A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes.

PubMed

Duan, Zhijun; Andronescu, Mirela; Schutz, Kevin; Lee, Choli; Shendure, Jay; Fields, Stanley; Noble, William S; Anthony Blau, C

2012-11-01

Accumulating evidence demonstrates that the three-dimensional (3D) organization of chromosomes within the eukaryotic nucleus reflects and influences genomic activities, including transcription, DNA replication, recombination and DNA repair. In order to uncover structure-function relationships, it is necessary first to understand the principles underlying the folding and the 3D arrangement of chromosomes. Chromosome conformation capture (3C) provides a powerful tool for detecting interactions within and between chromosomes. A high throughput derivative of 3C, chromosome conformation capture on chip (4C), executes a genome-wide interrogation of interaction partners for a given locus. We recently developed a new method, a derivative of 3C and 4C, which, similar to Hi-C, is capable of comprehensively identifying long-range chromosome interactions throughout a genome in an unbiased fashion. Hence, our method can be applied to decipher the 3D architectures of genomes. Here, we provide a detailed protocol for this method. Published by Elsevier Inc.

78 FR 19580 - Proposed Collection; Comment Request for Information Collection Tools

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-01

... transmit W-2 series forms to the Social Security Administration. Forms W-2c, W-3c and W-3cPR are used to.... Income Tax Return, Schedule B- Additional Information for Schedule M-3 Filers, Schedule D-Capital Gains... gains and losses from the sale of capital assets. Schedule H (Form 1120) is used by personal service...

An open source software tool to assign the material properties of bone for ABAQUS finite element simulations.

PubMed

Pegg, Elise C; Gill, Harinderjit S

2016-09-06

A new software tool to assign the material properties of bone to an ABAQUS finite element mesh was created and compared with Bonemat, a similar tool originally designed to work with Ansys finite element models. Our software tool (py_bonemat_abaqus) was written in Python, which is the chosen scripting language for ABAQUS. The purpose of this study was to compare the software packages in terms of the material assignment calculation and processing speed. Three element types were compared (linear hexahedral (C3D8), linear tetrahedral (C3D4) and quadratic tetrahedral elements (C3D10)), both individually and as part of a mesh. Comparisons were made using a CT scan of a hemi-pelvis as a test case. A small difference, of -0.05kPa on average, was found between Bonemat version 3.1 (the current version) and our Python package. Errors were found in the previous release of Bonemat (version 3.0 downloaded from www.biomedtown.org) during calculation of the quadratic tetrahedron Jacobian, and conversion of the apparent density to modulus when integrating over the Young׳s modulus field. These issues caused up to 2GPa error in the modulus assignment. For these reasons, we recommend users upgrade to the most recent release of Bonemat. Processing speeds were assessed for the three different element types. Our Python package took significantly longer (110s on average) to perform the calculations compared with the Bonemat software (10s). Nevertheless, the workflow advantages of the package and added functionality makes 'py_bonemat_abaqus' a useful tool for ABAQUS users. Copyright © 2016 Elsevier Ltd. All rights reserved.

Digital mono- and 3D stereo-photogrammetry for geological and geomorphological mapping

NASA Astrophysics Data System (ADS)

Scapozza, Cristian; Schenker, Filippo Luca; Castelletti, Claudio; Bozzini, Claudio; Ambrosi, Christian

2016-04-01

The generalization of application of digital tools for managing, mapping and updating geological data have become widely accepted in the last decennia. Despite the increasing quality and availability of digital topographical maps, orthorectified aerial photographs (orthophotos) and high resolution (5 up to 0.5 m) Digital Elevation Models (DEMs), a correct recognition of the kind, the nature and the boundaries of geological formations and geomophological landforms, unconsolidated sedimentary deposits or slope instabilities is often very difficult on conventional two-dimensional (2D) products, in particular in steep zones (rock walls and talus slopes), under the forest cover, for a very complex topography and in deeply urbanised zones. In many cases, photo-interpretative maps drawn only by 2D data sets must be improved by field verifications or, at least, by field oblique photographs. This is logical, because our natural perception of the real world is three-dimensional (3D), which is partially disabled by the application of 2D visualization techniques. Here we present some examples of application of digital mapping based on a 3D visualization (for aerial and satellite images photo-interpretation) or on a terrestrial perception by digital mono-photogrammetry (for oblique photographs). The 3D digital mapping was performed thanks to an extension of the software ESRI® ArcGIS™ called ArcGDS™. This methodology was also applied on historical aerial photographs (normally analysed by optical stereo-photogrammetry), which were digitized by scanning and then oriented and aero-triangulated thanks to the ArcGDS™ software, allowing the 3D visualisation and the mapping in a GIS environment (Ambrosi and Scapozza, 2015). The mono-photogrammetry (or monoplotting) is the technique of photogrammetrical georeferentiation of single oblique unrectified photographs, which are related to a DEM. In other words, the monoplotting allows relating each pixel of the photograph to the corresponding real world pixel on the DEM, and then extract georeferenced vector data and orthorectified raster data from terrestrial photographs (Bozzini et al., 2012; Scapozza et al., 2014). Through some case studies, we show (1) how 3D digital stereo-photogrammetry makes it possible the production of Quaternary geological and geomorphological maps, (2) how digital mono-photogrammetry is a powerful tool for supporting geological mapping in very steep zones and (3) how the combination of these two digital tools permits diachronical mapping of phenomena evolution (such as landslides or rockglaciers) during the entire twentieth century. Ambrosi C. and Scapozza C. 2015. Improvements in 3-D digital mapping for geomorphological and Quaternary geological cartography. Geographica Helvetica 70: 121-133. doi: 10.5194/gh-70-121-2015 Bozzini C., Conedera M. and Krebs P. 2012. A new monoplotting tool to extract georeferenced vector data and orthorectified raster data from oblique non-metric photographs. International Journal of Heritage in the Digital Era 1: 499-518. doi: 10.1260/2047-4970.1.3.499 Scapozza C., Lambiel C., Bozzini C., Mari S. and Conedera M. 2014. Assessing the rock glacier kinematics on three different timescales: a case study from the southern Swiss Alps. Earth Surface Processes and Landforms 39: 2056-2069. doi: 10.1002/esp.3599

Spatial Modeling Tools for Cell Biology

DTIC Science & Technology

2006-10-01

multiphysics modeling expertise. A graphical user interface (GUI) for CoBi, JCoBi, was written in Java and interactive 3D graphics. CoBi has been...tools (C++ and Java ) to simulate complex cell and organ biology problems. CoBi has been designed to interact with the other Bio-SPICE software...fall of 2002. VisIt supports C++, Python and Java interfaces. The C++ and Java interfaces make it possible to provide alternate user interfaces for

Sandia MEMS Visualization Tools v. 3.0

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

Yarberry, Victor; Jorgensen, Craig R.; Young, Andrew I.

This is a revision to the Sandia MEMS Visualization Tools. It replaces all previous versions. New features in this version: Support for AutoCAD 2014 and 2015 . This CD contains an integrated set of electronic files that: a) Provides a 2D Process Visualizer that generates cross-section images of devices constructed using the SUMMiT V fabrication process. b) Provides a 3D Visualizer that generates 3D images of devices constructed using the SUMMiT V fabrication process. c) Provides a MEMS 3D Model generator that creates 3D solid models of devices constructed using the SUMMiT V fabrication process. While there exists some filesmore » on the CD that are used in conjunction with software package AutoCAD , these files are not intended for use independent of the CD. Note that the customer must purchase his/her own copy of AutoCAD to use with these files.« less

Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy: An evaluation of single-cell Hi-C protocols.

PubMed

Lando, David; Stevens, Tim J; Basu, Srinjan; Laue, Ernest D

2018-01-01

Single-cell chromosome conformation capture approaches are revealing the extent of cell-to-cell variability in the organization and packaging of genomes. These single-cell methods, unlike their multi-cell counterparts, allow straightforward computation of realistic chromosome conformations that may be compared and combined with other, independent, techniques to study 3D structure. Here we discuss how single-cell Hi-C and subsequent 3D genome structure determination allows comparison with data from microscopy. We then carry out a systematic evaluation of recently published single-cell Hi-C datasets to establish a computational approach for the evaluation of single-cell Hi-C protocols. We show that the calculation of genome structures provides a useful tool for assessing the quality of single-cell Hi-C data because it requires a self-consistent network of interactions, relating to the underlying 3D conformation, with few errors, as well as sufficient longer-range cis- and trans-chromosomal contacts.

Reconstruction of Mammary Gland Structure Using Three-Dimensional Computer-Based Microscopy

DTIC Science & Technology

2001-08-01

Segmentation of Mammary Gland Ductal Structure Using Geometric Methods. P.l.’s Malladi R . and Ortiz de Solorzano C. Submitted to the LBNL Laboratory...mammary gland biology". Fernandez-Gonzalez, R ., Jones A., Garcia-Rodriguez E., Knowles D., Sudar D. Ortiz de Solorzano, C. Proceedings of Microscopy...the text. 25 3DRcn4rclr FieC4 eto m oosOtosMCUCP suto 5 2 3p4 eto 6 ’lw r 26o W ~Fl. Case Section Area Tools Opt~ons Micoscope

Geometric Methods for ATR: Shape Spaces, Metrics, Object/Image Relations, and Shapelets

DTIC Science & Technology

2007-09-30

our techniques as a tool for adding depth information to existing video content. In addition, we learned that researchers at the University of...and only if Kr - 4 C L r - 3 C H r - l C r This fact and the incidence relations given in Theorem I, §5, Chapter VII of Hodge and Pedoe [4] give us our...Springer-Verlag, 1992. 4. W.V.D. Hodge and D. Pedoe , Methods of Algebraic Geometry, nos. 1, 2, and 3, in Mathematical Library Series, Cambridge

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution.

PubMed

Ma, Wenxiu; Ay, Ferhat; Lee, Choli; Gulsoy, Gunhan; Deng, Xinxian; Cook, Savannah; Hesson, Jennifer; Cavanaugh, Christopher; Ware, Carol B; Krumm, Anton; Shendure, Jay; Blau, C Anthony; Disteche, Christine M; Noble, William S; Duan, ZhiJun

2018-06-01

The folding and three-dimensional (3D) organization of chromatin in the nucleus critically impacts genome function. The past decade has witnessed rapid advances in genomic tools for delineating 3D genome architecture. Among them, chromosome conformation capture (3C)-based methods such as Hi-C are the most widely used techniques for mapping chromatin interactions. However, traditional Hi-C protocols rely on restriction enzymes (REs) to fragment chromatin and are therefore limited in resolution. We recently developed DNase Hi-C for mapping 3D genome organization, which uses DNase I for chromatin fragmentation. DNase Hi-C overcomes RE-related limitations associated with traditional Hi-C methods, leading to improved methodological resolution. Furthermore, combining this method with DNA capture technology provides a high-throughput approach (targeted DNase Hi-C) that allows for mapping fine-scale chromatin architecture at exceptionally high resolution. Hence, targeted DNase Hi-C will be valuable for delineating the physical landscapes of cis-regulatory networks that control gene expression and for characterizing phenotype-associated chromatin 3D signatures. Here, we provide a detailed description of method design and step-by-step working protocols for these two methods. Copyright © 2018 Elsevier Inc. All rights reserved.

On the upper bound of the thermodynamic stability of fullerenes from small to giant

NASA Astrophysics Data System (ADS)

Pankratyev, Evgeniy Yu; Khatymov, Rustem V.; Sabirov, Denis Sh; Yuldashev, Arthur V.

2018-07-01

From the large variety of C20sbnd C720 fullerenes, the energetically most stable isomers were chosen and studied within the PBE/3ζ quantum-chemical approximation. A phenomenological model of the dependence of the standard enthalpy of formation and entropy of the selected isomers on the number of the carbon atoms is developed. From the analysis of the constants of the phenomenological model, it follows that the C60, C70, C180, and C1500 molecules hold a prominent position among the hypothetical and/or experimentally discovered fullerenes. For the selected energy-stable isomers, the values of the singlet-triplet splitting were calculated. The ground state of the C260sbnd C3, C320sbnd D3d and C500sbnd D3d molecules were found to be of triplet multiplicity that may indicate their low kinetic stability and/or possibility of existence in the derivatized forms. In view of the lack of relevant experimental thermodynamic data on fullerenes, the obtained in this work approximation dependences, expressed in a simple analytical form, may provide useful tool for fast assessing the energetic characteristics of fullerenes, as well as for prediction of those undiscovered yet.

Highly Omnidirectional and Frequency Controllable Carbon/Polyaniline-based 2D and 3D Monopole Antenna

NASA Astrophysics Data System (ADS)

Shin, Keun-Young; Kim, Minkyu; Lee, James S.; Jang, Jyongsik

2015-09-01

Highly omnidirectional and frequency controllable carbon/polyaniline (C/PANI)-based, two- (2D) and three-dimensional (3D) monopole antennas were fabricated using screen-printing and a one-step, dimensionally confined hydrothermal strategy, respectively. Solvated C/PANI was synthesized by low-temperature interfacial polymerization, during which strong π-π interactions between graphene and the quinoid rings of PANI resulted in an expanded PANI conformation with enhanced crystallinity and improved mechanical and electrical properties. Compared to antennas composed of pristine carbon or PANI-based 2D monopole structures, 2D monopole antennas composed of this enhanced hybrid material were highly efficient and amenable to high-frequency, omnidirectional electromagnetic waves. The mean frequency of C/PANI fiber-based 3D monopole antennas could be controlled by simply cutting and stretching the antenna. These antennas attained high peak gain (3.60 dBi), high directivity (3.91 dBi) and radiation efficiency (92.12%) relative to 2D monopole antenna. These improvements were attributed the high packing density and aspect ratios of C/PANI fibers and the removal of the flexible substrate. This approach offers a valuable and promising tool for producing highly omnidirectional and frequency-controllable, carbon-based monopole antennas for use in wireless networking communications on industrial, scientific, and medical (ISM) bands.

Highly Omnidirectional and Frequency Controllable Carbon/Polyaniline-based 2D and 3D Monopole Antenna

PubMed Central

Shin, Keun-Young; Kim, Minkyu; Lee, James S.; Jang, Jyongsik

2015-01-01

Highly omnidirectional and frequency controllable carbon/polyaniline (C/PANI)-based, two- (2D) and three-dimensional (3D) monopole antennas were fabricated using screen-printing and a one-step, dimensionally confined hydrothermal strategy, respectively. Solvated C/PANI was synthesized by low-temperature interfacial polymerization, during which strong π–π interactions between graphene and the quinoid rings of PANI resulted in an expanded PANI conformation with enhanced crystallinity and improved mechanical and electrical properties. Compared to antennas composed of pristine carbon or PANI-based 2D monopole structures, 2D monopole antennas composed of this enhanced hybrid material were highly efficient and amenable to high-frequency, omnidirectional electromagnetic waves. The mean frequency of C/PANI fiber-based 3D monopole antennas could be controlled by simply cutting and stretching the antenna. These antennas attained high peak gain (3.60 dBi), high directivity (3.91 dBi) and radiation efficiency (92.12%) relative to 2D monopole antenna. These improvements were attributed the high packing density and aspect ratios of C/PANI fibers and the removal of the flexible substrate. This approach offers a valuable and promising tool for producing highly omnidirectional and frequency-controllable, carbon-based monopole antennas for use in wireless networking communications on industrial, scientific, and medical (ISM) bands. PMID:26338090

Assessing similarity analysis of chromatographic fingerprints of Cyclopia subternata extracts as potential screening tool for in vitro glucose utilisation.

PubMed

Schulze, Alexandra E; De Beer, Dalene; Mazibuko, Sithandiwe E; Muller, Christo J F; Roux, Candice; Willenburg, Elize L; Nyunaï, Nyemb; Louw, Johan; Manley, Marena; Joubert, Elizabeth

2016-01-01

Similarity analysis of the phenolic fingerprints of a large number of aqueous extracts of Cyclopia subternata, obtained by high-performance liquid chromatography (HPLC), was evaluated as a potential tool to screen extracts for relative bioactivity. The assessment was based on the (dis)similarity of their fingerprints to that of a reference active extract of C. subternata, proven to enhance glucose uptake in vitro and in vivo. In vitro testing of extracts, selected as being most similar (n = 5; r ≥ 0.962) and most dissimilar (n = 5; r ≤ 0.688) to the reference active extract, showed that no clear pattern in terms of relative glucose uptake efficacy in C2C12 myocytes emerged, irrespective of the dose. Some of the most dissimilar extracts had higher glucose-lowering activity than the reference active extract. Principal component analysis revealed the major compounds responsible for the most variation within the chromatographic fingerprints, as mangiferin, isomangiferin, iriflophenone-3-C-β-D-glucoside-4-O-β-D-glucoside, iriflophenone-3-C-β-D-glucoside, scolymoside, and phloretin-3',5'-di-C-β-D-glucoside. Quantitative analysis of the selected extracts showed that the most dissimilar extracts contained the highest mangiferin and isomangiferin levels, whilst the most similar extracts had the highest scolymoside content. These compounds demonstrated similar glucose uptake efficacy in C2C12 myocytes. It can be concluded that (dis)similarity of chromatographic fingerprints of extracts of unknown activity to that of a proven bioactive extract does not necessarily translate to lower or higher bioactivity.

