral body were calculated. Using deformable image registration, nodes were mapped to a template computed tomogram to provide a visual impression of nodal frequencies and anatomic distribution. Results: We identified 72 PET-positive para-aortic lymph nodes (37 LPA, 32 AC, 3 RPC). All RPC lymph nodes were in the inferior third of the para-aortic region. The mean distance from aorta for all lymph nodes was 8.3 mm (range, 3-17 mm), and from the inferior vena cava was 5.6 mm (range, 2-10 mm). Of the 72 lymph nodes, 60% were in the inferior third, 36% were in the middle third, and 4% were in the upper third of the para-aortic region. In all, 29 of 30 patients also had FDG-avid pelvic lymph nodes. Conclusions: A total of 96% of PET positive nodes were adjacent to the aorta; PET positive nodes to the right of the IVC were rare and were all located distally, within 3 cm of the aortic bifurcation. Our findings suggest that circumferential margins around the vessels do not accurately define the nodal region at risk. Instead, the anatomical extent of the nodal basin should be contoured on each axial image to provide optimal coverage of the para-aortic nodal compartment.« less

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

NASA Astrophysics Data System (ADS)

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

1995-05-01

Electron beam computed tomography is unparalleled in its ability to consistently produce high quality dynamic images of the human heart. Its use in quantification of left ventricular dynamics is well established in both clinical and research applications. However, the image analysis tools supplied with the scanners offer a limited number of analysis options. They are based on embedded computer systems which have not been significantly upgraded since the scanner was introduced over a decade ago in spite of the explosive improvements in available computer power which have occured during this period. To address these shortcomings, a workstation-based ventricular analysis system has been developed at our institution. This system, which has been in use for over five years, is based on current workstation technology and therefore has benefited from the periodic upgrades in processor performance available to these systems. The dynamic image segmentation component of this system is an interactively supervised, semi-automatic surface identification and tracking system. It characterizes the endocardial and epicardial surfaces of the left ventricle as two concentric 4D hyper-space polyhedrons. Each of these polyhedrons have nearly ten thousand vertices which are deposited into a relational database. The right ventricle is also processed in a similar manner. This database is queried by other custom components which extract ventricular function parameters such as regional ejection fraction and wall stress. The interactive tool which supervises dynamic image segmentation has been enhanced with a temporal domain display. The operator interactively chooses the spatial location of the endpoints of a line segment while the corresponding space/time image is displayed. These images, with content resembling M-Mode echocardiography, benefit form electron beam computed tomography's high spatial and contrast resolution. The segmented surfaces are displayed along with the imagery. These displays give the operator valuable feedback pertaining to the contiguity of the extracted surfaces. As with M-Mode echocardiography, the velocity of moving structures can be easily visualized and measured. However, many views inaccessible to standard transthoracic echocardiography are easily generated. These features have augmented the interpretability of cine electron beam computed tomography and have prompted the recent cloning of this system into an 'omni-directional M-Mode display' system for use in digital post-processing of echocardiographic parasternal short axis tomograms. This enhances the functional assessment in orthogonal views of the left ventricle, accounting for shape changes particularly in the asymmetric post-infarction ventricle. Conclusions: A new tool has been developed for analysis and visualization of cine electron beam computed tomography. It has been found to be very useful in verifying the consistency of myocardial surface definition with a semi-automated segmentation tool. By drawing on M-Mode echocardiography experience, electron beam tomography's interpretability has been enhanced. Use of this feature, in conjunction with the existing image processing tools, will enhance the presentations of data on regional systolic and diastolic functions to clinicians in a format that is familiar to most cardiologists. Additionally, this tool reinforces the advantages of electron beam tomography as a single imaging modality for the assessment of left and right ventricular size, shape, and regional functions.

Use of conventional tomography to evaluate changes in the nasal cavity with rapid palatal expansion.

PubMed

Palaisa, Jacqueline; Ngan, Peter; Martin, Chris; Razmus, Thomas

2007-10-01

The relationship between nasal airway resistance and the use of rapid palatal expansion appliances remains controversial. The purpose of this study was to use conventional tomography to determine the anatomical changes in the nasal cavity after maxillary expansion. Nineteen patients (aged 8-15 years) were included in the study. Tomograms were taken before expansion (T1), immediately after expansion (T2), and 3 months after expansion (T3). Areas for the left and right anterior, middle, and posterior nasal cavity and total volume were calculated by using the computer software, AutoCAD LT 2005. Data were analyzed with paired t tests. Significant increases in area were found in the anterior nasal cavity from T1 to T2 (0.85 +/- 1.19 cm2, 11.7% increase), T2 to T3 (1.18 +/- 1.2 cm2, 22.2% increase), and T1 to T3 (2.6 +/- 1.7 cm2, 35.7% increase) (P <.05). Similar increases were found in the middle and posterior nasal cavity. Significant increases in volume were found from T1 to T2 (2.1 +/- 2.7 cm3, 10.7% increase), T2 to T3 (4.9 +/- 2.3 cm3, 22.6% increase), and T1 to T3 (6.99 +/- 2.45 cm3, 27.8% increase). No significant differences were found in the area or the volume of the left and right sides of the nasal cavity. Individual variations in response to maxillary expansion were large for most of the parameters tested. These data suggest that rapid palatal expansion is usually accompanied by increases in area and volume of the nasal cavity, and these changes remain stable 3 months after maxillary expansion.

A comparison of visual and quantitative methods to identify interstitial lung abnormalities.

PubMed

Kliment, Corrine R; Araki, Tetsuro; Doyle, Tracy J; Gao, Wei; Dupuis, Josée; Latourelle, Jeanne C; Zazueta, Oscar E; Fernandez, Isis E; Nishino, Mizuki; Okajima, Yuka; Ross, James C; Estépar, Raúl San José; Diaz, Alejandro A; Lederer, David J; Schwartz, David A; Silverman, Edwin K; Rosas, Ivan O; Washko, George R; O'Connor, George T; Hatabu, Hiroto; Hunninghake, Gary M

2015-10-29

Evidence suggests that individuals with interstitial lung abnormalities (ILA) on a chest computed tomogram (CT) may have an increased risk to develop a clinically significant interstitial lung disease (ILD). Although methods used to identify individuals with ILA on chest CT have included both automated quantitative and qualitative visual inspection methods, there has been not direct comparison between these two methods. To investigate this relationship, we created lung density metrics and compared these to visual assessments of ILA. To provide a comparison between ILA detection methods based on visual assessment we generated measures of high attenuation areas (HAAs, defined by attenuation values between -600 and -250 Hounsfield Units) in >4500 participants from both the COPDGene and Framingham Heart studies (FHS). Linear and logistic regressions were used for analyses. Increased measures of HAAs (in ≥ 10 % of the lung) were significantly associated with ILA defined by visual inspection in both cohorts (P < 0.0001); however, the positive predictive values were not very high (19 % in COPDGene and 13 % in the FHS). In COPDGene, the association between HAAs and ILA defined by visual assessment were modified by the percentage of emphysema and body mass index. Although increased HAAs were associated with reductions in total lung capacity in both cohorts, there was no evidence for an association between measurement of HAAs and MUC5B promoter genotype in the FHS. Our findings demonstrate that increased measures of lung density may be helpful in determining the severity of lung volume reduction, but alone, are not strongly predictive of ILA defined by visual assessment. Moreover, HAAs were not associated with MUC5B promoter genotype.

Differential expression levels of collagen 1A2, tissue inhibitor of metalloproteinase 4, and cathepsin B in intracranial aneurysms.

PubMed

Babu, R Arun; Paul, Pradip; Purushottam, Meera; Srinivas, Dwarakanath; Somanna, Sampath; Jain, Sanjeev

2016-01-01

Intracranial aneurysms (IAs) express a variety of differentially expressed genes when compared to the normal artery. The aim of this study was to evaluate the expression level of a few genes in the aneurysm wall and to correlate them with various clinicoradiological factors. The mRNA level of collagen 1A2 (COL1A2), tissue inhibitor of metalloproteinase 4 (TIMP4), and cathepsin B (CTSB) genes were studied in 23 aneurysmal walls and 19 superficial temporal arteries harvested from 23 patients undergoing clipping of IAs, by real-time polymerase chain reaction method. The mean fold change of COL1A2 gene between the aneurysm sample and the superficial temporal artery (STA) sample was 2.46 ± 0.12, that of TIMP4 gene was 0.31 ± 0, and that of CTSB gene was 31.47 ± 39.01. There was a positive correlation of TIMP4 expression level with maximum diameter of aneurysm (P = 0.008) and fundus of aneurysm (P = 0.012). The mean fold change of CTSB of patients who had preoperative hydrocephalus in the computed tomogram (CT) scan of the head at admission was 56.16 and that of the patients who did not have hydrocephalus was 13.51 (P = 0.008). The mean fold change of CTSB of patients who developed fresh postoperative deficits or worsening of the preexisting deficits was 23.64 and that of the patients who did not develop was 42.22 (P = 0.039). COL1A2 gene and CTSB genes were overexpressed, and TIMP4 gene was underexpressed in the aneurysmal sac compared to STA and their expression levels were associated with a few clinicoradiological factors.

Paramedian vertical palatal bone height for mini-implant insertion: a systematic review.

PubMed

Winsauer, H; Vlachojannis, C; Bumann, A; Vlachojannis, J; Chrubasik, S

2014-10-01

Paramedian insertion of orthodontic mini-implants is increasingly used to anchor molar distalizers. The aim of this review was to systematically examine the available measurements of vertical palatal bone height (VBH). PUBMED, MEDLINE and the Cochrane Controlled Trials Register were searched using specific search terms. Hand searches of bibliographies of articles were also performed to identify studies measuring VBH or bone thickness in the human palate. Sixteen studies were included, arising from 19 published articles. Repeat presentations were excluded. Ten of the 11 computed tomogram (CT)-based studies presented data from 956 orthodontic patients on average VBH and its variation at a range of palatal sites. Individual data were not available, and pooling of data was not feasible because of heterogeneity of subjects, different measurement sites, different CT methods and their associated software. The compilation of data did indicate that the region 3-4mm behind the incisive foramen and 3-9mm lateral to the midpalatal suture should normally provide sufficient VBH to anchor molar distalizers. The risks of unwanted effects during distalization should be small, but the limitations listed above and the small numbers of studies available impair the precision of the estimates and do not allow the results to be generalized. Paramedian anchorage in the anterior palate can be recommended for molar distalization but, given the great inter-individual variability of the palatal bone height, it must be preceded by reliable CT-based imaging in patients identified by routine investigations as being at risk. © The Author 2012. Published by Oxford University Press on behalf of the European Orthodontic Society. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Augmented corticotomy-assisted surgical orthodontics decompensates lower incisors in Class III malocclusion patients.

PubMed

Wang, Bo; Shen, Guofang; Fang, Bing; Yu, Hongbo; Wu, Yong; Sun, Liangyan

2014-03-01

To quantitatively evaluate lower incisor decompensation and the surrounding periodontal region after augmented corticotomy-assisted surgical orthodontics in patients with Class III malocclusion. This prospective study enrolled patients with severe Class III malocclusion who underwent augmented corticotomy in the lower anterior region before orthodontic surgery. Cone-beam computed tomograms and lateral cephalograms were obtained before treatment (T0), after presurgical orthodontic treatment (T1), and at removal of the orthodontic surgical appliances (T2). Repeated measures analysis of variance was used to compare variables at each time point: root length (RL), anterior vertical alveolar bone level at the labial side (AVBL), posterior vertical alveolar bone level at the lingual side (PVBL), labial alveolar bone thickness at the apex (LA), lingual alveolar bone thickness at the apex (LP), and angle of the incisor to the mandibular plane (L1-MP). In the 8 subjects studied, RL was maintained from T0 to T2 (P > .05), whereas AVBL and PVBL increased from T0 to T1 (P < .05) and then decreased from T1 to T2 (P < .05). LA and L1-MP increased from T0 to T1 (P < .001) but remained steady from T1 to T2 (P > .05). LP decreased from T0 to T1 (P < .05) but increased from T1 to T2 (P < .05) with no further change. Augmented corticotomy-assisted surgical orthodontics can achieve adequate tooth decompensation with minimal periodontal side-effects in the lower anterior region in patients with Class III malocclusion. Copyright © 2014 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

Metric on the space of quantum states from relative entropy. Tomographic reconstruction

NASA Astrophysics Data System (ADS)

Man'ko, Vladimir I.; Marmo, Giuseppe; Ventriglia, Franco; Vitale, Patrizia

2017-08-01

In the framework of quantum information geometry, we derive, from quantum relative Tsallis entropy, a family of quantum metrics on the space of full rank, N level quantum states, by means of a suitably defined coordinate free differential calculus. The cases N=2, N=3 are discussed in detail and notable limits are analyzed. The radial limit procedure has been used to recover quantum metrics for lower rank states, such as pure states. By using the tomographic picture of quantum mechanics we have obtained the Fisher-Rao metric for the space of quantum tomograms and derived a reconstruction formula of the quantum metric of density states out of the tomographic one. A new inequality obtained for probabilities of three spin-1/2 projections in three perpendicular directions is proposed to be checked in experiments with superconducting circuits.

3D radar wavefield tomography of comet interiors

NASA Astrophysics Data System (ADS)

Sava, Paul; Asphaug, Erik

2018-04-01

Answering fundamental questions about the origin and evolution of small planetary bodies hinges on our ability to image their surface and interior structure in detail and at high resolution. The interior structure is not easily accessible without systematic imaging using, e.g., radar transmission and reflection data from multiple viewpoints, as in medical tomography. Radar tomography can be performed using methodology adapted from terrestrial exploration seismology. Our feasibility study primarily focuses on full wavefield methods that facilitate high quality imaging of small body interiors. We consider the case of a monostatic system (co-located transmitters and receivers) operated in various frequency bands between 5 and 15 MHz, from a spacecraft in slow polar orbit around a spinning comet nucleus. Using realistic numerical experiments, we demonstrate that wavefield techniques can generate high resolution tomograms of comets nuclei with arbitrary shape and complex interior properties.

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

PubMed Central

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

2011-01-01

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

Audible sonar images generated with proprioception for target analysis.

PubMed

Kuc, Roman B

2017-05-01

Some blind humans have demonstrated the ability to detect and classify objects with echolocation using palatal clicks. An audible-sonar robot mimics human click emissions, binaural hearing, and head movements to extract interaural time and level differences from target echoes. Targets of various complexity are examined by transverse displacements of the sonar and by target pose rotations that model movements performed by the blind. Controlled sonar movements executed by the robot provide data that model proprioception information available to blind humans for examining targets from various aspects. The audible sonar uses this sonar location and orientation information to form two-dimensional target images that are similar to medical diagnostic ultrasound tomograms. Simple targets, such as single round and square posts, produce distinguishable and recognizable images. More complex targets configured with several simple objects generate diffraction effects and multiple reflections that produce image artifacts. The presentation illustrates the capabilities and limitations of target classification from audible sonar images.

Combined scanning transmission electron microscopy tilt- and focal series.

PubMed

Dahmen, Tim; Baudoin, Jean-Pierre; Lupini, Andrew R; Kübel, Christian; Slusallek, Philipp; de Jonge, Niels

2014-04-01

In this study, a combined tilt- and focal series is proposed as a new recording scheme for high-angle annular dark-field scanning transmission electron microscopy (STEM) tomography. Three-dimensional (3D) data were acquired by mechanically tilting the specimen, and recording a through-focal series at each tilt direction. The sample was a whole-mount macrophage cell with embedded gold nanoparticles. The tilt-focal algebraic reconstruction technique (TF-ART) is introduced as a new algorithm to reconstruct tomograms from such combined tilt- and focal series. The feasibility of TF-ART was demonstrated by 3D reconstruction of the experimental 3D data. The results were compared with a conventional STEM tilt series of a similar sample. The combined tilt- and focal series led to smaller "missing wedge" artifacts, and a higher axial resolution than obtained for the STEM tilt series, thus improving on one of the main issues of tilt series-based electron tomography.

Optical coherence tomography imaging for evaluating the photo biomodulation effects on tissue regeneration in the oral cavity

NASA Astrophysics Data System (ADS)

Gimbel, Craig B.

2008-03-01

Optical Coherence Tomography (OCT) is a noninvasive method for imaging dental microstructure which has the potential of evaluating the health of periodontal tissue. OCT provides an "optical biopsy" of tissue 2-3 mm in depth. Optical biopsy is a measurement of the localized optical properties based on tissue type and pathology. This sixth modality of imaging was pioneered at Lawrence Livermore National Laboratory. OCT is based on the optical scattering signatures within tissue structure. With the use of a broad spectrum bandwidth light source, high resolution images, 10 times the resolution of radiographs, can detect important tissue interfaces within the periodontal sulcus and its' relationship to the attachment apparatus of the tooth. Multiple cross-sectional tomograms can be stacked to create two and three dimensional images providing information as to health of periodontal tissue important to both the clinician and researcher.

Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography.

PubMed

Yu, Young-Sang; Farmand, Maryam; Kim, Chunjoong; Liu, Yijin; Grey, Clare P; Strobridge, Fiona C; Tyliszczak, Tolek; Celestre, Rich; Denes, Peter; Joseph, John; Krishnan, Harinarayan; Maia, Filipe R N C; Kilcoyne, A L David; Marchesini, Stefano; Leite, Talita Perciano Costa; Warwick, Tony; Padmore, Howard; Cabana, Jordi; Shapiro, David A

2018-03-02

Battery function is determined by the efficiency and reversibility of the electrochemical phase transformations at solid electrodes. The microscopic tools available to study the chemical states of matter with the required spatial resolution and chemical specificity are intrinsically limited when studying complex architectures by their reliance on two-dimensional projections of thick material. Here, we report the development of soft X-ray ptychographic tomography, which resolves chemical states in three dimensions at 11 nm spatial resolution. We study an ensemble of nano-plates of lithium iron phosphate extracted from a battery electrode at 50% state of charge. Using a set of nanoscale tomograms, we quantify the electrochemical state and resolve phase boundaries throughout the volume of individual nanoparticles. These observations reveal multiple reaction points, intra-particle heterogeneity, and size effects that highlight the importance of multi-dimensional analytical tools in providing novel insight to the design of the next generation of high-performance devices.

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

PubMed

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

2016-07-01

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

Three-dimensional spectral domain optical coherence tomography in X linked foveal retinoschisis

PubMed Central

Saxena, Sandeep; Manisha; Meyer, Carsten H

2013-01-01

Spectral domain optical coherence tomography (SD-OCT) was performed in two cases of bilateral X linked foveal retinoschisis of different age groups. On fundus examination spoke wheel and honeycomb pattern of cysts were observed along with retinal nerve fibre layer (RNFL) defects. On SD-OCT, schisis was observed in the outer plexiform layer. External limiting membrane disruption was observed in the subfoveal area, along with disruption of outer nuclear layer (ONL) and inner–outer segment junction. Elevation of ONL due to tractional pull of central palisade was a novel observation. Retinoschisis extended beyond the optic disc up to the nasal region. Extracted RNFL tomogram presented an unprecedented visualisation of schisis along 360° of the optic disc. Tractional elevation in the foveal area and schisis involving nasal region, not observed upon clinical examination, was highlighted on SD-OCT. This investigative modality is an important adjunct in the assessment of foveal retinoschisis. PMID:23563673

Merging information in geophysics: the triumvirat of geology, geophysics, and petrophysics

NASA Astrophysics Data System (ADS)

Revil, A.

2016-12-01

We know that geophysical inversion is non-unique and that many classical regularization techniques are unphysical. Despite this, we like to use them because of their simplicity and because geophysicists are often afraid to bias the inverse problem by introducing too much prior information (in a broad sense). It is also clear that geophysics is done on geological objects that are not random structures. Spending some time with a geologist in the field, before organizing a field geophysical campaign, is always an instructive experience. Finally, the measured properties are connected to physicochemical and textural parameters of the porous media and the interfaces between the various phases of a porous body. .Some fundamental parameters may control the geophysical observtions or their time variations. If we want to improve our geophysical tomograms, we need to be risk-takers and acknowledge, or rather embrqce, the cross-fertilization arising by coupling geology, geophysics, and ptrophysics. In this presentation, I will discuss various techniques to do so. They will include non-stationary geostatistical descriptors, facies deformation, cross-coupled petrophysical properties using petrophysical clustering, and image-guided inversion. I will show various applications to a number of relevant cases in hydrogeophysics. From these applications, it may become clear that there are many ways to address inverse or time-lapse inverse problems and geophysicists have to be pragmatic regarding the methods used depending on the degree of available prior information.

Spectral optical coherence tomography vs. fluorescein pattern for rigid gas-permeable lens fit.

PubMed

Piotrowiak, Ilona; Kaluzny, Bartłomiej Jan; Danek, Beata; Chwiędacz, Adam; Sikorski, Bartosz Lukasz; Malukiewicz, Grażyna

2014-07-04

This study aimed to evaluate anterior segment spectral optical coherence tomography (AS SOCT) for assessing the lens-to-cornea fit of rigid gas-permeable (RGP) lenses. The results were verified with the fluorescein pattern method, considered the criterion standard for RGP lens alignment evaluations. Twenty-six eyes of 14 patients were enrolled in the study. Initial base curve radius (BCR) of each RGP lens was determined on the basis of keratometry readings. The fluorescein pattern and AS SOCT tomograms were evaluated, starting with an alignment fit, and subsequently, with BCR reductions in increments of 0.1 mm, up to 3 consecutive changes. AS SOCT examination was performed with the use of RTVue (Optovue, California, USA). The average BCR for alignment fits, defined according to the fluorescein pattern, was 7.8 mm (SD=0.26). Repeatability of the measurements was 18.2%. BCR reductions of 0.1, 0.2, and 0.3 mm resulted in average apical clearances detected with AS SOCT of 12.38 (SD=9.91, p<0.05), 28.79 (SD=15.39, p<0.05), and 33.25 (SD=10.60, p>0.05), respectively. BCR steepening of 0.1 mm or more led to measurable changes in lens-to-cornea fits. Although AS SOCT represents a new method of assessing lens-to-cornea fit, apical clearance detection with current commercial technology showed lower sensitivity than the fluorescein pattern assessment.

Generation of a three-dimensional ultrastructural model of human respiratory cilia.

PubMed

Burgoyne, Thomas; Dixon, Mellisa; Luther, Pradeep; Hogg, Claire; Shoemark, Amelia

2012-12-01

The ultrastructures of cilia and flagella are highly similar and well conserved through evolution. Consequently, Chlamydomonas is commonly used as a model organism for the study of human respiratory cilia. Since detailed models of Chlamydomonas axonemes were generated using cryoelectron tomography, disparities among some of the ultrastructural features have become apparent when compared with human cilia. Extrapolating information on human disease from the Chlamydomonas model may lead to discrepancies in translational research. This study aimed to establish the first three-dimensional ultrastructural model of human cilia. Tomograms of transverse sections (n = 6) and longitudinal sections (n = 9) of human nasal respiratory cilia were generated from three healthy volunteers. Key features of the cilium were resolved using subatomic averaging, and were measured. For validation of the method, a model of the well characterized structure of Chlamydomonas reinhardtii was simultaneously generated. Data were combined to create a fully quantified three-dimensional reconstruction of human nasal respiratory cilia. We highlight key differences in the axonemal sheath, microtubular doublets, radial spokes, and dynein arms between the two structures. We show a decreased axial periodicity of the radial spokes, inner dynein arms, and central pair protrusions in the human model. We propose that this first human model will provide a basis for research into the function and structure of human respiratory cilia in health and in disease.

Systematic Review and Meta-Analysis of Recombinant Human Bone Morphogenetic Protein-2 in Localized Alveolar Ridge and Maxillary Sinus Augmentation.

PubMed

Kelly, Mick P; Vaughn, Olushola L Akinshemoyin; Anderson, Paul A

2016-05-01

Recombinant human bone morphogenetic protein-2 (rhBMP-2) is approved by the Food and Drug Administration as a viable alternative to bone graft in spinal fusion and maxillary sinus lift. The research questions for meta-analysis were: Is rhBMP-2 an effective bone graft substitute in localized alveolar ridge augmentation and maxillary sinus floor augmentation? What are the potential adverse events? A search of MEDLINE from January 1980 to January 2014 using PubMed, the Cochrane Database of Systematic Reviews and Controlled Trials, CINAHL, and EMBASE was performed. Searches were performed from Medical Subject Headings. The quality of each study included was graded by Review Manager software. The primary outcome variable was bone formation measured as change in bone height on computed tomogram. A systematic review of adverse events also was performed. A random-effects model was chosen. Continuous variables were calculated using the standardized mean difference and 95% confidence intervals (CIs) comparing improvement from baseline of the experimental group with that of the control group. Change in bone height was calculated using logarithmic odds ratio. Test of significance used the Z statistic with a P value of .05. Ten studies met the criteria for systematic review; 8 studies were included in the meta-analysis. Five studies assessed localized alveolar ridge augmentation and resulted in an overall standardized mean difference of 0.56 (CI, 0.20-0.92) in favor of BMP; this result was statistically important. Three studies assessed maxillary sinus floor augmentation and resulted in an overall standardized mean difference of -0.50 (CI, -0.93 to -0.09), which was meaningfully different in favor of the control group. Adverse events were inconsistently reported, ranging from no complications to widespread adverse events. For localized alveolar ridge augmentation, this meta-analysis showed that rhBMP-2 substantially increases bone height. However, rhBMP-2 does not perform as well as the autograft or allograft in maxillary sinus floor augmentation. Long-term clinical success and adverse events need to be reported with more consistency before definitive conclusions can be made. Copyright © 2016 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

In situ detection of tree root distribution and biomass by multi-electrode resistivity imaging.

PubMed

Amato, Mariana; Basso, Bruno; Celano, Giuseppe; Bitella, Giovanni; Morelli, Gianfranco; Rossi, Roberta

2008-10-01

Traditional methods for studying tree roots are destructive and labor intensive, but available nondestructive techniques are applicable only to small scale studies or are strongly limited by soil conditions and root size. Soil electrical resistivity measured by geoelectrical methods has the potential to detect belowground plant structures, but quantitative relationships of these measurements with root traits have not been assessed. We tested the ability of two-dimensional (2-D) DC resistivity tomography to detect the spatial variability of roots and to quantify their biomass in a tree stand. A high-resolution resistivity tomogram was generated along a 11.75 m transect under an Alnus glutinosa (L.) Gaertn. stand based on an alpha-Wenner configuration with 48 electrodes spaced 0.25 m apart. Data were processed by a 2-D finite-element inversion algorithm, and corrected for soil temperature. Data acquisition, inversion and imaging were completed in the field within 60 min. Root dry mass per unit soil volume (root mass density, RMD) was measured destructively on soil samples collected to a depth of 1.05 m. Soil sand, silt, clay and organic matter contents, electrical conductivity, water content and pH were measured on a subset of samples. The spatial pattern of soil resistivity closely matched the spatial distribution of RMD. Multiple linear regression showed that only RMD and soil water content were related to soil resistivity along the transect. Regression analysis of RMD against soil resistivity revealed a highly significant logistic relationship (n = 97), which was confirmed on a separate dataset (n = 67), showing that soil resistivity was quantitatively related to belowground tree root biomass. This relationship provides a basis for developing quick nondestructive methods for detecting root distribution and quantifying root biomass, as well as for optimizing sampling strategies for studying root-driven phenomena.

Characterizing submarine ground‐water discharge using fiber‐optic distributed temperature sensing and marine electrical resistivity

USGS Publications Warehouse

Henderson, Rory; Day-Lewis, Frederick D.; Lane, John W.; Harvey, Charles F.; Liu, Lanbo

2008-01-01

Submarine ground‐water discharge (SGD) contributes important solute fluxes to coastal waters. Pollutants are transported to coastal ecosystems by SGD at spatially and temporally variable rates. New approaches are needed to characterize the effects of storm‐event, tidal, and seasonal forcing on SGD. Here, we evaluate the utility of two geophysical methods‐fiber‐optic distributed temperature sensing (FO‐DTS) and marine electrical resistivity (MER)—for observing the spatial and temporal variations in SGD and the configuration of the freshwater/saltwater interface within submarine sediments. FO‐DTS and MER cables were permanently installed into the estuary floor on a transect extending 50 meters offshore under Waquoit Bay, Massachusetts, at the Waquoit Bay National Estuarine Research Reserve, and nearly continuous data were collected for 4 weeks in summer 2007. Initial results indicate that the methods are extremely useful for monitoring changes in the complex estuarine environment. The FO‐DTS produced time‐series data at approximately 1‐meter increments along the length of the fiber at approximately 29‐second intervals. The temperature time‐series data show that the temperature at near‐shore locations appears to be dominated by a semi‐diurnal (tidal) signal, whereas the temperature at off‐shore locations is dominated by a diurnal signal (day/night heating and cooling). Dipole‐dipole MER surveys were completed about every 50 minutes, allowing for production of high‐resolution time‐lapse tomograms, which provide insight into the variations of the subsurface freshwater/saltwater interface. Preliminary results from the MER data show a high‐resistivity zone near the shore at low tide, indicative of SGD, and consistent with the FO‐DTS results.

Evaluation of noise and blur effects with SIRT-FISTA-TV reconstruction algorithm: Application to fast environmental transmission electron tomography.

PubMed

Banjak, Hussein; Grenier, Thomas; Epicier, Thierry; Koneti, Siddardha; Roiban, Lucian; Gay, Anne-Sophie; Magnin, Isabelle; Peyrin, Françoise; Maxim, Voichita

2018-06-01

Fast tomography in Environmental Transmission Electron Microscopy (ETEM) is of a great interest for in situ experiments where it allows to observe 3D real-time evolution of nanomaterials under operating conditions. In this context, we are working on speeding up the acquisition step to a few seconds mainly with applications on nanocatalysts. In order to accomplish such rapid acquisitions of the required tilt series of projections, a modern 4K high-speed camera is used, that can capture up to 100 images per second in a 2K binning mode. However, due to the fast rotation of the sample during the tilt procedure, noise and blur effects may occur in many projections which in turn would lead to poor quality reconstructions. Blurred projections make classical reconstruction algorithms inappropriate and require the use of prior information. In this work, a regularized algebraic reconstruction algorithm named SIRT-FISTA-TV is proposed. The performance of this algorithm using blurred data is studied by means of a numerical blur introduced into simulated images series to mimic possible mechanical instabilities/drifts during fast acquisitions. We also present reconstruction results from noisy data to show the robustness of the algorithm to noise. Finally, we show reconstructions with experimental datasets and we demonstrate the interest of fast tomography with an ultra-fast acquisition performed under environmental conditions, i.e. gas and temperature, in the ETEM. Compared to classically used SIRT and SART approaches, our proposed SIRT-FISTA-TV reconstruction algorithm provides higher quality tomograms allowing easier segmentation of the reconstructed volume for a better final processing and analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

Use of borehole radar tomography to monitor steam injection in fractured limestone

USGS Publications Warehouse

Gregoire, C.; Joesten, P.K.