STRING 3: An Advanced Groundwater Flow Visualization Tool

NASA Astrophysics Data System (ADS)

Schröder, Simon; Michel, Isabel; Biedert, Tim; Gräfe, Marius; Seidel, Torsten; König, Christoph

2016-04-01

The visualization of 3D groundwater flow is a challenging task. Previous versions of our software STRING [1] solely focused on intuitive visualization of complex flow scenarios for non-professional audiences. STRING, developed by Fraunhofer ITWM (Kaiserslautern, Germany) and delta h Ingenieurgesellschaft mbH (Witten, Germany), provides the necessary means for visualization of both 2D and 3D data on planar and curved surfaces. In this contribution we discuss how to extend this approach to a full 3D tool and its challenges in continuation of Michel et al. [2]. This elevates STRING from a post-production to an exploration tool for experts. In STRING moving pathlets provide an intuition of velocity and direction of both steady-state and transient flows. The visualization concept is based on the Lagrangian view of the flow. To capture every detail of the flow an advanced method for intelligent, time-dependent seeding is used building on the Finite Pointset Method (FPM) developed by Fraunhofer ITWM. Lifting our visualization approach from 2D into 3D provides many new challenges. With the implementation of a seeding strategy for 3D one of the major problems has already been solved (see Schröder et al. [3]). As pathlets only provide an overview of the velocity field other means are required for the visualization of additional flow properties. We suggest the use of Direct Volume Rendering and isosurfaces for scalar features. In this regard we were able to develop an efficient approach for combining the rendering through raytracing of the volume and regular OpenGL geometries. This is achieved through the use of Depth Peeling or A-Buffers for the rendering of transparent geometries. Animation of pathlets requires a strict boundary of the simulation domain. Hence, STRING needs to extract the boundary, even from unstructured data, if it is not provided. In 3D we additionally need a good visualization of the boundary itself. For this the silhouette based on the angle of neighboring faces is extracted. Similar algorithms help to find the 2D boundary of cuts through the 3D model. As interactivity plays a big role for an exploration tool the speed of the drawing routines is also important. To achieve this, different pathlet rendering solutions have been developed and benchmarked. These provide a trade-off between the usage of geometry and fragment shaders. We show that point sprite shaders have superior performance and visual quality over geometry-based approaches. Admittedly, the point sprite-based approach has many non-trivial problems of joining the different parts of the pathlet geometry. This research is funded by the Federal Ministry for Economic Affairs and Energy (Germany). [1] T. Seidel, C. König, M. Schäfer, I. Ostermann, T. Biedert, D. Hietel (2014). Intuitive visualization of transient groundwater flow. Computers & Geosciences, Vol. 67, pp. 173-179 [2] I. Michel, S. Schröder, T. Seidel, C. König (2015). Intuitive Visualization of Transient Flow: Towards a Full 3D Tool. Geophysical Research Abstracts, Vol. 17, EGU2015-1670 [3] S. Schröder, I. Michel, T. Seidel, C.M. König (2015). STRING 3: Full 3D visualization of groundwater Flow. In Proceedings of IAMG 2015 Freiberg, pp. 813-822

Multi-modal imaging, model-based tracking, and mixed reality visualisation for orthopaedic surgery

PubMed Central

Fuerst, Bernhard; Tateno, Keisuke; Johnson, Alex; Fotouhi, Javad; Osgood, Greg; Tombari, Federico; Navab, Nassir

2017-01-01

Orthopaedic surgeons are still following the decades old workflow of using dozens of two-dimensional fluoroscopic images to drill through complex 3D structures, e.g. pelvis. This Letter presents a mixed reality support system, which incorporates multi-modal data fusion and model-based surgical tool tracking for creating a mixed reality environment supporting screw placement in orthopaedic surgery. A red–green–blue–depth camera is rigidly attached to a mobile C-arm and is calibrated to the cone-beam computed tomography (CBCT) imaging space via iterative closest point algorithm. This allows real-time automatic fusion of reconstructed surface and/or 3D point clouds and synthetic fluoroscopic images obtained through CBCT imaging. An adapted 3D model-based tracking algorithm with automatic tool segmentation allows for tracking of the surgical tools occluded by hand. This proposed interactive 3D mixed reality environment provides an intuitive understanding of the surgical site and supports surgeons in quickly localising the entry point and orienting the surgical tool during screw placement. The authors validate the augmentation by measuring target registration error and also evaluate the tracking accuracy in the presence of partial occlusion. PMID:29184659

2D- and 3D SIMS investigations on hot-pressed steel powder HS 6-5-3-8.

PubMed

Rosner, M; Pöckl, G; Danninger, H; Hutter, H

2002-10-01

Processing of steel with powder metallurgical methods such as sintering or hot-pressing have proven to be a powerful tool for the production of industrial parts and for components in the automotive industry. Series of steel-powders (HS 6-5-3-8) produced by gas atomization has been hot-pressed in a graphite tube at temperatures from 820 degrees C to 1050 degrees C. The samples have been characterized with a Secondary Electron Microscope (SEM) due to their porosity and then investigated with 2D- and 3D- SIMS. The spatial distribution of the non-metallic impurities and the covering oxide layer of the single particles has been traced dependent to the pressing temperature. Powders pressed at temperatures higher than 880 degrees C exhibited different precipitation behavior of the impurities and an excessive loss of the covering oxide layer of the single powder particles.

Evaluation of CERT Secure Coding Rules through Integration with Source Code Analysis Tools

DTIC Science & Technology

2008-06-01

Fortify SCA 3 2.2 Compass / ROSE 6 3 Project Analysis 9 3.1 Measuring and Analysis 9 4 Results 13 4.1 Fortify Results 13 4.1.1 CERT C++ Secure...Fortify C Rules 23 Appendix B Fortify C++ Rules 35 Appendix C C Rules Implemented in Compass Rose 43 Appendix D ROSE C++ Rules 51 References...to Daniel Quinlan at Lawrence Livermore National Laboratory for all his help getting us up and running with Compass /ROSE. Thanks to our SEI editor

An Examination of Selected Software Testing Tools: 1993 Supplement

DTIC Science & Technology

1993-10-01

tool users. They have recently established a relationship with a U.S. company, Texel & Co., who will market and support AdaTEST in this country. AdaTEST...was first marketed in 1991 and is now used at more than 15 sites internationally. It is machine and operating system independent, relying only on the...uin~ ugc ~zin~f224.64 N&MOSNOtRaD.YC 625.36, O •OMamm c 0.26 MZ~jVJO~ZAL.WW .00 mISIW...2aV3...OW.)b!UWZOU0.01mu.muw...mnav._ohawM3C2Ut’c 0.04 ,85152.88

Molecular Dynamics Visualization (MDV): Stereoscopic 3D Display of Biomolecular Structure and Interactions Using the Unity Game Engine.

PubMed

Wiebrands, Michael; Malajczuk, Chris J; Woods, Andrew J; Rohl, Andrew L; Mancera, Ricardo L

2018-06-21

Molecular graphics systems are visualization tools which, upon integration into a 3D immersive environment, provide a unique virtual reality experience for research and teaching of biomolecular structure, function and interactions. We have developed a molecular structure and dynamics application, the Molecular Dynamics Visualization tool, that uses the Unity game engine combined with large scale, multi-user, stereoscopic visualization systems to deliver an immersive display experience, particularly with a large cylindrical projection display. The application is structured to separate the biomolecular modeling and visualization systems. The biomolecular model loading and analysis system was developed as a stand-alone C# library and provides the foundation for the custom visualization system built in Unity. All visual models displayed within the tool are generated using Unity-based procedural mesh building routines. A 3D user interface was built to allow seamless dynamic interaction with the model while being viewed in 3D space. Biomolecular structure analysis and display capabilities are exemplified with a range of complex systems involving cell membranes, protein folding and lipid droplets.

Lightweight Object Oriented Structure analysis: Tools for building Tools to Analyze Molecular Dynamics Simulations

PubMed Central

Romo, Tod D.; Leioatts, Nicholas; Grossfield, Alan

2014-01-01

LOOS (Lightweight Object-Oriented Structure-analysis) is a C++ library designed to facilitate making novel tools for analyzing molecular dynamics simulations by abstracting out the repetitive tasks, allowing developers to focus on the scientifically relevant part of the problem. LOOS supports input using the native file formats of most common biomolecular simulation packages, including CHARMM, NAMD, Amber, Tinker, and Gromacs. A dynamic atom selection language based on the C expression syntax is included and is easily accessible to the tool-writer. In addition, LOOS is bundled with over 120 pre-built tools, including suites of tools for analyzing simulation convergence, 3D histograms, and elastic network models. Through modern C++ design, LOOS is both simple to develop with (requiring knowledge of only 4 core classes and a few utility functions) and is easily extensible. A python interface to the core classes is also provided, further facilitating tool development. PMID:25327784

Papers on Program Testing,

DTIC Science & Technology

1979-01-01

tractability for scientific analysis. Although much remains to be learned about mutation as a testing tool, there is a considerable body of written material...explicitly address classifications (2) may not have been affected at all! In general, the and (3) in this article , except to point out that even relative...34 ARTICLE B=B’B C IN CACM 1971). C=C*02 INTEGER AiN),N.F D=B+C INTEGER M.NS.R.I.J.W IF (A.NE.D) GOTO 200 MI PRINT 150 NS=N 150 FORMATIIH .RIGHT ANGLED

A CAD System for Hemorrhagic Stroke.

PubMed

Nowinski, Wieslaw L; Qian, Guoyu; Hanley, Daniel F

2014-09-01

Computer-aided detection/diagnosis (CAD) is a key component of routine clinical practice, increasingly used for detection, interpretation, quantification and decision support. Despite a critical need, there is no clinically accepted CAD system for stroke yet. Here we introduce a CAD system for hemorrhagic stroke. This CAD system segments, quantifies, and displays hematoma in 2D/3D, and supports evacuation of hemorrhage by thrombolytic treatment monitoring progression and quantifying clot removal. It supports seven-step workflow: select patient, add a new study, process patient's scans, show segmentation results, plot hematoma volumes, show 3D synchronized time series hematomas, and generate report. The system architecture contains four components: library, tools, application with user interface, and hematoma segmentation algorithm. The tools include a contour editor, 3D surface modeler, 3D volume measure, histogramming, hematoma volume plot, and 3D synchronized time-series hematoma display. The CAD system has been designed and implemented in C++. It has also been employed in the CLEAR and MISTIE phase-III, multicenter clinical trials. This stroke CAD system is potentially useful in research and clinical applications, particularly for clinical trials.

Expression of ZO-1 and claudin-1 in a 3D epidermal equivalent using canine progenitor epidermal keratinocytes.

PubMed

Teramoto, Keiji; Asahina, Ryota; Nishida, Hidetaka; Kamishina, Hiroaki; Maeda, Sadatoshi

2018-05-21

Previous studies indicate that tight junctions are involved in the pathogenesis of canine atopic dermatitis (cAD). An in vitro skin model is needed to elucidate the specific role of tight junctions in cAD. A 3D epidermal equivalent model using canine progenitor epidermal keratinocytes (CPEK) has been established; the expression of tight junctions within this model is uncharacterized. To investigate the expression of tight junctions in the 3D epidermal equivalent. Two normal laboratory beagle dogs served as donors of full-thickness skin biopsy samples for comparison to the in vitro model. Immunohistochemical techniques were employed to investigate the expression of tight junctions including zonula occludens (ZO)-1 and claudin-1 in normal canine skin, and in the CPEK 3D epidermal equivalent. Results demonstrated the expression of ZO-1 and claudin-1 in the CPEK 3D epidermal equivalent, with staining patterns that were similar to those in normal canine skin. The CPEK 3D epidermal equivalent has the potential to be a suitable in vitro research tool for clarifying the specific role of tight junctions in cAD. © 2018 ESVD and ACVD.

A browser-based 3D Visualization Tool designed for comparing CERES/CALIOP/CloudSAT level-2 data sets.

NASA Astrophysics Data System (ADS)

Chu, C.; Sun-Mack, S.; Chen, Y.; Heckert, E.; Doelling, D. R.

2017-12-01

In Langley NASA, Clouds and the Earth's Radiant Energy System (CERES) and Moderate Resolution Imaging Spectroradiometer (MODIS) are merged with Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) on the Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) and CloudSat Cloud Profiling Radar (CPR). The CERES merged product (C3M) matches up to three CALIPSO footprints with each MODIS pixel along its ground track. It then assigns the nearest CloudSat footprint to each of those MODIS pixels. The cloud properties from MODIS, retrieved using the CERES algorithms, are included in C3M with the matched CALIPSO and CloudSat products along with radiances from 18 MODIS channels. The dataset is used to validate the CERES retrieved MODIS cloud properties and the computed TOA and surface flux difference using MODIS or CALIOP/CloudSAT retrieved clouds. This information is then used to tune the computed fluxes to match the CERES observed TOA flux. A visualization tool will be invaluable to determine the cause of these large cloud and flux differences in order to improve the methodology. This effort is part of larger effort to allow users to order the CERES C3M product sub-setted by time and parameter as well as the previously mentioned visualization capabilities. This presentation will show a new graphical 3D-interface, 3D-CERESVis, that allows users to view both passive remote sensing satellites (MODIS and CERES) and active satellites (CALIPSO and CloudSat), such that the detailed vertical structures of cloud properties from CALIPSO and CloudSat are displayed side by side with horizontally retrieved cloud properties from MODIS and CERES. Similarly, the CERES computed profile fluxes whether using MODIS or CALIPSO and CloudSat clouds can also be compared. 3D-CERESVis is a browser-based visualization tool that makes uses of techniques such as multiple synchronized cursors, COLLADA format data and Cesium.

Open source 3D visualization and interaction dedicated to hydrological models

NASA Astrophysics Data System (ADS)

Richard, Julien; Giangola-Murzyn, Agathe; Gires, Auguste; Tchiguirinskaia, Ioulia; Schertzer, Daniel

2014-05-01

Climate change and surface urbanization strongly modify the hydrological cycle in urban areas, increasing the consequences of extreme events such as floods or draughts. These issues lead to the development of the Multi-Hydro model at the Ecole des Ponts ParisTech (A. Giangola-Murzyn et al., 2012). This fully distributed model allows to compute the hydrological response of urban and peri-urban areas. Unfortunately such models are seldom user friendly. Indeed generating the inputs before launching a new simulation is usually a tricky tasks, and understanding and interpreting the outputs remains specialist tasks not accessible to the wider public. The MH-AssimTool was developed to overcome these issues. To enable an easier and improved understanding of the model outputs, we decided to convert the raw output data (grids file in ascii format) to a 3D display. Some commercial paying models provide a 3D visualization. Because of the cost of their licenses, this kind of tools may not be accessible to the most concerned stakeholders. So, we are developing a new tool based on C++ for the computation, Qt for the graphic user interface, QGIS for the geographical side and OpenGL for the 3D display. All these languages and libraries are open source and multi-platform. We will discuss some preprocessing issues for the data conversion from 2.5D to 3D. Indeed, the GIS data, is considered as a 2.5D (e.i. 2D polygon + one height) and the its transform to 3D display implies a lot of algorithms. For example,to visualize in 3D one building, it is needed to have for each point the coordinates and the elevation according to the topography. Furthermore one have to create new points to represent the walls. Finally the interactions between the model and stakeholders through this new interface and how this helps converting a research tool into a an efficient operational decision tool will be discussed. This ongoing research on the improvement of the visualization methods is supported by the KIC-Climate Blue Green Dream project.

Innovative Methods for Engine Health Monitoring

DTIC Science & Technology

2006-11-30

ELEMENT NUMBER 6. AUTHOR(S) 6d. PROJECT NUMBER C. L. Philip Chen, Z. Pantic-Tanner, H. Millwater , S. Hudak, Y. Huang, P. Cotae, D. Tanner, E. John, K. Chan...Philip Chen’, Z. Pantic-Tanner 2, H. Millwater 3, S. Hudak 4, Y. Huang5, P. Cotae6, D. Tanner 7, E. Johns, K.Chan9, X. Wang𔃺 1 - Professor and Chair... Millwater , R.C. McClung, M.P. Enright, "A new tool for design and certification of aircraft turbine rotors," Journal of Engineering for Gas Turbines

Development of a 3D Tissue Culture-Based High-Content Screening Platform That Uses Phenotypic Profiling to Discriminate Selective Inhibitors of Receptor Tyrosine Kinases.

PubMed

Booij, Tijmen H; Klop, Maarten J D; Yan, Kuan; Szántai-Kis, Csaba; Szokol, Balint; Orfi, Laszlo; van de Water, Bob; Keri, Gyorgy; Price, Leo S

2016-10-01

3D tissue cultures provide a more physiologically relevant context for the screening of compounds, compared with 2D cell cultures. Cells cultured in 3D hydrogels also show complex phenotypes, increasing the scope for phenotypic profiling. Here we describe a high-content screening platform that uses invasive human prostate cancer cells cultured in 3D in standard 384-well assay plates to study the activity of potential therapeutic small molecules and antibody biologics. Image analysis tools were developed to process 3D image data to measure over 800 phenotypic parameters. Multiparametric analysis was used to evaluate the effect of compounds on tissue morphology. We applied this screening platform to measure the activity and selectivity of inhibitors of the c-Met and epidermal growth factor (EGF) receptor (EGFR) tyrosine kinases in 3D cultured prostate carcinoma cells. c-Met and EGFR activity was quantified based on the phenotypic profiles induced by their respective ligands, hepatocyte growth factor and EGF. The screening method was applied to a novel collection of 80 putative inhibitors of c-Met and EGFR. Compounds were identified that induced phenotypic profiles indicative of selective inhibition of c-Met, EGFR, or bispecific inhibition of both targets. In conclusion, we describe a fully scalable high-content screening platform that uses phenotypic profiling to discriminate selective and nonselective (off-target) inhibitors in a physiologically relevant 3D cell culture setting. © 2016 Society for Laboratory Automation and Screening.

Overview of 3D Documentation Data and Tools available for Archaeological Researches: case study of the Romanesque Church of Dugny-sur-Meuse (France)

NASA Astrophysics Data System (ADS)

Macher, H.; Grussenmeyer, P.; Kraemer, C.; Guillemin, S.

2015-08-01

In this paper, the 3D documentation of the full structure of the Romanesque church of Dugny-sur-Meuse is discussed. In 2012 and 2013, a 3D recording project was carried out under the supervision of the Photogrammetry and Geomatics Research Group from INSA Strasbourg (France) in cooperation with C. Kraemer, archaeologist from Nancy (France). The goal of the project was on one hand to propose new solutions and tools to the archaeologists in charge of the project especially for stone by stone measurements. On the other hand, a simplified 3D model was required by the local authorities for communication purposes. To achieve these goals several techniques were applied namely GNSS measurements and accurate traverse networks, photogrammetric recordings and terrestrial laser scanning acquisitions. The various acquired data are presented in this paper. Based on these data, several deliverables are also proposed. The generation of orthoimages from plane as well as cylindrical surfaces is considered. Moreover, the workflow for the creation of a 3D simplified model is also presented.

ATP-binding Cassette (ABC) Transport System Solute-binding Protein-guided Identification of Novel d-Altritol and Galactitol Catabolic Pathways in Agrobacterium tumefaciens C58*

PubMed Central

Wichelecki, Daniel J.; Vetting, Matthew W.; Chou, Liyushang; Al-Obaidi, Nawar; Bouvier, Jason T.; Almo, Steven C.; Gerlt, John A.

2015-01-01

Innovations in the discovery of the functions of uncharacterized proteins/enzymes have become increasingly important as advances in sequencing technology flood protein databases with an exponentially growing number of open reading frames. This study documents one such innovation developed by the Enzyme Function Initiative (EFI; U54GM093342), the use of solute-binding proteins for transport systems to identify novel metabolic pathways. In a previous study, this strategy was applied to the tripartite ATP-independent periplasmic transporters. Here, we apply this strategy to the ATP-binding cassette transporters and report the discovery of novel catabolic pathways for d-altritol and galactitol in Agrobacterium tumefaciens C58. These efforts resulted in the description of three novel enzymatic reactions as follows: 1) oxidation of d-altritol to d-tagatose via a dehydrogenase in Pfam family PF00107, a previously unknown reaction; 2) phosphorylation of d-tagatose to d-tagatose 6-phosphate via a kinase in Pfam family PF00294, a previously orphan EC number; and 3) epimerization of d-tagatose 6-phosphate C-4 to d-fructose 6-phosphate via a member of Pfam family PF08013, another previously unknown reaction. The epimerization reaction catalyzed by a member of PF08013 is especially noteworthy, because the functions of members of PF08013 have been unknown. These discoveries were assisted by the following two synergistic bioinformatics web tools made available by the Enzyme Function Initiative: the EFI-Enzyme Similarity Tool and the EFI-Genome Neighborhood Tool. PMID:26472925

A Multiscale Software Tool for Field/Circuit Co-Simulation

DTIC Science & Technology

2011-12-15

technology fields: Number of graduating undergraduates who achieved a 3.5 GPA to 4.0 (4.0 max scale): Number of graduating undergraduates funded by a...times more efficient than FDTD for such a problem in 3D . The techniques in class (c) above include the discontinuous Galerkin method and multidomain...implements a finite-differential-time-domain method on single field propagation in a 3D space. We consider a cavity model which includes two electric

Contamination Analysis Tools

NASA Technical Reports Server (NTRS)

Brieda, Lubos

2015-01-01

This talk presents 3 different tools developed recently for contamination analysis:HTML QCM analyzer: runs in a web browser, and allows for data analysis of QCM log filesJava RGA extractor: can load in multiple SRS.ana files and extract pressure vs. time dataC++ Contamination Simulation code: 3D particle tracing code for modeling transport of dust particulates and molecules. Uses residence time to determine if molecules stick. Particulates can be sampled from IEST-STD-1246 and be accelerated by aerodynamic forces.

Properties and Cutting Performance of TiAlSiN Coating Prepared by Cathode Arc Ion Plating

NASA Astrophysics Data System (ADS)

Zhang, Er-Geng; Chen, Qiang; Wang, Qin-Xue; Huang, Biao

2016-06-01

TiAlSiN coating was deposited on high-speed steel (HSS) samples and cemented carbide tool inserts, respectively, by a new coating preparation procedure, and its properties and cutting performance were characterized. The coating thickness, chemical composition, microstructure morphology and mechanical properties were investigated by X-ray fluorescence measurement system, energy dispersive spectrometer (EDS), scanning electron microscope (SEM), nanoindentation, Rockwell hardness tester and ball-on-disc tribometer. A 3D orthogonal cutting experiment model was established by DEFORM-3D to study the influences of different coating thicknesses on cutting force and temperature, and the field cutting experiment was carried out. The results show that the thickness of TiAlSiN coating is 3.14μm prepared by the 3μm preparation procedure, microhardness is 36.727GPa with the Si content of about 5.22at.% as well as good fracture toughness and adhesion strength. The TC4 and AISI 1045 cutting tool inserts with 4μm coating thickness have the minimum cutting forces of about 734.7N and 450.7N, respectively. Besides, tool inserts with a thickness of 3μm have the minimum cutting temperatures of about 510.2∘C and 230.6∘C, respectively.

Towards a Framework for Modeling Space Systems Architectures

NASA Technical Reports Server (NTRS)

Shames, Peter; Skipper, Joseph

2006-01-01

Topics covered include: 1) Statement of the problem: a) Space system architecture is complex; b) Existing terrestrial approaches must be adapted for space; c) Need a common architecture methodology and information model; d) Need appropriate set of viewpoints. 2) Requirements on a space systems model. 3) Model Based Engineering and Design (MBED) project: a) Evaluated different methods; b) Adapted and utilized RASDS & RM-ODP; c) Identified useful set of viewpoints; d) Did actual model exchanges among selected subset of tools. 4) Lessons learned & future vision.

Discovery of a cAMP Deaminase That Quenches Cyclic AMP-Dependent Regulation

PubMed Central

Goble, Alissa M.; Feng, Youjun; Raushel, Frank M.; Cronan, John E.

2013-01-01

An enzyme of unknown function within the amidohydrolase superfamily was discovered to catalyze the hydrolysis of the universal second messenger, cyclic-3’, 5’-adenosine monophosphate (cAMP). The enzyme, which we have named CadD, is encoded by the human pathogenic bacterium Leptospira interrogans. Although CadD is annotated as an adenosine deaminase, the protein specifically deaminates cAMP to cyclic-3’, 5’-inosine monophosphate (cIMP) with a kcat/Km of 2.7 ± 0.4 × 105 M−1 s−1 and has no activity on adenosine, adenine, or 5’-adenosine monophosphate (AMP). This is the first identification of a deaminase specific for cAMP. Expression of CadD in Escherichia coli mimics the loss of adenylate cyclase in that it blocks growth on carbon sources that require the cAMP-CRP transcriptional activator complex for expression of the cognate genes. The cIMP reaction product cannot replace cAMP as the ligand for CRP binding to DNA in vitro and cIMP is a very poor competitor of cAMP activation of CRP for DNA binding. Transcriptional analyses indicate that CadD expression represses expression of several cAMP-CRP dependent genes. CadD adds a new activity to the cAMP metabolic network and may be a useful tool in intracellular study of cAMP-dependent processes. PMID:24074367

Toward real-time endoscopically-guided robotic navigation based on a 3D virtual surgical field model

NASA Astrophysics Data System (ADS)

Gong, Yuanzheng; Hu, Danying; Hannaford, Blake; Seibel, Eric J.

2015-03-01

The challenge is to accurately guide the surgical tool within the three-dimensional (3D) surgical field for roboticallyassisted operations such as tumor margin removal from a debulked brain tumor cavity. The proposed technique is 3D image-guided surgical navigation based on matching intraoperative video frames to a 3D virtual model of the surgical field. A small laser-scanning endoscopic camera was attached to a mock minimally-invasive surgical tool that was manipulated toward a region of interest (residual tumor) within a phantom of a debulked brain tumor. Video frames from the endoscope provided features that were matched to the 3D virtual model, which were reconstructed earlier by raster scanning over the surgical field. Camera pose (position and orientation) is recovered by implementing a constrained bundle adjustment algorithm. Navigational error during the approach to fluorescence target (residual tumor) is determined by comparing the calculated camera pose to the measured camera pose using a micro-positioning stage. From these preliminary results, computation efficiency of the algorithm in MATLAB code is near real-time (2.5 sec for each estimation of pose), which can be improved by implementation in C++. Error analysis produced 3-mm distance error and 2.5 degree of orientation error on average. The sources of these errors come from 1) inaccuracy of the 3D virtual model, generated on a calibrated RAVEN robotic platform with stereo tracking; 2) inaccuracy of endoscope intrinsic parameters, such as focal length; and 3) any endoscopic image distortion from scanning irregularities. This work demonstrates feasibility of micro-camera 3D guidance of a robotic surgical tool.

Rapid and sensitive detection of Curvularia lunata associated with maize leaf spot based on its Clg2p gene using semi-nested PCR.

PubMed

Hou, J M; Ma, B C; Zuo, Y H; Guo, L L; Gao, S G; Wang, Y Y; Liu, T

2013-04-01

Curvularia lunata (Wakker) Boed, the causative agent of Curvularia leaf spot in maize, was determined according to conidiophore and conidium morphology in a previous study. In the current study, a sensitive polymerase chain reaction assay was developed for the detection of C. lunata. Two specific forward (ClgD1/ClgD2) and one reverse primers (ClgD3) were designed based on a Ras-related (Clg2p) gene. Eight C. lunata isolates that represent different virulent strains in maize, six other Curvularia spp., and 22 fungal plant pathogens were used to test the specificity of the primers. PCR amplification using ClgD1/ClgD3 as the first-round primers resulted in an 870-bp band from the C. lunata isolates. The detection sensitivity using ClgD1/ClgD3 was 100 pg of genomic DNA. In the second round of PCR, a 1 : 50 dilution of the first-round PCR products was used as a template with the ClgD2/ClgD3 primer pair, which increased the detection sensitivity to 1 fg. This semi-nested PCR procedure could also be used to detect C. lunata from infected maize leaves. The proposed PCR-based assay may be used for diagnosing and monitoring maize Curvularia leaf spot. The semi-nested PCR assay may provide researchers and laboratory technologists a tool to rapidly detect C. lunata, which causes maize Curvularia leaf spot, compared with histological examination. © 2012 The Society for Applied Microbiology.

Heightened Dopaminergic Response to Amphetamine at the D3 Dopamine Receptor in Methamphetamine Users

PubMed Central

Boileau, Isabelle; Payer, Doris; Rusjan, Pablo M; Houle, Sylvain; Tong, Junchao; McCluskey, Tina; Wilson, Alan A; Kish, Stephen J

2016-01-01

Neuroimaging studies in stimulant use (eg, cocaine, methamphetamine) disorders show that diminished dopamine release by dopamine-elevating drugs is a potential marker of relapse and suggest that increasing dopamine at the D2/3 receptors may be therapeutically beneficial. In contrast, recent investigations indicate heightened D3 receptor levels in stimulant users prompting the view that D3 antagonism may help prevent relapse. Here we tested whether a ‘blunted' response to amphetamine in methamphetamine (MA) users extends to D3-rich brain areas. Fourteen MA users and 15 healthy controls completed two positron emission tomographic scans with a D3-preferring probe [11C]-(+)-PHNO at baseline and after amphetamine (0.4 mg/kg). Relative to healthy controls, MA users had greater decreases in [11C]-(+)-PHNO binding (increased dopamine release) after amphetamine in D3-rich substantia nigra (36 vs 20%, p=0.03) and globus pallidus (30 vs 17%, p=0.06), which correlated with self-reported ‘drug wanting'. We did not observe a ‘blunted' dopamine response to amphetamine in D2-rich striatum; however, drug use severity was negatively associated with amphetamine-induced striatal changes in [11C]-(+)-PHNO binding. Our study provides evidence that dopamine transmission in extrastriatal ‘D3-areas' is not blunted but rather increased in MA users. Together with our previous finding of elevated D3 receptor level in MA users, the current observation suggests that greater dopaminergic transmission at the D3 dopamine receptor may contribute to motivation to use drugs and argues in favor of D3 antagonism as a possible therapeutic tool to reduce craving and relapse in MA addiction. PMID:27353309

Heightened Dopaminergic Response to Amphetamine at the D3 Dopamine Receptor in Methamphetamine Users.

PubMed

Boileau, Isabelle; Payer, Doris; Rusjan, Pablo M; Houle, Sylvain; Tong, Junchao; McCluskey, Tina; Wilson, Alan A; Kish, Stephen J

2016-12-01

Neuroimaging studies in stimulant use (eg, cocaine, methamphetamine) disorders show that diminished dopamine release by dopamine-elevating drugs is a potential marker of relapse and suggest that increasing dopamine at the D 2/3 receptors may be therapeutically beneficial. In contrast, recent investigations indicate heightened D 3 receptor levels in stimulant users prompting the view that D 3 antagonism may help prevent relapse. Here we tested whether a 'blunted' response to amphetamine in methamphetamine (MA) users extends to D 3 -rich brain areas. Fourteen MA users and 15 healthy controls completed two positron emission tomographic scans with a D 3 -preferring probe [ 11 C]-(+)-PHNO at baseline and after amphetamine (0.4 mg/kg). Relative to healthy controls, MA users had greater decreases in [ 11 C]-(+)-PHNO binding (increased dopamine release) after amphetamine in D 3 -rich substantia nigra (36 vs 20%, p=0.03) and globus pallidus (30 vs 17%, p=0.06), which correlated with self-reported 'drug wanting'. We did not observe a 'blunted' dopamine response to amphetamine in D 2 -rich striatum; however, drug use severity was negatively associated with amphetamine-induced striatal changes in [ 11 C]-(+)-PHNO binding. Our study provides evidence that dopamine transmission in extrastriatal 'D 3 -areas' is not blunted but rather increased in MA users. Together with our previous finding of elevated D 3 receptor level in MA users, the current observation suggests that greater dopaminergic transmission at the D 3 dopamine receptor may contribute to motivation to use drugs and argues in favor of D 3 antagonism as a possible therapeutic tool to reduce craving and relapse in MA addiction.

Environmental Geographic Information Systems (EGIS) at Stennis Space Center (SSC)

NASA Technical Reports Server (NTRS)

Carr, Hugh; Smoot, James; Parikh, Joy

2004-01-01

This viewgraph presentation includes: 1) Background of SSC Environmental GIS (EGIS); 2) Principal Center Activities; 3) SSC's GIS Applications: a) Environmental Emergency Response Tool, b) CERCLA, c) Facilities Master Planning, d) Natural Resource Management and Site Assessment.

Spacecraft Guidance, Navigation, and Control Visualization Tool

NASA Technical Reports Server (NTRS)

Mandic, Milan; Acikmese, Behcet; Blackmore, Lars

2011-01-01

G-View is a 3D visualization tool for supporting spacecraft guidance, navigation, and control (GN&C) simulations relevant to small-body exploration and sampling (see figure). The tool is developed in MATLAB using Virtual Reality Toolbox and provides users with the ability to visualize the behavior of their simulations, regardless of which programming language (or machine) is used to generate simulation results. The only requirement is that multi-body simulation data is generated and placed in the proper format before applying G-View.

Particles and forces. At the heart of matter. Readings from Scientific American magazine.

NASA Astrophysics Data System (ADS)

Carrigan, R. A., Jr.; Trower, W. P.

In this volume a selection of Scientific American articles chronicles the most recent developments in particle physics. In these twelve articles, distinguished physicists look at the tools, ideas, and experiments that shed light on events at the early moments of the universe, as well as the increasingly sophisticated instruments that will make further developments possible in the years to come. For the companion volume Particle physics in the cosmos see 49.003.059. Contents: Introduction. I. Ideas. 1. Elementary particles and forces (C. Quigg). 2. Quarks with color and flavor (S. L. Glashow). 3. The lattice theory of quark confinement (C. Rebbi). Postscript to Ideas (C. Quigg). II. Tools. 4. The next generation of particle accelerators (R. R. Wilson). 5. The Superconducting Super Collider (J. D. Jackson, M. Tigner, S. Wojcicki). Postscript to Tools (R. A. Carrigan Jr.). III. Weak interactions. 6. Heavy leptons (M. L. Perl, W. T. Kirk). 7. The search for intermediate vector bosons (D. B. Cline, C. Rubbia, S. van der Meer). IV. Strong interactions. 8. The Upsilon particle (L. M. Lederman). 9. Quarkonium (E. D. Bloom, G. J. Feldman). 10. Particles with naked beauty (N. B. Mistry, R. A. Poling, E. H. Thorndike). V. Now and beyond. 11. Superstrings (M. B. Green). 12. The structure of quarks and leptons (H. Harari). Postscript to Now and beyond (R. A. Carrigan Jr., W. P. Trower).

3D Virtual Reality Check: Learner Engagement and Constructivist Theory

ERIC Educational Resources Information Center

Bair, Richard A.

2013-01-01

The inclusion of three-dimensional (3D) virtual tools has created a need to communicate the engagement of 3D tools and specify learning gains that educators and the institutions, which are funding 3D tools, can expect. A review of literature demonstrates that specific models and theories for 3D Virtual Reality (VR) learning do not exist "per…

Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus.

PubMed

Zhang, Yan; An, Lin; Xu, Jie; Zhang, Bo; Zheng, W Jim; Hu, Ming; Tang, Jijun; Yue, Feng

2018-02-21

Although Hi-C technology is one of the most popular tools for studying 3D genome organization, due to sequencing cost, the resolution of most Hi-C datasets are coarse and cannot be used to link distal regulatory elements to their target genes. Here we develop HiCPlus, a computational approach based on deep convolutional neural network, to infer high-resolution Hi-C interaction matrices from low-resolution Hi-C data. We demonstrate that HiCPlus can impute interaction matrices highly similar to the original ones, while only using 1/16 of the original sequencing reads. We show that the models learned from one cell type can be applied to make predictions in other cell or tissue types. Our work not only provides a computational framework to enhance Hi-C data resolution but also reveals features underlying the formation of 3D chromatin interactions.

3D tissue formation by stacking detachable cell sheets formed on nanofiber mesh.

PubMed

Kim, Min Sung; Lee, Byungjun; Kim, Hong Nam; Bang, Seokyoung; Yang, Hee Seok; Kang, Seong Min; Suh, Kahp-Yang; Park, Suk-Hee; Jeon, Noo Li

2017-03-23

We present a novel approach for assembling 3D tissue by layer-by-layer stacking of cell sheets formed on aligned nanofiber mesh. A rigid frame was used to repeatedly collect aligned electrospun PCL (polycaprolactone) nanofiber to form a mesh structure with average distance between fibers 6.4 µm. When human umbilical vein endothelial cells (HUVECs), human foreskin dermal fibroblasts, and skeletal muscle cells (C2C12) were cultured on the nanofiber mesh, they formed confluent monolayers and could be handled as continuous cell sheets with areas 3 × 3 cm 2 or larger. Thicker 3D tissues have been formed by stacking multiple cell sheets collected on frames that can be nested (i.e. Matryoshka dolls) without any special tools. When cultured on the nanofiber mesh, skeletal muscle, C2C12 cells oriented along the direction of the nanofibers and differentiated into uniaxially aligned multinucleated myotube. Myotube cell sheets were stacked (upto 3 layers) in alternating or aligned directions to form thicker tissue with ∼50 µm thickness. Sandwiching HUVEC cell sheets with two dermal fibroblast cell sheets resulted in vascularized 3D tissue. HUVECs formed extensive networks and expressed CD31, a marker of endothelial cells. Cell sheets formed on nanofiber mesh have a number of advantages, including manipulation and stacking of multiple cell sheets for constructing 3D tissue and may find applications in a variety of tissue engineering applications.

Producing genome structure populations with the dynamic and automated PGS software.

PubMed

Hua, Nan; Tjong, Harianto; Shin, Hanjun; Gong, Ke; Zhou, Xianghong Jasmine; Alber, Frank

2018-05-01

Chromosome conformation capture technologies such as Hi-C are widely used to investigate the spatial organization of genomes. Because genome structures can vary considerably between individual cells of a population, interpreting ensemble-averaged Hi-C data can be challenging, in particular for long-range and interchromosomal interactions. We pioneered a probabilistic approach for the generation of a population of distinct diploid 3D genome structures consistent with all the chromatin-chromatin interaction probabilities from Hi-C experiments. Each structure in the population is a physical model of the genome in 3D. Analysis of these models yields new insights into the causes and the functional properties of the genome's organization in space and time. We provide a user-friendly software package, called PGS, which runs on local machines (for practice runs) and high-performance computing platforms. PGS takes a genome-wide Hi-C contact frequency matrix, along with information about genome segmentation, and produces an ensemble of 3D genome structures entirely consistent with the input. The software automatically generates an analysis report, and provides tools to extract and analyze the 3D coordinates of specific domains. Basic Linux command-line knowledge is sufficient for using this software. A typical running time of the pipeline is ∼3 d with 300 cores on a computer cluster to generate a population of 1,000 diploid genome structures at topological-associated domain (TAD)-level resolution.

A practical workflow for making anatomical atlases for biological research.

PubMed

Wan, Yong; Lewis, A Kelsey; Colasanto, Mary; van Langeveld, Mark; Kardon, Gabrielle; Hansen, Charles

2012-01-01

The anatomical atlas has been at the intersection of science and art for centuries. These atlases are essential to biological research, but high-quality atlases are often scarce. Recent advances in imaging technology have made high-quality 3D atlases possible. However, until now there has been a lack of practical workflows using standard tools to generate atlases from images of biological samples. With certain adaptations, CG artists' workflow and tools, traditionally used in the film industry, are practical for building high-quality biological atlases. Researchers have developed a workflow for generating a 3D anatomical atlas using accessible artists' tools. They used this workflow to build a mouse limb atlas for studying the musculoskeletal system's development. This research aims to raise the awareness of using artists' tools in scientific research and promote interdisciplinary collaborations between artists and scientists. This video (http://youtu.be/g61C-nia9ms) demonstrates a workflow for creating an anatomical atlas.