2006-01-01

Borehole radar tomography was used as part of a pilot study to monitor steam-enhanced remediation of a fractured limestone contaminated with volatile organic compounds at the former Loring Air Force Base, Maine, USA. Radar tomography data were collected using 100-MHz electric-dipole antennae before and during steam injection to evaluate whether cross-hole radar methods could detect changes in medium properties resulting from the steam injection. Cross-hole levelrun profiles, in which transmitting and receiving antennae are positioned at a common depth, were made before and after the collection of each full tomography data set to check the stability of the radar instruments. Before tomographic inversion, the levelrun profiles were used to calibrate the radar tomography data to compensate for changes in traveltime and antenna power caused by instrument drift. Observed changes in cross-hole radar traveltime and attenuation before and during steam injection were small. Slowness- and attenuation-difference tomograms indicate small increases in radar slowness and attenuation at depths greater than about 22 m below the surface, consistent with increases in water temperature observed in the boreholes used for the tomography. Based on theoretical modelling results, increases in slowness and attenuation are interpreted as delineating zones where steam injection heating increased the electrical conductivity of the limestone matrix and fluid. The results of this study show the potential of cross-hole radar tomography methods to monitor the effects of steam-induced heating in fractured rock environments. ?? 2006 European Association of Geoscientists & Engineers.

The Influence of Spatial Variation in Chromatin Density Determined by X-Ray Tomograms on the Time to Find DNA Binding Sites

PubMed Central

Larabell, Carolyn A.; Le Gros, Mark A.; McQueen, David M.; Peskin, Charles S.

2014-01-01

In this work, we examine how volume exclusion caused by regions of high chromatin density might influence the time required for proteins to find specific DNA binding sites. The spatial variation of chromatin density within mouse olfactory sensory neurons is determined from soft X-ray tomography reconstructions of five nuclei. We show that there is a division of the nuclear space into regions of low-density euchromatin and high-density heterochromatin. Volume exclusion experienced by a diffusing protein caused by this varying density of chromatin is modeled by a repulsive potential. The value of the potential at a given point in space is chosen to be proportional to the density of chromatin at that location. The constant of proportionality, called the volume exclusivity, provides a model parameter that determines the strength of volume exclusion. Numerical simulations demonstrate that the mean time for a protein to locate a binding site localized in euchromatin is minimized for a finite, nonzero volume exclusivity. For binding sites in heterochromatin, the mean time is minimized when the volume exclusivity is zero (the protein experiences no volume exclusion). An analytical theory is developed to explain these results. The theory suggests that for binding sites in euchromatin there is an optimal level of volume exclusivity that balances a reduction in the volume searched in finding the binding site, with the height of effective potential barriers the protein must cross during the search process. PMID:23955281

High resolution aquifer characterization using crosshole GPR full-waveform tomography

NASA Astrophysics Data System (ADS)

Gueting, N.; Vienken, T.; Klotzsche, A.; Van Der Kruk, J.; Vanderborght, J.; Caers, J.; Vereecken, H.; Englert, A.

2016-12-01

Limited knowledge about the spatial distribution of aquifer properties typically constrains our ability to predict subsurface flow and transport. Here, we investigate the value of using high resolution full-waveform inversion of cross-borehole ground penetrating radar (GPR) data for aquifer characterization. By stitching together GPR tomograms from multiple adjacent crosshole planes, we are able to image, with a decimeter scale resolution, the dielectric permittivity and electrical conductivity of an alluvial aquifer along cross-sections of 50 m length and 10 m depth. A logistic regression model is employed to predict the spatial distribution of lithological facies on the basis of the GPR results. Vertical profiles of porosity and hydraulic conductivity from direct-push, flowmeter and grain size data suggest that the GPR predicted facies classification is meaningful with regard to porosity and hydraulic conductivity, even though the distributions of individual facies show some overlap and the absolute hydraulic conductivities from the different methods (direct-push, flowmeter, grain size) differ up to approximately one order of magnitude. Comparison of the GPR predicted facies architecture with tracer test data suggests that the plume splitting observed in a tracer experiment was caused by a hydraulically low-conductive sand layer with a thickness of only a few decimeters. Because this sand layer is identified by GPR full-waveform inversion but not by conventional GPR ray-based inversion we conclude that the improvement in spatial resolution due to full-waveform inversion is crucial to detect small-scale aquifer structures that are highly relevant for solute transport.

Teleseismic P wave tomography of South Island, New Zealand upper mantle: Evidence of subduction of Pacific lithosphere since 45 Ma

NASA Astrophysics Data System (ADS)

Zietlow, Daniel W.; Molnar, Peter H.; Sheehan, Anne F.

2016-06-01

A P wave speed tomogram produced from teleseismic travel time measurements made on and offshore the South Island of New Zealand shows a nearly vertical zone with wave speeds that are 4.5% higher than the background average reaching to depths of approximately 450 km under the northwestern region of the island. This structure is consistent with oblique west-southwest subduction of Pacific lithosphere since about 45 Ma, when subduction beneath the region began. The high-speed zone reaches about 200-300 km below the depths of the deepest intermediate-depth earthquakes (subcrustal to ~200 km) and therefore suggests that ~200-300 km of slab below them is required to produce sufficient weight to induce the intermediate-depth seismicity. In the southwestern South Island, high P wave speeds indicate subduction of the Australian plate at the Puysegur Trench to approximately 200 km depth. A band with speeds ~2-3.5% lower than the background average is found along the east coast of the South Island to depths of ~150-200 km and underlies Miocene or younger volcanism; these low speeds are consistent with thinned lithosphere. A core of high speeds under the Southern Alps associated with a convergent margin and mountain building imaged in previous investigations is not well resolved in this study. This could suggest that such high speeds are limited in both width and depth and not resolvable by our data.

The effect of partial rostral hemimandibulectomy on mandibular mobility and temporomandibular joint morphology in the dog.

PubMed

Umphlet, R C; Johnson, A L; Eurell, J C; Losonsky, J

1988-01-01

Partial rostral hemimandibulectomy was performed in 10 adult dogs. The temporomandibular joints (TMJs) were examined radiographically and tomographically before surgery, and mandibular stability was evaluated before and immediately after surgery. Radiographic, tomographic, and hemimandibular mobility assessments were made again at months 3 and 6. The TMJs were examined grossly and histologically in five dogs euthanatized at month 3 and in five dogs euthanatized at month 6. Statistically significant hemimandibular instability (p less than 0.05) persisted in all subjects throughout the study. The radiographic appearance of the joints remained unaltered; however, space asymmetry was identified in postoperative tomograms of three dogs at month 3 and four dogs at month 6. The TMJs were grossly normal at necropsy. Histologically, there were degenerative changes in articular cartilage and subchondral bone in all of the joints. The authors conclude that partial rostral hemimandibulectomy causes TMJ degeneration, as a consequence of hemimandibular instability or abnormal loading, or both.

Theoretical limit of spatial resolution in diffuse optical tomography using a perturbation model

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

Konovalov, A B; Vlasov, V V

2014-03-28

We have assessed the limit of spatial resolution of timedomain diffuse optical tomography (DOT) based on a perturbation reconstruction model. From the viewpoint of the structure reconstruction accuracy, three different approaches to solving the inverse DOT problem are compared. The first approach involves reconstruction of diffuse tomograms from straight lines, the second – from average curvilinear trajectories of photons and the third – from total banana-shaped distributions of photon trajectories. In order to obtain estimates of resolution, we have derived analytical expressions for the point spread function and modulation transfer function, as well as have performed a numerical experiment onmore » reconstruction of rectangular scattering objects with circular absorbing inhomogeneities. It is shown that in passing from reconstruction from straight lines to reconstruction using distributions of photon trajectories we can improve resolution by almost an order of magnitude and exceed the accuracy of reconstruction of multi-step algorithms used in DOT. (optical tomography)« less

Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography

DOE PAGES

Yu, Young-Sang; Farmand, Maryam; Kim, Chunjoong; ...

2018-03-02

Battery function is determined by the efficiency and reversibility of the electrochemical phase transformations at solid electrodes. The microscopic tools available to study the chemical states of matter with the required spatial resolution and chemical specificity are intrinsically limited when studying complex architectures by their reliance on two-dimensional projections of thick material. Here in this paper, we report the development of soft X-ray ptychographic tomography, which resolves chemical states in three dimensions at 11 nm spatial resolution. We study an ensemble of nano-plates of lithium iron phosphate extracted from a battery electrode at 50% state of charge. Using a setmore » of nanoscale tomograms, we quantify the electrochemical state and resolve phase boundaries throughout the volume of individual nanoparticles. These observations reveal multiple reaction points, intra-particle heterogeneity, and size effects that highlight the importance of multi-dimensional analytical tools in providing novel insight to the design of the next generation of high-performance devices.« less

Solving cross-disciplinary problems by mathematical modelling

NASA Astrophysics Data System (ADS)

Panfilov, D. A.; Romanchikov, V. V.; Krupin, K. N.

2018-03-01

The article deals with the creation of a human tibia 3D model by means of “Autodesk Revit-2016” PC based on tomogram data. The model was imported into “Lira- SAPR2013 R4” software system. To assess the possibility of education and the nature of bone fracture (and their visualization), the Finite Element Analysis (FEA) method was used. The geometric parameters of the BBK model corresponded to the physical parameters of the individual. The compact plate different thickness is modeled by rigidity properties of the finite elements in accordance with the parameters on the roentgenogram. The BBK model included parameters of the outer compact plate and the spongy substance having a more developed structure of the epiphysic region. In the “Lira-SAPR2013 R4” software system, mathematical modeling of the traumatic effect was carried out and the analysis of the stress-strain state of the finite element model of the tibia was made to assess fracture conditions.

Structure of a bacterial type III secretion system in contact with a host membrane in situ

NASA Astrophysics Data System (ADS)

Nans, Andrea; Kudryashev, Mikhail; Saibil, Helen R.; Hayward, Richard D.

2015-12-01

Many bacterial pathogens of animals and plants use a conserved type III secretion system (T3SS) to inject virulence effector proteins directly into eukaryotic cells to subvert host functions. Contact with host membranes is critical for T3SS activation, yet little is known about T3SS architecture in this state or the conformational changes that drive effector translocation. Here we use cryo-electron tomography and sub-tomogram averaging to derive the intact structure of the primordial Chlamydia trachomatis T3SS in the presence and absence of host membrane contact. Comparison of the averaged structures demonstrates a marked compaction of the basal body (4 nm) occurs when the needle tip contacts the host cell membrane. This compaction is coupled to a stabilization of the cytosolic sorting platform-ATPase. Our findings reveal the first structure of a bacterial T3SS from a major human pathogen engaged with a eukaryotic host, and reveal striking `pump-action' conformational changes that underpin effector injection.

Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography

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

Yu, Young-Sang; Farmand, Maryam; Kim, Chunjoong

Battery function is determined by the efficiency and reversibility of the electrochemical phase transformations at solid electrodes. The microscopic tools available to study the chemical states of matter with the required spatial resolution and chemical specificity are intrinsically limited when studying complex architectures by their reliance on two-dimensional projections of thick material. Here in this paper, we report the development of soft X-ray ptychographic tomography, which resolves chemical states in three dimensions at 11 nm spatial resolution. We study an ensemble of nano-plates of lithium iron phosphate extracted from a battery electrode at 50% state of charge. Using a setmore » of nanoscale tomograms, we quantify the electrochemical state and resolve phase boundaries throughout the volume of individual nanoparticles. These observations reveal multiple reaction points, intra-particle heterogeneity, and size effects that highlight the importance of multi-dimensional analytical tools in providing novel insight to the design of the next generation of high-performance devices.« less

Structure of a bacterial type III secretion system in contact with a host membrane in situ.

PubMed

Nans, Andrea; Kudryashev, Mikhail; Saibil, Helen R; Hayward, Richard D

2015-12-11

Many bacterial pathogens of animals and plants use a conserved type III secretion system (T3SS) to inject virulence effector proteins directly into eukaryotic cells to subvert host functions. Contact with host membranes is critical for T3SS activation, yet little is known about T3SS architecture in this state or the conformational changes that drive effector translocation. Here we use cryo-electron tomography and sub-tomogram averaging to derive the intact structure of the primordial Chlamydia trachomatis T3SS in the presence and absence of host membrane contact. Comparison of the averaged structures demonstrates a marked compaction of the basal body (4 nm) occurs when the needle tip contacts the host cell membrane. This compaction is coupled to a stabilization of the cytosolic sorting platform-ATPase. Our findings reveal the first structure of a bacterial T3SS from a major human pathogen engaged with a eukaryotic host, and reveal striking 'pump-action' conformational changes that underpin effector injection.

The Effects of Ethanol on the Morphological and Biochemical Properties of Individual Human Red Blood Cells.

PubMed

Lee, Sang Yun; Park, Hyun Joo; Best-Popescu, Catherine; Jang, Seongsoo; Park, Yong Keun

2015-01-01

Here, we report the results of a study on the effects of ethanol exposure on human red blood cells (RBCs) using quantitative phase imaging techniques at the level of individual cells. Three-dimensional refractive index tomograms and dynamic membrane fluctuations of RBCs were measured using common-path diffraction optical tomography, from which morphological (volume, surface area, and sphericity); biochemical (hemoglobin (Hb) concentration and Hb content); and biomechanical (membrane fluctuation) parameters were retrieved at various concentrations of ethanol. RBCs exposed to the ethanol concentration of 0.1 and 0.3% v/v exhibited cell sphericities higher than those of normal cells. However, mean surface area and sphericity of RBCs in a lethal alcoholic condition (0.5% v/v) are not statistically different with those of healthy RBCs. Meanwhile, significant decreases of Hb content and concentration in RBC cytoplasm at the lethal condition were observed. Furthermore, dynamic fluctuation of RBC membranes increased significantly upon ethanol treatments, indicating ethanol-induced membrane fluidization.

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

PubMed

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

2015-11-01

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

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

PubMed Central

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

2015-01-01

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

Association between an Alzheimer's Disease-Related Index and APOE ε4 Gene Dose.

PubMed

Schraml, Frank; Chen, Kewei; Ayutyanont, Napatkamon; Auttawut, Roontiva; Langbaum, Jessica B S; Lee, Wendy; Liu, Xiaofen; Bandy, Dan; Reeder, Stephanie Q; Alexander, Gene E; Caselli, Richard J; Fleisher, Adam S; Reiman, Eric M

2013-01-01

We introduced a hypometabolic convergence index (HCI) to characterize in a single measurement the extent to which a person's fluorodeoxyglucose positron emission tomogram (FDG PET) corresponds to that in Alzheimer's disease (AD). Apolipoprotein E ε4 (APOE ε4) gene dose is associated with three levels of risk for late-onset AD. We explored the association between gene dose and HCI in cognitively normal ε4 homozygotes, heterozygotes, and non-carriers. An algorithm was used to characterize and compare AD-related HCIs in cognitively normal individuals, including 36 ε4 homozygotes, 46 heterozygotes, and 78 non-carriers. These three groups differed significantly in their HCIs (ANOVA, p = 0.004), and there was a significant association between HCIs and gene dose (linear trend, p = 0.001). The HCI is associated with three levels of genetic risk for late-onset AD. This supports the possibility of using a single FDG PET measurement to help in the preclinical detection and tracking of AD.

Evaluation of the BreastSimulator software platform for breast tomography

NASA Astrophysics Data System (ADS)

Mettivier, G.; Bliznakova, K.; Sechopoulos, I.; Boone, J. M.; Di Lillo, F.; Sarno, A.; Castriconi, R.; Russo, P.

2017-08-01

The aim of this work was the evaluation of the software BreastSimulator, a breast x-ray imaging simulation software, as a tool for the creation of 3D uncompressed breast digital models and for the simulation and the optimization of computed tomography (CT) scanners dedicated to the breast. Eight 3D digital breast phantoms were created with glandular fractions in the range 10%-35%. The models are characterised by different sizes and modelled realistic anatomical features. X-ray CT projections were simulated for a dedicated cone-beam CT scanner and reconstructed with the FDK algorithm. X-ray projection images were simulated for 5 mono-energetic (27, 32, 35, 43 and 51 keV) and 3 poly-energetic x-ray spectra typically employed in current CT scanners dedicated to the breast (49, 60, or 80 kVp). Clinical CT images acquired from two different clinical breast CT scanners were used for comparison purposes. The quantitative evaluation included calculation of the power-law exponent, β, from simulated and real breast tomograms, based on the power spectrum fitted with a function of the spatial frequency, f, of the form S(f)  =  α/f   β . The breast models were validated by comparison against clinical breast CT and published data. We found that the calculated β coefficients were close to that of clinical CT data from a dedicated breast CT scanner and reported data in the literature. In evaluating the software package BreastSimulator to generate breast models suitable for use with breast CT imaging, we found that the breast phantoms produced with the software tool can reproduce the anatomical structure of real breasts, as evaluated by calculating the β exponent from the power spectral analysis of simulated images. As such, this research tool might contribute considerably to the further development, testing and optimisation of breast CT imaging techniques.

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

PubMed

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

2016-06-01

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

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

PubMed Central

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

2016-01-01

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

Changes in the edentulous maxilla with ball and telescopic attachments of implant-retained mandibular overdentures: a 4-year retrospective study.

PubMed

Elsyad, Moustafa Abdou; Khairallah, Ahmed Samir; Shawky, Ahmad Fathalla

2013-07-01

This retrospective study investigated the clinical and radiographic changes in the edentulous maxilla in patients with either ball or telescopic attachments of implantretained mandibular overdentures. Thirty-two completely edentulous patients (21 males and 11 females) received two implants in the canine region of the mandible. New maxillary complete dentures and mandibular overdentures were fabricated. Overdentures were connected to the implants either with ball (group 1, n = 16) or telescopic (group 2, n = 16) attachments. Retention and stability of the maxillary denture as well as mucosal changes of the maxillary ridge were recorded after 4 years of denturewearing. Traced rotational tomograms were used for measurements of maxillary alveolar bone loss. The proportional value between bone areas and areas of reference not subject to resorption was expressed as a ratio (R). Change in R immediately before (T0) and after 4 years (T4) of overdenture insertion was calculated for the anterior and posterior regions of the maxilla. After 4 years of denture-wearing, maxillary denture retention was significantly higher in group 1 than in group 2, while occurrence of flabby ridges was significantly higher in group 2 than in group 1. The change in R of the anterior region of the maxilla was significantly higher than the change in the posterior region in both groups. Group 2 showed significant anterior residual ridge resorption compared to group 1. Telescopic attachments for implant-retained mandibular overdentures are associated with increased maxillary ridge resorption and flabbiness, and decreased maxillary denture retention when compared to ball attachments.

High resolution aquifer characterization using crosshole GPR full-waveform tomography: Comparison with direct-push and tracer test data

NASA Astrophysics Data System (ADS)

Gueting, Nils; Vienken, Thomas; Klotzsche, Anja; van der Kruk, Jan; Vanderborght, Jan; Caers, Jef; Vereecken, Harry; Englert, Andreas

2017-01-01

Limited knowledge about the spatial distribution of aquifer properties typically constrains our ability to predict subsurface flow and transport. Here we investigate the value of using high resolution full-waveform inversion of cross-borehole ground penetrating radar (GPR) data for aquifer characterization. By stitching together GPR tomograms from multiple adjacent crosshole planes, we are able to image, with a decimeter scale resolution, the dielectric permittivity and electrical conductivity of an alluvial aquifer along cross sections of 50 m length and 10 m depth. A logistic regression model is employed to predict the spatial distribution of lithological facies on the basis of the GPR results. Vertical profiles of porosity and hydraulic conductivity from direct-push, flowmeter and grain size data suggest that the GPR predicted facies classification is meaningful with regard to porosity and hydraulic conductivity, even though the distributions of individual facies show some overlap and the absolute hydraulic conductivities from the different methods (direct-push, flowmeter, grain size) differ up to approximately one order of magnitude. Comparison of the GPR predicted facies architecture with tracer test data suggests that the plume splitting observed in a tracer experiment was caused by a hydraulically low-conductive sand layer with a thickness of only a few decimeters. Because this sand layer is identified by GPR full-waveform inversion but not by conventional GPR ray-based inversion we conclude that the improvement in spatial resolution due to full-waveform inversion is crucial to detect small-scale aquifer structures that are highly relevant for solute transport.

Coexistence of both gyroid chiralities in individual butterfly wing scales of Callophrys rubi

PubMed Central

Winter, Benjamin; Butz, Benjamin; Dieker, Christel; Schröder-Turk, Gerd E.; Mecke, Klaus; Spiecker, Erdmann

2015-01-01

The wing scales of the Green Hairstreak butterfly Callophrys rubi consist of crystalline domains with sizes of a few micrometers, which exhibit a congenitally handed porous chitin microstructure identified as the chiral triply periodic single-gyroid structure. Here, the chirality and crystallographic texture of these domains are investigated by means of electron tomography. The tomograms unambiguously reveal the coexistence of the two enantiomeric forms of opposite handedness: the left- and right-handed gyroids. These two enantiomers appear with nonequal probabilities, implying that molecularly chiral constituents of the biological formation process presumably invoke a chiral symmetry break, resulting in a preferred enantiomeric form of the gyroid structure. Assuming validity of the formation model proposed by Ghiradella H (1989) J Morphol 202(1):69–88 and Saranathan V, et al. (2010) Proc Natl Acad Sci USA 107(26):11676–11681, where the two enantiomeric labyrinthine domains of the gyroid are connected to the extracellular and intra-SER spaces, our findings imply that the structural chirality of the single gyroid is, however, not caused by the molecular chirality of chitin. Furthermore, the wing scales are found to be highly textured, with a substantial fraction of domains exhibiting the <001> directions of the gyroid crystal aligned parallel to the scale surface normal. Both findings are needed to completely understand the photonic purpose of the single gyroid in gyroid-forming butterflies. More importantly, they show the level of control that morphogenesis exerts over secondary features of biological nanostructures, such as chirality or crystallographic texture, providing inspiration for biomimetic replication strategies for synthetic self-assembly mechanisms. PMID:26438839

Coexistence of both gyroid chiralities in individual butterfly wing scales of Callophrys rubi.

PubMed

Winter, Benjamin; Butz, Benjamin; Dieker, Christel; Schröder-Turk, Gerd E; Mecke, Klaus; Spiecker, Erdmann

2015-10-20

The wing scales of the Green Hairstreak butterfly Callophrys rubi consist of crystalline domains with sizes of a few micrometers, which exhibit a congenitally handed porous chitin microstructure identified as the chiral triply periodic single-gyroid structure. Here, the chirality and crystallographic texture of these domains are investigated by means of electron tomography. The tomograms unambiguously reveal the coexistence of the two enantiomeric forms of opposite handedness: the left- and right-handed gyroids. These two enantiomers appear with nonequal probabilities, implying that molecularly chiral constituents of the biological formation process presumably invoke a chiral symmetry break, resulting in a preferred enantiomeric form of the gyroid structure. Assuming validity of the formation model proposed by Ghiradella H (1989) J Morphol 202(1):69-88 and Saranathan V, et al. (2010) Proc Natl Acad Sci USA 107(26):11676-11681, where the two enantiomeric labyrinthine domains of the gyroid are connected to the extracellular and intra-SER spaces, our findings imply that the structural chirality of the single gyroid is, however, not caused by the molecular chirality of chitin. Furthermore, the wing scales are found to be highly textured, with a substantial fraction of domains exhibiting the <001> directions of the gyroid crystal aligned parallel to the scale surface normal. Both findings are needed to completely understand the photonic purpose of the single gyroid in gyroid-forming butterflies. More importantly, they show the level of control that morphogenesis exerts over secondary features of biological nanostructures, such as chirality or crystallographic texture, providing inspiration for biomimetic replication strategies for synthetic self-assembly mechanisms.

Radar attenuation tomography using the centroid frequency downshift method

USGS Publications Warehouse

Liu, L.; Lane, J.W.; Quan, Y.

1998-01-01

A method for tomographically estimating electromagnetic (EM) wave attenuation based on analysis of centroid frequency downshift (CFDS) of impulse radar signals is described and applied to cross-hole radar data. The method is based on a constant-Q model, which assumes a linear frequency dependence of attenuation for EM wave propagation above the transition frequency. The method uses the CFDS to construct the projection function. In comparison with other methods for estimating attenuation, the CFDS method is relatively insensitive to the effects of geometric spreading, instrument response, and antenna coupling and radiation pattern, but requires the data to be broadband so that the frequency shift and variance can be easily measured. The method is well-suited for difference tomography experiments using electrically conductive tracers. The CFDS method was tested using cross-hole radar data collected at the U.S. Geological Survey Fractured Rock Research Site at Mirror Lake, New Hampshire (NH) during a saline-tracer injection experiment. The attenuation-difference tomogram created with the CFDS method outlines the spatial distribution of saline tracer within the tomography plane. ?? 1998 Elsevier Science B.V. All rights reserved.

Automatic Segmentation and Quantification of Filamentous Structures in Electron Tomography

PubMed Central

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

2016-01-01

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

Automatic Segmentation and Quantification of Filamentous Structures in Electron Tomography.

PubMed

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

2012-10-01

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

Correlative Microscopy of Vitreous Sections Provides Insights into BAR-Domain Organization In Situ.

PubMed

Bharat, Tanmay A M; Hoffmann, Patrick C; Kukulski, Wanda

2018-04-10

Electron microscopy imaging of macromolecular complexes in their native cellular context is limited by the inherent difficulty to acquire high-resolution tomographic data from thick cells and to specifically identify elusive structures within crowded cellular environments. Here, we combined cryo-fluorescence microscopy with electron cryo-tomography of vitreous sections into a coherent correlative microscopy workflow, ideal for detection and structural analysis of elusive protein assemblies in situ. We used this workflow to address an open question on BAR-domain coating of yeast plasma membrane compartments known as eisosomes. BAR domains can sense or induce membrane curvature, and form scaffold-like membrane coats in vitro. Our results demonstrate that in cells, the BAR protein Pil1 localizes to eisosomes of varying membrane curvature. Sub-tomogram analysis revealed a dense protein coat on curved eisosomes, which was not present on shallow eisosomes, indicating that while BAR domains can assemble at shallow membranes in vivo, scaffold formation is tightly coupled to curvature generation. Copyright © 2018 MRC Laboratory of Molecular Biology. Published by Elsevier Ltd.. All rights reserved.

Comparison of dental maturity in children of different ethnic origins: international maturity curves for clinicians.

PubMed

Chaillet, Nils; Nyström, Marjatta; Demirjian, Arto

2005-09-01

Dental maturity was studied with 9577 dental panoramic tomograms of healthy subjects from 8 countries, aged between 2 and 25 years of age. Demirjian's method based on 7 teeth was used for determining dental maturity scores, establishing gender-specific tables of maturity scores and development graphs. The aim of this study was to give dental maturity standards when the ethnic origin is unknown and to compare the efficiency and applicability of this method to forensic sciences and dental clinicians. The second aim was to compare the dental maturity of these different populations. We noted an high efficiency for International Demirjian's method at 99% CI (0.85% of misclassified and a mean accuracy between 2 to 18 years +/- 2.15 years), which makes it useful for forensic purposes. Nevertheless, this international method is less accurate than Demirjian's method developed for a specific country, because of the inter-ethnic variability obtained by the addition of 8 countries in the dental database. There are inter-ethnic differences classified in three major groups. Australians have the fastest dental maturation and Koreans have the slowest.

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

PubMed

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

2011-01-01

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

Macromolecular organization of ATP synthase and complex I in whole mitochondria

PubMed Central

Davies, Karen M.; Strauss, Mike; Daum, Bertram; Kief, Jan H.; Osiewacz, Heinz D.; Rycovska, Adriana; Zickermann, Volker; Kühlbrandt, Werner

2011-01-01

We used electron cryotomography to study the molecular arrangement of large respiratory chain complexes in mitochondria from bovine heart, potato, and three types of fungi. Long rows of ATP synthase dimers were observed in intact mitochondria and cristae membrane fragments of all species that were examined. The dimer rows were found exclusively on tightly curved cristae edges. The distance between dimers along the rows varied, but within the dimer the distance between F1 heads was constant. The angle between monomers in the dimer was 70° or above. Complex I appeared as L-shaped densities in tomograms of reconstituted proteoliposomes. Similar densities were observed in flat membrane regions of mitochondrial membranes from all species except Saccharomyces cerevisiae and identified as complex I by quantum-dot labeling. The arrangement of respiratory chain proton pumps on flat cristae membranes and ATP synthase dimer rows along cristae edges was conserved in all species investigated. We propose that the supramolecular organization of respiratory chain complexes as proton sources and ATP synthase rows as proton sinks in the mitochondrial cristae ensures optimal conditions for efficient ATP synthesis. PMID:21836051

Model for the architecture of caveolae based on a flexible, net-like assembly of Cavin1 and Caveolin discs

PubMed Central

Stoeber, Miriam; Schellenberger, Pascale; Siebert, C. Alistair; Leyrat, Cedric; Helenius, Ari

2016-01-01

Caveolae are invaginated plasma membrane domains involved in mechanosensing, signaling, endocytosis, and membrane homeostasis. Oligomers of membrane-embedded caveolins and peripherally attached cavins form the caveolar coat whose structure has remained elusive. Here, purified Cavin1 60S complexes were analyzed structurally in solution and after liposome reconstitution by electron cryotomography. Cavin1 adopted a flexible, net-like protein mesh able to form polyhedral lattices on phosphatidylserine-containing vesicles. Mutating the two coiled-coil domains in Cavin1 revealed that they mediate distinct assembly steps during 60S complex formation. The organization of the cavin coat corresponded to a polyhedral nano-net held together by coiled-coil segments. Positive residues around the C-terminal coiled-coil domain were required for membrane binding. Purified caveolin 8S oligomers assumed disc-shaped arrangements of sizes that are consistent with the discs occupying the faces in the caveolar polyhedra. Polygonal caveolar membrane profiles were revealed in tomograms of native caveolae inside cells. We propose a model with a regular dodecahedron as structural basis for the caveolae architecture. PMID:27834731

A Toolbox for Ab Initio 3-D Reconstructions in Single-particle Electron Microscopy

PubMed Central

Voss, Neil R; Lyumkis, Dmitry; Cheng, Anchi; Lau, Pick-Wei; Mulder, Anke; Lander, Gabriel C; Brignole, Edward J; Fellmann, Denis; Irving, Christopher; Jacovetty, Erica L; Leung, Albert; Pulokas, James; Quispe, Joel D; Winkler, Hanspeter; Yoshioka, Craig; Carragher, Bridget; Potter, Clinton S

2010-01-01

Structure determination of a novel macromolecular complex via single-particle electron microscopy depends upon overcoming the challenge of establishing a reliable 3-D reconstruction using only 2-D images. There are a variety of strategies that deal with this issue, but not all of them are readily accessible and straightforward to use. We have developed a “toolbox” of ab initio reconstruction techniques that provide several options for calculating 3-D volumes in an easily managed and tightly controlled work-flow that adheres to standard conventions and formats. This toolbox is designed to streamline the reconstruction process by removing the necessity for bookkeeping, while facilitating transparent data transfer between different software packages. It currently includes procedures for calculating ab initio reconstructions via random or orthogonal tilt geometry, tomograms, and common lines, all of which have been tested using the 50S ribosomal subunit. Our goal is that the accessibility of multiple independent reconstruction algorithms via this toolbox will improve the ease with which models can be generated, and provide a means of evaluating the confidence and reliability of the final reconstructed map. PMID:20018246

Analogous on-axis interference topographic phase microscopy (AOITPM).