An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization.

PubMed

Szałaj, Przemysław; Tang, Zhonghui; Michalski, Paul; Pietal, Michal J; Luo, Oscar J; Sadowski, Michał; Li, Xingwang; Radew, Kamen; Ruan, Yijun; Plewczynski, Dariusz

2016-12-01

ChIA-PET is a high-throughput mapping technology that reveals long-range chromatin interactions and provides insights into the basic principles of spatial genome organization and gene regulation mediated by specific protein factors. Recently, we showed that a single ChIA-PET experiment provides information at all genomic scales of interest, from the high-resolution locations of binding sites and enriched chromatin interactions mediated by specific protein factors, to the low resolution of nonenriched interactions that reflect topological neighborhoods of higher-order chromosome folding. This multilevel nature of ChIA-PET data offers an opportunity to use multiscale 3D models to study structural-functional relationships at multiple length scales, but doing so requires a structural modeling platform. Here, we report the development of 3D-GNOME (3-Dimensional Genome Modeling Engine), a complete computational pipeline for 3D simulation using ChIA-PET data. 3D-GNOME consists of three integrated components: a graph-distance-based heat map normalization tool, a 3D modeling platform, and an interactive 3D visualization tool. Using ChIA-PET and Hi-C data derived from human B-lymphocytes, we demonstrate the effectiveness of 3D-GNOME in building 3D genome models at multiple levels, including the entire genome, individual chromosomes, and specific segments at megabase (Mb) and kilobase (kb) resolutions of single average and ensemble structures. Further incorporation of CTCF-motif orientation and high-resolution looping patterns in 3D simulation provided additional reliability of potential biologically plausible topological structures. © 2016 Szałaj et al.; Published by Cold Spring Harbor Laboratory Press.

Inhibition of Ovarian Cancer Chemoresistance and Metastasis with Antagonists of Hyaluronan-CD44-CD147 Interactions

DTIC Science & Technology

2014-07-01

attached but most leucocytes did not. The attached cells were washed and used for FACS analysis as described previously (Slomiany et al., 2009b...SKOV3 cells, Hey-A8-MDR cells and ascites-derived cells were subject to FACS analysis in the same manner, as follows. We first separated live cells...Cancer 11, 254-267. Zucker, S., Hymowitz, M., Rollo, E. E., Mann, R., Conner, C. E., Cao, J., Foda , H. D., Tompkins, D. C. and Toole, B. P. (2001

3D Graphene Oxide-encapsulated Gold Nanoparticles to Detect Neural Stem Cell Differentiation

PubMed Central

Kim, Tae-Hyung; Lee, Ki-Bum; Choi, Jeong-Woo

2013-01-01

Monitoring of stem cell differentiation and pluripotency is an important step for the practical use of stem cells in the field of regenerative medicine. Hence, a new non-destructive detection tool capable of in situ monitoring of stem cell differentiation is highly needed. In this study, we report a 3D graphene oxide-encapsulated gold nanoparticle that is very effective for the detection of the differentiation potential of neural stem cells (NSCs) based on surface-enhanced Raman spectroscopy (SERS). A new material, 3D GO-encapsulated gold nanoparticle, is developed to induce the double enhancement effect of graphene oxide and gold nanoparticle on SERS signals which is only effective for undifferentiated NSCs. The Raman peaks achieved from undifferentiated NSCs on the graphene oxide (GO)-encapsulated gold nanoparticles were 3.5 times higher than peaks obtained from normal metal structures and were clearly distinguishable from those of differentiated cells. The number of C=C bonds and the raman instensity at 1656cm−1 was found to show a positive correlation, which matches the differentiation state of the NSCs. Moreover, the substrate composed of 3D GO-encapsulated gold nanoparticles was also effective at distinguishing the differentiation state of single NSC by using electrochemical and electrical techniques. Hence, the proposed technique can be used as a powerful non-destructive in situ monitoring tool for the identification of the differentiation potential of various kinds of stem cells (mesenchymal, hematopoietic, and neural stem cells). PMID:23937915

Can Vitamin A be Improved to Prevent Blindness due to Age-Related Macular Degeneration, Stargardt Disease and Other Retinal Dystrophies?

PubMed

Saad, Leonide; Washington, Ilyas

2016-01-01

We discuss how an imperfect visual cycle results in the formation of vitamin A dimers, thought to be involved in the pathogenesis of various retinal diseases, and summarize how slowing vitamin A dimerization has been a therapeutic target of interest to prevent blindness. To elucidate the molecular mechanism of vitamin A dimerization, an alternative form of vitamin A, one that forms dimers more slowly yet maneuvers effortlessly through the visual cycle, was developed. Such a vitamin A, reinforced with deuterium (C20-D3-vitamin A), can be used as a non-disruptive tool to understand the contribution of vitamin A dimers to vision loss. Eventually, C20-D3-vitamin A could become a disease-modifying therapy to slow or stop vision loss associated with dry age-related macular degeneration (AMD), Stargardt disease and retinal diseases marked by such vitamin A dimers. Human clinical trials of C20-D3-vitamin A (ALK-001) are underway.

TU-C-17A-03: An Integrated Contour Evaluation Software Tool Using Supervised Pattern Recognition for Radiotherapy

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

Chen, H; Tan, J; Kavanaugh, J

Purpose: Radiotherapy (RT) contours delineated either manually or semiautomatically require verification before clinical usage. Manual evaluation is very time consuming. A new integrated software tool using supervised pattern contour recognition was thus developed to facilitate this process. Methods: The contouring tool was developed using an object-oriented programming language C# and application programming interfaces, e.g. visualization toolkit (VTK). The C# language served as the tool design basis. The Accord.Net scientific computing libraries were utilized for the required statistical data processing and pattern recognition, while the VTK was used to build and render 3-D mesh models from critical RT structures in real-timemore » and 360° visualization. Principal component analysis (PCA) was used for system self-updating geometry variations of normal structures based on physician-approved RT contours as a training dataset. The inhouse design of supervised PCA-based contour recognition method was used for automatically evaluating contour normality/abnormality. The function for reporting the contour evaluation results was implemented by using C# and Windows Form Designer. Results: The software input was RT simulation images and RT structures from commercial clinical treatment planning systems. Several abilities were demonstrated: automatic assessment of RT contours, file loading/saving of various modality medical images and RT contours, and generation/visualization of 3-D images and anatomical models. Moreover, it supported the 360° rendering of the RT structures in a multi-slice view, which allows physicians to visually check and edit abnormally contoured structures. Conclusion: This new software integrates the supervised learning framework with image processing and graphical visualization modules for RT contour verification. This tool has great potential for facilitating treatment planning with the assistance of an automatic contour evaluation module in avoiding unnecessary manual verification for physicians/dosimetrists. In addition, its nature as a compact and stand-alone tool allows for future extensibility to include additional functions for physicians’ clinical needs.« less

Sequence Diversity in the Dickeya fliC Gene: Phylogeny of the Dickeya Genus and TaqMan® PCR for 'D. solani', New Biovar 3 Variant on Potato in Europe

PubMed Central

Van Vaerenbergh, Johan; Baeyen, Steve; De Vos, Paul; Maes, Martine

2012-01-01

Worldwide, Dickeya (formerly Erwinia chrysanthemi) is causing soft rot diseases on a large diversity of crops and ornamental plants. Strains affecting potato are mainly found in D. dadantii, D. dianthicola and D. zeae, which appear to have a marked geographical distribution. Furthermore, a few Dickeya isolates from potato are attributed to D. chrysanthemi and D. dieffenbachiae. In Europe, isolates of Erwinia chrysanthemi biovar 1 and biovar 7 from potato are now classified in D. dianthicola. However, in the past few years, a new Dickeya biovar 3 variant, tentatively named ‘Dickeya solani’, has emerged as a common major threat, in particular in seed potatoes. Sequences of a fliC gene fragment were used to generate a phylogeny of Dickeya reference strains from culture collections and with this reference backbone, to classify pectinolytic isolates, i.e. Dickeya spp. from potato and ornamental plants. The reference strains of the currently recognized Dickeya species and ‘D. solani’ were unambiguously delineated in the fliC phylogram. D. dadantii, D. dianthicola and ‘D. solani’ displayed unbranched clades, while D. chrysanthemi, D. zeae and D. dieffenbachiae branched into subclades and lineages. Moreover, Dickeya isolates from diagnostic samples, in particular biovar 3 isolates from greenhouse ornamentals, formed several new lineages. Most of these isolates were positioned between the clade of ‘D. solani’ and D. dadantii as transition variants. New lineages also appeared in D. dieffenbachiae and in D. zeae. The strains and isolates of D. dianthicola and ‘D. solani’ were differentiated by a fliC sequence useful for barcode identification. A fliC TaqMan®real-time PCR was developed for ‘D. solani’ and the assay was provisionally evaluated in direct analysis of diagnostic potato samples. This molecular tool can support the efforts to control this particular phytopathogen in seed potato certification. PMID:22570692

Tools for Management of Chlorinated Solvent - Contaminated Sites

DTIC Science & Technology

2009-12-03

Equations coded into  RT3D reaction module   Spreadsheet as series of  CSTRs ● Model assumes No NAPL present   ( , , , )ij i I S i j i M MD v M F C...ER‐0623 ● Mechanics  MnO4 transport and consumption  Based on series of  CSTRs  NOD kinetics  identical to RT3D  Includes cost estimating tool to

Estimation of construction and demolition waste volume generation in new residential buildings in Spain.

PubMed

Villoria Sáez, Paola; del Río Merino, Mercedes; Porras-Amores, César

2012-02-01

The management planning of construction and demolition (C&D) waste uses a single indicator which does not provide enough detailed information. Therefore the determination and implementation of other innovative and precise indicators should be determined. The aim of this research work is to improve existing C&D waste quantification tools in the construction of new residential buildings in Spain. For this purpose, several housing projects were studied to determine an estimation of C&D waste generated during their construction process. This paper determines the values of three indicators to estimate the generation of C&D waste in new residential buildings in Spain, itemizing types of waste and construction stages. The inclusion of two more accurate indicators, in addition to the global one commonly in use, provides a significant improvement in C&D waste quantification tools and management planning.

5D imaging approaches reveal the formation of distinct intracellular cAMP spatial gradients

NASA Astrophysics Data System (ADS)

Rich, Thomas C.; Annamdevula, Naga; Trinh, Kenny; Britain, Andrea L.; Mayes, Samuel A.; Griswold, John R.; Deal, Joshua; Hoffman, Chase; West, Savannah; Leavesley, Silas J.

2017-02-01

Cyclic AMP (cAMP) is a ubiquitous second messenger known to differentially regulate many cellular functions. Several lines of evidence suggest that the distribution of cAMP within cells is not uniform. However, to date, no studies have measured the kinetics of 3D cAMP distributions within cells. This is largely due to the low signal-tonoise ratio of FRET-based probes. We previously reported that hyperspectral imaging improves the signal-to-noise ratio of FRET measurements. Here we utilized hyperspectral imaging approaches to measure FRET signals in five dimensions (5D) - three spatial (x, y, z), wavelength (λ), and time (t) - allowing us to visualize cAMP gradients in pulmonary endothelial cells. cAMP levels were measured using a FRET-based sensor (H188) comprised of a cAMP binding domain sandwiched between FRET donor and acceptor - Turquoise and Venus fluorescent proteins. We observed cAMP gradients in response to 0.1 or 1 μM isoproterenol, 0.1 or 1 μM PGE1, or 50 μM forskolin. Forskolin- and isoproterenol-induced cAMP gradients formed from the apical (high cAMP) to basolateral (low cAMP) face of cells. In contrast, PGE1-induced cAMP gradients originated from both the basolateral and apical faces of cells. Data suggest that 2D (x,y) studies of cAMP compartmentalization may lead to erroneous conclusions about the existence of cAMP gradients, and that 3D (x,y,z) studies are required to assess mechanisms of signaling specificity. Results demonstrate that 5D imaging technologies are powerful tools for measuring biochemical processes in discrete subcellular domains.

A recipe for consistent 3D management of velocity data and time-depth conversion using Vel-IO 3D

NASA Astrophysics Data System (ADS)

Maesano, Francesco E.; D'Ambrogi, Chiara

2017-04-01

3D geological model production and related basin analyses need large and consistent seismic dataset and hopefully well logs to support correlation and calibration; the workflow and tools used to manage and integrate different type of data control the soundness of the final 3D model. Even though seismic interpretation is a basic early step in such workflow, the most critical step to obtain a comprehensive 3D model useful for further analyses is represented by the construction of an effective 3D velocity model and a well constrained time-depth conversion. We present a complex workflow that includes comprehensive management of large seismic dataset and velocity data, the construction of a 3D instantaneous multilayer-cake velocity model, the time-depth conversion of highly heterogeneous geological framework, including both depositional and structural complexities. The core of the workflow is the construction of the 3D velocity model using Vel-IO 3D tool (Maesano and D'Ambrogi, 2017; https://github.com/framae80/Vel-IO3D) that is composed by the following three scripts, written in Python 2.7.11 under ArcGIS ArcPy environment: i) the 3D instantaneous velocity model builder creates a preliminary 3D instantaneous velocity model using key horizons in time domain and velocity data obtained from the analysis of well and pseudo-well logs. The script applies spatial interpolation to the velocity parameters and calculates the value of depth of each point on each horizon bounding the layer-cake velocity model. ii) the velocity model optimizer improves the consistency of the velocity model by adding new velocity data indirectly derived from measured depths, thus reducing the geometrical uncertainties in the areas located far from the original velocity data. iii) the time-depth converter runs the time-depth conversion of any object located inside the 3D velocity model The Vel-IO 3D tool allows one to create 3D geological models consistent with the primary geological constraints (e.g. depth of the markers on wells). The workflow and Vel-IO 3D tool have been developed and tested for the construction of the 3D geological model of a flat region, 5700 km2 in area, located in the central part of the Po Plain (Northern Italy) in the frame of the European funded Project GeoMol. The study area was covered by a dense dataset of seismic lines (ca. 12000 km) and exploration wells (130 drilling), mainly deriving from oil and gas exploration activities. The interpretation of the seismic dataset leads to the construction of a 3D model in time domain that has been depth converted using Vel-IO 3D, with a 4 layer-cake 3D instantaneous velocity model. The resulting final 3D geological model, composed of 15 horizons and 150 faults, has been used for basin analysis at regional scale, for geothermal assessment, and for the update of the seismotectonic knowledge of the Po Plain. The Vel-IO 3D has been further used for the depth conversion of the accretionary prism of the Calabrian subduction (Southern Italy) and for a basin scale analysis of the Po Plain Plio-Pleistocene evolution. Maesano F.E. and D'Ambrogi C., (2017), Computers and Geosciences, doi: 10.1016/j.cageo.2016.11.013 Vel-IO 3D is available at: https://github.com/framae80/Vel-IO3D

To select the best tool for generating 3D maintenance data and to set the detailed process for obtaining the 3D maintenance data

NASA Astrophysics Data System (ADS)

Prashanth, B. N.; Roy, Kingshuk

2017-07-01

Three Dimensional (3D) maintenance data provides a link between design and technical documentation creating interactive 3D graphical training and maintenance material. It becomes difficult for an operator to always go through huge paper manuals or come running to the computer for doing maintenance of a machine which makes the maintenance work fatigue. Above being the case, a 3D animation makes maintenance work very simple since, there is no language barrier. The research deals with the generation of 3D maintenance data of any given machine. The best tool for obtaining the 3D maintenance is selected and the tool is analyzed. Using the same tool, a detailed process for extracting the 3D maintenance data for any machine is set. This project aims at selecting the best tool for obtaining 3D maintenance data and to select the detailed process for obtaining 3D maintenance data. 3D maintenance reduces use of big volumes of manuals which creates human errors and makes the work of an operator fatiguing. Hence 3-D maintenance would help in training and maintenance and would increase productivity. 3Dvia when compared with Cortona 3D and Deep Exploration proves to be better than them. 3Dvia is good in data translation and it has the best renderings compared to the other two 3D maintenance software. 3Dvia is very user friendly and it has various options for creating 3D animations. Its Interactive Electronic Technical Publication (IETP) integration is also better than the other two software. Hence 3Dvia proves to be the best software for obtaining 3D maintenance data of any machine.

Combining fluorescence imaging with Hi-C to study 3D genome architecture of the same single cell.

PubMed

Lando, David; Basu, Srinjan; Stevens, Tim J; Riddell, Andy; Wohlfahrt, Kai J; Cao, Yang; Boucher, Wayne; Leeb, Martin; Atkinson, Liam P; Lee, Steven F; Hendrich, Brian; Klenerman, Dave; Laue, Ernest D

2018-05-01

Fluorescence imaging and chromosome conformation capture assays such as Hi-C are key tools for studying genome organization. However, traditionally, they have been carried out independently, making integration of the two types of data difficult to perform. By trapping individual cell nuclei inside a well of a 384-well glass-bottom plate with an agarose pad, we have established a protocol that allows both fluorescence imaging and Hi-C processing to be carried out on the same single cell. The protocol identifies 30,000-100,000 chromosome contacts per single haploid genome in parallel with fluorescence images. Contacts can be used to calculate intact genome structures to better than 100-kb resolution, which can then be directly compared with the images. Preparation of 20 single-cell Hi-C libraries using this protocol takes 5 d of bench work by researchers experienced in molecular biology techniques. Image acquisition and analysis require basic understanding of fluorescence microscopy, and some bioinformatics knowledge is required to run the sequence-processing tools described here.

A non-disruptive technology for robust 3D tool tracking for ultrasound-guided interventions.

PubMed

Mung, Jay; Vignon, Francois; Jain, Ameet

2011-01-01

In the past decade ultrasound (US) has become the preferred modality for a number of interventional procedures, offering excellent soft tissue visualization. The main limitation however is limited visualization of surgical tools. A new method is proposed for robust 3D tracking and US image enhancement of surgical tools under US guidance. Small US sensors are mounted on existing surgical tools. As the imager emits acoustic energy, the electrical signal from the sensor is analyzed to reconstruct its 3D coordinates. These coordinates can then be used for 3D surgical navigation, similar to current day tracking systems. A system with real-time 3D tool tracking and image enhancement was implemented on a commercial ultrasound scanner and 3D probe. Extensive water tank experiments with a tracked 0.2mm sensor show robust performance in a wide range of imaging conditions and tool position/orientations. The 3D tracking accuracy was 0.36 +/- 0.16mm throughout the imaging volume of 55 degrees x 27 degrees x 150mm. Additionally, the tool was successfully tracked inside a beating heart phantom. This paper proposes an image enhancement and tool tracking technology with sub-mm accuracy for US-guided interventions. The technology is non-disruptive, both in terms of existing clinical workflow and commercial considerations, showing promise for large scale clinical impact.

Analysis of Ten Reverse Engineering Tools

NASA Astrophysics Data System (ADS)

Koskinen, Jussi; Lehmonen, Tero

Reverse engineering tools can be used in satisfying the information needs of software maintainers. Especially in case of maintaining large-scale legacy systems tool support is essential. Reverse engineering tools provide various kinds of capabilities to provide the needed information to the tool user. In this paper we analyze the provided capabilities in terms of four aspects: provided data structures, visualization mechanisms, information request specification mechanisms, and navigation features. We provide a compact analysis of ten representative reverse engineering tools for supporting C, C++ or Java: Eclipse Java Development Tools, Wind River Workbench (for C and C++), Understand (for C++), Imagix 4D, Creole, Javadoc, Javasrc, Source Navigator, Doxygen, and HyperSoft. The results of the study supplement the earlier findings in this important area.

Screening for hearing loss in the elderly using distortion product otoacoustic emissions, pure tones, and a self-assessment tool.

PubMed

Jupiter, Tina

2009-12-01

To determine whether distortion product otoacoustic emissions (DPOAEs) could be used as a hearing screening tool with elderly individuals living independently, and to compare the utility of different screening protocols: (a) 3 pure-tone screening protocols consisting of 30 dB HL at 1, 2, and 3 kHz; 40 dB HL at 1, 2, and 3 kHz; or 40 dB HL at 1 and 2 kHz; (b) the Hearing Handicap Inventory for the Elderly-Screening version (HHIE-S); (c) pure tones at 40 dB HL at 1 and 2 kHz plus the HHIE-S; and (d) DPOAEs. A total of 106 elderly individuals age 65-91 years were screened using the above protocols. Pass/fail results showed that most individuals failed at 30 dB HL, followed by DPOAEs, the 40-dB HL protocols, the HHIE-S alone, and the combined pure-tone/HHIE-S protocol. All screening results were associated except the HHIE-S and 30 dB HL and the HHIE-S and DPOAEs. A McNemar analysis revealed that the differences between the correlated pass/fail results were significant except for the HHIE-S and 40 dB at 1 and 2 kHz. DPOAEs can be used to screen the elderly, with the advantage that individuals do not have to voluntarily respond to the test.

2D and 3D Method of Characteristic Tools for Complex Nozzle Development

NASA Technical Reports Server (NTRS)

Rice, Tharen

2003-01-01

This report details the development of a 2D and 3D Method of Characteristic (MOC) tool for the design of complex nozzle geometries. These tools are GUI driven and can be run on most Windows-based platforms. The report provides a user's manual for these tools as well as explains the mathematical algorithms used in the MOC solutions.

Characterization and Evolution of Salmonella CRISPR-Cas Systems

DTIC Science & Technology

2014-01-01

aeruginosa and Streptococcus pyogenes ( Cady et al., 2011; Deltcheva et al., 2011). In the former, CRISPR-Cas has been linked to the regulation of...Science 321, 960–964. Cady , K. C., White, A. S., Hammond, J. H., Abendroth, M. D., Karthikeyan, R. S., Lalitha, P., Zegans, M. E. & O’Toole, G. A...40, 5569–5576. Zegans, M. E., Wagner, J. C., Cady , K. C., Murphy, D. M., Hammond, J. H. & O’Toole, G. A. (2009). Interaction between bacteriophage

Human common acute lymphoblastic leukemia-derived cell lines are competent to recombine their T-cell receptor delta/alpha regions along a hierarchically ordered pathway.

PubMed

Hansen-Hagge, T E; Yokota, S; Reuter, H J; Schwarz, K; Bartram, C R

1992-11-01

Rearrangements of the T-cell receptor (TCR) delta locus are observed in the majority of human B-cell precursor acute lymphoblastic leukemias (ALL) with a striking predominance of V delta 2(D)D delta 3 recombinations in common ALL (cALL) patients. Recently, we and others showed that almost 20% of cALL cases are characterized by further recombination of V delta 2(D)D delta 3 segments to J alpha elements, thereby deleting the TCR delta locus in analogy to the delta Rec/psi J alpha pathway in differentiating alpha/beta-positive T cells. We report here that two human cALL-derived cell lines, REH and Nalm-6, are competent to recombine the TCR delta/alpha locus under standard tissue culture conditions. Analysis of different REH subclones obtained by limiting dilution of the initial culture showed a biased recombination of V delta 2D delta 3 to distinct J alpha elements. During prolonged tissue culture, a subclone acquired growth advantage and displaced parental cells as well as other subclones. Frequently, the DJ junctions of REH subclones contained extended stretches of palindromic sequences derived from modified D delta 3 coding elements. The other cell line, Nalm-6, started the TCR delta/alpha recombination with an unusual signal joint of a cryptic recombinase signal sequence (RSS) upstream of D delta 3 to the 3' RSS of D delta 3. The RSS dimer was subsequently rearranged in all investigated subclones to an identical J alpha element. Both cell lines might become valuable tools to unravel the complex regulation of TCR delta/alpha recombination pathways in malignant and normal lymphopoiesis.

Quantitative Analysis of Three-Dimensional Human Mammary Epithelial Tissue Architecture Reveals a Role for Tenascin-C in Regulating c-Met Function

PubMed Central

Taraseviciute, Agne; Vincent, Benjamin T.; Schedin, Pepper; Jones, Peter Lloyd

2010-01-01

Remodeling of the stromal extracellular matrix and elevated expression of specific proto-oncogenes within the adjacent epithelium represent cardinal features of breast cancer, yet how these events become integrated is not fully understood. To address this question, we focused on tenascin-C (TN-C), a stromal extracellular matrix glycoprotein whose expression increases with disease severity. Initially, nonmalignant human mammary epithelial cells (MCF-10A) were cultured within a reconstituted basement membrane (BM) where they formed three-dimensional (3-D) polarized, growth-attenuated, multicellular acini, enveloped by a continuous endogenous BM. In the presence of TN-C, however, acini failed to generate a normal BM, and net epithelial cell proliferation increased. To quantify how TN-C alters 3-D tissue architecture and function, we developed a computational image analysis algorithm, which showed that although TN-C disrupted acinar surface structure, it had no effect on their volume. Thus, TN-C promoted epithelial cell proliferation leading to luminal filling, a process that we hypothesized involved c-met, a proto-oncogene amplified in breast tumors that promotes intraluminal filling. Indeed, TN-C increased epithelial c-met expression and promoted luminal filling, whereas blockade of c-met function reversed this phenotype, resulting in normal BM deposition, proper lumen formation, and decreased cell proliferation. Collectively, these studies, combining a novel quantitative image analysis tool with 3-D organotypic cultures, demonstrate that stromal changes associated with breast cancer can control proto-oncogene function. PMID:20042668

Concrete shaver. Innovative technology summary report

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

NONE

1998-12-01

The US Department of Energy (DOE) is in the process of decontamination and decommissioning (D and D) for many of its nuclear facilities throughout the United States. These facilities must be dismantled and the demolition waste sized into manageable pieces for handling and disposal. The facilities undergoing D and D are typically chemically and/or radiologically contaminated. To facilitate this work, DOE requires a tool capable of removing the surface of radiologically contaminated concrete floors. Operating requirements for the tool include simple and economical operation, the capability of operating in ambient temperatures from 3 C to 40 C (37 F tomore » 104 F), and the ability to be easily decontaminated. The tool also must be safe for workers. The Marcrist Industries Limited concrete shaver is an electrically driven, self-propelled concrete and coating removal system. This technology consists of a 25-cm (10-in.)-wide diamond impregnated shaving drum powered by an electric motor and contains a vacuum port for dust extraction. The concrete shaver is ideal for use on open, flat, floor areas. The shaver may also be used on slightly curved surfaces. This shaver is self-propelled and produces a smooth, even surface with little vibration. The concrete shaver is an attractive alternative to traditional pneumatic scabbling tools, which were considered the baseline in this demonstration. The use of this tool reduces worker fatigue (compared to the baseline) due to lower vibration. The shaver is more than five times faster than the five-piston pneumatic scabbler at removing contamination from concrete. Because of this increased productivity, the shaver is 50% less costly to operate than baseline technologies. The DOE has successfully demonstrated the concrete shaver for decontaminating floors for free-release surveys prior to demolition work.« less

Carbon and metal-carbon implantations into tool steels for improved tribological performance

NASA Astrophysics Data System (ADS)

Hirvonen, J.-P.; Harskamp, F.; Torri, P.; Willers, H.; Fusari, A.; Gibson, N.; Haupt, J.

1997-05-01

The high-fluence implantation of carbon and dual implantations of metal-metalloid pairs into steels with different microstructures are briefly reviewed. A previously unexamined system, the implantation of Si and C into two kinds of tool steels, M3 and D2, have been studied in terms of microstructure and tribological performance. In both cases ion implantation transfers a surface into an amorphous layer. However, the tribological behavior of these two materials differs remarkably: in the case of ion-implanted M3 a reduction of wear in a steel pin is observed even at high pin loads, whereas in the case of ion-implanted D2 the beneficial effects of ion implantation were limited to the lowest pin load. The importance of an initial phase at the onset of sliding is emphasized and a number of peculiarities observed in ion-implanted M3 steel are discussed.

3D TRUMP - A GBI launch window tool

NASA Astrophysics Data System (ADS)

Karels, Steven N.; Hancock, John; Matchett, Gary

3D TRUMP is a novel GPS and communicatons-link software analysis tool developed for the SDIO's Ground-Based Interceptor (GBI) program. 3D TRUMP uses a computationally efficient analysis tool which provides key GPS-based performance measures for an entire GBI mission's reentry vehicle and interceptor trajectories. Algorithms and sample outputs are presented.

Towards clinical translation of augmented orthopedic surgery: from pre-op CT to intra-op x-ray via RGBD sensing

NASA Astrophysics Data System (ADS)

Tucker, Emerson; Fotouhi, Javad; Unberath, Mathias; Lee, Sing Chun; Fuerst, Bernhard; Johnson, Alex; Armand, Mehran; Osgood, Greg M.; Navab, Nassir

2018-03-01

Pre-operative CT data is available for several orthopedic and trauma interventions, and is mainly used to identify injuries and plan the surgical procedure. In this work we propose an intuitive augmented reality environment allowing visualization of pre-operative data during the intervention, with an overlay of the optical information from the surgical site. The pre-operative CT volume is first registered to the patient by acquiring a single C-arm X-ray image and using 3D/2D intensity-based registration. Next, we use an RGBD sensor on the C-arm to fuse the optical information of the surgical site with patient pre-operative medical data and provide an augmented reality environment. The 3D/2D registration of the pre- and intra-operative data allows us to maintain a correct visualization each time the C-arm is repositioned or the patient moves. An overall mean target registration error (mTRE) and standard deviation of 5.24 +/- 3.09 mm was measured averaged over 19 C-arm poses. The proposed solution enables the surgeon to visualize pre-operative data overlaid with information from the surgical site (e.g. surgeon's hands, surgical tools, etc.) for any C-arm pose, and negates issues of line-of-sight and long setup times, which are present in commercially available systems.

Feeding Concept, Military Vs Civilian System

DTIC Science & Technology

1990-12-01

Pudding d 3 c Chocolate Pudding w/Whipped Topping d 3 c Cowboy Cookies d 3 c Cream Puffs d 3 c Donuts d...c Fruit Won Tons d 3 c Gelatin Cubes d 3 c Hermits d 3 c Ice Box Cookies d : c Ice Cream d...I c Jelly Bar Spritz d 3 c Jelly Roll d : c Lemon Meringue Pie d : c Lime Gelatin Cubes d : c Oatmeal Cookies

Gemcitabine treatment of rat soft tissue sarcoma with phosphatidyldiglycerol-based thermosensitive liposomes.

PubMed

Limmer, Simone; Hahn, Jasmin; Schmidt, Rebecca; Wachholz, Kirsten; Zengerle, Anja; Lechner, Katharina; Eibl, Hansjörg; Issels, Rolf D; Hossann, Martin; Lindner, Lars H

2014-09-01

The pyrimidine analogue gemcitabine (dFdC) is frequently used in the treatment of patients with solid tumors. However, after i.v. application dFdC is rapidly inactivated by metabolization. Here, the potential of thermosensitive liposomes based on 1,2-dipalmitoyl-sn-glycero-3-phosphodiglycerol (DPPG2-TSL) were investigated as carrier and targeting system for delivery of dFdC in combination with local hyperthermia (HT). DPPG2-TSL were prepared by the lipid film hydration and extrusion method and characterized by dynamic light scattering, thin layer chromatography, phosphate assay and HPLC. In vivo experiments were performed in Brown Norway rats with a syngeneic soft tissue sarcoma. Local HT treatment was performed by light exposure. DPPG2-TSL were stable at 37°C in serum and showed a temperature dependent dFdC release >40°C. Plasma half-life of dFdC was strongly increased from 0.07 h (non-liposomal) to 0.53 h (liposomal, vesicle size 105 nm) or 2.59 h (liposomal, 129 nm). Therapy of BN175 tumors with dFdC encapsulated in DPPG2-TSL + HT showed significant improvement in tumor growth delay compared to non-liposomal dFdC without HT (p < 0.05), non-liposomal dFdC with HT (p < 0.01), and liposomal dFdC without HT (p < 0.05), respectively. Gemcitabine encapsulated in DPPG2-TSL in combination with local HT is a promising tool for the treatment of solid tumors. Therefore, these encouraging results ask for further investigation and evaluation.

FRET Imaging in Three-dimensional Hydrogels

PubMed Central

Taboas, Juan M.

2016-01-01

Imaging of Förster resonance energy transfer (FRET) is a powerful tool for examining cell biology in real-time. Studies utilizing FRET commonly employ two-dimensional (2D) culture, which does not mimic the three-dimensional (3D) cellular microenvironment. A method to perform quenched emission FRET imaging using conventional widefield epifluorescence microscopy of cells within a 3D hydrogel environment is presented. Here an analysis method for ratiometric FRET probes that yields linear ratios over the probe activation range is described. Measurement of intracellular cyclic adenosine monophosphate (cAMP) levels is demonstrated in chondrocytes under forskolin stimulation using a probe for EPAC1 activation (ICUE1) and the ability to detect differences in cAMP signaling dependent on hydrogel material type, herein a photocrosslinking hydrogel (PC-gel, polyethylene glycol dimethacrylate) and a thermoresponsive hydrogel (TR-gel). Compared with 2D FRET methods, this method requires little additional work. Laboratories already utilizing FRET imaging in 2D can easily adopt this method to perform cellular studies in a 3D microenvironment. It can further be applied to high throughput drug screening in engineered 3D microtissues. Additionally, it is compatible with other forms of FRET imaging, such as anisotropy measurement and fluorescence lifetime imaging (FLIM), and with advanced microscopy platforms using confocal, pulsed, or modulated illumination. PMID:27500354

Vel-IO 3D: A tool for 3D velocity model construction, optimization and time-depth conversion in 3D geological modeling workflow

NASA Astrophysics Data System (ADS)

Maesano, Francesco E.; D'Ambrogi, Chiara

2017-02-01

We present Vel-IO 3D, a tool for 3D velocity model creation and time-depth conversion, as part of a workflow for 3D model building. The workflow addresses the management of large subsurface dataset, mainly seismic lines and well logs, and the construction of a 3D velocity model able to describe the variation of the velocity parameters related to strong facies and thickness variability and to high structural complexity. Although it is applicable in many geological contexts (e.g. foreland basins, large intermountain basins), it is particularly suitable in wide flat regions, where subsurface structures have no surface expression. The Vel-IO 3D tool is composed by three scripts, written in Python 2.7.11, that automate i) the 3D instantaneous velocity model building, ii) the velocity model optimization, iii) the time-depth conversion. They determine a 3D geological model that is consistent with the primary geological constraints (e.g. depth of the markers on wells). The proposed workflow and the Vel-IO 3D tool have been tested, during the EU funded Project GeoMol, by the construction of the 3D geological model of a flat region, 5700 km2 in area, located in the central part of the Po Plain. The final 3D model showed the efficiency of the workflow and Vel-IO 3D tool in the management of large amount of data both in time and depth domain. A 4 layer-cake velocity model has been applied to a several thousand (5000-13,000 m) thick succession, with 15 horizons from Triassic up to Pleistocene, complicated by a Mesozoic extensional tectonics and by buried thrusts related to Southern Alps and Northern Apennines.

AceTree: a major update and case study in the long term maintenance of open-source scientific software.

PubMed

Katzman, Braden; Tang, Doris; Santella, Anthony; Bao, Zhirong

2018-04-04

AceTree, a software application first released in 2006, facilitates exploration, curation and editing of tracked C. elegans nuclei in 4-dimensional (4D) fluorescence microscopy datasets. Since its initial release, AceTree has been continuously used to interact with, edit and interpret C. elegans lineage data. In its 11 year lifetime, AceTree has been periodically updated to meet the technical and research demands of its community of users. This paper presents the newest iteration of AceTree which contains extensive updates, demonstrates the new applicability of AceTree in other developmental contexts, and presents its evolutionary software development paradigm as a viable model for maintaining scientific software. Large scale updates have been made to the user interface for an improved user experience. Tools have been grouped according to functionality and obsolete methods have been removed. Internal requirements have been changed that enable greater flexibility of use both in C. elegans contexts and in other model organisms. Additionally, the original 3-dimensional (3D) viewing window has been completely reimplemented. The new window provides a new suite of tools for data exploration. By responding to technical advancements and research demands, AceTree has remained a useful tool for scientific research for over a decade. The updates made to the codebase have extended AceTree's applicability beyond its initial use in C. elegans and enabled its usage with other model organisms. The evolution of AceTree demonstrates a viable model for maintaining scientific software over long periods of time.

Eddy current NDE performance demonstrations using simulation tools

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

Maurice, L.; Costan, V.; Guillot, E.

2013-01-25

To carry out performance demonstrations of the Eddy-Current NDE processes applied on French nuclear power plants, EDF studies the possibility of using simulation tools as an alternative to measurements on steam generator tube mocks-up. This paper focuses on the strategy led by EDF to assess and use code{sub C}armel3D and Civa, on the case of Eddy-Current NDE on wears problem which may appear in the U-shape region of steam generator tubes due to the rubbing of anti-vibration bars.

Two-photon holographic optogenetics of neural circuits (Conference Presentation)

NASA Astrophysics Data System (ADS)

Yang, Weijian; Carrillo-Reid, Luis; Peterka, Darcy S.; Yuste, Rafael

2016-03-01

Optical manipulation of in vivo neural circuits with cellular resolution could be important for understanding cortical function. Despite recent progress, simultaneous optogenetic activation with cellular precision has either been limited to 2D planes, or a very small numbers of neurons over a limited volume. Here we demonstrate a novel paradigm for simultaneous 3D activation using a low repetition rate pulse-amplified fiber laser system and a spatial light modulator (SLM) to project 3D holographic excitation patterns on the cortex of mice in vivo for targeted volumetric 3D photoactivation. This method is compatible with two-photon imaging, and enables the simultaneous activation of multiple cells in 3D, using red-shifted opsins, such as C1V1 or ReaChR, while simultaneously imaging GFP-based sensors such as GCaMP6. This all-optical imaging and 3D manipulation approach achieves simultaneous reading and writing of cortical activity, and should be a powerful tool for the study of neuronal circuits.

All Prime Contract Awards by State or Country, Place, and Contractor, FY83, Part 1 (Argentina-Goodyear, Arizona).