PubMed

Xiu, P; Liu, Q; Zhou, X; Xu, Y; Kuang, C; Liu, X

2018-05-01

The refractive index (RI) of a sample as an endogenous contrast agent plays an important role in transparent live cell imaging. In tomographic phase microscopy (TPM), 3D quantitative RI maps can be reconstructed based on the measured projections of the RI in multiple directions. The resolution of the RI maps not only depends on the numerical aperture of the employed objective lens, but also is determined by the accuracy of the quantitative phase of the sample measured at multiple scanning illumination angles. This paper reports an analogous on-axis interference TPM, where the interference angle between the sample and reference beams is kept constant for projections in multiple directions to improve the accuracy of the phase maps and the resolution of RI tomograms. The system has been validated with both silica beads and red blood cells. Compared with conventional TPM, the proposed system acquires quantitative RI maps with higher resolution (420 nm @λ = 633 nm) and signal-to-noise ratio that can be beneficial for live cell imaging in biomedical applications. © 2018 The Authors Journal of Microscopy © 2018 Royal Microscopical Society.

Optical diffraction tomography using a digital micromirror device for stable measurements of 4D refractive index tomography of cells

NASA Astrophysics Data System (ADS)

Shin, Seungwoo; Kim, Kyoohyun; Kim, Taeho; Yoon, Jonghee; Hong, Kihyun; Park, Jinah; Park, YongKeun

2016-03-01

Optical diffraction tomography (ODT) is an interferometric microscopy technique capable of measuring 3-D refractive index (RI) distribution of transparent samples. Multiple 2-D holograms of a sample illuminated with various angles are measured, from which 3-D RI map of the sample is reconstructed via the diffraction theory. ODT has been proved as a powerful tool for the study of biological cells, due to its non-invasiveness, label-free and quantitative imaging capability. Recently, our group has demonstrated that a digital micromirror device (DMD) can be exploited for fast and precise control of illumination beams for ODT. In this work, we systematically study the precision and stability of the ODT system equipped with a DMD and present measurements of 3-D and 4-D RI maps of various types of live cells including human red blood cells, white blood cells, hepatocytes, and HeLa cells. Furthermore, we also demonstrate the effective visualization of 3-D RI maps of live cells utilizing the measured information about the values and gradient of RI tomograms.

Three-dimensional imaging of hold baggage for airport security

NASA Astrophysics Data System (ADS)

Kolokytha, S.; Speller, R.; Robson, S.

2014-06-01

This study describes a cost-effective check-in baggage screening system, based on "on-belt tomosynthesis" (ObT) and close-range photogrammetry, that is designed to address the limitations of the most common system used, conventional projection radiography. The latter's limitations can lead to loss of information and an increase in baggage handling time, as baggage is manually searched or screened with more advanced systems. This project proposes a system that overcomes such limitations creating a cost-effective automated pseudo-3D imaging system, by combining x-ray and optical imaging to form digital tomograms. Tomographic reconstruction requires a knowledge of the change in geometry between multiple x-ray views of a common object. This is uniquely achieved using a close range photogrammetric system based on a small network of web-cameras. This paper presents the recent developments of the ObT system and describes recent findings of the photogrammetric system implementation. Based on these positive results, future work on the advancement of the ObT system as a cost-effective pseudo-3D imaging of hold baggage for airport security is proposed.

Preoperative Planning of Orthopedic Procedures using Digitalized Software Systems.

PubMed

Steinberg, Ely L; Segev, Eitan; Drexler, Michael; Ben-Tov, Tomer; Nimrod, Snir

2016-06-01

The progression from standard celluloid films to digitalized technology led to the development of new software programs to fulfill the needs of preoperative planning. We describe here preoperative digitalized programs and the variety of conditions for which those programs can be used to facilitate preparation for surgery. A PubMed search using the keywords "digitalized software programs," "preoperative planning" and "total joint arthroplasty" was performed for all studies regarding preoperative planning of orthopedic procedures that were published from 1989 to 2014 in English. Digitalized software programs are enabled to import and export all picture archiving communication system (PACS) files (i.e., X-rays, computerized tomograms, magnetic resonance images) from either the local working station or from any remote PACS. Two-dimension (2D) and 3D CT scans were found to be reliable tools with a high preoperative predicting accuracy for implants. The short learning curve, user-friendly features, accurate prediction of implant size, decreased implant stocks and low-cost maintenance makes digitalized software programs an attractive tool in preoperative planning of total joint replacement, fracture fixation, limb deformity repair and pediatric skeletal disorders.

Geophysical Investigation of Buried Slag at the Parrot Tailings Site, Butte, Montana

NASA Astrophysics Data System (ADS)

Ha, C. D. M.; Shepherd, K.; Mack, A.; Rutherford, B. S.; Speece, M. A.

2016-12-01

Butte, Montana, has served as an important mining district for more than 120 years. This area contains historic mine waste from decades of unregulated mining practices. In July 1881, the Parrot smelter in Butte started operations and was soon processing ore and producing copper. The Parrot smelter also had a concentrating plant that treated the ore prior to smelting. The Parrot smelter wastes (slag and tailings) were later covered with Berkeley Pit crushed quartz monzonite overburden. The slag is bricked because it was deposited hot and, as a consequence forms a laterally extensive, cohesive, hard body that is difficult to remove without blasting. With the mine waste being covered by unknown quantities of overburden and soil throughout the area, and core data being limited and expensive to retrieve, the only economical method of discovery is geophysics. Several geophysical techniques were used to determine the lateral boundaries and depth of the buried slag body. The geophysical methods used were seismic, gravity, electromagnetic induction, and magnetics. Not all of these geophysical surveys produced useful results due to the nature of the slag. For instance, electromagnetic induction could not distinguish between the slag and adjacent tailings; and, the microgravity profiles showed only a small gravitational field variation caused by the density contrast between slag and the surrounding tailings, sediment and granitic cover. On the other hand, the seismic surveys resulted in unexpected first arrival times that distinctly showed velocity variations due to the slag. In addition, the slag body produced a large magnetic response. Unpublished, proprietary well data allowed us to model the slag body from our magnetic data. This model was confirmed by projecting velocity tomograms, that we created using seismic diving waves, onto our magnetic models. Model results were combined to form a three-dimensional image of the slag body. These results will be used to help construct a remediation plan to remove the slag along with the associated tailings.

Full-waveform inversion of Crosshole GPR data: Implications for porosity estimation in chalk

NASA Astrophysics Data System (ADS)

Keskinen, Johanna; Klotzsche, Anja; Looms, Majken C.; Moreau, Julien; van der Kruk, Jan; Holliger, Klaus; Stemmerik, Lars; Nielsen, Lars

2017-05-01

The Maastrichtian-Danian chalk is a widely distributed hydrocarbon and groundwater reservoir rock in north-western Europe. Knowledge of lateral and vertical heterogeneity and porosity variation in this type of rock is essential, since they critically determine the reservoir properties. We have collected a densely sampled crosshole ground-penetrating radar (GPR) dataset from a highly heterogeneous section of the chalk and inverted it with a full-waveform inversion (FWI) approach. To date, successful crosshole FWI has only been reported for a handful of GPR field data, none of which include strongly heterogeneous environments like the one considered in this study. Testing different starting models shows that all FWI results converge to very similar subsurface structures indicating that the results are robust with regard to local variations in the permittivity starting models and are not very sensitive to the conductivity starting models. Compared to their ray-based counterparts, the obtained FWI models show significantly higher resolution and improved localization of fine-scale heterogeneity. The final FWI permittivity tomogram was converted to a bulk porosity model using the Complex Refractive Index Model (CRIM) and comparisons with plug sample porosities and televiewer image logs verify that variations in the obtained permittivity are related to facies and lithology changes. The inferred porosity varies from 30 to 54%, which is consistent with values in the chalk cores from the investigated boreholes and in agreement with other studies conducted in similar rocks onshore. Moreover, porosities vary significantly over scales of less than a meter both laterally and vertically. The FWI constrains porosity variation with decimeter scale resolution in our 5 m (horizontally) by 10 m (vertically) model section bridging the gap between what is measured on the core sample scale and the scale typical of hydrogeophysical field experiments conducted to characterize fluid flow in the subsurface. The results provide complementary knowledge to traditional chalk reservoir characterization.

Optical coherence tomography of the eye

NASA Astrophysics Data System (ADS)

Hee, Michael Richard

1997-10-01

Optical Coherence Tomography (OCT) is a new technique for high-resolution, cross-sectional imaging of tissue in which the time-of-flight delay of light reflected from internal tissue structures is resolved with high precision using interferometry. Tomographic images are obtained which are analogous to those provided by ultrasound except that image contrast relies on differences in optical rather than acoustic properties of tissue. The use of light rather than sound enables higher resolution (10 μm) and non-contact imaging. A clinically viable high-sensitivity, fiber-optic based OCT instrument has been constructed based on engineering principles derived from optical communication theory. Computer algorithms have also been developed for quantitative image analysis and restoration. OCT has been used to image patients with a variety of ocular diseases. In patients with macular pathology, OCT images have been correlated with conventional clinical examination and fluorescein angiography. Optical coherence tomograms are effective in staging macular holes, evaluating the vitreoretinal interface in eyes at risk for a macular hole, and providing a structural assessment of macular hole surgery. In eyes with central serous chorioretinopathy, OCT can evaluate sensory retinal separations undetected at the slit-lamp. Serial OCT images of macular edema are able to track both the progression of macular thickening and the resolution of macular edema following laser photocoagulation. In patients with diabetic retinopathy, measurements of macular thickness correlate with visual acuity and OCT is more sensitive to small changes in retinal thickness than slit-lamp biomicroscopy. OCT may provide a novel method of defining occult choroidal neovascular membranes in patients with age-related macular degeneration. OCT can also profile the thickness of the retinal nerve fiber layer with high resolution which is potentially important for the objective assessment of early glaucoma progression. OCT images have been correlated with visual field performance and optic nerve appearance in a cross- section of patients with various stages of glaucoma. These studies suggest that OCT has the potential to become an important diagnostic tool for the practicing ophthalmologist. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)

Impact of small-scale saline tracer heterogeneity on electrical resistivity monitoring in fully and partially saturated porous media: Insights from geoelectrical milli-fluidic experiments

NASA Astrophysics Data System (ADS)

Jougnot, Damien; Jiménez-Martínez, Joaquín; Legendre, Raphaël; Le Borgne, Tanguy; Méheust, Yves; Linde, Niklas

2018-03-01

Time-lapse electrical resistivity tomography (ERT) is a geophysical method widely used to remotely monitor the migration of electrically-conductive tracers and contaminant plumes in the subsurface. Interpretations of time-lapse ERT inversion results are generally based on the assumption of a homogeneous solute concentration below the resolution limits of the tomogram depicting inferred electrical conductivity variations. We suggest that ignoring small-scale solute concentration variability (i.e., at the sub-resolution scale) is a major reason for the often-observed apparent loss of solute mass in ERT tracer studies. To demonstrate this, we developed a geoelectrical milli-fluidic setup where the bulk electric conductivity of a 2D analogous porous medium, consisting of cylindrical grains positioned randomly inside a Hele-Shaw cell, is monitored continuously in time while saline tracer tests are performed through the medium under fully and partially saturated conditions. High resolution images of the porous medium are recorded with a camera at regular time intervals, and provide both the spatial distribution of the fluid phases (aqueous solution and air), and the saline solute concentration field (where the solute consists of a mixture of salt and fluorescein, the latter being used as a proxy for the salt concentration). Effective bulk electrical conductivities computed numerically from the measured solute concentration field and the spatial distributions of fluid phases agree well with the measured bulk conductivities. We find that the effective bulk electrical conductivity is highly influenced by the connectivity of high electrical conductivity regions. The spatial distribution of air, saline tracer fingering, and mixing phenomena drive temporal changes in the effective bulk electrical conductivity by creating preferential paths or barriers for electrical current at the pore-scale. The resulting heterogeneities in the solute concentrations lead to strong anisotropy of the effective bulk electrical conductivity, especially for partially saturated conditions. We highlight how these phenomena contribute to the typically large apparent mass loss observed when conducting field-scale time-lapse ERT.

Three-dimensional imaging of aquifer and aquitard heterogeneity via transient hydraulic tomography at a highly heterogeneous field site

NASA Astrophysics Data System (ADS)

Zhao, Zhanfeng; Illman, Walter A.

2018-04-01

Previous studies have shown that geostatistics-based transient hydraulic tomography (THT) is robust for subsurface heterogeneity characterization through the joint inverse modeling of multiple pumping tests. However, the hydraulic conductivity (K) and specific storage (Ss) estimates can be smooth or even erroneous for areas where pumping/observation densities are low. This renders the imaging of interlayer and intralayer heterogeneity of highly contrasting materials including their unit boundaries difficult. In this study, we further test the performance of THT by utilizing existing and newly collected pumping test data of longer durations that showed drawdown responses in both aquifer and aquitard units at a field site underlain by a highly heterogeneous glaciofluvial deposit. The robust performance of the THT is highlighted through the comparison of different degrees of model parameterization including: (1) the effective parameter approach; (2) the geological zonation approach relying on borehole logs; and (3) the geostatistical inversion approach considering different prior information (with/without geological data). Results reveal that the simultaneous analysis of eight pumping tests with the geostatistical inverse model yields the best results in terms of model calibration and validation. We also find that the joint interpretation of long-term drawdown data from aquifer and aquitard units is necessary in mapping their full heterogeneous patterns including intralayer variabilities. Moreover, as geological data are included as prior information in the geostatistics-based THT analysis, the estimated K values increasingly reflect the vertical distribution patterns of permeameter-estimated K in both aquifer and aquitard units. Finally, the comparison of various THT approaches reveals that differences in the estimated K and Ss tomograms result in significantly different transient drawdown predictions at observation ports.

Three-Dimensional Electrical Resistivity Tomography of the Solfatara Crater (Italy): Implication for the Multiphase Flow Structure of the Shallow Hydrothermal System

NASA Astrophysics Data System (ADS)

Gresse, Marceau; Vandemeulebrouck, Jean; Byrdina, Svetlana; Chiodini, Giovanni; Revil, André; Johnson, Timothy C.; Ricci, Tullio; Vilardo, Giuseppe; Mangiacapra, Annarita; Lebourg, Thomas; Grangeon, Jacques; Bascou, Pascale; Metral, Laurent

2017-11-01

The Solfatara volcano is the main degassing area of the Campi Flegrei caldera, characterized by 60 years of unrest. Assessing such renewal activity is a challenging task because hydrothermal interactions with magmatic gases remain poorly understood. In this study, we decipher the complex structure of the shallow Solfatara hydrothermal system by performing the first 3-D, high-resolution, electrical resistivity tomography of the volcano. The 3-D resistivity model was obtained from the inversion of 43,432 resistance measurements performed on an area of 0.68 km2. The proposed interpretation of the multiphase hydrothermal structures is based on the resistivity model, a high-resolution infrared surface temperature image, and 1,136 soil CO2 flux measurements. In addition, we realized 27 soil cation exchange capacity and pH measurements demonstrating a negligible contribution of surface conductivity to the shallow bulk electrical conductivity. Hence, we show that the resistivity changes are mainly controlled by fluid content and temperature. The high-resolution tomograms identify for the first time the structure of the gas-dominated reservoir at 60 m depth that feeds the Bocca Grande fumarole through a 10 m thick channel. In addition, the resistivity model reveals a channel-like conductive structure where the liquid produced by steam condensation around the main fumaroles flows down to the Fangaia area within a buried fault. The model delineates the emplacement of the main geological structures: Mount Olibano, Solfatara cryptodome, and tephra deposits. It also reveals the anatomy of the hydrothermal system, especially two liquid-dominated plumes, the Fangaia mud pool and the Pisciarelli fumarole, respectively.

The Transformation of Enterovirus Replication Structures: a Three-Dimensional Study of Single- and Double-Membrane Compartments

PubMed Central

Limpens, Ronald W. A. L.; van der Schaar, Hilde M.; Kumar, Darshan; Koster, Abraham J.; Snijder, Eric J.; van Kuppeveld, Frank J. M.; Bárcena, Montserrat

2011-01-01

ABSTRACT All positive-strand RNA viruses induce membrane structures in their host cells which are thought to serve as suitable microenvironments for viral RNA synthesis. The structures induced by enteroviruses, which are members of the family Picornaviridae, have so far been described as either single- or double-membrane vesicles (DMVs). Aside from the number of delimiting membranes, their exact architecture has also remained elusive due to the limitations of conventional electron microscopy. In this study, we used electron tomography (ET) to solve the three-dimensional (3-D) ultrastructure of these compartments. At different time points postinfection, coxsackievirus B3-infected cells were high-pressure frozen and freeze-substituted for ET analysis. The tomograms showed that during the exponential phase of viral RNA synthesis, closed smooth single-membrane tubules constituted the predominant virus-induced membrane structure, with a minor proportion of DMVs that were either closed or connected to the cytosol in a vase-like configuration. As infection progressed, the DMV number steadily increased, while the tubular single-membrane structures gradually disappeared. Late in infection, complex multilamellar structures, previously unreported, became apparent in the cytoplasm. Serial tomography disclosed that their basic unit is a DMV, which is enwrapped by one or multiple cisternae. ET also revealed striking intermediate structures that strongly support the conversion of single-membrane tubules into double-membrane and multilamellar structures by a process of membrane apposition, enwrapping, and fusion. Collectively, our work unravels the sequential appearance of distinct enterovirus-induced replication structures, elucidates their detailed 3-D architecture, and provides the basis for a model for their transformation during the course of infection. PMID:21972238

The influence of resilient liner and clip attachments for bar-implant-retained mandibular overdentures on opposing maxillary ridge. A 5-year randomised clinical trial.

PubMed

Elsyad, M A; Ashmawy, T M; Faramawy, A G

2014-01-01

This study aimed to compare the influence of resilient liner and clip attachments for bar-implant-retained mandibular overdentures on opposing maxillary ridge after 5 years of denture wearing. Thirty edentulous male patients (mean age 62·5 years) received two implants in the anterior mandible after being allocated into two equal groups using balanced randomisation. After 3 months, implants were connected with resilient bars. New maxillary complete dentures were then constructed, and mandibular overdentures were retained to the bars with either clips (group I, GI) or silicone resilient liners (group II, GII). The prosthetic and soft tissue complications of the maxillary dentures were recorded 6 months (T6 m ), 1 year (T1), 3 years (T3) and 5 years (T5) after overdenture insertion. Traced rotational tomograms were used for measurements of maxillary alveolar bone loss. The proportional value between bone areas and areas of reference not subject to resorption was expressed as a ratio (R). Change in R immediately before (T0) and after 5 years (T5) of overdenture insertion was calculated. Maxillary denture relining times and frequency of flabby anterior maxillary ridge occurred significantly more often in GI compared with GII. The change of R in anterior part of maxilla was significantly higher than change of R in posterior part in both groups. GI showed significant resorption of anterior residual ridge compared with GII. Relining times and frequencies of flabby ridge were significantly correlated with change in R. Within the limitations of this study, resilient liner attachments for bar-implant-retained mandibular overdentures are associated with decreased resorption and flabbiness of maxillary anterior residual ridge and fewer maxillary denture relining times when compared with clip attachments. © 2013 John Wiley & Sons Ltd.

Label-free identification of white blood cell using optical diffraction tomography (Conference Presentation)

NASA Astrophysics Data System (ADS)

Yoon, Jonghee; Kim, Kyoohyun; Kim, Min-hyeok; Kang, Suk-Jo; Park, YongKeun

2016-03-01

White blood cells (WBC) have crucial roles in immune systems which defend the host against from disease conditions and harmful invaders. Various WBC subsets have been characterized and reported to be involved in many pathophysiologic conditions. It is crucial to isolate a specific WBC subset to study its pathophysiological roles in diseases. Identification methods for a specific WBC population are rely on invasive approaches, including Wright-Gimesa staining for observing cellular morphologies and fluorescence staining for specific protein markers. While these methods enable precise classification of WBC populations, they could disturb cellular viability or functions. In order to classify WBC populations in a non-invasive manner, we exploited optical diffraction tomography (ODT). ODT is a three-dimensional (3-D) quantitative phase imaging technique that measures 3-D refractive index (RI) distributions of individual WBCs. To test feasibility of label-free classification of WBC populations using ODT, we measured four subtypes of WBCs, including B cell, CD4 T cell, CD8 T cell, and natural killer (NK) cell. From measured 3-D RI tomograms of WBCs, we obtain quantitative structural and biochemical information and classify each WBC population using a machine learning algorithm.

Clinical trials of the prototype Rutherford Appleton Laboratory MWPC positron camera at the Royal Marsden Hospital

NASA Astrophysics Data System (ADS)

Flower, M. A.; Ott, R. J.; Webb, S.; Leach, M. O.; Marsden, P. K.; Clack, R.; Khan, O.; Batty, V.; McCready, V. R.; Bateman, J. E.

1988-06-01

Two clinical trials of the prototype RAL multiwire proportional chamber (MWPC) positron camera were carried out prior to the development of a clinical system with large-area detectors. During the first clinical trial, the patient studies included skeletal imaging using 18F, imaging of brain glucose metabolism using 18F FDG, bone marrow imaging using 52Fe citrate and thyroid imaging with Na 124I. Longitudinal tomograms were produced from the limited-angle data acquisition from the static detectors. During the second clinical trial, transaxial, coronal and sagittal images were produced from the multiview data acquisition. A more detailed thyroid study was performed in which the volume of the functioning thyroid tissue was obtained from the 3D PET image and this volume was used in estimating the radiation dose achieved during radioiodine therapy of patients with thyrotoxicosis. Despite the small field of view of the prototype camera, and the use of smaller than usual amounts of activity administered, the PET images were in most cases comparable with, and in a few cases visually better than, the equivalent planar view using a state-of-the-art gamma camera with a large field of view and routine radiopharmaceuticals.

Dark-field optical coherence microscopy

NASA Astrophysics Data System (ADS)

Pache, C.; Villiger, M. L.; Lasser, T.

2010-02-01

Many solutions have been proposed to produce phase quantitative images of biological cell samples. Among these, Spectral Domain Phase Microscopy combines the fast imaging speed and high sensitivity of Optical Coherence Microscopy (OCM) in the Fourier domain with the high phase stability of common-path interferometry. We report on a new illumination scheme for OCM that enhances the sensitivity for backscattered light and detects the weak sample signal, otherwise buried by the signal from specular reflection. With the use of a Bessel-like beam, a dark-field configuration was realized. Sensitivity measurements for three different illumination configurations were performed to compare our method to standard OCM and extended focus OCM. Using a well-defined scattering and reflecting object, we demonstrated an attenuation of -40 dB of the DC-component and a relative gain of 30 dB for scattered light, compared to standard OCM. In a second step, we applied this technique, referred to as dark-field Optical Coherence Microscopy (dfOCM), to living cells. Chinese hamster ovarian cells were applied in a drop of medium on a coverslide. The cells of ~15 μm in diameter and even internal cell structures were visualized in the acquired tomograms.

Three-Dimensional Microstructure of Biological Tissues during Freezing and Thawing

NASA Astrophysics Data System (ADS)

Ishiguro, Hiroshi; Horimizu, Takashi; Kataori, Akinobu; Kajigaya, Hiroshi

Three-dimensional behavior of ice crystals and cells during the freezing and thawing of biological tissues was investigated microscopically in real time by using a confocal laser scanning microscope(CLSM) and a fluorescent dye, acridine orange (AO). Fresh tender meat (2nd pectoral muscles) of chicken was stained with the AO in physiological saline to distinguish ice crystals and cells by their different colors, and then frozen and thawed under two different thermal protocols: a) slow-cooling and rapid-warming and b) rapid-cooling and rapid-warming. The CLSM noninvasively produced optical tomograms of the tissues to clarify the pattern of freezing, morphology of ice crystals in the tissues, and the interaction between ice crystals and cells. Also, the tissues were morphologically investigated by pathological means after the freezing and thawing. Typical freezing pattern during the slow-cooling was extracellular-freezing, and those during the rapid-cooling were extracellular-freezing and intracellular freezing with a lot of fine ice crystals in the cells. Cracks caused by the extracellular and intracellular ice crystals remained in the muscle tissues after the thawing. The results obtained by using the CLSM/dye method were consistent with pathologically morphological changes in the tissues through freezing and thawing.

Evaluating the potential for quantitative monitoring of in situ chemical oxidation of aqueous-phase TCE using in-phase and quadrature electrical conductivity

NASA Astrophysics Data System (ADS)

Hort, R. D.; Revil, A.; Munakata-Marr, J.; Mao, D.

2015-07-01

Electrical resistivity measurements can potentially be used to remotely monitor fate and transport of ionic oxidants such as permanganate (MnO4-) during in situ chemical oxidation (ISCO) of contaminants like trichloroethene (TCE). Time-lapse two-dimensional bulk conductivity and induced polarization surveys conducted during a sand tank ISCO simulation demonstrated that MnO4- plume movement could be monitored in a qualitative manner using bulk conductivity tomograms, although chargeability was below sensitivity limits. We also examined changes to in-phase and quadrature electrical conductivity resulting from ion injection, MnO2 and Cl- production, and pH change during TCE and humate oxidation by MnO4- in homogeneous aqueous solutions and saturated porous media samples. Data from the homogeneous samples demonstrated that inversion of the sand tank resistivity data using a common Tikhonov regularization approach was insufficient to recover an accurate conductivity distribution within the tank. While changes to in-phase conductivity could be successfully modeled, quadrature conductivity values could not be directly related to TCE oxidation product or MnO4- concentrations at frequencies consistent with field induced polarization surveys, limiting the utility of quadrature conductivity for monitoring ISCO.

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

PubMed

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

2017-02-01

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

Boolean logic analysis for flow regime recognition of gas-liquid horizontal flow

NASA Astrophysics Data System (ADS)

Ramskill, Nicholas P.; Wang, Mi

2011-10-01

In order to develop a flowmeter for the accurate measurement of multiphase flows, it is of the utmost importance to correctly identify the flow regime present to enable the selection of the optimal method for metering. In this study, the horizontal flow of air and water in a pipeline was studied under a multitude of conditions using electrical resistance tomography but the flow regimes that are presented in this paper have been limited to plug and bubble air-water flows. This study proposes a novel method for recognition of the prevalent flow regime using only a fraction of the data, thus rendering the analysis more efficient. By considering the average conductivity of five zones along the central axis of the tomogram, key features can be identified, thus enabling the recognition of the prevalent flow regime. Boolean logic and frequency spectrum analysis has been applied for flow regime recognition. Visualization of the flow using the reconstructed images provides a qualitative comparison between different flow regimes. Application of the Boolean logic scheme enables a quantitative comparison of the flow patterns, thus reducing the subjectivity in the identification of the prevalent flow regime.

Geophysical Investigation using Two Dimensional Electrical Resistivity Tomography method to delineate Subsurface Geological Structures at Dudhkoshi-II (230 MW) Hydroelectric Project, Solukhumbu District, Eastern Nepal

NASA Astrophysics Data System (ADS)

Ghimire, H.; Bhusal, U. C.; Khatiwada, B.; Pandey, D.

2017-12-01

Geophysical investigation using two dimensional electrical resistivity tomography (2D-ERT) method plays a significant role in determining the subsurface resistivity distribution by making measurement on the ground surface. This method was carried out at Dudhkoshi-II (230 MW) Hydroelectric Project, lies on Lesser Himalayan region of the Eastern Nepal to delineate the nature of the subsurface geology to assess its suitability for the construction of dam, desanding basin and powerhouse. The main objective of the proposed study consists of mapping vertical as well as horizontal variations of electrical resistivity to enable detection of the boundaries between unconsolidated materials and rocks of the different resistivity, possible geologic structures, such as possible presence of faults, fractures, and voids in intake and powerhouse area. For this purpose, the (WDJD-4 Multi-function Digital DC Resistivity/IP) equipment was used with Wenner array (60 electrodes). To fulfill these objectives of the study, the site area was mapped by Nine ERT profiles with different profile length and space between electrodes was 5 m. The depth of the investigation was 50 m. The acquired data were inverted to tomogram sections using tomographic inversion with RES2DINV commercial software. The Tomography sections show that the subsurface is classified into distinct geo-electric layers of dry unconsolidated overburden, saturated overburden, fractured rock and fresh bedrock of phyllites with quartzite and gneiss with different resistivity values. There were no voids and faults in the study area. Thickness of overburden at different region found to be different. Most of the survey area has bedrock of phyllites with quartzite; gneiss is also present in some location at intake area. Bedrock is found at the varies depth of 5-8 m at dam axis, 20-32 m at desanding basin and 3-10 m at powerhouse area. These results are confirmed and verified by using several boreholes data were drilled on the survey area. The results obtained from the study showed that the site is suitable for the construction of the proposed dam, desanding basin and powerhouse.

Joint inversion of geophysical data using petrophysical clustering and facies deformation wth the level set technique

NASA Astrophysics Data System (ADS)

Revil, A.