DTIC Science & Technology

1983-01-01

C Z 5 2 2 5110 000 69 HAND TOOLS EDGED NONPOWERED 7 9 3 5 L 06 1 B 4 1 0 100 WAESCHEREI KRAUSE GERMANY 088616 0000 GY I L OJA37 2913 DAJA37-82-00210 B...0 27 WOLFGANG PRAYON GERMANY 090010 0000 GY I D OJA37 0369 DAJA37-82-DO261 B C 2 5 3 2 V212 000 S MOTOR PASSENGER SERVICE 7 9 4 5 L 06 1 B J 1 J 34

The Need For Continued Development Of Ricin Countermeasures

DTIC Science & Technology

2012-01-01

ricin was code named compound W and considered for weapon - ization during the US offensive Biological Warfare Program [3]. The US intelligence community...similarly maintained that ricin is more compatible with a tool of assassination instead of a weapon of mass destruc- tion [42]. However, Radosavljevic...Nottingham, A Survey of Chemical and Bio - logical Warfare, vol. 6, Monthly Review Press, New York, NY, USA, 1969. [4] M. A. Poli, C. Roy, K. D. Huebner, D. R

Adoptive immunotherapy mediated by ex vivo expanded natural killer T cells against CD1d-expressing lymphoid neoplasms.

PubMed

Bagnara, Davide; Ibatici, Adalberto; Corselli, Mirko; Sessarego, Nadia; Tenca, Claudya; De Santanna, Amleto; Mazzarello, Andrea; Daga, Antonio; Corvò, Renzo; De Rossi, Giulio; Frassoni, Francesco; Ciccone, Ermanno; Fais, Franco

2009-07-01

CD1d is a monomorphic antigen presentation molecule expressed in several hematologic malignancies. Alpha-galactosylceramide (alpha-GalCer) is a glycolipid that can be presented to cytotoxic CD1d-restricted T cells. These reagents represent a potentially powerful tool for cell mediated immunotherapy. We set up an experimental model to evaluate the use of adoptively transferred cytotoxic CD1d-restricted T cells and alpha-GalCer in the treatment of mice engrafted with CD1d(+) lymphoid neoplastic cells. To this end the C1R cell line was transfected with CD1c or CD1d molecules. In addition, upon retroviral infection firefly luciferase was expressed on C1R transfected cell lines allowing the evaluation of tumor growth in xenografted immunodeficient NOD/SCID mice. The C1R-CD1d cell line was highly susceptible to specific CD1d-restricted T cell cytotoxicity in the presence alpha-GalCer in vitro. After adoptive transfer of CD1d-restricted T cells and alpha-GalCer to mice engrafted with both C1R-CD1c and C1R-CD1d, a reduction in tumor growth was observed only in CD1d(+) masses. In addition, CD1d-restricted T-cell treatment plus alpha-GalCer eradicated small C1R-CD1d(+) nodules. Immunohistochemical analysis revealed that infiltrating NKT cells were mainly observed in CD1d nodules. Our results indicate that ex vivo expanded cytotoxic CD1d-restricted T cells and alpha-GalCer may represent a new immunotherapeutic tool for treatment of CD1d(+) hematologic malignancies.

Adoptive immunotherapy mediated by ex vivo expanded natural killer T cells against CD1d-expressing lymphoid neoplasms

PubMed Central

Bagnara, Davide; Ibatici, Adalberto; Corselli, Mirko; Sessarego, Nadia; Tenca, Claudya; De Santanna, Amleto; Mazzarello, Andrea; Daga, Antonio; Corvò, Renzo; De Rossi, Giulio; Frassoni, Francesco; Ciccone, Ermanno; Fais, Franco

2009-01-01

Background CD1d is a monomorphic antigen presentation molecule expressed in several hematologic malignancies. Alpha-galactosylceramide (α-GalCer) is a glycolipid that can be presented to cytotoxic CD1d-restricted T cells. These reagents represent a potentially powerful tool for cell mediated immunotherapy. Design and Methods We set up an experimental model to evaluate the use of adoptively transferred cytotoxic CD1d-restricted T cells and α-GalCer in the treatment of mice engrafted with CD1d+ lymphoid neoplastic cells. To this end the C1R cell line was transfected with CD1c or CD1d molecules. In addition, upon retroviral infection firefly luciferase was expressed on C1R transfected cell lines allowing the evaluation of tumor growth in xenografted immunodeficient NOD/SCID mice. Results The C1R-CD1d cell line was highly susceptible to specific CD1d-restricted T cell cytotoxicity in the presence α-GalCer in vitro. After adoptive transfer of CD1d-restricted T cells and α-GalCer to mice engrafted with both C1R-CD1c and C1R-CD1d, a reduction in tumor growth was observed only in CD1d+ masses. In addition, CD1d-restricted T-cell treatment plus α-GalCer eradicated small C1R-CD1d+ nodules. Immunohistochemical analysis revealed that infiltrating NKT cells were mainly observed in CD1d nodules. Conclusions Our results indicate that ex vivo expanded cytotoxic CD1d-restricted T cells and α-GalCer may represent a new immunotherapeutic tool for treatment of CD1d+ hematologic malignancies. PMID:19454494

M3T: Morphable Multithreaded Memory Tiles

DTIC Science & Technology

2004-01-01

4 5 6 7 8 9 10 A B C D E F G H I J K L x[0] x[1] x[2] x[3] x[4] x[5] x[6] x[7] y[0] y[4] y[2] y[6] y[1] y[5] y[3] y[7] Figure 4: 8-point radix-2...CONPAR 94, September. 33. [NAR95] Narayan, S. and Gajski , D. (1995) “Interfacing Incompatible Protocols Using Interface Process Generation,” 32nd...Parallel and Distributed Tools, August. 42. [SOH95] Sohi, G ., Breach, S. and Vajapeyam, S. (1995) “Multiscalar Processors,” Proceedings of the 22nd

Voice and gesture-based 3D multimedia presentation tool

NASA Astrophysics Data System (ADS)

Fukutake, Hiromichi; Akazawa, Yoshiaki; Okada, Yoshihiro

2007-09-01

This paper proposes a 3D multimedia presentation tool that allows the user to manipulate intuitively only through the voice input and the gesture input without using a standard keyboard or a mouse device. The authors developed this system as a presentation tool to be used in a presentation room equipped a large screen like an exhibition room in a museum because, in such a presentation environment, it is better to use voice commands and the gesture pointing input rather than using a keyboard or a mouse device. This system was developed using IntelligentBox, which is a component-based 3D graphics software development system. IntelligentBox has already provided various types of 3D visible, reactive functional components called boxes, e.g., a voice input component and various multimedia handling components. IntelligentBox also provides a dynamic data linkage mechanism called slot-connection that allows the user to develop 3D graphics applications by combining already existing boxes through direct manipulations on a computer screen. Using IntelligentBox, the 3D multimedia presentation tool proposed in this paper was also developed as combined components only through direct manipulations on a computer screen. The authors have already proposed a 3D multimedia presentation tool using a stage metaphor and its voice input interface. This time, we extended the system to make it accept the user gesture input besides voice commands. This paper explains details of the proposed 3D multimedia presentation tool and especially describes its component-based voice and gesture input interfaces.

Developing an Ear Prosthesis Fabricated in Polyvinylidene Fluoride by a 3D Printer with Sensory Intrinsic Properties of Pressure and Temperature

PubMed Central

Suaste-Gómez, Ernesto; Rodríguez-Roldán, Grissel; Reyes-Cruz, Héctor; Terán-Jiménez, Omar

2016-01-01

An ear prosthesis was designed in 3D computer graphics software and fabricated using a 3D printing process of polyvinylidene fluoride (PVDF) for use as a hearing aid. In addition, the prosthesis response to pressure and temperature was observed. Pyroelectric and piezoelectric properties of this ear prosthesis were investigated using an astable multivibrator circuit, as changes in PVDF permittivity were observed according to variations of pressure and temperature. The results show that this prosthesis is reliable for use under different conditions of pressure (0 Pa to 16,350 Pa) and temperature (2 °C to 90 °C). The experimental results show an almost linear and inversely proportional behavior between the stimuli of pressure and temperature with the frequency response. This 3D-printed ear prosthesis is a promising tool and has a great potentiality in the biomedical engineering field because of its ability to generate an electrical potential proportional to pressure and temperature, and it is the first time that such a device has been processed by the additive manufacturing process (3D printing). More work needs to be carried out to improve the performance, such as electrical stimulation of the nervous system, thereby extending the purpose of a prosthesis to the area of sensory perception. PMID:26959026

Developing an Ear Prosthesis Fabricated in Polyvinylidene Fluoride by a 3D Printer with Sensory Intrinsic Properties of Pressure and Temperature.

PubMed

Suaste-Gómez, Ernesto; Rodríguez-Roldán, Grissel; Reyes-Cruz, Héctor; Terán-Jiménez, Omar

2016-03-04

An ear prosthesis was designed in 3D computer graphics software and fabricated using a 3D printing process of polyvinylidene fluoride (PVDF) for use as a hearing aid. In addition, the prosthesis response to pressure and temperature was observed. Pyroelectric and piezoelectric properties of this ear prosthesis were investigated using an astable multivibrator circuit, as changes in PVDF permittivity were observed according to variations of pressure and temperature. The results show that this prosthesis is reliable for use under different conditions of pressure (0 Pa to 16,350 Pa) and temperature (2 °C to 90 °C). The experimental results show an almost linear and inversely proportional behavior between the stimuli of pressure and temperature with the frequency response. This 3D-printed ear prosthesis is a promising tool and has a great potentiality in the biomedical engineering field because of its ability to generate an electrical potential proportional to pressure and temperature, and it is the first time that such a device has been processed by the additive manufacturing process (3D printing). More work needs to be carried out to improve the performance, such as electrical stimulation of the nervous system, thereby extending the purpose of a prosthesis to the area of sensory perception.

Rosetta CONSERT operations and data analysis preparation: simulation software tools.

NASA Astrophysics Data System (ADS)

Rogez, Yves; Hérique, Alain; Cardiet, Maël; Zine, Sonia; Westphal, Mathieu; Micallef, Mickael; Berquin, Yann; Kofman, Wlodek

2014-05-01

The CONSERT experiment onboard Rosetta and Philae will perform the tomography of the 67P/CG comet nucleus by measuring radio waves transmission from the Rosetta S/C to the Philae Lander. The accurate analysis of travel time measurements will deliver unique knowledge of the nucleus interior dielectric properties. The challenging complexity of CONSERT operations requirements, combining both Rosetta and Philae, allows only a few set of opportunities to acquire data. Thus, we need a fine analysis of the impact of Rosetta trajectory, Philae position and comet shape on CONSERT measurements, in order to take optimal decisions in a short time. The integration of simulation results and mission parameters provides synthetic information to evaluate performances and risks for each opportunity. The preparation of CONSERT measurements before space operations is a key to achieve the best science return of the experiment. In addition, during Rosetta space operations, these software tools will allow a "real-time" first analysis of the latest measurements to improve the next acquisition sequences. The software tools themselves are built around a 3D electromagnetic radio wave simulation, taking into account the signal polarization. It is based on ray-tracing algorithms specifically designed for quick orbit analysis and radar signal generation. This allows computation on big domains relatively to the wavelength. The extensive use of 3D visualization tools provides comprehensive and synthetic views of the results. The software suite is designed to be extended, after Rosetta operations, to the full 3D measurement data analysis using inversion methods.

Inter-algorithm lesion volumetry comparison of real and 3D simulated lung lesions in CT

NASA Astrophysics Data System (ADS)

Robins, Marthony; Solomon, Justin; Hoye, Jocelyn; Smith, Taylor; Ebner, Lukas; Samei, Ehsan

2017-03-01

The purpose of this study was to establish volumetric exchangeability between real and computational lung lesions in CT. We compared the overall relative volume estimation performance of segmentation tools when used to measure real lesions in actual patient CT images and computational lesions virtually inserted into the same patient images (i.e., hybrid datasets). Pathologically confirmed malignancies from 30 thoracic patient cases from Reference Image Database to Evaluate Therapy Response (RIDER) were modeled and used as the basis for the comparison. Lesions included isolated nodules as well as those attached to the pleura or other lung structures. Patient images were acquired using a 16 detector row or 64 detector row CT scanner (Lightspeed 16 or VCT; GE Healthcare). Scans were acquired using standard chest protocols during a single breath-hold. Virtual 3D lesion models based on real lesions were developed in Duke Lesion Tool (Duke University), and inserted using a validated image-domain insertion program. Nodule volumes were estimated using multiple commercial segmentation tools (iNtuition, TeraRecon, Inc., Syngo.via, Siemens Healthcare, and IntelliSpace, Philips Healthcare). Consensus based volume comparison showed consistent trends in volume measurement between real and virtual lesions across all software. The average percent bias (+/- standard error) shows -9.2+/-3.2% for real lesions versus -6.7+/-1.2% for virtual lesions with tool A, 3.9+/-2.5% and 5.0+/-0.9% for tool B, and 5.3+/-2.3% and 1.8+/-0.8% for tool C, respectively. Virtual lesion volumes were statistically similar to those of real lesions (< 4% difference) with p >.05 in most cases. Results suggest that hybrid datasets had similar inter-algorithm variability compared to real datasets.

B97-3c: A revised low-cost variant of the B97-D density functional method

NASA Astrophysics Data System (ADS)

Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas; Grimme, Stefan

2018-02-01

A revised version of the well-established B97-D density functional approximation with general applicability for chemical properties of large systems is proposed. Like B97-D, it is based on Becke's power-series ansatz from 1997 and is explicitly parametrized by including the standard D3 semi-classical dispersion correction. The orbitals are expanded in a modified valence triple-zeta Gaussian basis set, which is available for all elements up to Rn. Remaining basis set errors are mostly absorbed in the modified B97 parametrization, while an established atom-pairwise short-range potential is applied to correct for the systematically too long bonds of main group elements which are typical for most semi-local density functionals. The new composite scheme (termed B97-3c) completes the hierarchy of "low-cost" electronic structure methods, which are all mainly free of basis set superposition error and account for most interactions in a physically sound and asymptotically correct manner. B97-3c yields excellent molecular and condensed phase geometries, similar to most hybrid functionals evaluated in a larger basis set expansion. Results on the comprehensive GMTKN55 energy database demonstrate its good performance for main group thermochemistry, kinetics, and non-covalent interactions, when compared to functionals of the same class. This also transfers to metal-organic reactions, which is a major area of applicability for semi-local functionals. B97-3c can be routinely applied to hundreds of atoms on a single processor and we suggest it as a robust computational tool, in particular, for more strongly correlated systems where our previously published "3c" schemes might be problematic.

3D analysis of vortical structures in an abdominal aortic aneurysm by stereoscopic PIV

NASA Astrophysics Data System (ADS)

Deplano, Valérie; Guivier-Curien, Carine; Bertrand, Eric

2016-11-01

The present work presents an experimental in vitro three-dimensional analysis of the flow dynamics in an abdominal aortic aneurysm (AAA) through stereoscopic particle image velocimetry (SPIV) measurements. The experimental set-up mimics the pathophysiological context involving a shear thinning blood analogue fluid, compliant AAA and aorto-iliac bifurcation walls and controlled inlet and outlet flow rate and pressure waveforms as well as working fluid temperature. SPIV was carefully calibrated and conducted to assess the three velocity components in the AAA volume. For the first time in the literature, the 3D vortex ring genesis, propagation, and vanishing in the AAA bulge are experimentally described and quantified. In comparison with classical 2-component PIV measurements (2C PIV), the third component of the velocity vector was shown to be of importance in such a geometry, especially, during the deceleration phase of the flow rate. The 3D velocity magnitude reached up more than 20 % of the 2D one showing that 2C PIV are definitively not accurate enough to provide a complete description of flow behaviour in an AAA. In addition to potential clinical implications of a full 3D vortex ring description in AAA evolution, the 3D in vitro experimental quantification of the flow dynamics carried out in the present study offers an interesting tool for the validation of fluid-structure interaction numerical studies dealing with AAA.

SF3M 2.0: improvement of 3D photo-reconstruction interface based on freely available software

NASA Astrophysics Data System (ADS)

Castillo, Carlos; James, Michael R.; Pérez, Rafael; Gómez, Jose A.

2016-04-01

During recent years, a number of tools based on Structure-from-Motion algorithms have been released for full image-based 3D reconstruction either freely (e.g. Bundler, PMVS2, VisualSFM, MicMac) or commercially (e.g. Agisoft PhotoScan). The SF3M interface was developed in Matlab® to use link software developments (VisualSFM, CloudCompare) and new applications to create a semi-automated workflow including reconstruction, georeferencing and point-cloud filtering, and has been tested for gully erosion assessment with terrestrial images (Castillo et al., 2015). The main aim of this work to provide an improved freely-available and easy-to-use alternative for 3D reconstruction intended for public agencies, non-profit organisations, researchers and other stakeholders interested in 3D modelling. In this communication we present SF3M 2.0, a new version of the graphical user interface. In this case, the SfM module is based on MicMac, an open-software tool (Pierrot-Deseilligny and Cléry, 2011) which provides advanced features such as camera calibration and constrained bundle adjustment using ground control points. SF3M 2.0 will be tested in two scenarios: a) using the same ground-based image set tested in Castillo et al. (2015) to compare the performance of both versions and b) using aerial images taken from a helium balloon to assess a gully network in a 40-hectares catchment. In this study we explore the advantages of SF3M 2.0, explain its operation and evaluate its accuracy and performance. This tool will be also available for free download. References Castillo, C., James, M.R., Redel-Macías, M. D., Pérez, R., and Gómez, J.A.: SF3M software: 3-D photo-reconstruction for non-expert users and its application to a gully network, SOIL, 1, 583-594. Pierrot-Deseilligny, M and Cléry, I. APERO, an Open Source Bundle Adjusment Software for Automatic Calibration and Orientation of a Set of Images. Proceedings of the ISPRS Commission V Symposium, Image Engineering and Vision Metrology, Trento, Italy, 2-4 March 2011.

Delta: a new web-based 3D genome visualization and analysis platform.

PubMed

Tang, Bixia; Li, Feifei; Li, Jing; Zhao, Wenming; Zhang, Zhihua

2018-04-15

Delta is an integrative visualization and analysis platform to facilitate visually annotating and exploring the 3D physical architecture of genomes. Delta takes Hi-C or ChIA-PET contact matrix as input and predicts the topologically associating domains and chromatin loops in the genome. It then generates a physical 3D model which represents the plausible consensus 3D structure of the genome. Delta features a highly interactive visualization tool which enhances the integration of genome topology/physical structure with extensive genome annotation by juxtaposing the 3D model with diverse genomic assay outputs. Finally, by visually comparing the 3D model of the β-globin gene locus and its annotation, we speculated a plausible transitory interaction pattern in the locus. Experimental evidence was found to support this speculation by literature survey. This served as an example of intuitive hypothesis testing with the help of Delta. Delta is freely accessible from http://delta.big.ac.cn, and the source code is available at https://github.com/zhangzhwlab/delta. zhangzhihua@big.ac.cn. Supplementary data are available at Bioinformatics online.

Optical 3D surface digitizing in forensic medicine: 3D documentation of skin and bone injuries.

PubMed

Thali, Michael J; Braun, Marcel; Dirnhofer, Richard

2003-11-26

Photography process reduces a three-dimensional (3D) wound to a two-dimensional level. If there is a need for a high-resolution 3D dataset of an object, it needs to be three-dimensionally scanned. No-contact optical 3D digitizing surface scanners can be used as a powerful tool for wound and injury-causing instrument analysis in trauma cases. The 3D skin wound and a bone injury documentation using the optical scanner Advanced TOpometric Sensor (ATOS II, GOM International, Switzerland) will be demonstrated using two illustrative cases. Using this 3D optical digitizing method the wounds (the virtual 3D computer model of the skin and the bone injuries) and the virtual 3D model of the injury-causing tool are graphically documented in 3D in real-life size and shape and can be rotated in the CAD program on the computer screen. In addition, the virtual 3D models of the bone injuries and tool can now be compared in a 3D CAD program against one another in virtual space, to see if there are matching areas. Further steps in forensic medicine will be a full 3D surface documentation of the human body and all the forensic relevant injuries using optical 3D scanners.

Infusion of a Gaming Paradigm into Computer-Aided Engineering Design Tools

DTIC Science & Technology

2012-05-03

Virtual Test Bed (VTB), and the gaming tool, Unity3D . This hybrid gaming environment coupled a three-dimensional (3D) multibody vehicle system model...from Google Earth to the 3D visual front-end fabricated around Unity3D . The hybrid environment was sufficiently developed to support analyses of the...ndFr Cti3r4 G’OjrdFr ctior-2 The VTB simulation of the vehicle dynamics ran concurrently with and interacted with the gaming engine, Unity3D which

Monoclonal antibodies to snakehead, Channa striata immunoglobulins: detection and quantification of immunoglobulin-positive cells in blood and lymphoid organs.

PubMed

Sood, Neeraj; Chaudhary, Dharmendra K; Rathore, Gaurav; Singh, Akhilesh; Lakra, W S

2011-02-01

Snakehead Channa striata is an important freshwater food fish in many Southeast Asian countries. Three monoclonal antibodies (C9, C10 and D10) were developed against purified serum immunoglobulins of Channa striata (Cs-Ig) and characterized. C9 and D10 MAbs were specific to heavy chain, while C10 MAb detected only unreduced Cs-Ig in western blotting. In competitive ELISA, C9 and C10 MAbs were specific to C. striata Ig and showed no cross reactivity with serum Ig of other fish species i.e. Channa punctatus, Channa marulius, Clarias batrachus and Labeo rohita. D10 MAb showed reactivity to serum Ig of C. striata and C. marulius. In FACS analysis of gated lymphocytes, the percentage of Ig+ cells detected by C9 MAb was 18.2%, 27.7% and 10.3% in blood, spleen and kidney, respectively (n=3, body weight 500-600 g). However, only a few cells (0.5%) were found to be Ig+ in thymus (n=5). C9 MAb was also successfully employed to demonstrate Ig+ cells in blood smears and formalin fixed sections of spleen and kidney. These findings suggest that the spleen plays an important role in humoral immunity as compared to head kidney. Further, these MAbs can be useful immunological tool in monitoring health status of cultured C. striata. Copyright © 2010 Elsevier Ltd. All rights reserved.

Scale and the isotopic record of C4 plants in pedogenic carbonate: from the biome to the rhizospere.

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

Monger, Dr. H Curtis; Cole, David R; Buck, Dr. Brenda

2009-01-01

The 13C/12C ratio in pedogenic carbonate (i.e., CaCO3 formed in soil) is a significant tool for investigating C4 biomes of the past. However, the paleoecological meaning of d13C values in pedogenic carbonate can change with the scale at which one considers the data. We describe studies of modern soils, fossil soils, and vegetation change in the Chihuahuan Desert of North America and elsewhere that reveal four scales important for paleoecologic interpretations. (1) At the broadest scale, the biome scale (hundreds to millions of km2), an isotopic record interpreted as C3 vegetation replacing C4 grasslands may indicate invading C3 woody shrubsmore » instead of expanding C3 forests (a common interpretation). (2) At the landscape scale (several tens of m2 to hundreds of km2), the accuracy of scaling up paleoclimatic interpretations to a regional level is affected by the landform containing the isotopic record. (3) At the soil-profile scale (cm2 to m2), soil profiles with multiple generations of carbonate mixed together have a lower-resolution paleoecologic record than soil profiles repeatedly buried. (4) At the rhizosphere scale (lm2 to cm2), carbonate formed on roots lack the 14 17 enrichment observed at broader scales, revealing different fractionation processes at different scales. A multi-scale approach in dealing with d13C in pedogenic carbonate will increase the accuracy of paleoecologic interpretations and understanding of soil geomorphic climatic interactions that affect boundaries between C4 and C3 vegetation.« less

Scale and the isotopic record of C4 plants in pedogenic carbonate: from the biome to the rhizosphere

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

Monger, Dr. H Curtis; Cole, David; Buck, Dr. Brenda

2009-01-01

The 13C/12C ratio in pedogenic carbonate (i.e., CaCO3 formed in soil) is a significant tool for investigating C4 biomes of the past. However, the paleoecological meaning of d13C values in pedogenic carbonate can change with the scale at which one considers the data. We describe studies of modern soils, fossil soils, and vegetation change in the Chihuahuan Desert of North America and elsewhere that reveal four scales important for paleoecologic interpretations. (1) At the broadest scale, the biome scale (hundreds to millions of km2), an isotopic record interpreted as C3 vegetation replacing C4 grasslands may indicate invading C3 woody shrubsmore » instead of expanding C3 forests (a common interpretation). (2) At the landscape scale (several tens of m2 to hundreds of km2), the accuracy of scaling up paleoclimatic interpretations to a regional level is affected by the landform containing the isotopic record. (3) At the soil-profile scale (cm2 to m2), soil profiles with multiple generations of carbonate mixed together have a lower-resolution paleoecologic record than soil profiles repeatedly buried. (4) At the rhizosphere scale (lm2 to cm2), carbonate formed on roots lack the 14 17 enrichment observed at broader scales, revealing different fractionation processes at different scales. A multi-scale approach in dealing with d13C in pedogenic carbonate will increase the accuracy of paleoecologic interpretations and understanding of soil geomorphic climatic interactions that affect boundaries between C4 and C3 vegetation.« less

Comparison of biotyping methods as alternative identification tools to molecular typing of pathogenic Cryptococcus species in sub-Saharan Africa.

PubMed

Nyazika, Tinashe K; Robertson, Valerie J; Nherera, Brenda; Mapondera, Prichard T; Meis, Jacques F; Hagen, Ferry

2016-03-01

Cryptococcal meningitis is the leading fungal infection and AIDS defining opportunistic illness in patients with late stage HIV infection, particularly in South-East Asia and sub-Saharan Africa. Given the high mortality, clinical differences and the extensive ecological niche of Cryptococcus neoformans and Cryptococcus gattii species complexes, there is need for laboratories in sub-Sahara African countries to adopt new and alternative reliable diagnostic algorithms that rapidly identify and distinguish these species. We biotyped 74 and then amplified fragment length polymorphism (AFLP) genotyped 66 Cryptococcus isolates from a cohort of patients with HIV-associated cryptococcal meningitis. C. gattii sensu lato was isolated at a prevalence of 16.7% (n = 11/66) and C. neoformans sensu stricto was responsible for 83.3% (n = 55/66) of the infections. l-Canavanine glycine bromothymol blue, yeast-carbon-base-d-proline-d-tryptophan and creatinine dextrose bromothymol blue thymine were able to distinguish pathogenic C. gattii sensu lato from C. neoformans sensu stricto species when compared with AFLP genotyping. This study demonstrates high C. gattii sensu lato prevalence in Zimbabwe. In addition, biotyping methods can be used as alternative diagnostic tools to molecular typing in resource-limited areas for differentiating pathogenic Cryptococcus species. © 2015 Blackwell Verlag GmbH.

Recent developments in turning hardened steels - A review

NASA Astrophysics Data System (ADS)

Sivaraman, V.; Prakash, S.

2017-05-01

Hard materials ranging from HRC 45 - 68 such as hardened AISI H13, AISI 4340, AISI 52100, D2 STL, D3 STEEL Steel etc., need super hard tool materials to machine. Turning of these hard materials is termed as hard turning. Hard turning makes possible direct machining of the hard materials and also eliminates the lubricant requirement and thus favoring dry machining. Hard turning is a finish turning process and hence conventional grinding is not required. Development of the new advanced super hard tool materials such as ceramic inserts, Cubic Boron Nitride, Polycrystalline Cubic Boron Nitride etc. enabled the turning of these materials. PVD and CVD methods of coating have made easier the production of single and multi layered coated tool inserts. Coatings of TiN, TiAlN, TiC, Al2O3, AlCrN over cemented carbide inserts has lead to the machining of difficult to machine materials. Advancement in the process of hard machining paved way for better surface finish, long tool life, reduced tool wear, cutting force and cutting temperatures. Micro and Nano coated carbide inserts, nanocomposite coated PCBN inserts, micro and nano CBN coated carbide inserts and similar developments have made machining of hardened steels much easier and economical. In this paper, broad literature review on turning of hardened steels including optimizing process parameters, cooling requirements, different tool materials etc., are done.

Grassystatins A–C from Marine Cyanobacteria, Potent Cathepsin E Inhibitors that Reduce Antigen Presentation

PubMed Central

Kwan, Jason C.; Eksioglu, Erika A.; Liu, Chen; Paul, Valerie J.; Luesch, Hendrik

2009-01-01

In our efforts to explore marine cyanobacteria as a source of novel bioactive compounds we discovered a statine unit-containing linear decadepsipeptide, grassystatin A (1), which we screened against a diverse set of 59 proteases. We describe the structure determination of 1 and two natural analogs, grassystatins B (2) and C (3), using NMR, MS, and chiral HPLC techniques. Compound 1 selectively inhibited cathepsins D and E with IC50s of 26.5 nM and 886 pM, respectively. Compound 2 showed similar potency and selectivity against cathepsins D and E (IC50s 7.27 nM and 354 pM, respectively), whereas the truncated peptide analog grassystatin C (3), which consists of two fewer residues than 1 and 2, was less potent against both but still selective for cathepsin E. The selectivity of compounds 1–3 for cathepsin E over D (20- to 38-fold) suggests that these natural products may be useful tools to probe cathepsin E function. We investigated the structural basis of this selectivity using molecular docking. We also show that 1 can reduce antigen presentation by dendritic cells, a process thought to rely on cathepsin E. PMID:19715320

Associations of the Levels of C4d-bearing Reticulocytes and High-avidity Anti-dsDNA Antibodies with Disease Activity in Systemic Lupus Erythematosus.

PubMed

Mora, Claudia; Medina-Rosas, Jorge; Santos, Ana Maria; Jaimes, Diego A; Arbeláez, Ana M; Romero, Consuelo; Cortes, Annie; Londono, John

2016-09-01

There are no laboratory tools that detect early flares in systemic lupus erythematosus (SLE). Our aim was to validate in our population the previous findings of the association of C4d-bearing reticulocytes (R-C4d) compared to anti-dsDNA antibodies, with disease activity assessed by the Safety of Estrogens in Lupus Erythematosus National Assessment-Systemic Lupus Erythematosus Disease Activity Index (SELENA-SLEDAI) and the British Isles Lupus Assessment Group (BILAG) 2004 scales. All patients who met the 1987 American College of Rheumatology classification criteria and were seen consecutively in 2013 at a specialized SLE care clinic were included. Disease activity was established by the SELENA-SLEDAI and BILAG 2004. Anti-dsDNA and R-C4d were quantified in peripheral blood. Comparisons were made between values of active and inactive patients, and the correlations between the SELENA-SLEDAI and serum levels of anti-dsDNA and R-C4d were measured. Sixty-two patients (83.9% women) were included. A total of 32.3% had active disease according to the SELENA-SLEDAI. There was a significant statistical difference (p = 0.0001) in the distribution of R-C4d between disease activity groups. The correlation coefficient between R-C4d and the SELENA-SLEDAI score was rs = 0.738 (p = 0.0001). R-C4d differed between patients with and without activity in the BILAG 2004 constitutional, mucocutaneous, gastrointestinal, renal, and hematological domains. R-C4d showed a higher correlation with SLE activity measured by the SELENA-SLEDAI and BILAG 2004 than anti-dsDNA did, suggesting a possible involvement in diagnosing disease activity. Prospective studies that confirm these findings and evaluate its involvement in followup are needed.

3D Visualization Tools to Support Soil Management In Relation to Sustainable Agriculture and Ecosystem Services

NASA Astrophysics Data System (ADS)

Wang, Chen

2017-04-01

Visualization tools [1][2][6] have been used increasingly as part of information, consultation, and collaboration in relation to issues of global significance. Visualization techniques can be used in a variety of different settings, depending on their association with specific types of decision. Initially, they can be used to improve awareness of the local community and landscape, either individually or in groups [5]. They can also be used to communicate different aspects of change, such as digital soil mapping, ecosystem services and climate change [7][8]. A prototype 3D model was developed to present Tarland Catchment on the North East Scotland which includes 1:25000 soil map data and 1:50000 land capability for agriculture (LCA) data [4]. The model was used to identify issues arising between the growing interest soil monitoring and management, and the potential effects on existing soil characteristics. The online model was also created which can capture user/stakeholder comments they associate with soil features. In addition, people are located physically within the real-world bounds of the current soil management scenario, they can use Augmented Reality to see the scenario overlaid on their immediate surroundings. Models representing alternative soil use and management were used in the virtual landscape theatre (VLT) [3]with electronic voting designed to elicit public aspirations and concerns regarding future soil uses, and to develop scenarios driven by local input. Preliminary findings suggest positive audience responses to the relevance of the inclusion of soil data within a scene when considering questions regarding the impact of land-use change, such as woodland, agricultural land and open spaces. A future development is the use of the prototype virtual environment in a preference survey of scenarios of changes in land use, and in stakeholder consultations on such changes.END Rua, H. and Alvito, P. (2011) Living the past: 3D models, virtual reality and game engines as tools for supporting archaeology and the reconstruction of cultural heritage - the case-study of the Roman villa of Casal de Freiria, Journal of Archaeological Science, 38(12): 3296-3308. Wang, C., Miller, D.R., Brown I., Jiang Y., Castellazzi M, "Visualisation Techniques to Support Public Interpretation of Future Climate Change and Land Use Choices: A Case Study from N-E Scotland", International Journal of Digital Earth, Volume 9, Issue 6, pp.586-605, 2016. VLT, http://www.hutton.ac.uk/learning/exhibits/vlt Scotland's soil, http://www.soils-scotland.gov.uk/ Wang, C., Miller, D.R., Jiang Y., Donaldson-Selby, "Use of 3D Visualisation Tools for Representing Urban Greenspace Spatial Planning", 2015 IEEE International Conference on Information Science and Control Engineering Shanghai, China, April 24-26, 2015. Tobias, S., Buser, T., Buchecker, M. (2016) Does real-time visualization support local stakeholders in developing landscape visions? Environment and Planning B:Planning and Design, 43: 84¨ C197. Li.Y, Zhu. A-Xing, Shi. Z, Liu. J and Du. F, "Supplemental sampling for digital soil mapping based on prediction uncertainty from both the feature domain and the spatial domain", The Global Journal of Soil Science, Volume 284, pp 73-84, 2016. Warren-Kretzschmar. B and Haaren, C, "Communicating spatial planning decisions at the landscape and farm level with landscape visualization", Journal of Biogeosciences and Forestry, volume 7, pp 434-442, 2014.

Metabolite Differentiation and Discovery Lab (MeDDL): A New Tool for Biomarker Discovery and Mass Spectral Visualization

DTIC Science & Technology

2010-06-01

Jeremy Nicholson, Elaine Holmes , and John Lindon at the Imperial College in London1 utilizing nuclear magnetic resonance (NMR) based analysis, has...Lindon, J. C.; Holmes , E. Xenobiotica 1999, 29, 1181– 1189. (2) Pham-Tuan, H.; Kaskavelis, L.; Daykin, C.; Janssen, H. J. Chromatogr. B 2003, 789, 283...301. (3) Lindon, J.; Holmes , E.; Nicholson, J. Pharm. Res. 2006, 23, 1075–1088. (4) Robertson, D. Toxicol. Sci. 2005, 85, 809–822. (5) Nicholson, J

HIBAL Program. Preliminary Warhead-Design. Volume II. Appendices.

DTIC Science & Technology

1980-09-15

Mild Steel (iAi i018). ............. 11-2 B. SAE 4130 .. .. .. .... ...... ....... 11-3 C. SAE 4140 ......... .... .... ......... 11-3 D, SAE 4340...11-7 - Test Data for SAE 4140 Steel Frag- ments ...... ................ 11-14 Figure II-7A - 4142 ... .............. 11-15 Figure 11-8 - Test Data...included the following types of steel: SAE 1018, 4130, 4140 and 4340; 5-317 and 5-876 Carpenter tool steel; Anico HY-80 and SSS-100 steel; AISI-S7

The in-situ 3D measurement system combined with CNC machine tools

NASA Astrophysics Data System (ADS)

Zhao, Huijie; Jiang, Hongzhi; Li, Xudong; Sui, Shaochun; Tang, Limin; Liang, Xiaoyue; Diao, Xiaochun; Dai, Jiliang

2013-06-01

With the development of manufacturing industry, the in-situ 3D measurement for the machining workpieces in CNC machine tools is regarded as the new trend of efficient measurement. We introduce a 3D measurement system based on the stereovision and phase-shifting method combined with CNC machine tools, which can measure 3D profile of the machining workpieces between the key machining processes. The measurement system utilizes the method of high dynamic range fringe acquisition to solve the problem of saturation induced by specular lights reflected from shiny surfaces such as aluminum alloy workpiece or titanium alloy workpiece. We measured two workpieces of aluminum alloy on the CNC machine tools to demonstrate the effectiveness of the developed measurement system.

3DProIN: Protein-Protein Interaction Networks and Structure Visualization.

PubMed

Li, Hui; Liu, Chunmei

2014-06-14

3DProIN is a computational tool to visualize protein-protein interaction networks in both two dimensional (2D) and three dimensional (3D) view. It models protein-protein interactions in a graph and explores the biologically relevant features of the tertiary structures of each protein in the network. Properties such as color, shape and name of each node (protein) of the network can be edited in either 2D or 3D views. 3DProIN is implemented using 3D Java and C programming languages. The internet crawl technique is also used to parse dynamically grasped protein interactions from protein data bank (PDB). It is a java applet component that is embedded in the web page and it can be used on different platforms including Linux, Mac and Window using web browsers such as Firefox, Internet Explorer, Chrome and Safari. It also was converted into a mac app and submitted to the App store as a free app. Mac users can also download the app from our website. 3DProIN is available for academic research at http://bicompute.appspot.com.