2015-12-01

Geological expertise and petrophysical relationships can be brought together to provide prior information while inverting multiple geophysical datasets. The merging of such information can result in more realistic solution in the distribution of the model parameters, reducing ipse facto the non-uniqueness of the inverse problem. We consider two level of heterogeneities: facies, described by facies boundaries and heteroegenities inside each facies determined by a correlogram. In this presentation, we pose the geophysical inverse problem in terms of Gaussian random fields with mean functions controlled by petrophysical relationships and covariance functions controlled by a prior geological cross-section, including the definition of spatial boundaries for the geological facies. The petrophysical relationship problem is formulated as a regression problem upon each facies. The inversion of the geophysical data is performed in a Bayesian framework. We demonstrate the usefulness of this strategy using a first synthetic case for which we perform a joint inversion of gravity and galvanometric resistivity data with the stations located at the ground surface. The joint inversion is used to recover the density and resistivity distributions of the subsurface. In a second step, we consider the possibility that the facies boundaries are deformable and their shapes are inverted as well. We use the level set approach to perform such deformation preserving prior topological properties of the facies throughout the inversion. With the help of prior facies petrophysical relationships and topological characteristic of each facies, we make posterior inference about multiple geophysical tomograms based on their corresponding geophysical data misfits. The method is applied to a second synthetic case showing that we can recover the heterogeneities inside the facies, the mean values for the petrophysical properties, and, to some extent, the facies boundaries using the 2D joint inversion of gravity and galvanometric resistivity data. For this 2D synthetic example, we note that the position of the facies are well-recovered except far from the ground surfce where the sensitivity is too low. The figure shows the evolution of the shape of the facies during the inversion itertion by iteration.

AFM stiffness nanotomography of normal, metaplastic and dysplastic human esophageal cells

NASA Astrophysics Data System (ADS)

Fuhrmann, A.; Staunton, J. R.; Nandakumar, V.; Banyai, N.; Davies, P. C. W.; Ros, R.

2011-02-01

The mechanical stiffness of individual cells is important in tissue homeostasis, cell growth, division and motility, and the epithelial-mesenchymal transition in the initiation of cancer. In this work, a normal squamous cell line (EPC2) and metaplastic (CP-A) as well as dysplastic (CP-D) Barrett's Esophagus columnar cell lines are studied as a model of pre-neoplastic progression in the human esophagus. We used the combination of an atomic force microscope (AFM) with a scanning confocal fluorescence lifetime imaging microscope to study the mechanical properties of single adherent cells. Sixty four force indentation curves were taken over the nucleus of each cell in an 8 × 8 grid pattern. Analyzing the force indentation curves, indentation depth-dependent Young's moduli were found for all cell lines. Stiffness tomograms demonstrate distinct differences between the mechanical properties of the studied cell lines. Comparing the stiffness for indentation forces of 1 nN, most probable Young's moduli were calculated to 4.7 kPa for EPC2 (n = 18 cells), 3.1 kPa for CP-A (n = 10) and 2.6 kPa for CP-D (n = 19). We also tested the influence of nuclei and nucleoli staining organic dyes on the mechanical properties of the cells. For stained EPC2 cells (n = 5), significant stiffening was found (9.9 kPa), while CP-A cells (n = 5) showed no clear trend (2.9 kPa) and a slight softening was observed (2.1 kPa) in the case of CP-D cells (n = 16). Some force-indentation curves show non-monotonic discontinuities with segments of negative slope, resembling a sawtooth pattern. We found the incidence of these 'breakthrough events' to be highest in the dysplastic CP-D cells, intermediate in the metaplastic CP-A cells and lowest in the normal EPC2 cells. This observation suggests that the microscopic explanation for the increased compliance of cancerous and pre-cancerous cells may lie in their susceptibility to 'crumble and yield' rather than their ability to 'bend and flex'.

Reliability of third molar development for age estimation in Gujarati population: A comparative study.

PubMed

Gandhi, Neha; Jain, Sandeep; Kumar, Manish; Rupakar, Pratik; Choyal, Kanaram; Prajapati, Seema

2015-01-01

Age assessment may be a crucial step in postmortem profiling leading to confirmative identification. In children, Demirjian's method based on eight developmental stages was developed to determine maturity scores as a function of age and polynomial functions to determine age as a function of score. Of this study was to evaluate the reliability of age estimation using Demirjian's eight teeth method following the French maturity scores and Indian-specific formula from developmental stages of third molar with the help of orthopantomograms using the Demirjian method. Dental panoramic tomograms from 30 subjects each of known chronological age and sex were collected and were evaluated according to Demirjian's criteria. Age calculations were performed using Demirjian's formula and Indian formula. Statistical analysis used was Chi-square test and ANOVA test and the P values obtained were statistically significant. There was an average underestimation of age with both Indian and Demirjian's formulas. The mean absolute error was lower using Indian formula hence it can be applied for age estimation in present Gujarati population. Also, females were ahead of achieving dental maturity than males thus completion of dental development is attained earlier in females. Greater accuracy can be obtained if population-specific formulas considering the ethnic and environmental variation are derived performing the regression analysis.

A Freeze Substitution Fixation-Based Gold Enlarging Technique for EM Studies of Endocytosed Nanogold-Labeled Molecules

PubMed Central

He, Wanzhong; Kivork, Christine; Machinani, Suman; Morphew, Mary K.; Gail, Anna M.; Tesar, Devin B.; Tiangco, Noreen E.; McIntosh, J. Richard; Bjorkman, Pamela J.

2007-01-01

We have developed methods to locate individual ligands that can be used for electron microscopy studies of dynamic events during endocytosis and subsequent intracellular trafficking. The methods are based on enlargement of 1.4 nm Nanogold attached to an endocytosed ligand. Nanogold, a small label that does not induce misdirection of ligand-receptor complexes, is ideal for labeling ligands endocytosed by live cells, but is too small to be routinely located in cells by electron microscopy. Traditional pre-embedding enhancement protocols to enlarge Nanogold are not compatible with high pressure freezing/freeze substitution fixation (HPF/FSF), the most accurate method to preserve ultrastructure and dynamic events during trafficking. We have developed an improved enhancement procedure for chemically-fixed samples that reduced autonucleation, and a new pre-embedding gold-enlarging technique for HPF/FSF samples that preserved contrast and ultrastructure and can be used for high-resolution tomography. We evaluated our methods using labeled Fc as a ligand for the neonatal Fc receptor. Attachment of Nanogold to Fc did not interfere with receptor binding or uptake, and gold-labeled Fc could be specifically enlarged to allow identification in 2D projections and in tomograms. These methods should be broadly applicable to many endocytosis and transcytosis studies. PMID:17723309

Travel-time-based thermal tracer tomography

NASA Astrophysics Data System (ADS)

Somogyvári, Márk; Bayer, Peter; Brauchler, Ralf

2016-05-01

Active thermal tracer testing is a technique to get information about the flow and transport properties of an aquifer. In this paper we propose an innovative methodology using active thermal tracers in a tomographic setup to reconstruct cross-well hydraulic conductivity profiles. This is facilitated by assuming that the propagation of the injected thermal tracer is mainly controlled by advection. To reduce the effects of density and viscosity changes and thermal diffusion, early-time diagnostics are used and specific travel times of the tracer breakthrough curves are extracted. These travel times are inverted with an eikonal solver using the staggered grid method to reduce constraints from the pre-defined grid geometry and to improve the resolution. Finally, non-reliable pixels are removed from the derived hydraulic conductivity tomograms. The method is applied to successfully reconstruct cross-well profiles as well as a 3-D block of a high-resolution fluvio-aeolian aquifer analog data set. Sensitivity analysis reveals a negligible role of the injection temperature, but more attention has to be drawn to other technical parameters such as the injection rate. This is investigated in more detail through model-based testing using diverse hydraulic and thermal conditions in order to delineate the feasible range of applications for the new tomographic approach.

Precision ephemerides for gravitational-wave searches - III. Revised system parameters of Sco X-1

NASA Astrophysics Data System (ADS)

Wang, L.; Steeghs, D.; Galloway, D. K.; Marsh, T.; Casares, J.

2018-06-01

Neutron stars in low-mass X-ray binaries are considered promising candidate sources of continuous gravitational-waves. These neutron stars are typically rotating many hundreds of times a second. The process of accretion can potentially generate and support non-axisymmetric distortions to the compact object, resulting in persistent emission of gravitational-waves. We present a study of existing optical spectroscopic data for Sco X-1, a prime target for continuous gravitational-wave searches, with the aim of providing revised constraints on key orbital parameters required for a directed search with advanced-LIGO data. From a circular orbit fit to an improved radial velocity curve of the Bowen emission components, we derived an updated orbital period and ephemeris. Centre of symmetry measurements from the Bowen Doppler tomogram yield a centre of the disc component of 90 km s-1, which we interpret as a revised upper limit to the projected orbital velocity of the NS K1. By implementing Monte Carlo binary parameter calculations, and imposing new limits on K1 and the rotational broadening, we obtained a complete set of dynamical system parameter constraints including a new range for K1 of 40-90 km s-1. Finally, we discussed the implications of the updated orbital parameters for future continuous-waves searches.

THz - ToF Optical Layer Analysis (OLA) to determine optical properties of dielectric materials

NASA Astrophysics Data System (ADS)

Spranger, Holger; Beckmann, Jörg

2017-02-01

Electromagnetic waves with frequencies between 0.1 and 10 THz are described as THz-radiation (T-ray). The ability to penetrate dielectric materials makes T-rays attractive to reveal discontinuities in polymer and ceramic materials. THz-Time Domain Spectroscopy Systems (THz-TDS) are available on the market today which operates with THz-pulses transmitted and received by optically pumped semiconductor antennas. In THz-TDS the travelling time (ToF) and shape of the pulse is changed if it interacts with the dielectric material and its inherent discontinuities. A tomogram of the object under the test can be reconstructed from time of flight diffraction (ToFD) scans if a synthetic focusing aperture (SAFT) algorithm is applied. The knowledge of the base materials shape and optical properties is essential for a proper reconstruction result. To obtain these properties a model is assumed which describes the device under the test as multilayer structure composed of thin layers with different dielectric characteristics. The Optical Layer Analysis (OLA) is able to fulfill these requirements. A short description why the optical properties are crucial for meaningful SAFT reconstruction results will be given first. Afterwards the OLA will be derived and applied on representative samples to discuss and evaluate its benefits and limits.

Computer Maintenance Operations Center (CMOC), showing duplexed cyber 170174 computers ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Computer Maintenance Operations Center (CMOC), showing duplexed cyber 170-174 computers - Beale Air Force Base, Perimeter Acquisition Vehicle Entry Phased-Array Warning System, Techinical Equipment Building, End of Spencer Paul Road, north of Warren Shingle Road (14th Street), Marysville, Yuba County, CA

Geological and Seismic Data Mining For The Development of An Interpretation System Within The Alptransit Project

NASA Astrophysics Data System (ADS)

Klose, C. D.; Giese, R.; Löw, S.; Borm, G.

Especially for deep underground excavations, the prediction of the locations of small- scale hazardous geotechnical structures is nearly impossible when exploration is re- stricted to surface based methods. Hence, for the AlpTransit base tunnels, exploration ahead has become an essential component of the excavation plan. The project de- scribed in this talk aims at improving the technology for the geological interpretation of reflection seismic data. The discovered geological-seismic relations will be used to develop an interpretation system based on artificial intelligence to predict hazardous geotechnical structures of the advancing tunnel face. This talk gives, at first, an overview about the data mining of geological and seismic properties of metamorphic rocks within the Penninic gneiss zone in Southern Switzer- land. The data results from measurements of a specific geophysical prediction system developed by the GFZ Potsdam, Germany, along the 2600 m long and 1400 m deep Faido access tunnel. The goal is to find those seismic features (i.e. compression and shear wave velocities, velocity ratios and velocity gradients) which show a significant relation to geological properties (i.e. fracturing and fabric features). The seismic properties were acquired from different tomograms, whereas the geolog- ical features derive from tunnel face maps. The features are statistically compared with the seismic rock properties taking into account the different methods used for the tunnel excavation (TBM and Drill/Blast). Fracturing and the mica content stay in a positive relation to the velocity values. Both, P- and S-wave velocities near the tunnel surface describe the petrology better, whereas in the interior of the rock mass they correlate to natural micro- and macro-scopic fractures surrounding tectonites, i.e. cataclasites. The latter lie outside of the excavation damage zone and the tunnel loos- ening zone. The shear wave velocities are better indicators for rock fracturing than compression wave velocities. The velocity ratios indicate the mica content and the water content of the rocks.

A high resolution 3D velocity model beneath the Tokyo Metropolitan area by MeSO-net

NASA Astrophysics Data System (ADS)

Nakagawa, S.; Sakai, S.; Honda, R.; Kimura, H.; Hirata, N.

2015-12-01

Beneath the Tokyo metropolitan area, the Philippine Sea Plate (PSP) subducts and causes devastating mega-thrust earthquakes, such as the 1703 Genroku earthquake (M8.0) and the 1923 Kanto earthquake (M7.9). An M7 or greater (M7+) earthquake in this area at present has high potential to produce devastating serious loss of life and property with even greater global economic repercussions. The Central Disaster Management Council of Japan estimates that an M7+ earthquake will cause 23,000 fatalities and 95 trillion yen (about 1 trillion US$) economic loss. We have launched the Special Project for Reducing Vulnerability for Urban Mega Earthquake Disasters in collaboration with scientists, engineers, and social-scientists in nationwide institutions since 2012. We analyze data from the dense seismic array called Metropolitan Seismic Observation network (MeSO-net), which has 296 seismic stations with spacing of 5 km (Sakai and Hirata, 2009; Kasahara et al., 2009). We applied the double-difference tomography method (Zhang and Thurber, 2003) and estimated the velocity structure and the upper boundary of PSP (Nakagawa et al., 2010). The 2011 Tohoku-oki earthquake (M9.0) has activated seismicity also in Kanto region, providing better coverage of ray paths for tomographic analysis. We obtain much higher resolution velocity models from whole dataset observed by MeSO-net between 2008 and 2015. A detailed image of tomograms shows that PSP contacts Pacific plate at a depth of 50 km beneath northern Tokyo bay. A variation of velocity along the oceanic crust suggests dehydration reaction to produce seismicity in a slab, which may related to the M7+ earthquake. Acknowledgement: This study was supported by the Special Project for Reducing Vulnerability for Urban Mega Earthquake Disasters of MEXT, Japan and the Earthquake Research Institute cooperative research program.

Value of speckle tracking echocardiography for detection of clinically silent left ventricular dysfunction in patients with β-thalassemia.

PubMed

Parsaee, Mozhgan; Saedi, Sedigheh; Joghataei, Pegah; Azarkeivan, Azita; Alizadeh Sani, Zahra

2017-10-01

β-Thalassemia is an inherited hemoglobin disorder resulting in chronic hemolytic anemia requiring chronic transfusion therapy. Cardiac involvement is the main cause of death in patients with thalassemia major. The narrow border is between overt myocardial dysfunction and clinically silent left ventricular (LV) dysfunction in patients with thalassemia. Therefore, we need novel parameters in different imaging techniques to discover cardiac involvement in an early and subtle stage. We explore to find a novel, straightforward and informative parameter in echocardiography as a noninvasive, economical and really routine in clinical practice. In this prospective study, 55 patients, who are known cases of β-thalassemia major, receiving long-term blood transfusions and undergoing iron chelation therapy were enrolled. Ferritin level, cardiac magnetic resonance (CMR) T2 * value, full conventional echocardiography and speckle tracking, LV regional circumferential and longitudinal strain values (%) and time-to-peak strain (ms) of 17 segments cardiac model in eyeball tomogram were measured. There was a significant reduction in global longitudinal strain (GLS) (-20.9% ± 1.9 vs. -22.2 ± 1.03) and also basal segments longitudinal strain compared to normal subjects group (-17.4% ± 2.7 vs. -19.6% ± 1.2). There was no significant difference in circumferential strain value between thalassemia patients and normal control group. Interestingly, there was no significant correlation between GLS and CMR T2 * values showing no association between cardiac iron load and longitudinal strain. Speckle tracking echocardiography could be used as a feasible method for evaluating subclinical myocardial dysfunction in patients with thalassemia major. Echocardiography, using GLS, could predict clinically silent myocardial dysfunction independent of CMR (T2 * value) and extension of iron deposition. Our study also puts forward other causes such as chronic tissue hypoxia resulting from chronic anemia as a root cause and initiating factor for subsequent injury by the iron deposition. Speckle tracking can recognize the cardiac involvement in really early stages.

C2 Primary leiomyoma in an immunocompetent woman: A case report and review of literature

PubMed Central

Patibandla, Mohana Rao; Nayak, Madhukar T.; Purohit, A. K.; Uppin, Megha; Challa, Sundaram; Addagada, Gokul Chowdary; Nukavarapu, Manisha

2017-01-01

Clinical case report and review of the literature. This is the first case of primary leiomyoma in an immunocompetent woman without previous history of uterine leiomyoma being reported in the literature to the best of our knowledge. Leiomyoma, a type of smooth muscle cell tumor, involving the vertebra is extremely rare. There were very few primary leiomyoma in patients with AIDS or in the immune-suppressed patients. This 48-year-old female came with H/o neck pain, weakness and bladder retention. On examination, tone increased in all four limbs, power on the right side of the limbs 4/5, power on the left upper limb 0/5, lower limb 3/5, left plantar was up going, decreased sensation over the left second cervical vertebra (C2) dermatome and all modalities decreased below C2. X-ray and magnetic resonance imaging (MRI) of the cervical spine showed kyphosis of the cervical spine with destruction of the C2 vertebral body along with pathological fracture. The patient underwent decompression of the C2 lesion through the C2 right pedicle with occipito-C1-C3 lateral mass screws fixation. Lesion anterior to the cord was reached by a transpedicular approach and decompression was performed. The lesion was pinkish grey, firm and moderately vascular and was destroying the C2 vertebral body. The patient improved symptomatically in power in the left upper limb and lower limb over the next 1 week duration from 0/5 to 4+/5. Histopathology revealed primary leiomyoma. The patient was evaluated with ultrasound abdomen and contrast tomogram of the chest, abdomen and pelvis to rule out other possible lesions in the lung, intestines and uterus. We suggest that leiomyoma should be included in the differential diagnosis of destructive lytic lesions involving the C2 vertebra. Histopathological examination with immunohistochemistry is necessary for the definitive diagnosis. Treatment of choice is surgery with complete removal. PMID:28413557

Monte Carlo Optimization of Crystal Configuration for Pixelated Molecular SPECT Scanners

NASA Astrophysics Data System (ADS)

Mahani, Hojjat; Raisali, Gholamreza; Kamali-Asl, Alireza; Ay, Mohammad Reza

2017-02-01

Resolution-sensitivity-PDA tradeoff is the most challenging problem in design and optimization of pixelated preclinical SPECT scanners. In this work, we addressed such a challenge from a crystal point-of-view by looking for an optimal pixelated scintillator using GATE Monte Carlo simulation. Various crystal configurations have been investigated and the influence of different pixel sizes, pixel gaps, and three scintillators on tomographic resolution, sensitivity, and PDA of the camera were evaluated. The crystal configuration was then optimized using two objective functions: the weighted-sum and the figure-of-merit methods. The CsI(Na) reveals the highest sensitivity of the order of 43.47 cps/MBq in comparison to the NaI(Tl) and the YAP(Ce), for a 1.5×1.5 mm2 pixel size and 0.1 mm gap. The results show that the spatial resolution, in terms of FWHM, improves from 3.38 to 2.21 mm while the sensitivity simultaneously deteriorates from 42.39 cps/MBq to 27.81 cps/MBq when pixel size varies from 2×2 mm2 to 0.5×0.5 mm2 for a 0.2 mm gap, respectively. The PDA worsens from 0.91 to 0.42 when pixel size decreases from 0.5×0.5 mm2 to 1×1 mm2 for a 0.2 mm gap at 15° incident-angle. The two objective functions agree that the 1.5×1.5 mm2 pixel size and 0.1 mm Epoxy gap CsI(Na) configuration provides the best compromise for small-animal imaging, using the HiReSPECT scanner. Our study highlights that crystal configuration can significantly affect the performance of the camera, and thereby Monte Carlo optimization of pixelated detectors is mandatory in order to achieve an optimal quality tomogram.

Resistivity and self-potential tomography applied to groundwater remediation and contaminant plumes: Sandbox and field experiments

NASA Astrophysics Data System (ADS)

Mao, D.; Revil, A.; Hort, R. D.; Munakata-Marr, J.; Atekwana, E. A.; Kulessa, B.

2015-11-01

Geophysical methods can be used to remotely characterize contaminated sites and monitor in situ enhanced remediation processes. We have conducted one sandbox experiment and one contaminated field investigation to show the robustness of electrical resistivity tomography and self-potential (SP) tomography for these applications. In the sandbox experiment, we injected permanganate in a trichloroethylene (TCE)-contaminated environment under a constant hydraulic gradient. Inverted resistivity tomograms are able to track the evolution of the permanganate plume in agreement with visual observations made on the side of the tank. Self-potential measurements were also performed at the surface of the sandbox using non-polarizing Ag-AgCl electrodes. These data were inverted to obtain the source density distribution with and without the resistivity information. A compact horizontal dipole source located at the front of the plume was obtained from the inversion of these self-potential data. This current dipole may be related to the redox reaction occurring between TCE and permanganate and the strong concentration gradient at the front of the plume. We demonstrate that time-lapse self-potential signals can be used to track the kinetics of an advecting oxidizer plume with acceptable accuracy and, if needed, in real time, but are unable to completely resolve the shape of the plume. In the field investigation, a 3D resistivity tomography is used to characterize an organic contaminant plume (resistive domain) and an overlying zone of solid waste materials (conductive domain). After removing the influence of the streaming potential, the identified source current density had a magnitude of 0.5 A m-2. The strong source current density may be attributed to charge movement between the neighboring zones that encourage abiotic and microbially enhanced reduction and oxidation reactions. In both cases, the self-potential source current density is located in the area of strong resistivity gradient.

Time-lapse Seismic Refraction Monitoring of an Active Landslide in Lias Group Mudrocks, North Yorkshire, UK

NASA Astrophysics Data System (ADS)

Uhlemann, S.; Whiteley, J.; Chambers, J. E.; Inauen, C.; Swift, R. T.

2017-12-01

Geophysical monitoring of the internal moisture content and processes of landslides is an increasingly common approach to the characterisation and assessment of the hydrogeological condition of rainfall-triggered landslides. Geoelectrical monitoring methods are sensitive to changes in the subsurface moisture conditions that cause the failure of unstable slopes, typically through the increase of pore water pressures and softening of materials within the landslide system. The application of seismic methods to the monitoring of landslides has not been as extensively applied as geoelectrical approaches, but the seismic method can determine elastic properties of landslide materials that can characterise and identify changes in the geomechanical condition of landslide systems that also lead to slope failure. We present the results of a seismic refraction monitoring campaign undertaken at the Hollin Hill Landslide Observatory in North Yorkshire, UK. This campaign has involved the repeat acquisition of surface acquired high resolution P- and S-wave seismic refraction data. The monitoring profile traverses a 142m long section from the crest to the toe of an active landslide comprising of mudstone and sandstone. Data were acquired at six to nine week intervals between October 2016 and October 2017. This repeat acquisition approach allowed for the imaging of seismically determined property changes of the landslide throughout the annual climatic cycle. Initial results showed that changes in the moisture dynamics of the landslide are reflected by changes in the seismic character of the inverted tomograms. Changes in the seismic properties are linked to the changes in the annual climatic cycle, particularly in relation to effective rainfall. The results indicate that the incorporation of seismic monitoring data into ongoing geoelectrical monitoring programmes can provide complementary geomechanical data to enhance our understanding of the internal condition of landslide systems. Future development of this integrated approach will allow for the imaging and monitoring of these systems at unprecedented spatial and temporal scales.

Markov Random Field Based Automatic Image Alignment for ElectronTomography

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

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

2007-11-30

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

The crustal and mantle velocity structure in central Asia from 3D traveltime tomography

NASA Astrophysics Data System (ADS)

Sun, Y.; Martin, R. V.; Toksoz, M. N.; Pei, S.

2010-12-01

The lithospheric structure in central Asia features large blocks such as the Indian plate, the Afghan block, the Turan plate, and the Tarim block. This geologically and tectonically complicated area is also one of the most seismically active regions in the world. We developed P- and S- wave velocity structures of the central Asia in the crust using the traveltime data from Kyrgyzstan, Tajikistan, Kazakhstan, and Uzbek. We chose the events and stations between 32N65E and 45N85E and focused on the areas of Pamir and western Tianshan. In this data set, there are more than 6000 P and S arrivals received at 80 stations from about 300 events. The double difference tomography is applied to relocate events and to invert for seismic structures simultaneously. Our results provide accurate locations of earthquakes and high resolution crustal structure in this region. To extend the model deeper into the mantle through the upper mantle transition zone, ISC/EHB data for P and PP phases are combined with the ABCE data. To counteract the “smearing effect,” the crust and upper mantle velocity structure, derived from regional travel-times, is used. An adaptive grid method based on ray density is used in the inversion. A P-wave velocity model extending down to a depth of 2000 km is obtained. regional-teleseismic tomography provides a high-resolution, 3-D P-wave velocity model for the crust, upper mantle, and the transition zone. The crustal models correlate well with geologic and tectonic features. The upper mantle tomograms show the images of Tian Shan. The slab geometry is quite complex, reflecting the history of the changes in the plate motions and collision processes. Vp/Vs tomography was also determined in the study region, and an attenuation tomography was obtained as well.

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

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

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

2010-10-22

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

Advantages of the full-waveform inversion: real data example from the Polish Basin

NASA Astrophysics Data System (ADS)

Malinowski, M.; Operto, S.

2006-12-01

Modern acquisition techniques allow us to gather high-density seismic data even in case of crustal-scale investigations. In combination with increasing availability of computational resources (eg. PC clusters), this allow us to image the Earth's structure on much finer scale than offered by ray-theory based methods (like travel time tomography) by applying the full waveform inversion/tomography method (FWT). Recently, the FWT method was for the first time successfully applied to the real wide-aperture data: 100-km long OBS profile (Operto et al. 2006) and a 15-km long land profile (Operto et al. 2004, Ravaut et al., 2004). We present the results of the application of the FWT method to the GRUNDY 2003 experiment data, which is standing in between the scale of the mentioned datasets. This project was targeted at recognition of the pre-Zechstein strata within the Polish Basin. For a successful investigations relatively low-frequencies and wide-apertures were used. In the 50 by 10 km rectangular area ca. 800 RefTek 125 "Texan" stations with 4.5 Hz geophones were deployed, forming high-density central line (receiver spacing 100 m) and additional 4 parallel profiles. Previously the data were modelled using conventional methods: CDP processing and traveltime tomography. In order to utilise secondary arrivals, we used the frequency-domain FWT method of Pratt et al. (1998). The wide-aperture content of our data leads to a redundant wavenumber coverage which can be partially removed without loss of information by limiting the inversion to few frequencies only. The inversion proceeds by stepping from low to high frequencies and uses the model inferred for one component as the starting one for the next frequency. Before full waveform inversion, the data were preprocessed by QC editing, spectral deconvolution (whitening), bandpass filtering and muting in narrow window around the first arrival. Traveltime tomogram was choosen as the starting model for 2D waveform inversion. The model size was 50x10 km with 25 m FD grid step. We have selected 10 frequencies from 4 to 13 Hz. For each frequency 10 iterations were computed (on a Linux cluster). There is a clear improvement in resolution of the obtained tomographic images by exploiting the full wavefield. The model allows to predict also fairly well the observed seismograms and is consistent with both the geological horizons projected from industrial reflection profiles as well as check-shot velocity log. Benefits of FWT in application to our data seems to be clear: in one step, without the need for performing the forward raytracing modelling, we gained both the quasi-structural image (perturbational model) and the detailed velocity model. In this way we fully exploited the broad range of recorded offsets and reflection angles from pre- to postcritical ones for a successful imaging beneath the Zechstein strata.

Interfacing External Quantum Devices to a Universal Quantum Computer

PubMed Central

Lagana, Antonio A.; Lohe, Max A.; von Smekal, Lorenz

2011-01-01

We present a scheme to use external quantum devices using the universal quantum computer previously constructed. We thereby show how the universal quantum computer can utilize networked quantum information resources to carry out local computations. Such information may come from specialized quantum devices or even from remote universal quantum computers. We show how to accomplish this by devising universal quantum computer programs that implement well known oracle based quantum algorithms, namely the Deutsch, Deutsch-Jozsa, and the Grover algorithms using external black-box quantum oracle devices. In the process, we demonstrate a method to map existing quantum algorithms onto the universal quantum computer. PMID:22216276

Interfacing external quantum devices to a universal quantum computer.

PubMed

Lagana, Antonio A; Lohe, Max A; von Smekal, Lorenz

2011-01-01

We present a scheme to use external quantum devices using the universal quantum computer previously constructed. We thereby show how the universal quantum computer can utilize networked quantum information resources to carry out local computations. Such information may come from specialized quantum devices or even from remote universal quantum computers. We show how to accomplish this by devising universal quantum computer programs that implement well known oracle based quantum algorithms, namely the Deutsch, Deutsch-Jozsa, and the Grover algorithms using external black-box quantum oracle devices. In the process, we demonstrate a method to map existing quantum algorithms onto the universal quantum computer. © 2011 Lagana et al.

Conjunctival impression cytology in computer users.

PubMed

Kumar, S; Bansal, R; Khare, A; Malik, K P S; Malik, V K; Jain, K; Jain, C

2013-01-01

It is known that the computer users develop the features of dry eye. To study the cytological changes in the conjunctiva using conjunctival impression cytology in computer users and a control group. Fifteen eyes of computer users who had used computers for more than one year and ten eyes of an age-and-sex matched control group (those who had not used computers) were studied by conjunctival impression cytology. Conjunctival impression cytology (CIC) results in the control group were of stage 0 and stage I while the computer user group showed CIC results between stages II to stage IV. Among the computer users, the majority ( > 90 %) showed stage III and stage IV changes. We found that those who used computers daily for long hours developed more CIC changes than those who worked at the computer for a shorter daily duration. © NEPjOPH.

Bringing MapReduce Closer To Data With Active Drives

NASA Astrophysics Data System (ADS)

Golpayegani, N.; Prathapan, S.; Warmka, R.; Wyatt, B.; Halem, M.; Trantham, J. D.; Markey, C. A.

2017-12-01

Moving computation closer to the data location has been a much theorized improvement to computation for decades. The increase in processor performance, the decrease in processor size and power requirement combined with the increase in data intensive computing has created a push to move computation as close to data as possible. We will show the next logical step in this evolution in computing: moving computation directly to storage. Hypothetical systems, known as Active Drives, have been proposed as early as 1998. These Active Drives would have a general-purpose CPU on each disk allowing for computations to be performed on them without the need to transfer the data to the computer over the system bus or via a network. We will utilize Seagate's Active Drives to perform general purpose parallel computing using the MapReduce programming model directly on each drive. We will detail how the MapReduce programming model can be adapted to the Active Drive compute model to perform general purpose computing with comparable results to traditional MapReduce computations performed via Hadoop. We will show how an Active Drive based approach significantly reduces the amount of data leaving the drive when performing several common algorithms: subsetting and gridding. We will show that an Active Drive based design significantly improves data transfer speeds into and out of drives compared to Hadoop's HDFS while at the same time keeping comparable compute speeds as Hadoop.

Effects of spatially variable resolution on field-scale estimates of tracer concentration from electrical inversions using Archie's law

USGS Publications Warehouse

Singha, Kamini; Gorelick, Steven M.

2006-01-01

Two important mechanisms affect our ability to estimate solute concentrations quantitatively from the inversion of field-scale electrical resistivity tomography (ERT) data: (1) the spatially variable physical processes that govern the flow of current as well as the variation of physical properties in space and (2) the overparameterization of inverse models, which requires the imposition of a smoothing constraint (regularization) to facilitate convergence of the inverse solution. Based on analyses of field and synthetic data, we find that the ability of ERT to recover the 3D shape and magnitudes of a migrating conductive target is spatially variable. Additionally, the application of Archie's law to tomograms from field ERT data produced solute concentrations that are consistently less than 10% of point measurements collected in the field and estimated from transport modeling. Estimates of concentration from ERT using Archie's law only fit measured solute concentrations if the apparent formation factor is varied with space and time and allowed to take on unreasonably high values. Our analysis suggests that the inability to find a single petrophysical relation in space and time between concentration and electrical resistivity is largely an effect of two properties of ERT surveys: (1) decreased sensitivity of ERT to detect the target plume with increasing distance from the electrodes and (2) the smoothing imprint of regularization used in inversion.

Comparison between GPR measurements and ultrasonic tomography with different inversion algorithms: an application to the base of an ancient Egyptian sculpture

NASA Astrophysics Data System (ADS)

Sambuelli, L.; Bohm, G.; Capizzi, P.; Cardarelli, E.; Cosentino, P.

2011-09-01

By late 2008 one of the most important pieces of the 'Museo delle Antichità Egizie' of Turin, the sculpture of the Pharaoh with god Amun, was planned to be one of the masterpieces of a travelling exhibition in Japan. The 'Fondazione Museo delle Antichità Egizie di Torino', who manages the museum, was concerned with the integrity of the base of the statue which actually presents visible signs of restoration dating back to the early 19th century. It was required to estimate the persistence of the visible fractures, to search for unknown ones and to provide information about the overall mechanical strength of the base. To tackle the first question a GPR reflection survey along three sides of the base was performed and the results were assembled in a 3D rendering. As far as the second question is concerned, two parallel, horizontal ultrasonic 2D tomograms across the base were made. We acquired, for each section, 723 ultrasonic signals corresponding to different transmitter and receiver positions. The tomographic data were inverted using four different software packages based upon different algorithms. The obtained velocity images were then compared each other, with the GPR results and with the visible fractures in the base. A critical analysis of the comparisons is finally presented.

Reliability of third molar development for age estimation in Gujarati population: A comparative study

PubMed Central

Gandhi, Neha; Jain, Sandeep; Kumar, Manish; Rupakar, Pratik; Choyal, Kanaram; Prajapati, Seema

2015-01-01

Background: Age assessment may be a crucial step in postmortem profiling leading to confirmative identification. In children, Demirjian's method based on eight developmental stages was developed to determine maturity scores as a function of age and polynomial functions to determine age as a function of score. Aim: Of this study was to evaluate the reliability of age estimation using Demirjian's eight teeth method following the French maturity scores and Indian-specific formula from developmental stages of third molar with the help of orthopantomograms using the Demirjian method. Materials and Methods: Dental panoramic tomograms from 30 subjects each of known chronological age and sex were collected and were evaluated according to Demirjian's criteria. Age calculations were performed using Demirjian's formula and Indian formula. Statistical analysis used was Chi-square test and ANOVA test and the P values obtained were statistically significant. Results: There was an average underestimation of age with both Indian and Demirjian's formulas. The mean absolute error was lower using Indian formula hence it can be applied for age estimation in present Gujarati population. Also, females were ahead of achieving dental maturity than males thus completion of dental development is attained earlier in females. Conclusion: Greater accuracy can be obtained if population-specific formulas considering the ethnic and environmental variation are derived performing the regression analysis. PMID:26005298

3-dimensional orthodontics visualization system with dental study models and orthopantomograms

NASA Astrophysics Data System (ADS)

Zhang, Hua; Ong, S. H.; Foong, K. W. C.; Dhar, T.

2005-04-01

The aim of this study is to develop a system that provides 3-dimensional visualization of orthodontic treatments. Dental plaster models and corresponding orthopantomogram (dental panoramic tomogram) are first digitized and fed into the system. A semi-auto segmentation technique is applied to the plaster models to detect the dental arches, tooth interstices and gum margins, which are used to extract individual crown models. 3-dimensional representation of roots, generated by deforming generic tooth models with orthopantomogram using radial basis functions, is attached to corresponding crowns to enable visualization of complete teeth. An optional algorithm to close the gaps between deformed roots and actual crowns by using multi-quadratic radial basis functions is also presented, which is capable of generating smooth mesh representation of complete 3-dimensional teeth. User interface is carefully designed to achieve a flexible system with as much user friendliness as possible. Manual calibration and correction is possible throughout the data processing steps to compensate occasional misbehaviors of automatic procedures. By allowing the users to move and re-arrange individual teeth (with their roots) on a full dentition, this orthodontic visualization system provides an easy and accurate way of simulation and planning of orthodontic treatment. Its capability of presenting 3-dimensional root information with only study models and orthopantomogram is especially useful for patients who do not undergo CT scanning, which is not a routine procedure in most orthodontic cases.

Imaging of forced-imbibition in carbonate rocks using synchrotron X-ray micro-tomography

NASA Astrophysics Data System (ADS)

Singh, K.; Menke, H. P.; Andrew, M. G.; Lin, Q.; Saif, T.; Al-Khulaifi, Y.; Reynolds, C. A.; Bijeljic, B.; Rau, C.; Blunt, M. J.

2016-12-01

We have investigated the pore-scale behavior of brine-oil systems and oil trapping during forced-imbibition in a water-wet carbonate rock in a capillary-dominated flow regime at reservoir pressure conditions. To capture the dynamics of the brine-oil front progression and snap-off process, real-time tomograms with a time resolution of 38 s (24 s for imaging and 14 s for recording the data) and a spatial resolution of 3.28 µm were acquired at Diamond Light Source (UK). The data were first analyzed at global scale (complete imaged rock) for overall front behavior. From the saturation profiles, we obtain the location of the tail of the desaturation front that progresses with a velocity of 13 µm/min. This velocity is smaller than average flow velocity 16.88 µm/min, which explains why it needs slightly more than 1 pore volume of brine injection to reach the residual saturation of oil in a water-wet rock. The data were further analyzed at local scale to investigate the pore-scale mechanisms of oil trapping during brine flooding. We isolated various trapping events which resulted in the creation of discrete oil ganglia occupying one to several pore bodies. We perform pore-scale curvature analysis of brine-oil interfaces to obtain local capillary pressure that will be related to the shape and the size of throats in which ganglia were trapped.

Grating-based tomography applications in biomedical engineering

NASA Astrophysics Data System (ADS)

Schulz, Georg; Thalmann, Peter; Khimchenko, Anna; Müller, Bert

2017-10-01

For the investigation of soft tissues or tissues consisting of soft and hard tissues on the microscopic level, hard X-ray phase tomography has become one of the most suitable imaging techniques. Besides other phase contrast methods grating interferometry has the advantage of higher sensitivity than inline methods and the quantitative results. One disadvantage of the conventional double-grating setup (XDGI) compared to inline methods is the limitation of the spatial resolution. This limitation can be overcome by removing the analyser grating resulting in a single-grating setup (XSGI). In order to verify the performance of XSGI concerning contrast and spatial resolution, a quantitative comparison of XSGI and XDGI tomograms of a human nerve was performed. Both techniques provide sufficient contrast to allow for the distinction of tissue types. The spatial resolution of the two-fold binned XSGI data set is improved by a factor of two in comparison to XDGI which underlies its performance in tomography of soft tissues. Another application for grating-based X-ray phase tomography is the simultaneous visualization of soft and hard tissues of a plaque-containing coronary artery. The simultaneous visualization of both tissues is important for the segmentation of the lumen. The segmented data can be used for flow simulations in order to obtain information about the three-dimensional wall shear stress distribution needed for the optimization of mechano-sensitive nanocontainers used for drug delivery.

Characterizations of individual human red blood cells from patients with diabetes mellitus (Conference Presentation)

NASA Astrophysics Data System (ADS)

Lee, SangYun; Jang, Seongsoo; Park, HyunJoo; Park, YongKeun

2016-03-01

We systematically measure the morphological, biochemical, and biomechanical properties of individual human red blood cells (RBCs) from patients with diabetes mellitus using quantitative phase imaging technique to characterize the diabetic red cells with respect to those of the healthy. The 3-D refractive index tomograms and 2-D dynamic membrane fluctuation maps of individual RBCs are reconstructed from a set of the retrieved complex optical fields at various laser incidence angles using the Common-path diffraction optical tomography, from which volume, surface area, sphericity, hemoglobin (Hb) concentration, Hb content, and membrane fluctuation are obtained simultaneously. The correlative relations among the retrieved red cell indices of diabetic and healthy RBCs are also investigated with capabilities of individual cell measurement. As expected, there are no significant alterations in morphologies (cellular volumes, surface area, and sphericity) between diabetic and healthy RBCs. However, despite the minute mean corpuscular Hb differences in cell blood count datasheet, the measured Hb concentrations and Hb contents of diabetic RBCs are statistically higher than those of healthy RBCs, which might be related to the glycation of Hb molecules by hyperglycemia. Meanwhile, the membrane fluctuations of diabetic RBCs are clearly diminished compared to healthy red cells, implying the significantly decreased RBC deformability. In particular, it seems that the membrane fluctuations have mild negative relationships with the reported HbA1c levels.

3-D Resistivity Tomography for Cliff Stability Study at the D-Day Pointe du Hoc Historic Site in Normandy, France

NASA Astrophysics Data System (ADS)

Udphuay, S.; Everett, M. E.; Guenther, T.; Warden, R. R.

2007-12-01

The D-Day invasion site at Pointe du Hoc in Normandy, France is one of the most important World War II battlefields. The site remains today a valuable historic cultural resource. However the site is vulnerable to cliff collapses that could endanger the observation post building and U.S. Ranger memorial located just landward of the sea stack, and an anti-aircraft gun emplacement, Col. Rudder's command post, located on the cliff edge about 200 m east of the observation post. A 3-D resistivity tomography incorporating extreme topography is used in this study to provide a detailed site stability assessment with special attention to these two buildings. Multi-electrode resistivity measurements were made across the cliff face and along the top of the cliff around the two at-risk buildings to map major subsurface fracture zones and void spaces that could indicate possible accumulations and pathways of groundwater. The ingress of acidic groundwater through the underlying carbonate formations enlarges pre-existing tectonic fractures via limestone dissolution and weakens the overall structural integrity of the cliff. The achieved 3-D resistivity tomograms provide diagnostic subsurface resistivity distributions. Resistive zones associated with subsurface void spaces have been located. These void spaces constitute a stability geohazard as they become significant drainage routes during and after periods of heavy rainfalls.

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

PubMed Central

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

2015-01-01

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

Fast X-Ray Fluorescence Microtomography of Hydrated Biological Samples

PubMed Central

Lombi, Enzo; de Jonge, Martin D.; Donner, Erica; Kopittke, Peter M.; Howard, Daryl L.; Kirkham, Robin; Ryan, Chris G.; Paterson, David

2011-01-01

Metals and metalloids play a key role in plant and other biological systems as some of them are essential to living organisms and all can be toxic at high concentrations. It is therefore important to understand how they are accumulated, complexed and transported within plants. In situ imaging of metal distribution at physiological relevant concentrations in highly hydrated biological systems is technically challenging. In the case of roots, this is mainly due to the possibility of artifacts arising during sample preparation such as cross sectioning. Synchrotron x-ray fluorescence microtomography has been used to obtain virtual cross sections of elemental distributions. However, traditionally this technique requires long data acquisition times. This has prohibited its application to highly hydrated biological samples which suffer both radiation damage and dehydration during extended analysis. However, recent advances in fast detectors coupled with powerful data acquisition approaches and suitable sample preparation methods can circumvent this problem. We demonstrate the heightened potential of this technique by imaging the distribution of nickel and zinc in hydrated plant roots. Although 3D tomography was still impeded by radiation damage, we successfully collected 2D tomograms of hydrated plant roots exposed to environmentally relevant metal concentrations for short periods of time. To our knowledge, this is the first published example of the possibilities offered by a new generation of fast fluorescence detectors to investigate metal and metalloid distribution in radiation-sensitive, biological samples. PMID:21674049

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.

Seismic Travel Time Tomography in Modeling Low Velocity Anomalies between the Boreholes

NASA Astrophysics Data System (ADS)

Octova, A.; Sule, R.

2018-04-01

Travel time cross-hole seismic tomography is applied to describing the structure of the subsurface. The sources are placed at one borehole and some receivers are placed in the others. First arrival travel time data that received by each receiver is used as the input data in seismic tomography method. This research is devided into three steps. The first step is reconstructing the synthetic model based on field parameters. Field parameters are divided into 24 receivers and 45 receivers. The second step is applying inversion process for the field data that consists of five pairs bore holes. The last step is testing quality of tomogram with resolution test. Data processing using FAST software produces an explicit shape and resemble the initial model reconstruction of synthetic model with 45 receivers. The tomography processing in field data indicates cavities in several place between the bore holes. Cavities are identified on BH2A-BH1, BH4A-BH2A and BH4A-BH5 with elongated and rounded structure. In resolution tests using a checker-board, anomalies still can be identified up to 2 meter x 2 meter size. Travel time cross-hole seismic tomography analysis proves this mothod is very good to describing subsurface structure and boundary layer. Size and anomalies position can be recognized and interpreted easily.

In situ Compressive Loading and Correlative Noninvasive Imaging of the Bone-periodontal Ligament-tooth Fibrous Joint

PubMed Central

Jang, Andrew T.; Lin, Jeremy D.; Seo, Youngho; Etchin, Sergey; Merkle, Arno; Fahey, Kevin; Ho, Sunita P.

2014-01-01

This study demonstrates a novel biomechanics testing protocol. The advantage of this protocol includes the use of an in situ loading device coupled to a high resolution X-ray microscope, thus enabling visualization of internal structural elements under simulated physiological loads and wet conditions. Experimental specimens will include intact bone-periodontal ligament (PDL)-tooth fibrous joints. Results will illustrate three important features of the protocol as they can be applied to organ level biomechanics: 1) reactionary force vs. displacement: tooth displacement within the alveolar socket and its reactionary response to loading, 2) three-dimensional (3D) spatial configuration and morphometrics: geometric relationship of the tooth with the alveolar socket, and 3) changes in readouts 1 and 2 due to a change in loading axis, i.e. from concentric to eccentric loads. Efficacy of the proposed protocol will be evaluated by coupling mechanical testing readouts to 3D morphometrics and overall biomechanics of the joint. In addition, this technique will emphasize on the need to equilibrate experimental conditions, specifically reactionary loads prior to acquiring tomograms of fibrous joints. It should be noted that the proposed protocol is limited to testing specimens under ex vivo conditions, and that use of contrast agents to visualize soft tissue mechanical response could lead to erroneous conclusions about tissue and organ-level biomechanics. PMID:24638035

Three-dimensional refractive index tomograms and deformability of individual human red blood cells from cord blood of newborn infants and maternal blood.

PubMed

Park, HyunJoo; Ahn, Taegyu; Kim, Kyoohyun; Lee, Sangyun; Kook, Song-Yi; Lee, Dongheon; Suh, In Bum; Na, Sunghun; Park, YongKeun

2015-01-01

Red blood cells (RBCs) from the cord blood of newborn infants have distinctive functions in fetal and infant development. To systematically investigate the biophysical characteristics of individual cord RBCs in newborn infants, a comparative study was performed on RBCs from the cord blood of newborn infants and from adult mothers or nonpregnant women using optical holographic microtomography. Optical measurements of the distributions of the three-dimensional refractive indices and the dynamic membrane fluctuations of individual RBCs were used to investigate the morphological, biochemical, and mechanical properties of cord, maternal, and adult RBCs at the individual cell level. The volume and surface area of the cord RBCs were significantly larger than those of the RBCs from nonpregnant women, and the cord RBCs had more flattened shapes than that of the RBCs in adults. In addition, the hemoglobin (Hb) content in the cord RBCs from newborns was significantly higher. The Hb concentration in the cord RBCs was higher than that in the nonpregnant women or maternal RBCs, but they were within the physiological range of adults. Interestingly, the amplitudes of the dynamic membrane fluctuations in cord RBCs were comparable to those in nonpregnant women and maternal RBCs, suggesting that the deformability of cord RBCs is similar to that of healthy RBCs in adults.

Giga-pixel lensfree holographic microscopy and tomography using color image sensors.

PubMed

Isikman, Serhan O; Greenbaum, Alon; Luo, Wei; Coskun, Ahmet F; Ozcan, Aydogan

2012-01-01

We report Giga-pixel lensfree holographic microscopy and tomography using color sensor-arrays such as CMOS imagers that exhibit Bayer color filter patterns. Without physically removing these color filters coated on the sensor chip, we synthesize pixel super-resolved lensfree holograms, which are then reconstructed to achieve ~350 nm lateral resolution, corresponding to a numerical aperture of ~0.8, across a field-of-view of ~20.5 mm(2). This constitutes a digital image with ~0.7 Billion effective pixels in both amplitude and phase channels (i.e., ~1.4 Giga-pixels total). Furthermore, by changing the illumination angle (e.g., ± 50°) and scanning a partially-coherent light source across two orthogonal axes, super-resolved images of the same specimen from different viewing angles are created, which are then digitally combined to synthesize tomographic images of the object. Using this dual-axis lensfree tomographic imager running on a color sensor-chip, we achieve a 3D spatial resolution of ~0.35 µm × 0.35 µm × ~2 µm, in x, y and z, respectively, creating an effective voxel size of ~0.03 µm(3) across a sample volume of ~5 mm(3), which is equivalent to >150 Billion voxels. We demonstrate the proof-of-concept of this lensfree optical tomographic microscopy platform on a color CMOS image sensor by creating tomograms of micro-particles as well as a wild-type C. elegans nematode.

High-pressure freezing and freeze substitution of Arabidopsis for electron microscopy.

PubMed

Austin, Jotham R

2014-01-01

The objectives of electron microscopy ultrastructural studies are to examine cellular architecture and relate the cell's structural machinery to dynamic functional roles. This aspiration is difficult to achieve if specimens have not been adequately preserved in a "living state"; hence specimen preparation is of the utmost importance for the success of any electron micrographic study. High-pressure freezing (HPF)/freeze substitution (FS) has long been recognized as the primer technique for the preservation of ultrastructure in biological samples. In most cases a basic HPF/freeze substitution protocol is sufficient to obtain superior ultrastructural preservation and structural contrast, which allows one to use more advanced microscopy techniques such as 3D electron tomography. However, for plant tissues, which have a thick cell wall, large water-filled vacuoles, and air spaces (all of which are detrimental to cryopreservation), these basic HPF/FS protocols often yield undesirable results. In particular, ice crystal artifacts and the staining of membrane systems are often poorly or negatively stained, which make 3D segmentation of a tomogram difficult. To overcome these problems, various aspects of the HPF/FS protocol can be altered, including the cryo-filler(s) used, freeze substitution cocktail, and the resin infiltration process. This chapter will describe these modifications for the preparation of plant tissues for routine electron microscopic studies, immunocytochemistry, and 3D tomographic electron imaging.

Elucidating Reaction Mechanisms on Quantum Computers

NASA Astrophysics Data System (ADS)

Wiebe, Nathan; Reiher, Markus; Svore, Krysta; Wecker, Dave; Troyer, Matthias

We show how a quantum computer can be employed to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical-computer simulations for such problems, to significantly increase their accuracy and enable hitherto intractable simulations. Detailed resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. This demonstrates that quantum computers will realistically be able to tackle important problems in chemistry that are both scientifically and economically significant.

A vectorized Lanczos eigensolver for high-performance computers

NASA Technical Reports Server (NTRS)

Bostic, Susan W.

1990-01-01

The computational strategies used to implement a Lanczos-based-method eigensolver on the latest generation of supercomputers are described. Several examples of structural vibration and buckling problems are presented that show the effects of using optimization techniques to increase the vectorization of the computational steps. The data storage and access schemes and the tools and strategies that best exploit the computer resources are presented. The method is implemented on the Convex C220, the Cray 2, and the Cray Y-MP computers. Results show that very good computation rates are achieved for the most computationally intensive steps of the Lanczos algorithm and that the Lanczos algorithm is many times faster than other methods extensively used in the past.

Presentation Software and the Single Computer.

ERIC Educational Resources Information Center

Brown, Cindy A.

1998-01-01

Shows how the "Kid Pix" software and a single multimedia computer can aid classroom instruction for kindergarten through second grade. Topics include using the computer as a learning center for small groups of students; making a "Kid Pix" slide show; using it as an electronic chalkboard; and creating curriculum-related…

Surface Curvatures Computation from Equidistance Contours

NASA Astrophysics Data System (ADS)

Tanaka, Hiromi T.; Kling, Olivier; Lee, Daniel T. L.

1990-03-01

The subject of our research is on the 3D shape representation problem for a special class of range image, one where the natural mode of the acquired range data is in the form of equidistance contours, as exemplified by a moire interferometry range system. In this paper we present a novel surface curvature computation scheme that directly computes the surface curvatures (the principal curvatures, Gaussian curvature and mean curvature) from the equidistance contours without any explicit computations or implicit estimates of partial derivatives. We show how the special nature of the equidistance contours, specifically, the dense information of the surface curves in the 2D contour plane, turns into an advantage for the computation of the surface curvatures. The approach is based on using simple geometric construction to obtain the normal sections and the normal curvatures. This method is general and can be extended to any dense range image data. We show in details how this computation is formulated and give an analysis on the error bounds of the computation steps showing that the method is stable. Computation results on real equidistance range contours are also shown.

Computer-based personality judgments are more accurate than those made by humans

PubMed Central

Youyou, Wu; Kosinski, Michal; Stillwell, David

2015-01-01

Judging others’ personalities is an essential skill in successful social living, as personality is a key driver behind people’s interactions, behaviors, and emotions. Although accurate personality judgments stem from social-cognitive skills, developments in machine learning show that computer models can also make valid judgments. This study compares the accuracy of human and computer-based personality judgments, using a sample of 86,220 volunteers who completed a 100-item personality questionnaire. We show that (i) computer predictions based on a generic digital footprint (Facebook Likes) are more accurate (r = 0.56) than those made by the participants’ Facebook friends using a personality questionnaire (r = 0.49); (ii) computer models show higher interjudge agreement; and (iii) computer personality judgments have higher external validity when predicting life outcomes such as substance use, political attitudes, and physical health; for some outcomes, they even outperform the self-rated personality scores. Computers outpacing humans in personality judgment presents significant opportunities and challenges in the areas of psychological assessment, marketing, and privacy. PMID:25583507

Computer-based personality judgments are more accurate than those made by humans.

PubMed

Youyou, Wu; Kosinski, Michal; Stillwell, David

2015-01-27

Judging others' personalities is an essential skill in successful social living, as personality is a key driver behind people's interactions, behaviors, and emotions. Although accurate personality judgments stem from social-cognitive skills, developments in machine learning show that computer models can also make valid judgments. This study compares the accuracy of human and computer-based personality judgments, using a sample of 86,220 volunteers who completed a 100-item personality questionnaire. We show that (i) computer predictions based on a generic digital footprint (Facebook Likes) are more accurate (r = 0.56) than those made by the participants' Facebook friends using a personality questionnaire (r = 0.49); (ii) computer models show higher interjudge agreement; and (iii) computer personality judgments have higher external validity when predicting life outcomes such as substance use, political attitudes, and physical health; for some outcomes, they even outperform the self-rated personality scores. Computers outpacing humans in personality judgment presents significant opportunities and challenges in the areas of psychological assessment, marketing, and privacy.

The Easy Way to Create Computer Slide Shows.

ERIC Educational Resources Information Center

Anderson, Mary Alice

1995-01-01

Discusses techniques for creating computer slide shows. Topics include memory; format; color use; HyperCard and CD-ROM; font styles and sizes; graphs and graphics; the slide show option; special effects; and tips for effective presentation. (Author/AEF)

Deformation processes in orogenic wedges: New methods and application to Northwestern Washington State

NASA Astrophysics Data System (ADS)

Thissen, Christopher J.

Permanent deformation records aspects of how material moves through a tectonic environment. The methods required to measure deformation vary based on rock type, deformation process, and the geological question of interest. In this thesis we develop two new methods for measuring permanent deformation in rocks. The first method uses the autocorrelation function to measure the anisotropy present in two-dimensional photomicrographs and three-dimensional X-ray tomograms of rocks. The method returns very precise estimates for the deformation parameters and works best for materials where the deformation is recorded as a shape change of distinct fabric elements, such as grains. Our method also includes error estimates. Image analysis techniques can focus the method on specific fabric elements, such as quartz grains. The second method develops a statistical technique for measuring the symmetry in a distribution of crystal orientations, called a lattice-preferred orientation (LPO). We show that in many cases the symmetry of the LPO directly constrains the symmetry of the deformation, such axial flattening vs. pure shear vs. simple shear. In addition to quantifying the symmetry, the method uses the full crystal orientation to estimate symmetry rather than pole figures. Pole figure symmetry can often be misleading. This method works best for crystal orientations measured in samples deformed by dislocation creep, but otherwise can be used on any mineral without requiring information about slip systems. In Chapter 4 we show how deformation measurements can be used to inform regional tectonic and orogenic models in the Pacific Northwestern United States. A suite of measurements from the Olympic Mountains shows that uplift and deformation of the range is consistent with an orogenic wedge model driven by subduction of the Juan de Fuca plate, and not northward forearc migration of the Oregon block. The deformation measurements also show that deformation within the Olympic Mountains is essentially two-dimensional. We use this constraint to develop a suite of orogenic deformation models that use slab height and erosion rate data as boundary conditions. We use the models to show that influx of sediments distributed along an accretionary front can greatly reduce deformation required to maintain wedge taper. Due to the two-dimensional nature of deformation in the Olympics, a series of two-dimensional transects across the peninsula provides an approximation for non-elastic deformation across the Peninsula. We show how the shallow slab height and deeper exhumation at the core of peninsula led to the domal structure of the Olympics. This model also explains the counter-clockwise vertical axis rotations north of the peninsula, and clockwise rotations south of the peninsula through horizontal shear, similar to opening a gate. Finally, the horizontal surface velocities predicted by the models suggests that up to 15% of GPS velocities may reflect non-elastic, permanent translation of material towards the rear of the wedge.

Comparative Analysis Between Computed and Conventional Inferior Alveolar Nerve Block Techniques.

PubMed

Araújo, Gabriela Madeira; Barbalho, Jimmy Charles Melo; Dias, Tasiana Guedes de Souza; Santos, Thiago de Santana; Vasconcellos, Ricardo José de Holanda; de Morais, Hécio Henrique Araújo

2015-11-01

The aim of this randomized, double-blind, controlled trial was to compare the computed and conventional inferior alveolar nerve block techniques in symmetrically positioned inferior third molars. Both computed and conventional anesthetic techniques were performed in 29 healthy patients (58 surgeries) aged between 18 and 40 years. The anesthetic of choice was 2% lidocaine with 1: 200,000 epinephrine. The Visual Analogue Scale assessed the pain variable after anesthetic infiltration. Patient satisfaction was evaluated using the Likert Scale. Heart and respiratory rates, mean time to perform technique, and the need for additional anesthesia were also evaluated. Pain variable means were higher for the conventional technique as compared with computed, 3.45 ± 2.73 and 2.86 ± 1.96, respectively, but no statistically significant differences were found (P > 0.05). Patient satisfaction showed no statistically significant differences. The average computed technique runtime and the conventional were 3.85 and 1.61 minutes, respectively, showing statistically significant differences (P <0.001). The computed anesthetic technique showed lower mean pain perception, but did not show statistically significant differences when contrasted to the conventional technique.

Iterated Gate Teleportation and Blind Quantum Computation.

PubMed

Pérez-Delgado, Carlos A; Fitzsimons, Joseph F

2015-06-05

Blind quantum computation allows a user to delegate a computation to an untrusted server while keeping the computation hidden. A number of recent works have sought to establish bounds on the communication requirements necessary to implement blind computation, and a bound based on the no-programming theorem of Nielsen and Chuang has emerged as a natural limiting factor. Here we show that this constraint only holds in limited scenarios, and show how to overcome it using a novel method of iterated gate teleportations. This technique enables drastic reductions in the communication required for distributed quantum protocols, extending beyond the blind computation setting. Applied to blind quantum computation, this technique offers significant efficiency improvements, and in some scenarios offers an exponential reduction in communication requirements.

Elucidating reaction mechanisms on quantum computers.

PubMed

Reiher, Markus; Wiebe, Nathan; Svore, Krysta M; Wecker, Dave; Troyer, Matthias

2017-07-18

With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources.

Elucidating reaction mechanisms on quantum computers

PubMed Central

Reiher, Markus; Wiebe, Nathan; Svore, Krysta M.; Wecker, Dave; Troyer, Matthias

2017-01-01

With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources. PMID:28674011

Elucidating reaction mechanisms on quantum computers

NASA Astrophysics Data System (ADS)

Reiher, Markus; Wiebe, Nathan; Svore, Krysta M.; Wecker, Dave; Troyer, Matthias

2017-07-01

With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources.

Usefulness of the automatic quantitative estimation tool for cerebral blood flow: clinical assessment of the application software tool AQCEL.

PubMed

Momose, Mitsuhiro; Takaki, Akihiro; Matsushita, Tsuyoshi; Yanagisawa, Shin; Yano, Kesato; Miyasaka, Tadashi; Ogura, Yuka; Kadoya, Masumi

2011-01-01

AQCEL enables automatic reconstruction of single-photon emission computed tomogram (SPECT) without image degradation and quantitative analysis of cerebral blood flow (CBF) after the input of simple parameters. We ascertained the usefulness and quality of images obtained by the application software AQCEL in clinical practice. Twelve patients underwent brain perfusion SPECT using technetium-99m ethyl cysteinate dimer at rest and after acetazolamide (ACZ) loading. Images reconstructed using AQCEL were compared with those reconstructed using conventional filtered back projection (FBP) method for qualitative estimation. Two experienced nuclear medicine physicians interpreted the image quality using the following visual scores: 0, same; 1, slightly superior; 2, superior. For quantitative estimation, the mean CBF values of the normal hemisphere of the 12 patients using ACZ calculated by the AQCEL method were compared with those calculated by the conventional method. The CBF values of the 24 regions of the 3-dimensional stereotaxic region of interest template (3DSRT) calculated by the AQCEL method at rest and after ACZ loading were compared to those calculated by the conventional method. No significant qualitative difference was observed between the AQCEL and conventional FBP methods in the rest study. The average score by the AQCEL method was 0.25 ± 0.45 and that by the conventional method was 0.17 ± 0.39 (P = 0.34). There was a significant qualitative difference between the AQCEL and conventional methods in the ACZ loading study. The average score for AQCEL was 0.83 ± 0.58 and that for the conventional method was 0.08 ± 0.29 (P = 0.003). During quantitative estimation using ACZ, the mean CBF values of 12 patients calculated by the AQCEL method were 3-8% higher than those calculated by the conventional method. The square of the correlation coefficient between these methods was 0.995. While comparing the 24 3DSRT regions of 12 patients, the squares of the correlation coefficient between AQCEL and conventional methods were 0.973 and 0.986 for the normal and affected sides at rest, respectively, and 0.977 and 0.984 for the normal and affected sides after ACZ loading, respectively. The quality of images reconstructed using the application software AQCEL were superior to that obtained using conventional method after ACZ loading, and high correlations were shown in quantity at rest and after ACZ loading. This software can be applied to clinical practice and is a useful tool for improvement of reproducibility and throughput.

On Undecidability Aspects of Resilient Computations and Implications to Exascale

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

Rao, Nageswara S

2014-01-01

Future Exascale computing systems with a large number of processors, memory elements and interconnection links, are expected to experience multiple, complex faults, which affect both applications and operating-runtime systems. A variety of algorithms, frameworks and tools are being proposed to realize and/or verify the resilience properties of computations that guarantee correct results on failure-prone computing systems. We analytically show that certain resilient computation problems in presence of general classes of faults are undecidable, that is, no algorithms exist for solving them. We first show that the membership verification in a generic set of resilient computations is undecidable. We describe classesmore » of faults that can create infinite loops or non-halting computations, whose detection in general is undecidable. We then show certain resilient computation problems to be undecidable by using reductions from the loop detection and halting problems under two formulations, namely, an abstract programming language and Turing machines, respectively. These two reductions highlight different failure effects: the former represents program and data corruption, and the latter illustrates incorrect program execution. These results call for broad-based, well-characterized resilience approaches that complement purely computational solutions using methods such as hardware monitors, co-designs, and system- and application-specific diagnosis codes.« less

Simple proof of equivalence between adiabatic quantum computation and the circuit model.

PubMed

Mizel, Ari; Lidar, Daniel A; Mitchell, Morgan

2007-08-17

We prove the equivalence between adiabatic quantum computation and quantum computation in the circuit model. An explicit adiabatic computation procedure is given that generates a ground state from which the answer can be extracted. The amount of time needed is evaluated by computing the gap. We show that the procedure is computationally efficient.

Gender Differences in the Use of Computers, Programming, and Peer Interactions in Computer Science Classrooms

ERIC Educational Resources Information Center

Stoilescu, Dorian; Egodawatte, Gunawardena

2010-01-01

Research shows that female and male students in undergraduate computer science programs view computer culture differently. Female students are interested more in the use of computers than in doing programming, whereas male students see computer science mainly as a programming activity. The overall purpose of our research was not to find new…

High school computer science education paves the way for higher education: the Israeli case

NASA Astrophysics Data System (ADS)

Armoni, Michal; Gal-Ezer, Judith

2014-07-01

The gap between enrollments in higher education computing programs and the high-tech industry's demands is widely reported, and is especially prominent for women. Increasing the availability of computer science education in high school is one of the strategies suggested in order to address this gap. We look at the connection between exposure to computer science in high school and pursuing computing in higher education. We also examine the gender gap, in the context of high school computer science education. We show that in Israel, students who took the high-level computer science matriculation exam were more likely to pursue computing in higher education. Regarding the issue of gender, we will show that, in general, in Israel the difference between males and females who take computer science in high school is relatively small, and a larger, though still not very large difference exists only for the highest exam level. In addition, exposing females to high-level computer science in high school has more relative impact on pursuing higher education in computing.

Assessing the physical loading of wearable computers.

PubMed

Knight, James F; Baber, Chris

2007-03-01

Wearable computers enable workers to interact with computer equipment in situations where previously they were unable. Attaching a computer to the body though has an unknown physical effect. This paper reports a methodology for addressing this, by assessing postural effects and the effect of added weight. Using the example of arm-mounted computers (AMCs), the paper shows that adopting a posture to interact with an AMC generates fatiguing levels of stress and a load of 0.54 kg results in increased level of stress and increased rate of fatigue. The paper shows that, due to poor postures adopted when wearing and interacting with computers and the weight of the device attached to the body, one possible outcome for prolonged exposure is the development of musculoskeletal disorders.

Universal quantum computation with little entanglement.

PubMed

Van den Nest, Maarten

2013-02-08

We show that universal quantum computation can be achieved in the standard pure-state circuit model while the entanglement entropy of every bipartition is small in each step of the computation. The entanglement entropy required for large-scale quantum computation even tends to zero. Moreover we show that the same conclusion applies to many entanglement measures commonly used in the literature. This includes e.g., the geometric measure, localizable entanglement, multipartite concurrence, squashed entanglement, witness-based measures, and more generally any entanglement measure which is continuous in a certain natural sense. These results demonstrate that many entanglement measures are unsuitable tools to assess the power of quantum computers.

Computer Series, 87.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1987-01-01

Included are two articles related to the use of computers. One activity is a computer exercise in chemical reaction engineering and applied kinetics for undergraduate college students. The second article shows how computer-assisted analysis can be used with reaction rate data. (RH)

Making classical ground-state spin computing fault-tolerant.

PubMed

Crosson, I J; Bacon, D; Brown, K R

2010-09-01

We examine a model of classical deterministic computing in which the ground state of the classical system is a spatial history of the computation. This model is relevant to quantum dot cellular automata as well as to recent universal adiabatic quantum computing constructions. In its most primitive form, systems constructed in this model cannot compute in an error-free manner when working at nonzero temperature. However, by exploiting a mapping between the partition function for this model and probabilistic classical circuits we are able to show that it is possible to make this model effectively error-free. We achieve this by using techniques in fault-tolerant classical computing and the result is that the system can compute effectively error-free if the temperature is below a critical temperature. We further link this model to computational complexity and show that a certain problem concerning finite temperature classical spin systems is complete for the complexity class Merlin-Arthur. This provides an interesting connection between the physical behavior of certain many-body spin systems and computational complexity.

26 CFR 1.513-3 - Qualified convention and trade show activity.

Code of Federal Regulations, 2011 CFR

2011-04-01

... purpose of the sponsoring organization in conducting the show is the education of its members, or the... digital computers produced by various computer manufacturers. X is a qualifying organization under section...

Efficient calibration for imperfect computer models

DOE PAGES

Tuo, Rui; Wu, C. F. Jeff

2015-12-01

Many computer models contain unknown parameters which need to be estimated using physical observations. Furthermore, the calibration method based on Gaussian process models may lead to unreasonable estimate for imperfect computer models. In this work, we extend their study to calibration problems with stochastic physical data. We propose a novel method, called the L 2 calibration, and show its semiparametric efficiency. The conventional method of the ordinary least squares is also studied. Theoretical analysis shows that it is consistent but not efficient. Here, numerical examples show that the proposed method outperforms the existing ones.

Loyalty to Computer Terminals: Is it Anthropomorphism or Consistency?

ERIC Educational Resources Information Center

Sundar, S. Shyam

2004-01-01

The psychological tendency to behave socially with a computer is quite well documented in the literature. But does the short-term socialness of human-computer interaction extend over to long-term social relationships with computers? In particular, do we show loyalty to particular computer terminals over a period of time? An electronic observation…

Parent's Guide to Computers in Education.

ERIC Educational Resources Information Center

Moursund, David

Addressed to the parents of children taking computer courses in school, this booklet outlines the rationales for computer use in schools and explains for a lay audience the features and functions of computers. A look at the school of the future shows computers aiding the study of reading, writing, arithmetic, geography, and history. The features…

Data Storage and Transfer | High-Performance Computing | NREL

Science.gov Websites

High-Performance Computing (HPC) systems. Photo of computer server wiring and lights, blurred to show data. WinSCP for Windows File Transfers Use to transfer files from a local computer to a remote computer. Robinhood for File Management Use this tool to manage your data files on Peregrine. Best

Ramsey numbers and adiabatic quantum computing.

PubMed

Gaitan, Frank; Clark, Lane

2012-01-06

The graph-theoretic Ramsey numbers are notoriously difficult to calculate. In fact, for the two-color Ramsey numbers R(m,n) with m, n≥3, only nine are currently known. We present a quantum algorithm for the computation of the Ramsey numbers R(m,n). We show how the computation of R(m,n) can be mapped to a combinatorial optimization problem whose solution can be found using adiabatic quantum evolution. We numerically simulate this adiabatic quantum algorithm and show that it correctly determines the Ramsey numbers R(3,3) and R(2,s) for 5≤s≤7. We then discuss the algorithm's experimental implementation, and close by showing that Ramsey number computation belongs to the quantum complexity class quantum Merlin Arthur.

Dental age assessment of Maltese children and adolescents. Development of a reference dataset and comparison with a United Kingdom Caucasian reference dataset.

PubMed

Elshehawi, Waleed; Alsaffar, Hani; Roberts, Graham; Lucas, Victoria; McDonald, Fraser; Camilleri, Simon

2016-04-01

The purpose of this study was to develop and validate a Reference Data Set for Dental Age Assessment of the Maltese population and compare the mean Age of Attainment to a UK Caucasian Reference Data Set. The Maltese Reference Data Set was developed from 1593 Dental Panoramic Tomograms of patients aged between 4 and 26 years, taken from the radiographic archives of the Dental Department, Mater Dei Hospital, Malta. Tooth Development Stages were recorded for all 16 maxillary and mandibular permanent teeth on the left side and both permanent third molars on the right, according to Demirjian's staging method. Summary and percentile data were calculated for each Tooth Development Stage, including the mean Age of Attainment. These means were used to estimate the Dental Age of each subject in the study sample using the simple unweighted average method. The estimated Dental Age was compared to the gold standard of the Chronological Age. Comparison of the Maltese and UK Caucasian Reference Data Set was by a series of t-tests, carried out for each paired Tooth Development Stage by gender. The mean Age of Attainment was slightly higher for the Maltese than the UK Caucasians in both males and females. However there was no statistically significant difference between the Chronological Age and Dental Age for either sex. Copyright © 2016 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Conceptual design and optimization of a plastic scintillator array for 2D tomography using a compact D-D fast neutron generator.

PubMed

Adams, Robert; Zboray, Robert; Cortesi, Marco; Prasser, Horst-Michael

2014-04-01

A conceptual design optimization of a fast neutron tomography system was performed. The system is based on a compact deuterium-deuterium fast neutron generator and an arc-shaped array of individual neutron detectors. The array functions as a position sensitive one-dimensional detector allowing tomographic reconstruction of a two-dimensional cross section of an object up to 10 cm across. Each individual detector is to be optically isolated and consists of a plastic scintillator and a Silicon Photomultiplier for measuring light produced by recoil protons. A deterministic geometry-based model and a series of Monte Carlo simulations were used to optimize the design geometry parameters affecting the reconstructed image resolution. From this, it is expected that with an array of 100 detectors a reconstructed image resolution of ~1.5mm can be obtained. Other simulations were performed in order to optimize the scintillator depth (length along the neutron path) such that the best ratio of direct to scattered neutron counts is achieved. This resulted in a depth of 6-8 cm and an expected detection efficiency of 33-37%. Based on current operational capabilities of a prototype neutron generator being developed at the Paul Scherrer Institute, planned implementation of this detector array design should allow reconstructed tomograms to be obtained with exposure times on the order of a few hours. Copyright © 2014 Elsevier Ltd. All rights reserved.

Geometric reconstruction using tracked ultrasound strain imaging

NASA Astrophysics Data System (ADS)

Pheiffer, Thomas S.; Simpson, Amber L.; Ondrake, Janet E.; Miga, Michael I.

2013-03-01

The accurate identification of tumor margins during neurosurgery is a primary concern for the surgeon in order to maximize resection of malignant tissue while preserving normal function. The use of preoperative imaging for guidance is standard of care, but tumor margins are not always clear even when contrast agents are used, and so margins are often determined intraoperatively by visual and tactile feedback. Ultrasound strain imaging creates a quantitative representation of tissue stiffness which can be used in real-time. The information offered by strain imaging can be placed within a conventional image-guidance workflow by tracking the ultrasound probe and calibrating the image plane, which facilitates interpretation of the data by placing it within a common coordinate space with preoperative imaging. Tumor geometry in strain imaging is then directly comparable to the geometry in preoperative imaging. This paper presents a tracked ultrasound strain imaging system capable of co-registering with preoperative tomograms and also of reconstructing a 3D surface using the border of the strain lesion. In a preliminary study using four phantoms with subsurface tumors, tracked strain imaging was registered to preoperative image volumes and then tumor surfaces were reconstructed using contours extracted from strain image slices. The volumes of the phantom tumors reconstructed from tracked strain imaging were approximately between 1.5 to 2.4 cm3, which was similar to the CT volumes of 1.0 to 2.3 cm3. Future work will be done to robustly characterize the reconstruction accuracy of the system.

The predictive value of 201Tl rest-redistribution and 18F-fluorodeoxyglucose SPECT for wall motion recovery after recent reperfused myocardial infarction.

PubMed

González, Patricio; Massardo, Teresa; Coll, Claudia; Humeres, Pamela; Sierralta, Paulina; Jofré, M Josefina; Yovanovich, Jorge; Aramburu, Ivonne; Brugère, Solange; Chamorro, Hernán

2004-04-01

201Tl and 18F-FDG are useful for acute myocardial infarction (MI) assessment. The goal of this study was to compare their predictive value for wall motion recovery in the culprit area after a recent reperfused MI using SPECT technique. Forty-one patients (mean age: 56 +/- 12 years) were included, 81% of them male; all were studied within 1-24 days post MI. They underwent angioplasty in 27 cases (12 primary); bypass grafting in 10 cases and successful thrombolysis in 4. SPECT 201Tl injected at rest and redistribution (R-R) and also 18F-FDG, were performed on different days. Processed tomograms were interpreted blinded to clinical or angiographic data. Segmental wall motion assessed with echocardiography at baseline was compared with the 3 month follow up. Sensitivity [Confidence Interval] for 201Tl R-R was 74.6% [60.5-84.5], for FDG it was 82.1% [70.8-90.4]; specificities were 73% [64.3-80.5] and 54.8% [45.6-63.7], respectively. 18F-FDG tended to be more sensitive than 201Tl R-R, but the latter was more specific (p < 0.0004). Both 201Tl RR and 18F-FDG presented high negative predictive value (p: ns). In recent MI, SPECT 201Tl R-R is a valuable and widely available technique for viability detection, with similar sensitivity and significant better specificity than SPECT 18F-FDG.

3D Doppler Tomography of the X-Ray Binary System Cygnus X-1 from Spectral Observations in 2007 in the HeII λ 4686 Å Line

NASA Astrophysics Data System (ADS)

Agafonov, M. I.; Karitskaya, E. A.; Sharova, O. I.; Bochkarev, N. G.; Zharikov, S. V.; Butenko, G. Z.; Bondar', A. V.; Sidorov, M. Yu.

2018-02-01

The results of a 3D Doppler tomography analysis for the X-ray binary system Cyg X-1 in the HeII λ 4686 Å line are presented. Information about the motions of gaseous flows outside the orbital plane has been obtained for the first time. Line profiles obtained in June 2007 on the 2-m telescope of the Terskol Branch of the Institute of Astronomy (Russia) and on the 2.1-m telescope of the National Astronomical Observatory of Mexico were used. A detailed analysis of these spectral data is presented: the distribution of the data in time, distribution of orbital phases for the projections, comparison of the line profile shapes for the data from two observatories. The geometry of the total transfer function obtained in the reconstruction is considered. The possibility of applying the profiles obtained to realize 3D tomography is justified. The resolution of the constructed 3D tomogram in velocity space is 60 × 60 × 40 km/s for V x , V y , V z . Fifteen cross sections for 15 different V z values perpendicular to the orbital plane are presented. The intensity distributions corresponding to the velocities of gaseous structures in the binary system are obtained. The reconstruction was realized using the radio-astronomical approach, developed for solving problems in tomography with a limited number of projections.

3D quantitative phase imaging of neural networks using WDT

NASA Astrophysics Data System (ADS)

Kim, Taewoo; Liu, S. C.; Iyer, Raj; Gillette, Martha U.; Popescu, Gabriel

2015-03-01

White-light diffraction tomography (WDT) is a recently developed 3D imaging technique based on a quantitative phase imaging system called spatial light interference microscopy (SLIM). The technique has achieved a sub-micron resolution in all three directions with high sensitivity granted by the low-coherence of a white-light source. Demonstrations of the technique on single cell imaging have been presented previously; however, imaging on any larger sample, including a cluster of cells, has not been demonstrated using the technique. Neurons in an animal body form a highly complex and spatially organized 3D structure, which can be characterized by neuronal networks or circuits. Currently, the most common method of studying the 3D structure of neuron networks is by using a confocal fluorescence microscope, which requires fluorescence tagging with either transient membrane dyes or after fixation of the cells. Therefore, studies on neurons are often limited to samples that are chemically treated and/or dead. WDT presents a solution for imaging live neuron networks with a high spatial and temporal resolution, because it is a 3D imaging method that is label-free and non-invasive. Using this method, a mouse or rat hippocampal neuron culture and a mouse dorsal root ganglion (DRG) neuron culture have been imaged in order to see the extension of processes between the cells in 3D. Furthermore, the tomogram is compared with a confocal fluorescence image in order to investigate the 3D structure at synapses.

Regional cerebral blood flow measurement with intravenous ( sup 15 O)water bolus and ( sup 18 F)fluoromethane inhalation

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

Herholz, K.; Pietrzyk, U.; Wienhard, K.

1989-09-01

In 20 patients with ischemic cerebrovascular disease, classic migraine, or angiomas, we compared paired dynamic positron emission tomographic measurements of regional cerebral blood flow using both ({sup 15}O)water and ({sup 18}F)fluoromethane as tracers. Cerebral blood flow was also determined according to the autoradiographic technique with a bolus injection of ({sup 15}O)water. There were reasonable overall correlations between dynamic ({sup 15}O)water and ({sup 18}F)fluoromethane values for cerebral blood flow (r = 0.82) and between dynamic and autoradiographic ({sup 15}O)water values for cerebral blood flow (r = 0.83). We found a close correspondence between abnormal pathologic findings and visually evaluated cerebral bloodmore » flow tomograms obtained with the two tracers. On average, dynamic ({sup 15}O)water cerebral blood flow was 6% lower than that measured with ({sup 18}F)fluoromethane. There also was a general trend toward a greater underestimation with ({sup 15}O)water in high-flow areas, particularly in hyperemic areas, probably due to incomplete first-pass extraction of ({sup 15}O)water. Underestimation was not detected in low-flow areas or in the cerebellum. Absolute cerebral blood flow values were less closely correlated between tracers and techniques than cerebral blood flow patterns. The variability of the relation between absolute flow values was probably caused by confounding effects of the variation in the circulatory delay time. The autoradiographic technique was most sensitive to this type error.« less

3D nanoscale imaging of biological samples with laboratory-based soft X-ray sources

NASA Astrophysics Data System (ADS)

Dehlinger, Aurélie; Blechschmidt, Anne; Grötzsch, Daniel; Jung, Robert; Kanngießer, Birgit; Seim, Christian; Stiel, Holger

2015-09-01

In microscopy, where the theoretical resolution limit depends on the wavelength of the probing light, radiation in the soft X-ray regime can be used to analyze samples that cannot be resolved with visible light microscopes. In the case of soft X-ray microscopy in the water-window, the energy range of the radiation lies between the absorption edges of carbon (at 284 eV, 4.36 nm) and oxygen (543 eV, 2.34 nm). As a result, carbon-based structures, such as biological samples, posses a strong absorption, whereas e.g. water is more transparent to this radiation. Microscopy in the water-window, therefore, allows the structural investigation of aqueous samples with resolutions of a few tens of nanometers and a penetration depth of up to 10μm. The development of highly brilliant laser-produced plasma-sources has enabled the transfer of Xray microscopy, that was formerly bound to synchrotron sources, to the laboratory, which opens the access of this method to a broader scientific community. The Laboratory Transmission X-ray Microscope at the Berlin Laboratory for innovative X-ray technologies (BLiX) runs with a laser produced nitrogen plasma that emits radiation in the soft X-ray regime. The mentioned high penetration depth can be exploited to analyze biological samples in their natural state and with several projection angles. The obtained tomogram is the key to a more precise and global analysis of samples originating from various fields of life science.

Numerical Analysis of the Effect of Particle Shape and Adhesion on the Segregation of Powder Mixtures

NASA Astrophysics Data System (ADS)

Alizadeh Behjani, Mohammadreza; Hassanpour, Ali; Ghadiri, Mojtaba; Bayly, Andrew

2017-06-01

Segregation of granules is an undesired phenomenon in which particles in a mixture separate from each other based on the differences in their physical and chemical properties. It is, therefore, crucial to control the homogeneity of the system by applying appropriate techniques. This requires a fundamental understanding of the underlying mechanisms. In this study, the effect of particle shape and cohesion has been analysed. As a model system prone to segregation, a ternary mixture of particles representing the common ingredients of home washing powders, namely, spray dried detergent powders, tetraacetylethylenediamine, and enzyme placebo (as the minor ingredient) during heap formation is modelled numerically by the Discrete Element Method (DEM) with an aim to investigate the effect of cohesion/adhesion of the minor components on segregation quality. Non-spherical particle shapes are created in DEM using the clumped-sphere method based on their X-ray tomograms. Experimentally, inter particle adhesion is generated by coating the minor ingredient (enzyme placebo) with Polyethylene Glycol 400 (PEG 400). The JKR theory is used to model the cohesion/adhesion of coated enzyme placebo particles in the simulation. Tests are carried out experimentally and simulated numerically by mixing the placebo particles (uncoated and coated) with the other ingredients and pouring them in a test box. The simulation and experimental results are compared qualitatively and quantitatively. It is found that coating the minor ingredient in the mixture reduces segregation significantly while the change in flowability of the system is negligible.

Concepts and Preliminary Data Toward the Realization of Image-guided Liver Surgery

PubMed Central

Cash, David M.; Miga, Michael I.; Glasgow, Sean C.; Dawant, Benoit M.; Clements, Logan W.; Cao, Zhujiang; Galloway, Robert L.; Chapman, William C.

2013-01-01

Image-guided surgery provides navigational assistance to the surgeon by displaying the surgical probe position on a set of preoperative tomograms in real time. In this study, the feasibility of implementing image-guided surgery concepts into liver surgery was examined during eight hepatic resection procedures. Preoperative tomographic image data were acquired and processed. Accompanying intraoperative data on liver shape and position were obtained through optically tracked probes and laser range scanning technology. The preoperative and intraoperative representations of the liver surface were aligned using the iterative closest point surface matching algorithm. Surface registrations resulted in mean residual errors from 2 to 6 mm, with errors of target surface regions being below a stated goal of 1 cm. Issues affecting registration accuracy include liver motion due to respiration, the quality of the intraoperative surface data, and intraoperative organ deformation. Respiratory motion was quantified during the procedures as cyclical, primarily along the cranial–caudal direction. The resulting registrations were more robust and accurate when using laser range scanning to rapidly acquire thousands of points on the liver surface and when capturing unique geometric regions on the liver surface, such as the inferior edge. Finally, finite element models recovered much of the observed intraoperative deformation, further decreasing errors in the registration. Image-guided liver surgery has shown the potential to provide surgeons with important navigation aids that could increase the accuracy of targeting lesions and the number of patients eligible for surgical resection. PMID:17458587

Monitoring groundwater-surface water interaction using time-series and time-frequency analysis of transient three-dimensional electrical resistivity changes

USGS Publications Warehouse

Johnson, Timothy C.; Slater, Lee D.; Ntarlagiannis, Dimitris; Day-Lewis, Frederick D.; Elwaseif, Mehrez

2012-01-01

Time-lapse resistivity imaging is increasingly used to monitor hydrologic processes. Compared to conventional hydrologic measurements, surface time-lapse resistivity provides superior spatial coverage in two or three dimensions, potentially high-resolution information in time, and information in the absence of wells. However, interpretation of time-lapse electrical tomograms is complicated by the ever-increasing size and complexity of long-term, three-dimensional (3-D) time series conductivity data sets. Here we use 3-D surface time-lapse electrical imaging to monitor subsurface electrical conductivity variations associated with stage-driven groundwater-surface water interactions along a stretch of the Columbia River adjacent to the Hanford 300 near Richland, Washington, USA. We reduce the resulting 3-D conductivity time series using both time-series and time-frequency analyses to isolate a paleochannel causing enhanced groundwater-surface water interactions. Correlation analysis on the time-lapse imaging results concisely represents enhanced groundwater-surface water interactions within the paleochannel, and provides information concerning groundwater flow velocities. Time-frequency analysis using the Stockwell (S) transform provides additional information by identifying the stage periodicities driving groundwater-surface water interactions due to upstream dam operations, and identifying segments in time-frequency space when these interactions are most active. These results provide new insight into the distribution and timing of river water intrusion into the Hanford 300 Area, which has a governing influence on the behavior of a uranium plume left over from historical nuclear fuel processing operations.

Computer Learning Through Piaget's Eyes.

ERIC Educational Resources Information Center

Huber, Leonard N.

1985-01-01

Discusses Piaget's pre-operational, concrete operational, and formal operational stages and shows how this information sheds light on how children approach computers and computing, particularly with the LOGO programming language. (JN)

PREVIEW: Computer Assistance for Visual Management of Forested Landscapes

Treesearch

Erik Myklestad; J. Alan Wagar

1976-01-01

The PREVIEW computer program facilitates visual management of forested landscapes by generating perspective drawings that show proposed timber harvesting and regrowth throughout a rotation. Drawings show how changes would appear from selected viewing points and show landscapes as either a grid of distorted squares or by symbols representing trees, clearings, water,...

Computer and video game addiction-a comparison between game users and non-game users.

PubMed

Weinstein, Aviv Malkiel

2010-09-01

Computer game addiction is excessive or compulsive use of computer and video games that may interfere with daily life. It is not clear whether video game playing meets diagnostic criteria for Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV). First objective is to review the literature on computer and video game addiction over the topics of diagnosis, phenomenology, epidemiology, and treatment. Second objective is to describe a brain imaging study measuring dopamine release during computer game playing. Article search of 15 published articles between 2000 and 2009 in Medline and PubMed on computer and video game addiction. Nine abstinent "ecstasy" users and 8 control subjects were scanned at baseline and after performing on a motorbike riding computer game while imaging dopamine release in vivo with [123I] IBZM and single photon emission computed tomography (SPECT). Psycho-physiological mechanisms underlying computer game addiction are mainly stress coping mechanisms, emotional reactions, sensitization, and reward. Computer game playing may lead to long-term changes in the reward circuitry that resemble the effects of substance dependence. The brain imaging study showed that healthy control subjects had reduced dopamine D2 receptor occupancy of 10.5% in the caudate after playing a motorbike riding computer game compared with baseline levels of binding consistent with increased release and binding to its receptors. Ex-chronic "ecstasy" users showed no change in levels of dopamine D2 receptor occupancy after playing this game. This evidence supports the notion that psycho-stimulant users have decreased sensitivity to natural reward. Computer game addicts or gamblers may show reduced dopamine response to stimuli associated with their addiction presumably due to sensitization.

Thrust chamber performance using Navier-Stokes solution. [space shuttle main engine viscous nozzle calculation

NASA Technical Reports Server (NTRS)

Chan, J. S.; Freeman, J. A.

1984-01-01

The viscous, axisymmetric flow in the thrust chamber of the space shuttle main engine (SSME) was computed on the CRAY 205 computer using the general interpolants method (GIM) code. Results show that the Navier-Stokes codes can be used for these flows to study trends and viscous effects as well as determine flow patterns; but further research and development is needed before they can be used as production tools for nozzle performance calculations. The GIM formulation, numerical scheme, and computer code are described. The actual SSME nozzle computation showing grid points, flow contours, and flow parameter plots is discussed. The computer system and run times/costs are detailed.

Empowering Middle School Teachers with Portable Computers.

ERIC Educational Resources Information Center

Weast, Jerry D.; And Others

1993-01-01

A Sioux Falls (South Dakota) project that supplied middle school teachers with Macintosh computers and training to use them showed gratifying results. Easy access to portable notebook computers made teachers more active computer users, increased teacher interaction and collaboration, enhanced teacher productivity regarding management tasks and…

The Story of Computers.

ERIC Educational Resources Information Center

Meadow, Charles T.

The aim of this book is to interest young people from the ages of ten to fourteen in computers, particularly to show them that computers are exciting machines, controlled by people, and to dispel myths that computers can do magic. This is not a detailed exposition of computers, nor is it a textbook. It is an attempt to impart flavor and general…

Evidence of Gender Disparity in Children's Computer Use and Activities.

ERIC Educational Resources Information Center

Land, M. J.

This multi-method study examines the differences in male and female computer use in the home of children ages 9-14. Long interviews, observations, and surveys with children show males spend more time on the computer, but not on-line, than females. Males and females engage in different computer activities. They play computer games about the same…

The Effects of Computer Games on the Achievement of Basic Mathematical Skills

ERIC Educational Resources Information Center

Sayan, Hamiyet

2015-01-01

This study aims to analyze the relationship between playing computer games and learning basic mathematics skills. It shows the role computer games play in the learning and achievement of basic mathematical skills by students. Nowadays it is clear that individuals, especially young persons are very fond of computer and computer games. Since…

In vitro molecular machine learning algorithm via symmetric internal loops of DNA.

PubMed

Lee, Ji-Hoon; Lee, Seung Hwan; Baek, Christina; Chun, Hyosun; Ryu, Je-Hwan; Kim, Jin-Woo; Deaton, Russell; Zhang, Byoung-Tak

2017-08-01

Programmable biomolecules, such as DNA strands, deoxyribozymes, and restriction enzymes, have been used to solve computational problems, construct large-scale logic circuits, and program simple molecular games. Although studies have shown the potential of molecular computing, the capability of computational learning with DNA molecules, i.e., molecular machine learning, has yet to be experimentally verified. Here, we present a novel molecular learning in vitro model in which symmetric internal loops of double-stranded DNA are exploited to measure the differences between training instances, thus enabling the molecules to learn from small errors. The model was evaluated on a data set of twenty dialogue sentences obtained from the television shows Friends and Prison Break. The wet DNA-computing experiments confirmed that the molecular learning machine was able to generalize the dialogue patterns of each show and successfully identify the show from which the sentences originated. The molecular machine learning model described here opens the way for solving machine learning problems in computer science and biology using in vitro molecular computing with the data encoded in DNA molecules. Copyright © 2017. Published by Elsevier B.V.

Distinguishing humans from computers in the game of go: A complex network approach

NASA Astrophysics Data System (ADS)

Coquidé, C.; Georgeot, B.; Giraud, O.

2017-08-01

We compare complex networks built from the game of go and obtained from databases of human-played games with those obtained from computer-played games. Our investigations show that statistical features of the human-based networks and the computer-based networks differ, and that these differences can be statistically significant on a relatively small number of games using specific estimators. We show that the deterministic or stochastic nature of the computer algorithm playing the game can also be distinguished from these quantities. This can be seen as a tool to implement a Turing-like test for go simulators.

A highly efficient multi-core algorithm for clustering extremely large datasets

PubMed Central

2010-01-01

Background In recent years, the demand for computational power in computational biology has increased due to rapidly growing data sets from microarray and other high-throughput technologies. This demand is likely to increase. Standard algorithms for analyzing data, such as cluster algorithms, need to be parallelized for fast processing. Unfortunately, most approaches for parallelizing algorithms largely rely on network communication protocols connecting and requiring multiple computers. One answer to this problem is to utilize the intrinsic capabilities in current multi-core hardware to distribute the tasks among the different cores of one computer. Results We introduce a multi-core parallelization of the k-means and k-modes cluster algorithms based on the design principles of transactional memory for clustering gene expression microarray type data and categorial SNP data. Our new shared memory parallel algorithms show to be highly efficient. We demonstrate their computational power and show their utility in cluster stability and sensitivity analysis employing repeated runs with slightly changed parameters. Computation speed of our Java based algorithm was increased by a factor of 10 for large data sets while preserving computational accuracy compared to single-core implementations and a recently published network based parallelization. Conclusions Most desktop computers and even notebooks provide at least dual-core processors. Our multi-core algorithms show that using modern algorithmic concepts, parallelization makes it possible to perform even such laborious tasks as cluster sensitivity and cluster number estimation on the laboratory computer. PMID:20370922

Computational work and time on finite machines.

NASA Technical Reports Server (NTRS)

Savage, J. E.

1972-01-01

Measures of the computational work and computational delay required by machines to compute functions are given. Exchange inequalities are developed for random access, tape, and drum machines to show that product inequalities between storage and time, number of drum tracks and time, number of bits in an address and time, etc., must be satisfied to compute finite functions on bounded machines.

A Longitudinal Investigation of the Effects of Computer Anxiety on Performance in a Computing-Intensive Environment

ERIC Educational Resources Information Center

Buche, Mari W.; Davis, Larry R.; Vician, Chelley

2007-01-01

Computers are pervasive in business and education, and it would be easy to assume that all individuals embrace technology. However, evidence shows that roughly 30 to 40 percent of individuals experience some level of computer anxiety. Many academic programs involve computing-intensive courses, but the actual effects of this exposure on computer…

Scaling predictive modeling in drug development with cloud computing.

PubMed

Moghadam, Behrooz Torabi; Alvarsson, Jonathan; Holm, Marcus; Eklund, Martin; Carlsson, Lars; Spjuth, Ola

2015-01-26

Growing data sets with increased time for analysis is hampering predictive modeling in drug discovery. Model building can be carried out on high-performance computer clusters, but these can be expensive to purchase and maintain. We have evaluated ligand-based modeling on cloud computing resources where computations are parallelized and run on the Amazon Elastic Cloud. We trained models on open data sets of varying sizes for the end points logP and Ames mutagenicity and compare with model building parallelized on a traditional high-performance computing cluster. We show that while high-performance computing results in faster model building, the use of cloud computing resources is feasible for large data sets and scales well within cloud instances. An additional advantage of cloud computing is that the costs of predictive models can be easily quantified, and a choice can be made between speed and economy. The easy access to computational resources with no up-front investments makes cloud computing an attractive alternative for scientists, especially for those without access to a supercomputer, and our study shows that it enables cost-efficient modeling of large data sets on demand within reasonable time.

Learning Universal Computations with Spikes

PubMed Central

Thalmeier, Dominik; Uhlmann, Marvin; Kappen, Hilbert J.; Memmesheimer, Raoul-Martin

2016-01-01

Providing the neurobiological basis of information processing in higher animals, spiking neural networks must be able to learn a variety of complicated computations, including the generation of appropriate, possibly delayed reactions to inputs and the self-sustained generation of complex activity patterns, e.g. for locomotion. Many such computations require previous building of intrinsic world models. Here we show how spiking neural networks may solve these different tasks. Firstly, we derive constraints under which classes of spiking neural networks lend themselves to substrates of powerful general purpose computing. The networks contain dendritic or synaptic nonlinearities and have a constrained connectivity. We then combine such networks with learning rules for outputs or recurrent connections. We show that this allows to learn even difficult benchmark tasks such as the self-sustained generation of desired low-dimensional chaotic dynamics or memory-dependent computations. Furthermore, we show how spiking networks can build models of external world systems and use the acquired knowledge to control them. PMID:27309381

Fully nonlocal inelastic scattering computations for spectroscopical transmission electron microscopy methods

NASA Astrophysics Data System (ADS)

Rusz, Ján; Lubk, Axel; Spiegelberg, Jakob; Tyutyunnikov, Dmitry

2017-12-01

The complex interplay of elastic and inelastic scattering amenable to different levels of approximation constitutes the major challenge for the computation and hence interpretation of TEM-based spectroscopical methods. The two major approaches to calculate inelastic scattering cross sections of fast electrons on crystals—Yoshioka-equations-based forward propagation and the reciprocal wave method—are founded in two conceptually differing schemes—a numerical forward integration of each inelastically scattered wave function, yielding the exit density matrix, and a computation of inelastic scattering matrix elements using elastically scattered initial and final states (double channeling). Here, we compare both approaches and show that the latter is computationally competitive to the former by exploiting analytical integration schemes over multiple excited states. Moreover, we show how to include full nonlocality of the inelastic scattering event, neglected in the forward propagation approaches, at no additional computing costs in the reciprocal wave method. Detailed simulations show in some cases significant errors due to the z -locality approximation and hence pitfalls in the interpretation of spectroscopical TEM results.

Computation in generalised probabilisitic theories

NASA Astrophysics Data System (ADS)

Lee, Ciarán M.; Barrett, Jonathan

2015-08-01

From the general difficulty of simulating quantum systems using classical systems, and in particular the existence of an efficient quantum algorithm for factoring, it is likely that quantum computation is intrinsically more powerful than classical computation. At present, the best upper bound known for the power of quantum computation is that {{BQP}}\\subseteq {{AWPP}}, where {{AWPP}} is a classical complexity class (known to be included in {{PP}}, hence {{PSPACE}}). This work investigates limits on computational power that are imposed by simple physical, or information theoretic, principles. To this end, we define a circuit-based model of computation in a class of operationally-defined theories more general than quantum theory, and ask: what is the minimal set of physical assumptions under which the above inclusions still hold? We show that given only an assumption of tomographic locality (roughly, that multipartite states and transformations can be characterized by local measurements), efficient computations are contained in {{AWPP}}. This inclusion still holds even without assuming a basic notion of causality (where the notion is, roughly, that probabilities for outcomes cannot depend on future measurement choices). Following Aaronson, we extend the computational model by allowing post-selection on measurement outcomes. Aaronson showed that the corresponding quantum complexity class, {{PostBQP}}, is equal to {{PP}}. Given only the assumption of tomographic locality, the inclusion in {{PP}} still holds for post-selected computation in general theories. Hence in a world with post-selection, quantum theory is optimal for computation in the space of all operational theories. We then consider whether one can obtain relativized complexity results for general theories. It is not obvious how to define a sensible notion of a computational oracle in the general framework that reduces to the standard notion in the quantum case. Nevertheless, it is possible to define computation relative to a ‘classical oracle’. Then, we show there exists a classical oracle relative to which efficient computation in any theory satisfying the causality assumption does not include {{NP}}.

Architectures for Quantum Simulation Showing a Quantum Speedup

NASA Astrophysics Data System (ADS)

Bermejo-Vega, Juan; Hangleiter, Dominik; Schwarz, Martin; Raussendorf, Robert; Eisert, Jens

2018-04-01

One of the main aims in the field of quantum simulation is to achieve a quantum speedup, often referred to as "quantum computational supremacy," referring to the experimental realization of a quantum device that computationally outperforms classical computers. In this work, we show that one can devise versatile and feasible schemes of two-dimensional, dynamical, quantum simulators showing such a quantum speedup, building on intermediate problems involving nonadaptive, measurement-based, quantum computation. In each of the schemes, an initial product state is prepared, potentially involving an element of randomness as in disordered models, followed by a short-time evolution under a basic translationally invariant Hamiltonian with simple nearest-neighbor interactions and a mere sampling measurement in a fixed basis. The correctness of the final-state preparation in each scheme is fully efficiently certifiable. We discuss experimental necessities and possible physical architectures, inspired by platforms of cold atoms in optical lattices and a number of others, as well as specific assumptions that enter the complexity-theoretic arguments. This work shows that benchmark settings exhibiting a quantum speedup may require little control, in contrast to universal quantum computing. Thus, our proposal puts a convincing experimental demonstration of a quantum speedup within reach in the near term.

Do-It-Yourself Learning Games: Software That Lets You Pick the Questions--and Answers.

ERIC Educational Resources Information Center

Hively, Wells

1984-01-01

Reviews user-adaptable learning games that can be customized for any subject, including Tic Tac Show and the Game Show from Computer Advanced Ideas, which are question-answer learning programs based on game shows, and Master Match from Computer Advanced Ideas and Square Pairs from Scholastic Inc., which are based on the card game Concentration.…

Quantum computing with incoherent resources and quantum jumps.

PubMed

Santos, M F; Cunha, M Terra; Chaves, R; Carvalho, A R R

2012-04-27

Spontaneous emission and the inelastic scattering of photons are two natural processes usually associated with decoherence and the reduction in the capacity to process quantum information. Here we show that, when suitably detected, these photons are sufficient to build all the fundamental blocks needed to perform quantum computation in the emitting qubits while protecting them from deleterious dissipative effects. We exemplify this by showing how to efficiently prepare graph states for the implementation of measurement-based quantum computation.

Psychology of computer use: XXXII. Computer screen-savers as distractors.

PubMed

Volk, F A; Halcomb, C G

1994-12-01

The differences in performance of 16 male and 16 female undergraduates on three cognitive tasks were investigated in the presence of visual distractors (computer-generated dynamic graphic images). These tasks included skilled and unskilled proofreading and listening comprehension. The visually demanding task of proofreading (skilled and unskilled) showed no significant decreases in performance in the distractor conditions. Results showed significant decrements, however, in performance on listening comprehension in at least one of the distractor conditions.

Affordable Emerging Computer Hardware for Neuromorphic Computing Applications

DTIC Science & Technology

2011-09-01

DATES COVERED (From - To) 4 . TITLE AND SUBTITLE AFFORDABLE EMERGING COMPUTER HARDWARE FOR NEUROMORPHIC COMPUTING APPLICATIONS 5a. CONTRACT NUMBER...speedup over software [3, 4 ]. 3 Table 1 shows a comparison of the computing performance, communication performance, power consumption...time is probably 5 frames per second, corresponding to 5 saccades. III. RESULTS AND DISCUSSION The use of IBM Cell-BE technology (Sony PlayStation

Computation of neutron fluxes in clusters of fuel pins arranged in hexagonal assemblies (2D and 3D)

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

Prabha, H.; Marleau, G.

2012-07-01

For computations of fluxes, we have used Carvik's method of collision probabilities. This method requires tracking algorithms. An algorithm to compute tracks (in 2D and 3D) has been developed for seven hexagonal geometries with cluster of fuel pins. This has been implemented in the NXT module of the code DRAGON. The flux distribution in cluster of pins has been computed by using this code. For testing the results, they are compared when possible with the EXCELT module of the code DRAGON. Tracks are plotted in the NXT module by using MATLAB, these plots are also presented here. Results are presentedmore » with increasing number of lines to show the convergence of these results. We have numerically computed volumes, surface areas and the percentage errors in these computations. These results show that 2D results converge faster than 3D results. The accuracy on the computation of fluxes up to second decimal is achieved with fewer lines. (authors)« less

New Computational Methods for the Prediction and Analysis of Helicopter Noise

NASA Technical Reports Server (NTRS)

Strawn, Roger C.; Oliker, Leonid; Biswas, Rupak

1996-01-01

This paper describes several new methods to predict and analyze rotorcraft noise. These methods are: 1) a combined computational fluid dynamics and Kirchhoff scheme for far-field noise predictions, 2) parallel computer implementation of the Kirchhoff integrations, 3) audio and visual rendering of the computed acoustic predictions over large far-field regions, and 4) acoustic tracebacks to the Kirchhoff surface to pinpoint the sources of the rotor noise. The paper describes each method and presents sample results for three test cases. The first case consists of in-plane high-speed impulsive noise and the other two cases show idealized parallel and oblique blade-vortex interactions. The computed results show good agreement with available experimental data but convey much more information about the far-field noise propagation. When taken together, these new analysis methods exploit the power of new computer technologies and offer the potential to significantly improve our prediction and understanding of rotorcraft noise.

On the Computation of Comprehensive Boolean Gröbner Bases

NASA Astrophysics Data System (ADS)

Inoue, Shutaro

We show that a comprehensive Boolean Gröbner basis of an ideal I in a Boolean polynomial ring B (bar A,bar X) with main variables bar X and parameters bar A can be obtained by simply computing a usual Boolean Gröbner basis of I regarding both bar X and bar A as variables with a certain block term order such that bar X ≫ bar A. The result together with a fact that a finite Boolean ring is isomorphic to a direct product of the Galois field mathbb{GF}_2 enables us to compute a comprehensive Boolean Gröbner basis by only computing corresponding Gröbner bases in a polynomial ring over mathbb{GF}_2. Our implementation in a computer algebra system Risa/Asir shows that our method is extremely efficient comparing with existing computation algorithms of comprehensive Boolean Gröbner bases.

Quantum walk computation

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

Kendon, Viv

2014-12-04

Quantum versions of random walks have diverse applications that are motivating experimental implementations as well as theoretical studies. Recent results showing quantum walks are “universal for quantum computation” relate to algorithms, to be run on quantum computers. We consider whether an experimental implementation of a quantum walk could provide useful computation before we have a universal quantum computer.

Computer Education and Instructional Technology Teacher Trainees' Opinions about Cloud Computing Technology

ERIC Educational Resources Information Center

Karamete, Aysen

2015-01-01

This study aims to show the present conditions about the usage of cloud computing in the department of Computer Education and Instructional Technology (CEIT) amongst teacher trainees in School of Necatibey Education, Balikesir University, Turkey. In this study, a questionnaire with open-ended questions was used. 17 CEIT teacher trainees…

Technopower and Technoppression: Some Abuses of Power and Control in Computer-Assisted Writing Environments (Computers and Controversy).

ERIC Educational Resources Information Center

Janangelo, Joseph

1991-01-01

Examines the exploitation of individuals that occurs within writing classrooms by those who organize computer systems. Discusses these abuses in three categories: teachers observing students, teachers observing teachers, and students observing students. Shows how computer-enhanced writing environments, if not designed carefully, can inhibit as…

Gender Differences in Attitudes toward Computers and Performance in the Accounting Information Systems Class

ERIC Educational Resources Information Center

Lenard, Mary Jane; Wessels, Susan; Khanlarian, Cindi

2010-01-01

Using a model developed by Young (2000), this paper explores the relationship between performance in the Accounting Information Systems course, self-assessed computer skills, and attitudes toward computers. Results show that after taking the AIS course, students experience a change in perception about their use of computers. Females'…

Sleep problems and computer use during work and leisure: Cross-sectional study among 7800 adults.

PubMed

Andersen, Lars Louis; Garde, Anne Helene

2015-01-01

Previous studies linked heavy computer use to disturbed sleep. This study investigates the association between computer use during work and leisure and sleep problems in working adults. From the 2010 round of the Danish Work Environment Cohort Study, currently employed wage earners on daytime schedule (N = 7883) replied to the Bergen insomnia scale and questions on weekly duration of computer use. Results showed that sleep problems for three or more days per week (average of six questions) were experienced by 14.9% of the respondents. Logistic regression analyses, controlled for gender, age, physical and psychosocial work factors, lifestyle, chronic disease and mental health showed that computer use during leisure for 30 or more hours per week (reference 0-10 hours per week) was associated with increased odds of sleep problems (OR 1.83 [95% CI 1.06-3.17]). Computer use during work and shorter duration of computer use during leisure were not associated with sleep problems. In conclusion, excessive computer use during leisure - but not work - is associated with sleep problems in adults working on daytime schedule.

Performance of parallel computation using CUDA for solving the one-dimensional elasticity equations

NASA Astrophysics Data System (ADS)

Darmawan, J. B. B.; Mungkasi, S.

2017-01-01

In this paper, we investigate the performance of parallel computation in solving the one-dimensional elasticity equations. Elasticity equations are usually implemented in engineering science. Solving these equations fast and efficiently is desired. Therefore, we propose the use of parallel computation. Our parallel computation uses CUDA of the NVIDIA. Our research results show that parallel computation using CUDA has a great advantage and is powerful when the computation is of large scale.

Modeling the state dependent impulse control for computer virus propagation under media coverage

NASA Astrophysics Data System (ADS)

Liang, Xiyin; Pei, Yongzhen; Lv, Yunfei

2018-02-01

A state dependent impulsive control model is proposed to model the spread of computer virus incorporating media coverage. By the successor function, the sufficient conditions for the existence and uniqueness of order-1 periodic solution are presented first. Secondly, for two classes of periodic solutions, the geometric property of successor function and the analogue of the Poincaré criterion are employed to obtain the stability results. These results show that the number of the infective computers is under the threshold all the time. Finally, the theoretic and numerical analysis show that media coverage can delay the spread of computer virus.

Enhanced delegated computing using coherence

NASA Astrophysics Data System (ADS)

Barz, Stefanie; Dunjko, Vedran; Schlederer, Florian; Moore, Merritt; Kashefi, Elham; Walmsley, Ian A.

2016-03-01

A longstanding question is whether it is possible to delegate computational tasks securely—such that neither the computation nor the data is revealed to the server. Recently, both a classical and a quantum solution to this problem were found [C. Gentry, in Proceedings of the 41st Annual ACM Symposium on the Theory of Computing (Association for Computing Machinery, New York, 2009), pp. 167-178; A. Broadbent, J. Fitzsimons, and E. Kashefi, in Proceedings of the 50th Annual Symposium on Foundations of Computer Science (IEEE Computer Society, Los Alamitos, CA, 2009), pp. 517-526]. Here, we study the first step towards the interplay between classical and quantum approaches and show how coherence can be used as a tool for secure delegated classical computation. We show that a client with limited computational capacity—restricted to an XOR gate—can perform universal classical computation by manipulating information carriers that may occupy superpositions of two states. Using single photonic qubits or coherent light, we experimentally implement secure delegated classical computations between an independent client and a server, which are installed in two different laboratories and separated by 50 m . The server has access to the light sources and measurement devices, whereas the client may use only a restricted set of passive optical devices to manipulate the information-carrying light beams. Thus, our work highlights how minimal quantum and classical resources can be combined and exploited for classical computing.

The effect of computer-assisted therapeutic practice for children with handwriting deficit: a comparison with the effect of the traditional sensorimotor approach.

PubMed

Chang, Shao-Hsia; Yu, Nan-Ying

2014-07-01

The objective of this study was to compare the effect of computer-assisted practice with the sensorimotor approach on the remediation of handwriting problems in children with dysgraphia. In a randomized controlled trial, experiments were conducted to verify the intervention effect. Forty two children with handwriting deficit were assigned to computer-assisted instruction, sensorimotor training, or a control group. Handwriting performance was measured using the elementary reading/writing test and computerized handwriting evaluation before and after 6 weeks of intervention. Repeated-measures ANOVA of changed scores were conducted to show whether statistically significant differences across the three groups were present. Significant differences in the elementary reading/writing test were found among the three groups. The computer group showed more significant improvements than the other two groups did. In the kinematic and kinetic analyses, the computer group showed promising results in the remediation of handwriting speed and fluency. This study provided clinical evidence for applying a computer-assisted handwriting program for children with dysgraphia. Clinicians and school teachers are provided with a systematic intervention for the improvement of handwriting difficulties. Copyright © 2014 Elsevier Ltd. All rights reserved.

The effects of a computer skill training programme adopting social comparison and self-efficacy enhancement strategies on self-concept and skill outcome in trainees with physical disabilities.

PubMed

Tam, S F

2000-10-15

The aim of this controlled, quasi-experimental study was to evaluate the effects of both self-efficacy enhancement and social comparison training strategy on computer skills learning and self-concept outcome of trainees with physical disabilities. The self-efficacy enhancement group comprised 16 trainees, the tutorial training group comprised 15 trainees, and there were 25 subjects in the control group. Both the self-efficacy enhancement group and the tutorial training group received a 15 week computer skills training course, including generic Chinese computer operation, Chinese word processing and Chinese desktop publishing skills. The self-efficacy enhancement group received training with tutorial instructions that incorporated self-efficacy enhancement strategies and experienced self-enhancing social comparisons. The tutorial training group received behavioural learning-based tutorials only, and the control group did not receive any training. The following measurements were employed to evaluate the outcomes: the Self-Concept Questionnaire for the Physically Disabled Hong Kong Chinese (SCQPD), the computer self-efficacy rating scale and the computer performance rating scale. The self-efficacy enhancement group showed significantly better computer skills learning outcome, total self-concept, and social self-concept than the tutorial training group. The self-efficacy enhancement group did not show significant changes in their computer self-efficacy: however, the tutorial training group showed a significant lowering of their computer self-efficacy. The training strategy that incorporated self-efficacy enhancement and positive social comparison experiences maintained the computer self-efficacy of trainees with physical disabilities. This strategy was more effective in improving the learning outcome (p = 0.01) and self-concept (p = 0.05) of the trainees than the conventional tutorial-based training strategy.

68Ga/177Lu-labeled DOTA-TATE shows similar imaging and biodistribution in neuroendocrine tumor model.

PubMed

Liu, Fei; Zhu, Hua; Yu, Jiangyuan; Han, Xuedi; Xie, Qinghua; Liu, Teli; Xia, Chuanqin; Li, Nan; Yang, Zhi

2017-06-01

Somatostatin receptors are overexpressed in neuroendocrine tumors, whose endogenous ligands are somatostatin. DOTA-TATE is an analogue of somatostatin, which shows high binding affinity to somatostatin receptors. We aim to evaluate the 68 Ga/ 177 Lu-labeling DOTA-TATE kit in neuroendocrine tumor model for molecular imaging and to try human-positron emission tomography/computed tomography imaging of 68 Ga-DOTA-TATE in neuroendocrine tumor patients. DOTA-TATE kits were formulated and radiolabeled with 68 Ga/ 177 Lu for 68 Ga/ 177 Lu-DOTA-TATE (M-DOTA-TATE). In vitro and in vivo stability of 177 Lu-DOTA-TATE were performed. Nude mice bearing human tumors were injected with 68 Ga-DOTA-TATE or 177 Lu-DOTA-TATE for micro-positron emission tomography and micro-single-photon emission computed tomography/computed tomography imaging separately, and clinical positron emission tomography/computed tomography images of 68 Ga-DOTA-TATE were obtained at 1 h post-intravenous injection from patients with neuroendocrine tumors. Micro-positron emission tomography and micro-single-photon emission computed tomography/computed tomography imaging of 68 Ga-DOTA-TATE and 177 Lu-DOTA-TATE both showed clear tumor uptake which could be blocked by excess DOTA-TATE. In addition, 68 Ga-DOTA-TATE-positron emission tomography/computed tomography imaging in neuroendocrine tumor patients could show primary and metastatic lesions. 68 Ga-DOTA-TATE and 177 Lu-DOTA-TATE could accumulate in tumors in animal models, paving the way for better clinical peptide receptor radionuclide therapy for neuroendocrine tumor patients in Asian population.

Counterfactual quantum computation through quantum interrogation

NASA Astrophysics Data System (ADS)

Hosten, Onur; Rakher, Matthew T.; Barreiro, Julio T.; Peters, Nicholas A.; Kwiat, Paul G.

2006-02-01

The logic underlying the coherent nature of quantum information processing often deviates from intuitive reasoning, leading to surprising effects. Counterfactual computation constitutes a striking example: the potential outcome of a quantum computation can be inferred, even if the computer is not run. Relying on similar arguments to interaction-free measurements (or quantum interrogation), counterfactual computation is accomplished by putting the computer in a superposition of `running' and `not running' states, and then interfering the two histories. Conditional on the as-yet-unknown outcome of the computation, it is sometimes possible to counterfactually infer information about the solution. Here we demonstrate counterfactual computation, implementing Grover's search algorithm with an all-optical approach. It was believed that the overall probability of such counterfactual inference is intrinsically limited, so that it could not perform better on average than random guesses. However, using a novel `chained' version of the quantum Zeno effect, we show how to boost the counterfactual inference probability to unity, thereby beating the random guessing limit. Our methods are general and apply to any physical system, as illustrated by a discussion of trapped-ion systems. Finally, we briefly show that, in certain circumstances, counterfactual computation can eliminate errors induced by decoherence.

Computational multicore on two-layer 1D shallow water equations for erodible dambreak

NASA Astrophysics Data System (ADS)

Simanjuntak, C. A.; Bagustara, B. A. R. H.; Gunawan, P. H.

2018-03-01

The simulation of erodible dambreak using two-layer shallow water equations and SCHR scheme are elaborated in this paper. The results show that the two-layer SWE model in a good agreement with the data experiment which is performed by Louvain-la-Neuve Université Catholique de Louvain. Moreover, the parallel algorithm with multicore architecture are given in the results. The results show that Computer I with processor Intel(R) Core(TM) i5-2500 CPU Quad-Core has the best performance to accelerate the computational time. Moreover, Computer III with processor AMD A6-5200 APU Quad-Core is observed has higher speedup and efficiency. The speedup and efficiency of Computer III with number of grids 3200 are 3.716050530 times and 92.9% respectively.

Computation of shock wave/target interaction

NASA Technical Reports Server (NTRS)

Mark, A.; Kutler, P.

1983-01-01

Computational results of shock waves impinging on targets and the ensuing diffraction flowfield are presented. A number of two-dimensional cases are computed with finite difference techniques. The classical case of a shock wave/cylinder interaction is compared with shock tube data and shows the quality of the computations on a pressure-time plot. Similar results are obtained for a shock wave/rectangular body interaction. Here resolution becomes important and the use of grid clustering techniques tend to show good agreement with experimental data. Computational results are also compared with pressure data resulting from shock impingement experiments for a complicated truck-like geometry. Here of significance are the grid generation and clustering techniques used. For these very complicated bodies, grids are generated by numerically solving a set of elliptic partial differential equations.

Numerical Computation of Sensitivities and the Adjoint Approach

NASA Technical Reports Server (NTRS)

Lewis, Robert Michael

1997-01-01

We discuss the numerical computation of sensitivities via the adjoint approach in optimization problems governed by differential equations. We focus on the adjoint problem in its weak form. We show how one can avoid some of the problems with the adjoint approach, such as deriving suitable boundary conditions for the adjoint equation. We discuss the convergence of numerical approximations of the costate computed via the weak form of the adjoint problem and show the significance for the discrete adjoint problem.

Limits on efficient computation in the physical world

NASA Astrophysics Data System (ADS)

Aaronson, Scott Joel

More than a speculative technology, quantum computing seems to challenge our most basic intuitions about how the physical world should behave. In this thesis I show that, while some intuitions from classical computer science must be jettisoned in the light of modern physics, many others emerge nearly unscathed; and I use powerful tools from computational complexity theory to help determine which are which. In the first part of the thesis, I attack the common belief that quantum computing resembles classical exponential parallelism, by showing that quantum computers would face serious limitations on a wider range of problems than was previously known. In particular, any quantum algorithm that solves the collision problem---that of deciding whether a sequence of n integers is one-to-one or two-to-one---must query the sequence O (n1/5) times. This resolves a question that was open for years; previously no lower bound better than constant was known. A corollary is that there is no "black-box" quantum algorithm to break cryptographic hash functions or solve the Graph Isomorphism problem in polynomial time. I also show that relative to an oracle, quantum computers could not solve NP-complete problems in polynomial time, even with the help of nonuniform "quantum advice states"; and that any quantum algorithm needs O (2n/4/n) queries to find a local minimum of a black-box function on the n-dimensional hypercube. Surprisingly, the latter result also leads to new classical lower bounds for the local search problem. Finally, I give new lower bounds on quantum one-way communication complexity, and on the quantum query complexity of total Boolean functions and recursive Fourier sampling. The second part of the thesis studies the relationship of the quantum computing model to physical reality. I first examine the arguments of Leonid Levin, Stephen Wolfram, and others who believe quantum computing to be fundamentally impossible. I find their arguments unconvincing without a "Sure/Shor separator"---a criterion that separates the already-verified quantum states from those that appear in Shor's factoring algorithm. I argue that such a separator should be based on a complexity classification of quantum states, and go on to create such a classification. Next I ask what happens to the quantum computing model if we take into account that the speed of light is finite---and in particular, whether Grover's algorithm still yields a quadratic speedup for searching a database. Refuting a claim by Benioff, I show that the surprising answer is yes. Finally, I analyze hypothetical models of computation that go even beyond quantum computing. I show that many such models would be as powerful as the complexity class PP, and use this fact to give a simple, quantum computing based proof that PP is closed under intersection. On the other hand, I also present one model---wherein we could sample the entire history of a hidden variable---that appears to be more powerful than standard quantum computing, but only slightly so.

Computer laboratory in medical education for medical students.

PubMed

Hercigonja-Szekeres, Mira; Marinović, Darko; Kern, Josipa

2009-01-01

Five generations of second year students at the Zagreb University School of Medicine were interviewed through an anonymous questionnaire on their use of personal computers, Internet, computer laboratories and computer-assisted education in general. Results show an advance in students' usage of information and communication technology during the period from 1998/99 to 2002/03. However, their positive opinion about computer laboratory depends on installed capacities: the better the computer laboratory technology, the better the students' acceptance and use of it.

Computer Use and Factors Related to Computer Use in Large Independent Secondary School Libraries.

ERIC Educational Resources Information Center

Currier, Heidi F.

Survey results about the use of computers in independent secondary school libraries are reported, and factors related to the presence of computers are identified. Data are from 104 librarians responding to a questionnaire sent to a sample of 136 large (over 400 students) independent secondary schools. Data are analyzed descriptively to show the…

Closing the Gender Gap: Girls and Computers.

ERIC Educational Resources Information Center

Fuchs, Lucy

While 15 years ago only a few schools had microcomputers, today a majority of public schools have some computers, although an adequate number of computers for students to use is still in the future. Unfortunately, statistics show that, in many states, a higher percentage of male students are enrolled in computer classes than female; boys seem to…

Computing with Neural Synchrony

PubMed Central

Brette, Romain

2012-01-01

Neurons communicate primarily with spikes, but most theories of neural computation are based on firing rates. Yet, many experimental observations suggest that the temporal coordination of spikes plays a role in sensory processing. Among potential spike-based codes, synchrony appears as a good candidate because neural firing and plasticity are sensitive to fine input correlations. However, it is unclear what role synchrony may play in neural computation, and what functional advantage it may provide. With a theoretical approach, I show that the computational interest of neural synchrony appears when neurons have heterogeneous properties. In this context, the relationship between stimuli and neural synchrony is captured by the concept of synchrony receptive field, the set of stimuli which induce synchronous responses in a group of neurons. In a heterogeneous neural population, it appears that synchrony patterns represent structure or sensory invariants in stimuli, which can then be detected by postsynaptic neurons. The required neural circuitry can spontaneously emerge with spike-timing-dependent plasticity. Using examples in different sensory modalities, I show that this allows simple neural circuits to extract relevant information from realistic sensory stimuli, for example to identify a fluctuating odor in the presence of distractors. This theory of synchrony-based computation shows that relative spike timing may indeed have computational relevance, and suggests new types of neural network models for sensory processing with appealing computational properties. PMID:22719243

A computer assisted tutorial for applications of computer spreadsheets in nursing financial management.

PubMed

Edwardson, S R; Pejsa, J

1993-01-01

A computer-based tutorial for teaching nursing financial management concepts was developed using the macro function of a commercially available spreadsheet program. The goals of the tutorial were to provide students with an experience with spreadsheets as a computer tool and to teach selected financial management concepts. Preliminary results show the tutorial was well received by students. Suggestions are made for overcoming the general lack of computer sophistication among students.

THE COMPUTER AND SMALL BUSINESS.

DTIC Science & Technology

The place of the computer in small business is investigated with respect to what type of problems it can solve for small business and how the small...firm can acquire time on one. The decision-making process and the importance of information is discussed in relation to small business . Several...applications of computers are examined to show how the firm can use the computer in day-to-day business operations. The capabilities of a digital computer

Reservoir computing with a single time-delay autonomous Boolean node

NASA Astrophysics Data System (ADS)

Haynes, Nicholas D.; Soriano, Miguel C.; Rosin, David P.; Fischer, Ingo; Gauthier, Daniel J.

2015-02-01

We demonstrate reservoir computing with a physical system using a single autonomous Boolean logic element with time-delay feedback. The system generates a chaotic transient with a window of consistency lasting between 30 and 300 ns, which we show is sufficient for reservoir computing. We then characterize the dependence of computational performance on system parameters to find the best operating point of the reservoir. When the best parameters are chosen, the reservoir is able to classify short input patterns with performance that decreases over time. In particular, we show that four distinct input patterns can be classified for 70 ns, even though the inputs are only provided to the reservoir for 7.5 ns.

Postmortem whole-body computed tomography angiography visualizing vascular rupture in a case of fatal car crash.

PubMed

Flach, Patricia M; Ross, Steffen G; Bolliger, Stephan A; Preiss, Ulrich S; Thali, Michael J; Spendlove, Danny

2010-01-01

In addition to the increasingly significant role of multislice computed tomography in forensic pathology, the performance of whole-body computed tomography angiography provides outstanding results. In this case, we were able to detect multiple injuries of the parenchymal organs in the upper abdomen as well as lesions of the brain parenchyma and vasculature of the neck. The radiologic findings showed complete concordance with the autopsy and even supplemented the autopsy findings in areas that are difficult to access via a manual dissection (such as the vasculature of the neck). This case shows how minimally invasive computed tomography angiography can serve as an invaluable adjunct to the classic autopsy procedure.

Convergence issues in domain decomposition parallel computation of hovering rotor

NASA Astrophysics Data System (ADS)

Xiao, Zhongyun; Liu, Gang; Mou, Bin; Jiang, Xiong

2018-05-01

Implicit LU-SGS time integration algorithm has been widely used in parallel computation in spite of its lack of information from adjacent domains. When applied to parallel computation of hovering rotor flows in a rotating frame, it brings about convergence issues. To remedy the problem, three LU factorization-based implicit schemes (consisting of LU-SGS, DP-LUR and HLU-SGS) are investigated comparatively. A test case of pure grid rotation is designed to verify these algorithms, which show that LU-SGS algorithm introduces errors on boundary cells. When partition boundaries are circumferential, errors arise in proportion to grid speed, accumulating along with the rotation, and leading to computational failure in the end. Meanwhile, DP-LUR and HLU-SGS methods show good convergence owing to boundary treatment which are desirable in domain decomposition parallel computations.

Low-Energy Truly Random Number Generation with Superparamagnetic Tunnel Junctions for Unconventional Computing

NASA Astrophysics Data System (ADS)

Vodenicarevic, D.; Locatelli, N.; Mizrahi, A.; Friedman, J. S.; Vincent, A. F.; Romera, M.; Fukushima, A.; Yakushiji, K.; Kubota, H.; Yuasa, S.; Tiwari, S.; Grollier, J.; Querlioz, D.

2017-11-01

Low-energy random number generation is critical for many emerging computing schemes proposed to complement or replace von Neumann architectures. However, current random number generators are always associated with an energy cost that is prohibitive for these computing schemes. We introduce random number bit generation based on specific nanodevices: superparamagnetic tunnel junctions. We experimentally demonstrate high-quality random bit generation that represents an orders-of-magnitude improvement in energy efficiency over current solutions. We show that the random generation speed improves with nanodevice scaling, and we investigate the impact of temperature, magnetic field, and cross talk. Finally, we show how alternative computing schemes can be implemented using superparamagentic tunnel junctions as random number generators. These results open the way for fabricating efficient hardware computing devices leveraging stochasticity, and they highlight an alternative use for emerging nanodevices.

Bayesian Parameter Inference and Model Selection by Population Annealing in Systems Biology

PubMed Central

Murakami, Yohei

2014-01-01

Parameter inference and model selection are very important for mathematical modeling in systems biology. Bayesian statistics can be used to conduct both parameter inference and model selection. Especially, the framework named approximate Bayesian computation is often used for parameter inference and model selection in systems biology. However, Monte Carlo methods needs to be used to compute Bayesian posterior distributions. In addition, the posterior distributions of parameters are sometimes almost uniform or very similar to their prior distributions. In such cases, it is difficult to choose one specific value of parameter with high credibility as the representative value of the distribution. To overcome the problems, we introduced one of the population Monte Carlo algorithms, population annealing. Although population annealing is usually used in statistical mechanics, we showed that population annealing can be used to compute Bayesian posterior distributions in the approximate Bayesian computation framework. To deal with un-identifiability of the representative values of parameters, we proposed to run the simulations with the parameter ensemble sampled from the posterior distribution, named “posterior parameter ensemble”. We showed that population annealing is an efficient and convenient algorithm to generate posterior parameter ensemble. We also showed that the simulations with the posterior parameter ensemble can, not only reproduce the data used for parameter inference, but also capture and predict the data which was not used for parameter inference. Lastly, we introduced the marginal likelihood in the approximate Bayesian computation framework for Bayesian model selection. We showed that population annealing enables us to compute the marginal likelihood in the approximate Bayesian computation framework and conduct model selection depending on the Bayes factor. PMID:25089832

Consulting room computers and their effect on general practitioner-patient communication.

PubMed

Noordman, Janneke; Verhaak, Peter; van Beljouw, Ilse; van Dulmen, Sandra

2010-12-01

in the western medical world, computers form part of the standard equipment in the consulting rooms of most GPs. As the use of a computer requires time and attention from GPs, this may well interfere with the communication process. Yet, the information accessed on the computer may also enhance communication. the present study affords insight into the relationship between computer use and GP-patient communication recorded by the same GPs over two periods. videotaped GP consultations collected in 2001 and 2008 were used to observe computer use and GP-patient communication. In addition, patients questionnaires about their experiences with communication by the GP were analysed using multilevel models with patients (Level 1) nested within GPs (Level 2). both in 2008 and in 2001, GPs used their computer in almost every consultation. Still, our study showed a change in computer use by the GPs over time. In addition, the results indicate that computer use is negatively related to some communication aspects: the patient-directed gaze of the GP and the amount of information given by GPs. There is also a negative association between computer use and the body posture of the GP. Computer use by GPs is not associated with other (analysed) non-verbal and verbal behaviour of GPs and patients. Moreover, computer use is scarcely related to patients' experiences with the communication behaviour of the GP. GPs show greater reluctance to use computers in 2008 compared to 2001. Computer use can indeed affect the communication between GPs and patients. Therefore, GPs ought to remain aware of their computer use during consultations and at the same time keep the interaction with the patient alive.

Evaluation of E-Rat, a Computer-based Rat Dissection in Terms of Student Learning Outcomes.

ERIC Educational Resources Information Center

Predavec, Martin

2001-01-01

Presents a study that used computer-based rat anatomy to compare student learning outcomes from computer-based instruction with a conventional dissection. Indicates that there was a significant relationship between the time spent on both classes and the marks gained. Shows that computer-based instruction can be a viable alternative to the use of…

Girls Save the World through Computer Science

ERIC Educational Resources Information Center

Murakami, Christine

2011-01-01

It's no secret that fewer and fewer women are entering computer science fields. Attracting high school girls to computer science is only part of the solution. Retaining them while they are in higher education or the workforce is also a challenge. To solve this, there is a need to show girls that computer science is a wide-open field that offers…

The Effects of Integrating Service Learning into Computer Science: An Inter-Institutional Longitudinal Study

ERIC Educational Resources Information Center

Payton, Jamie; Barnes, Tiffany; Buch, Kim; Rorrer, Audrey; Zuo, Huifang

2015-01-01

This study is a follow-up to one published in computer science education in 2010 that reported preliminary results showing a positive impact of service learning on student attitudes associated with success and retention in computer science. That paper described how service learning was incorporated into a computer science course in the context of…

Quaternions in computer vision and robotics

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

Pervin, E.; Webb, J.A.

1982-01-01

Computer vision and robotics suffer from not having good tools for manipulating three-dimensional objects. Vectors, coordinate geometry, and trigonometry all have deficiencies. Quaternions can be used to solve many of these problems. Many properties of quaternions that are relevant to computer vision and robotics are developed. Examples are given showing how quaternions can be used to simplify derivations in computer vision and robotics.

On finite element methods for the Helmholtz equation

NASA Technical Reports Server (NTRS)

Aziz, A. K.; Werschulz, A. G.

1979-01-01

The numerical solution of the Helmholtz equation is considered via finite element methods. A two-stage method which gives the same accuracy in the computed gradient as in the computed solution is discussed. Error estimates for the method using a newly developed proof are given, and the computational considerations which show this method to be computationally superior to previous methods are presented.

Use of Computer-Assisted Technologies (CAT) to Enhance Social, Communicative, and Language Development in Children with Autism Spectrum Disorders

ERIC Educational Resources Information Center

Ploog, Bertram O.; Scharf, Alexa; Nelson, DeShawn; Brooks, Patricia J.

2013-01-01

Major advances in multimedia computer technology over the past decades have made sophisticated computer games readily available to the public. This, combined with the observation that most children, including those with autism spectrum disorders (ASD), show an affinity to computers, has led researchers to recognize the potential of computer…

Bayesian Latent Class Analysis Tutorial.

PubMed

Li, Yuelin; Lord-Bessen, Jennifer; Shiyko, Mariya; Loeb, Rebecca

2018-01-01

This article is a how-to guide on Bayesian computation using Gibbs sampling, demonstrated in the context of Latent Class Analysis (LCA). It is written for students in quantitative psychology or related fields who have a working knowledge of Bayes Theorem and conditional probability and have experience in writing computer programs in the statistical language R . The overall goals are to provide an accessible and self-contained tutorial, along with a practical computation tool. We begin with how Bayesian computation is typically described in academic articles. Technical difficulties are addressed by a hypothetical, worked-out example. We show how Bayesian computation can be broken down into a series of simpler calculations, which can then be assembled together to complete a computationally more complex model. The details are described much more explicitly than what is typically available in elementary introductions to Bayesian modeling so that readers are not overwhelmed by the mathematics. Moreover, the provided computer program shows how Bayesian LCA can be implemented with relative ease. The computer program is then applied in a large, real-world data set and explained line-by-line. We outline the general steps in how to extend these considerations to other methodological applications. We conclude with suggestions for further readings.

Resolution of Infinite-Loop in Hyperincursive and Nonlocal Cellular Automata: Introduction to Slime Mold Computing

NASA Astrophysics Data System (ADS)

Aono, Masashi; Gunji, Yukio-Pegio

2004-08-01

How can non-algorithmic/non-deterministic computational syntax be computed? "The hyperincursive system" introduced by Dubois is an anticipatory system embracing the contradiction/uncertainty. Although it may provide a novel viewpoint for the understanding of complex systems, conventional digital computers cannot run faithfully as the hyperincursive computational syntax specifies, in a strict sense. Then is it an imaginary story? In this paper we try to argue that it is not. We show that a model of complex systems "Elementary Conflictable Cellular Automata (ECCA)" proposed by Aono and Gunji is embracing the hyperincursivity and the nonlocality. ECCA is based on locality-only type settings basically as well as other CA models, and/but at the same time, each cell is required to refer to globality-dominant regularity. Due to this contradictory locality-globality loop, the time evolution equation specifies that the system reaches the deadlock/infinite-loop. However, we show that there is a possibility of the resolution of these problems if the computing system has parallel and/but non-distributed property like an amoeboid organism. This paper is an introduction to "the slime mold computing" that is an attempt to cultivate an unconventional notion of computation.

Comparing the social skills of students addicted to computer games with normal students.

PubMed

Zamani, Eshrat; Kheradmand, Ali; Cheshmi, Maliheh; Abedi, Ahmad; Hedayati, Nasim

2010-01-01

This study aimed to investigate and compare the social skills of studentsaddicted to computer games with normal students. The dependentvariable in the present study is the social skills. The study population included all the students in the second grade ofpublic secondary school in the city of Isfahan at the educational year of2009-2010. The sample size included 564 students selected using thecluster random sampling method. Data collection was conducted usingQuestionnaire of Addiction to Computer Games and Social SkillsQuestionnaire (The Teenage Inventory of Social Skill or TISS). The results of the study showed that generally, there was a significantdifference between the social skills of students addicted to computer gamesand normal students. In addition, the results indicated that normal studentshad a higher level of social skills in comparison with students addicted tocomputer games. As the study results showed, addiction to computer games may affectthe quality and quantity of social skills. In other words, the higher theaddiction to computer games, the less the social skills. The individualsaddicted to computer games have less social skills.).

Comparing the Social Skills of Students Addicted to Computer Games with Normal Students

PubMed Central

Zamani, Eshrat; Kheradmand, Ali; Cheshmi, Maliheh; Abedi, Ahmad; Hedayati, Nasim

2010-01-01

Background This study aimed to investigate and compare the social skills of studentsaddicted to computer games with normal students. The dependentvariable in the present study is the social skills. Methods The study population included all the students in the second grade ofpublic secondary school in the city of Isfahan at the educational year of2009-2010. The sample size included 564 students selected using thecluster random sampling method. Data collection was conducted usingQuestionnaire of Addiction to Computer Games and Social SkillsQuestionnaire (The Teenage Inventory of Social Skill or TISS). Findings The results of the study showed that generally, there was a significantdifference between the social skills of students addicted to computer gamesand normal students. In addition, the results indicated that normal studentshad a higher level of social skills in comparison with students addicted tocomputer games. Conclusion As the study results showed, addiction to computer games may affectthe quality and quantity of social skills. In other words, the higher theaddiction to computer games, the less the social skills. The individualsaddicted to computer games have less social skills.). PMID:24494102

All-optical reservoir computing.

PubMed

Duport, François; Schneider, Bendix; Smerieri, Anteo; Haelterman, Marc; Massar, Serge

2012-09-24

Reservoir Computing is a novel computing paradigm that uses a nonlinear recurrent dynamical system to carry out information processing. Recent electronic and optoelectronic Reservoir Computers based on an architecture with a single nonlinear node and a delay loop have shown performance on standardized tasks comparable to state-of-the-art digital implementations. Here we report an all-optical implementation of a Reservoir Computer, made of off-the-shelf components for optical telecommunications. It uses the saturation of a semiconductor optical amplifier as nonlinearity. The present work shows that, within the Reservoir Computing paradigm, all-optical computing with state-of-the-art performance is possible.

Towards fault tolerant adiabatic quantum computation.

PubMed

Lidar, Daniel A

2008-04-25

I show how to protect adiabatic quantum computation (AQC) against decoherence and certain control errors, using a hybrid methodology involving dynamical decoupling, subsystem and stabilizer codes, and energy gaps. Corresponding error bounds are derived. As an example, I show how to perform decoherence-protected AQC against local noise using at most two-body interactions.

Some Unexpected Results Using Computer Algebra Systems.

ERIC Educational Resources Information Center

Alonso, Felix; Garcia, Alfonsa; Garcia, Francisco; Hoya, Sara; Rodriguez, Gerardo; de la Villa, Agustin

2001-01-01

Shows how teachers can often use unexpected outputs from Computer Algebra Systems (CAS) to reinforce concepts and to show students the importance of thinking about how they use the software and reflecting on their results. Presents different examples where DERIVE, MAPLE, or Mathematica does not work as expected and suggests how to use them as a…

8. DETAIL OF COMPUTER SCREEN AND CONTROL BOARDS: LEFT SCREEN ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

8. DETAIL OF COMPUTER SCREEN AND CONTROL BOARDS: LEFT SCREEN TRACKS RESIDUAL CHLORINE; INDICATES AMOUNT OF SUNLIGHT WHICH ENABLES OPERATOR TO ESTIMATE NEEDED CHLORINE; CENTER SCREEN SHOWS TURNOUT STRUCTURES; RIGHT SCREEN SHOWS INDICATORS OF ALUMINUM SULFATE TANK FARM. - F. E. Weymouth Filtration Plant, 700 North Moreno Avenue, La Verne, Los Angeles County, CA

Reconstruction of human brain spontaneous activity based on frequency-pattern analysis of magnetoencephalography data

PubMed Central

Llinás, Rodolfo R.; Ustinin, Mikhail N.; Rykunov, Stanislav D.; Boyko, Anna I.; Sychev, Vyacheslav V.; Walton, Kerry D.; Rabello, Guilherme M.; Garcia, John

2015-01-01

A new method for the analysis and localization of brain activity has been developed, based on multichannel magnetic field recordings, over minutes, superimposed on the MRI of the individual. Here, a high resolution Fourier Transform is obtained over the entire recording period, leading to a detailed multi-frequency spectrum. Further analysis implements a total decomposition of the frequency components into functionally invariant entities, each having an invariant field pattern localizable in recording space. The method, addressed as functional tomography, makes it possible to find the distribution of magnetic field sources in space. Here, the method is applied to the analysis of simulated data, to oscillating signals activating a physical current dipoles phantom, and to recordings of spontaneous brain activity in 10 healthy adults. In the analysis of simulated data, 61 dipoles are localized with 0.7 mm precision. Concerning the physical phantom the method is able to localize three simultaneously activated current dipoles with 1 mm precision. Spatial resolution 3 mm was attained when localizing spontaneous alpha rhythm activity in 10 healthy adults, where the alpha peak was specified for each subject individually. Co-registration of the functional tomograms with each subject's head MRI localized alpha range activity to the occipital and/or posterior parietal brain region. This is the first application of this new functional tomography to human brain activity. The method successfully provides an overall view of brain electrical activity, a detailed spectral description and, combined with MRI, the localization of sources in anatomical brain space. PMID:26528119

Biomechanics and strain mapping in bone as related to immediately-loaded dental implants

PubMed Central

Du, Jing; Lee, Jihyun; Jang, Andrew; Gu, Allen; Hossaini-Zadeh, Mehran; Prevost, Richard; Curtis, Don; Ho, Sunita

2015-01-01

The effects of alveolar bone socket geometry and bone-implant contact on implant biomechanics, and resulting strain distributions in bone were investigated. Following extraction of lateral incisors on a cadaver mandible, immediate implants were placed and bone-implant contact area, stability and bone strain were measured. In situ biomechanical testing coupled with micro X-ray microscope (μ-XRM) illustrated less stiff bone-implant complexes (701-822 N/mm) compared with bone-periodontal ligament (PDL)-tooth complexes (791-913 N/mm). X-ray tomograms illustrated that the cause of reduced stiffness was due to reduced and limited bone-implant contact. Heterogeneous elemental composition of bone was identified by using energy dispersive X-ray spectroscopy (EDS). The novel aspect of this study was the application of a new experimental mechanics method, that is, digital volume correlation, which allowed mapping of strains in volumes of alveolar bone in contact with a loaded implant. The identified surface and subsurface strain concentrations were a manifestation of load transferred to bone through bone-implant contact based on bone-implant geometry, quality of bone, implant placement, and implant design. 3D strain mapping indicated that strain concentrations are not exclusive to the bone-implant contact regions, but also extend into bone not directly in contact with the implant. The implications of the observed strain concentrations are discussed in the context of mechanobiology. Although a plausible explanation of surgical complications for immediate implant treatment is provided, extrapolation of results is only warranted by future systematic studies on more cadaver specimens and/or in vivo small scale animal models. PMID:26162549

Typhlitis: selective surgical management.

PubMed

Moir, C R; Scudamore, C H; Benny, W B

1986-05-01

Typhlitis is a neutropenic enterocolitis of varying severity. Its incidence is increasing, particularly in patients with acute myelogenous leukemia undergoing high dose cytosine arabinoside chemotherapy. The onset is heralded by prodromal fever, watery or bloody diarrhea, abdominal distension, and nausea during the phase of severe neutropenia. The symptoms may then localize to the right lower quadrant with an associated increase in systemic toxicity. The diagnosis can be confirmed in these and other less specific cases by serial reexamination and abdominal radiographs, ultrasonography, computerized tomograms, or radionucleotide scans. The mainstay of management is complete bowel rest with nasogastric suction and total parenteral nutrition. Broad-spectrum combination antibiotics are essential, as is the avoidance of laxatives or antidiarrheal agents. Granulocyte support may be helpful. Patients with a history of nonspecific gastrointestinal complaints or of true typhlitis, successfully managed nonoperatively, should have prophylactic bowel rest and total parenteral nutrition instituted at the beginning of further chemotherapy. Patients with ongoing severe systemic sepsis who do not respond to chemotherapy and those with overt perforation, obstruction, massive hemorrhage, or abscess formation require surgical intervention. All necrotic material must be resected, usually by a right hemicolectomy, ileostomy, and mucous fistula. Divided ileostomy for less severe cases may be useful. Failure to remove the necrotic focus in these severely immunocompromised patients is fatal. With adequate recognition of typhlitis and its precipitating factors, the incidence of complications can be reduced through prevention and timely surgical intervention. Although typhlitis developed in a quarter of our acute myeloblastic leukemia patients, use of this combined approach was successful in all cases.

4D ERT-based calibration and prediction of biostimulant induced changes in fluid conductivity

NASA Astrophysics Data System (ADS)

Johnson, T. C.; Versteeg, R. J.; Day-Lewis, F. D.; Major, W. R.; Wright, K. E.

2008-12-01

In-situ bioremediation is an emerging and cost-effective method of removing organic contaminants from groundwater. The performance of bioremedial systems depends on the adequate delivery and distribution of biostimulants to contaminated zones. Monitoring the distribution of biostimulants using monitoring wells is expensive, time consuming, and provides inadequate information between sampling wells. We discuss a Hydrogeophysical Performance Monitoring System (HPMS) deployed to monitor bioremediation efforts at a TCE-contaminated Superfund site in Brandywine MD. The HPMS enables autonomous electrical geophysical data acquisition, processing, quality-assurance/quality-control, and inversion. Our objective is to demonstrate the feasibility and cost effectiveness of the HPMS to provide near real-time information on the spatiotemporal behavior of injected biostimulants. As a first step, we use time-lapse electrical resistivity tomography (ERT) to estimate changes in bulk conductivity caused by the injectate. We demonstrate how ERT-based bulk conductivity estimates can be calibrated with a small number of fluid conductivity measurements to produce ERT-based estimates of fluid conductivity. The calibration procedure addresses the spatially variable resolution of the ERT tomograms. To test the validity of these estimates, we used the ERT results to predict the fluid conductivity at tens of points prior to field sampling of fluid conductivity at the same points. The comparison of ERT-predicted vs. observed fluid conductivity displays a high degree of correlation (correlation coefficient over 0.8), and demonstrates the ability of the HPMS to estimate the four-dimensional (4D) distribution of fluid conductivity caused by the biostimulant injection.

Trans-Dimensional Bayesian Imaging of 3-D Crustal and Upper Mantle Structure in Northeast Asia

NASA Astrophysics Data System (ADS)

Kim, S.; Tkalcic, H.; Rhie, J.; Chen, Y.

2016-12-01

Imaging 3-D structures using stepwise inversions of ambient noise and receiver function data is now a routine work. Here, we carry out the inversion in the trans-dimensional and hierarchical extension of the Bayesian framework to obtain rigorous estimates of uncertainty and high-resolution images of crustal and upper mantle structures beneath Northeast (NE) Asia. The methods inherently account for data sensitivities by means of using adaptive parameterizations and treating data noise as free parameters. Therefore, parsimonious results from the methods are balanced out between model complexity and data fitting. This allows fully exploiting data information, preventing from over- or under-estimation of the data fit, and increases model resolution. In addition, the reliability of results is more rigorously checked through the use of Bayesian uncertainties. It is shown by various synthetic recovery tests that complex and spatially variable features are well resolved in our resulting images of NE Asia. Rayleigh wave phase and group velocity tomograms (8-70 s), a 3-D shear-wave velocity model from depth inversions of the estimated dispersion maps, and regional 3-D models (NE China, the Korean Peninsula, and the Japanese islands) from joint inversions with receiver function data of dense networks are presented. High-resolution models are characterized by a number of tectonically meaningful features. We focus our interpretation on complex patterns of sub-lithospheric low velocity structures that extend from back-arc regions to continental margins. We interpret the anomalies in conjunction with distal and distributed intraplate volcanoes in NE Asia. Further discussion on other imaged features will be presented.

Statistical representative elementary volumes of porous media determined using greyscale analysis of 3D tomograms

NASA Astrophysics Data System (ADS)

Bruns, S.; Stipp, S. L. S.; Sørensen, H. O.

2017-09-01

Digital rock physics carries the dogmatic concept of having to segment volume images for quantitative analysis but segmentation rejects huge amounts of signal information. Information that is essential for the analysis of difficult and marginally resolved samples, such as materials with very small features, is lost during segmentation. In X-ray nanotomography reconstructions of Hod chalk we observed partial volume voxels with an abundance that limits segmentation based analysis. Therefore, we investigated the suitability of greyscale analysis for establishing statistical representative elementary volumes (sREV) for the important petrophysical parameters of this type of chalk, namely porosity, specific surface area and diffusive tortuosity, by using volume images without segmenting the datasets. Instead, grey level intensities were transformed to a voxel level porosity estimate using a Gaussian mixture model. A simple model assumption was made that allowed formulating a two point correlation function for surface area estimates using Bayes' theory. The same assumption enables random walk simulations in the presence of severe partial volume effects. The established sREVs illustrate that in compacted chalk, these simulations cannot be performed in binary representations without increasing the resolution of the imaging system to a point where the spatial restrictions of the represented sample volume render the precision of the measurement unacceptable. We illustrate this by analyzing the origins of variance in the quantitative analysis of volume images, i.e. resolution dependence and intersample and intrasample variance. Although we cannot make any claims on the accuracy of the approach, eliminating the segmentation step from the analysis enables comparative studies with higher precision and repeatability.

Resolution enhancement of partial coherence interferometry by dispersion compensation

NASA Astrophysics Data System (ADS)

Baumgartner, Angela; Hitzenberger, Christoph K.; Drexler, Wolfgang; Fercher, Adolf F.

1997-12-01

In the past ten years partial coherence interferometry and optical coherence tomography have been developed for high precision biometry and tomography of the human eye in vivo. The longitudinal resolution of the optical coherence tomography technique depends on the spectral bandwidth of the light source used and on the dispersion of the media to be measured. In nondispersive media the resolution is approximately equal to the coherence length of the light used, which is inversely proportional to the width of the emission spectrum. Hence, a broad emission spectrum yields a short coherence length and consequently a good resolution. However, if the tissue under investigation is dispersive, the coherence envelope of the signal broadens leading to a decrease in resolution and interference fringe contrast. This effect becomes predominant if measurements through the dispersive media of the eye to the retina are performed with source bandwidths larger than approximately 25 nm. In order to achieve optimum resolution of OCT by applying a light source with a broad emission spectrum, the dispersion of the object to be measured, i.e. in this case of the ocular media, has to be compensated. Within the scope of this work we demonstrate the resolution improvement that is obtained by compensating the dispersive effects of the ocular media and using broadband light sources. Furthermore, we present the first optical coherence tomogram recorded with this technique in the retina of a human eye in vivo with an axial geometrical resolution of approximately 6 micrometers which is a two-fold improvement compared to presently used technology.

Reciprocal Questioning and Computer-based Instruction in Introductory Auditing: Student Perceptions.

ERIC Educational Resources Information Center

Watters, Mike

2000-01-01

An auditing course used reciprocal questioning (Socratic method) and computer-based instruction. Separate evaluations by 67 students revealed a strong aversion to the Socratic method; students expected professors to lecture. They showed a strong preference for the computer-based assignment. (SK)