Dynamic three-dimensional model of the coronary circulation

NASA Astrophysics Data System (ADS)

Lehmann, Glen; Gobbi, David G.; Dick, Alexander J.; Starreveld, Yves P.; Quantz, M.; Holdsworth, David W.; Drangova, Maria

2001-05-01

A realistic numerical three-dimensional (3D) model of the dynamics of human coronary arteries has been developed. High- resolution 3D images of the coronary arteries of an excised human heart were obtained using a C-arm based computed tomography (CT) system. Cine bi-plane coronary angiograms were then acquired from a patient with similar coronary anatomy. These angiograms were used to determine the vessel motion, which was applied to the static 3D coronary tree. Corresponding arterial bifurcations were identified in the 3D CT image and in the 2D angiograms. The 3D positions of the angiographic landmarks, which were known throughout the cardiac cycle, were used to warp the 3D image via a non-linear thin-plate spline algorithm. The result was a set or 30 dynamic volumetric images sampling a complete cardiac cycle. To the best of our knowledge, the model presented here is the first dynamic 3D model that provides a true representation of both the geometry and motion of a human coronary artery tree. In the future, similar models can be generated to represent different coronary anatomy and motion. Such models are expected to become an invaluable tool during the development of dynamic imaging techniques such as MRI, multi-slice CT and 3D angiography.

Evaluation of serum free thyroxine and thyrotropin concentrations in the diagnosis of canine hypothyroidism.

PubMed

Dixon, R M; Mooney, C T

1999-02-01

Canine thyroid-stimulating hormone (cTSH), total thyroxine (T4) and free T4 by equilibrium dialysis (fT4d) were measured in serum samples from 107 dogs with clinical signs suggestive of hypothyroidism in which the diagnosis was either confirmed (n = 30) or excluded (n = 77) by exogenous TSH response testing. Median serum total T4 and fT4d concentrations were significantly lower and cTSH significantly higher (P < 0.001) in hypothyroid compared with euthyroid dogs. Differential positive rate analysis determined optimal cut-off values of less than 14.9 nmol/litre (total T4), less than 5.42 pmol/litre (fT4d), greater than 0.68 ng/ml (cTSH), less than 17.3 (T4 to cTSH ratio), and less than 7.5 (fT4d to cTSH ratio) for hypothyroidism. These had a sensitivity and specificity of 100 and 75.3 per cent, 80 and 93.5 per cent, 86.7 and 81.8 per cent, 86.7 and 92.2 per cent, and 80 and 97.4 per cent, respectively, for diagnosing hypothyroidism. Corresponding areas under the receiver operating characteristic curves were 0.92, 0.93, 0.87, 0.93 and 0.93. Unexpectedly low cTSH values in hypothyroid dogs may have resulted from concurrent non-thyroidal illness. Unexpectedly high serum cTSH values in the euthyroid dogs might have resulted from recovery from illness or concurrent potentiated sulphonamide therapy. Measurement of endogenous cTSH concentration is a valuable diagnostic tool for canine hypothyroidism if used in association with assessment of T4. Estimation of fT4d added only limited additional information over total T4 measurement.

Intensity-based segmentation and visualization of cells in 3D microscopic images using the GPU

NASA Astrophysics Data System (ADS)

Kang, Mi-Sun; Lee, Jeong-Eom; Jeon, Woong-ki; Choi, Heung-Kook; Kim, Myoung-Hee

2013-02-01

3D microscopy images contain abundant astronomical data, rendering 3D microscopy image processing time-consuming and laborious on a central processing unit (CPU). To solve these problems, many people crop a region of interest (ROI) of the input image to a small size. Although this reduces cost and time, there are drawbacks at the image processing level, e.g., the selected ROI strongly depends on the user and there is a loss in original image information. To mitigate these problems, we developed a 3D microscopy image processing tool on a graphics processing unit (GPU). Our tool provides efficient and various automatic thresholding methods to achieve intensity-based segmentation of 3D microscopy images. Users can select the algorithm to be applied. Further, the image processing tool provides visualization of segmented volume data and can set the scale, transportation, etc. using a keyboard and mouse. However, the 3D objects visualized fast still need to be analyzed to obtain information for biologists. To analyze 3D microscopic images, we need quantitative data of the images. Therefore, we label the segmented 3D objects within all 3D microscopic images and obtain quantitative information on each labeled object. This information can use the classification feature. A user can select the object to be analyzed. Our tool allows the selected object to be displayed on a new window, and hence, more details of the object can be observed. Finally, we validate the effectiveness of our tool by comparing the CPU and GPU processing times by matching the specification and configuration.

Reduction of nitrate in aquifer microcosms by carbon additions

USGS Publications Warehouse

Obenhuber, Donald C.; Lowrance , Richard

1991-01-01

Aquifer microcosms were used to examine the effects of NO−3 and C amendments on groundwater from the Claiborne aquifer. Nitrate concentrations of 12.17 mg L−1 in aquifer microcosms were reduced 0.92%/d to 5.84 mg L−1 by the addition of 10 mg C L−1 for 35 d. Nitrate disappearance correlated with increases in number of denitrifiers and dissolved N2O concentration and decreases in dissolved oxygen, suggesting biological denitrification. Nitrate/chloride ratios decreased in microcosms with 10 mg C L−1 added and then increased when the C addition was removed. Carbon additions of 0.4 mg C L−1 had no effect on the microbial or chemical properties of the microcosms. Nitrous oxide levels in wells sampling the Claiborne aquifer showed an increase with depth, indicating N2O production within the aquifer. Microcosms are useful tools to examine biological transformations of chemical contaminants in unconsolidated aquifer material. The remediation of NO−3 contaminated aquifers by organic infusion is possible and appears to be a function of microbial denitrification.

A Prototype Digital Library for 3D Collections: Tools To Capture, Model, Analyze, and Query Complex 3D Data.

ERIC Educational Resources Information Center

Rowe, Jeremy; Razdan, Anshuman

The Partnership for Research in Spatial Modeling (PRISM) project at Arizona State University (ASU) developed modeling and analytic tools to respond to the limitations of two-dimensional (2D) data representations perceived by affiliated discipline scientists, and to take advantage of the enhanced capabilities of three-dimensional (3D) data that…

Development and Assessment of a New 3D Neuroanatomy Teaching Tool for MRI Training

ERIC Educational Resources Information Center

Drapkin, Zachary A.; Lindgren, Kristen A.; Lopez, Michael J.; Stabio, Maureen E.

2015-01-01

A computerized three-dimensional (3D) neuroanatomy teaching tool was developed for training medical students to identify subcortical structures on a magnetic resonance imaging (MRI) series of the human brain. This program allows the user to transition rapidly between two-dimensional (2D) MRI slices, 3D object composites, and a combined model in…

CaveCAD: a tool for architectural design in immersive virtual environments

NASA Astrophysics Data System (ADS)

Schulze, Jürgen P.; Hughes, Cathleen E.; Zhang, Lelin; Edelstein, Eve; Macagno, Eduardo

2014-02-01

Existing 3D modeling tools were designed to run on desktop computers with monitor, keyboard and mouse. To make 3D modeling possible with mouse and keyboard, many 3D interactions, such as point placement or translations of geometry, had to be mapped to the 2D parameter space of the mouse, possibly supported by mouse buttons or keyboard keys. We hypothesize that had the designers of these existing systems had been able to assume immersive virtual reality systems as their target platforms, they would have been able to design 3D interactions much more intuitively. In collaboration with professional architects, we created a simple, but complete 3D modeling tool for virtual environments from the ground up and use direct 3D interaction wherever possible and adequate. In this publication, we present our approaches for interactions for typical 3D modeling functions, such as geometry creation, modification of existing geometry, and assignment of surface materials. We also discuss preliminary user experiences with this system.

Hyper-Fractal Analysis: A visual tool for estimating the fractal dimension of 4D objects

NASA Astrophysics Data System (ADS)

Grossu, I. V.; Grossu, I.; Felea, D.; Besliu, C.; Jipa, Al.; Esanu, T.; Bordeianu, C. C.; Stan, E.

2013-04-01

This work presents a new version of a Visual Basic 6.0 application for estimating the fractal dimension of images and 3D objects (Grossu et al. (2010) [1]). The program was extended for working with four-dimensional objects stored in comma separated values files. This might be of interest in biomedicine, for analyzing the evolution in time of three-dimensional images. New version program summaryProgram title: Hyper-Fractal Analysis (Fractal Analysis v03) Catalogue identifier: AEEG_v3_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEG_v3_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 745761 No. of bytes in distributed program, including test data, etc.: 12544491 Distribution format: tar.gz Programming language: MS Visual Basic 6.0 Computer: PC Operating system: MS Windows 98 or later RAM: 100M Classification: 14 Catalogue identifier of previous version: AEEG_v2_0 Journal reference of previous version: Comput. Phys. Comm. 181 (2010) 831-832 Does the new version supersede the previous version? Yes Nature of problem: Estimating the fractal dimension of 4D images. Solution method: Optimized implementation of the 4D box-counting algorithm. Reasons for new version: Inspired by existing applications of 3D fractals in biomedicine [3], we extended the optimized version of the box-counting algorithm [1, 2] to the four-dimensional case. This might be of interest in analyzing the evolution in time of 3D images. The box-counting algorithm was extended in order to support 4D objects, stored in comma separated values files. A new form was added for generating 2D, 3D, and 4D test data. The application was tested on 4D objects with known dimension, e.g. the Sierpinski hypertetrahedron gasket, Df=ln(5)/ln(2) (Fig. 1). The algorithm could be extended, with minimum effort, to higher number of dimensions. Easy integration with other applications by using the very simple comma separated values file format for storing multi-dimensional images. Implementation of χ2 test as a criterion for deciding whether an object is fractal or not. User friendly graphical interface. Hyper-Fractal Analysis-Test on the Sierpinski hypertetrahedron 4D gasket (Df=ln(5)/ln(2)≅2.32). Running time: In a first approximation, the algorithm is linear [2]. References: [1] V. Grossu, D. Felea, C. Besliu, Al. Jipa, C.C. Bordeianu, E. Stan, T. Esanu, Computer Physics Communications, 181 (2010) 831-832. [2] I.V. Grossu, C. Besliu, M.V. Rusu, Al. Jipa, C. C. Bordeianu, D. Felea, Computer Physics Communications, 180 (2009) 1999-2001. [3] J. Ruiz de Miras, J. Navas, P. Villoslada, F.J. Esteban, Computer Methods and Programs in Biomedicine, 104 Issue 3 (2011) 452-460.

Mobile Building Energy Audit and Modeling Tools: Cooperative Research and Development Final Report, CRADA Number CRD-11-00441

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

Brackney, L.

Broadly accessible, low cost, accurate, and easy-to-use energy auditing tools remain out of reach for managers of the aging U.S. building population (over 80% of U.S. commercial buildings are more than 10 years old*). concept3D and NREL's commercial buildings group will work to translate and extend NREL's existing spreadsheet-based energy auditing tool for a browser-friendly and mobile-computing platform. NREL will also work with concept3D to further develop a prototype geometry capture and materials inference tool operable on a smart phone/pad platform. These tools will be developed to interoperate with NREL's Building Component Library and OpenStudio energy modeling platforms, and willmore » be marketed by concept3D to commercial developers, academic institutions and governmental agencies. concept3D is NREL's lead developer and subcontractor of the Building Component Library.« less

Assigning Treatment to HCC Patients for Transplantation: Utility of a New Decision-Making Tool.

PubMed

Shah, Najmul Hassan; Dar, Faisal Saud; Bhatti, Abu Bakar Hafeez; Rana, Atif; Salih, Mohammad

2016-10-28

BACKGROUND The Barcelona clinic liver cancer (BCLC) staging system is considered the standard of care for hepatocellular carcinoma (HCC) management. It has various limitations, including lack of second-line treatment options and combination therapy. We prospectively collected data on our HCC patients based on a new decision-making tool (NDT). The objective of this study was to determine the applicability of this tool and compare it with BCLC for treatment allocation, in particular with respect to liver transplantation. MATERIAL AND METHODS We retrospectively reviewed HCC patients who were managed based on an NDT that was developed in 2012. All patients whose treatment decision was based on this tool between 2012 and 2015 were included. Comparison was made with BCLC. Survival was compared for patients who underwent liver transplantation. RESULTS Based on the NDT, 406 (40.6%) patients were eligible for curative treatment versus only 22 (2.2%) patients based on BCLC. A total of 58 (5.8%) patients underwent liver transplant based on the NDT, while only 2 (0.2%) were transplantable based on BCLC. Estimated 3-year survival for transplanted patients based on the NDT was 73%. There were 41 (4.1%) stage C and 15 (1.5%) stage D BCLC patients who received transplant based on the NDT. Estimated 3-year survival for stage A, C, and D BCLC patients who received transplantation was 100%,72%, and 67%, respectively (P=0.6). CONCLUSIONS The NDT correctly identified a group of HCC patients for liver transplantation who would otherwise have received palliative treatment based on the BCLC algorithm.

Discussion on the 3D visualizing of 1:200 000 geological map

NASA Astrophysics Data System (ADS)

Wang, Xiaopeng

2018-01-01

Using United States National Aeronautics and Space Administration Shuttle Radar Topography Mission (SRTM) terrain data as digital elevation model (DEM), overlap scanned 1:200 000 scale geological map, program using Direct 3D of Microsoft with C# computer language, the author realized the three-dimensional visualization of the standard division geological map. User can inspect the regional geology content with arbitrary angle, rotating, roaming, and can examining the strata synthetical histogram, map section and legend at any moment. This will provide an intuitionistic analyzing tool for the geological practitioner to do structural analysis with the assistant of landform, dispose field exploration route etc.

Interfaces and Integration of Medical Image Analysis Frameworks: Challenges and Opportunities.

PubMed

Covington, Kelsie; McCreedy, Evan S; Chen, Min; Carass, Aaron; Aucoin, Nicole; Landman, Bennett A

2010-05-25

Clinical research with medical imaging typically involves large-scale data analysis with interdependent software toolsets tied together in a processing workflow. Numerous, complementary platforms are available, but these are not readily compatible in terms of workflows or data formats. Both image scientists and clinical investigators could benefit from using the framework which is a most natural fit to the specific problem at hand, but pragmatic choices often dictate that a compromise platform is used for collaboration. Manual merging of platforms through carefully tuned scripts has been effective, but exceptionally time consuming and is not feasible for large-scale integration efforts. Hence, the benefits of innovation are constrained by platform dependence. Removing this constraint via integration of algorithms from one framework into another is the focus of this work. We propose and demonstrate a light-weight interface system to expose parameters across platforms and provide seamless integration. In this initial effort, we focus on four platforms Medical Image Analysis and Visualization (MIPAV), Java Image Science Toolkit (JIST), command line tools, and 3D Slicer. We explore three case studies: (1) providing a system for MIPAV to expose internal algorithms and utilize these algorithms within JIST, (2) exposing JIST modules through self-documenting command line interface for inclusion in scripting environments, and (3) detecting and using JIST modules in 3D Slicer. We review the challenges and opportunities for light-weight software integration both within development language (e.g., Java in MIPAV and JIST) and across languages (e.g., C/C++ in 3D Slicer and shell in command line tools).

RAG-3D: A search tool for RNA 3D substructures

DOE PAGES

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; ...

2015-08-24

In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

RAG-3D: a search tool for RNA 3D substructures

PubMed Central

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

2015-01-01

To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding. PMID:26304547

RAG-3D: A search tool for RNA 3D substructures

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

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef

In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

Subsurface observations of white shark Carcharodon carcharias predatory behaviour using an autonomous underwater vehicle.

PubMed

Skomal, G B; Hoyos-Padilla, E M; Kukulya, A; Stokey, R

2015-12-01

In this study, an autonomous underwater vehicle (AUV) was used to test this technology as a viable tool for directly observing the behaviour of marine animals and to investigate the behaviour, habitat use and feeding ecology of white sharks Carcharodon carcharias near Guadalupe Island off the coast of Mexico. During the period 31 October to 7 November 2013, six AUV missions were conducted to track one male and three female C. carcharias, ranging in estimated total length (LT ) from 3·9 to 5·7 m, off the north-east coast of Guadalupe Island. In doing so, the AUV generated over 13 h of behavioural data for C. carcharias at depths down to 90 m. The sharks remained in the area for the duration of each mission and moved through broad depth and temperature ranges from the surface to 163·8 m depth (mean ± S.D. = 112·5 ± 40·3 m) and 7·9-27·1° C (mean ± S.D. = 12·7 ± 2·9° C), respectively. Video footage and AUV sensor data revealed that two of the C. carcharias being tracked and eight other C. carcharias in the area approached (n = 17), bumped (n = 4) and bit (n = 9) the AUV during these tracks. This study demonstrated that an AUV can be used to effectively track and observe the behaviour of a large pelagic animal, C. carcharias. In doing so, the first observations of subsurface predatory behaviour were generated for this species. At its current state of development, this technology clearly offers a new and innovative tool for tracking the fine-scale behaviour of marine animals. © 2015 The Fisheries Society of the British Isles.

The 3D widgets for exploratory scientific visualization

NASA Technical Reports Server (NTRS)

Herndon, Kenneth P.; Meyer, Tom

1995-01-01

Computational fluid dynamics (CFD) techniques are used to simulate flows of fluids like air or water around such objects as airplanes and automobiles. These techniques usually generate very large amounts of numerical data which are difficult to understand without using graphical scientific visualization techniques. There are a number of commercial scientific visualization applications available today which allow scientists to control visualization tools via textual and/or 2D user interfaces. However, these user interfaces are often difficult to use. We believe that 3D direct-manipulation techniques for interactively controlling visualization tools will provide opportunities for powerful and useful interfaces with which scientists can more effectively explore their datasets. A few systems have been developed which use these techniques. In this paper, we will present a variety of 3D interaction techniques for manipulating parameters of visualization tools used to explore CFD datasets, and discuss in detail various techniques for positioning tools in a 3D scene.

Shared Memory Parallelism for 3D Cartesian Discrete Ordinates Solver

NASA Astrophysics Data System (ADS)

Moustafa, Salli; Dutka-Malen, Ivan; Plagne, Laurent; Ponçot, Angélique; Ramet, Pierre

2014-06-01

This paper describes the design and the performance of DOMINO, a 3D Cartesian SN solver that implements two nested levels of parallelism (multicore+SIMD) on shared memory computation nodes. DOMINO is written in C++, a multi-paradigm programming language that enables the use of powerful and generic parallel programming tools such as Intel TBB and Eigen. These two libraries allow us to combine multi-thread parallelism with vector operations in an efficient and yet portable way. As a result, DOMINO can exploit the full power of modern multi-core processors and is able to tackle very large simulations, that usually require large HPC clusters, using a single computing node. For example, DOMINO solves a 3D full core PWR eigenvalue problem involving 26 energy groups, 288 angular directions (S16), 46 × 106 spatial cells and 1 × 1012 DoFs within 11 hours on a single 32-core SMP node. This represents a sustained performance of 235 GFlops and 40:74% of the SMP node peak performance for the DOMINO sweep implementation. The very high Flops/Watt ratio of DOMINO makes it a very interesting building block for a future many-nodes nuclear simulation tool.

3D-atom probe characterization of nano-precipitates in a PM processed tool steels

NASA Astrophysics Data System (ADS)

Niederkofler, M.; Leisch, M.

2004-07-01

The microstructure of a powder metallurgical processed high speed steel (nom. composition (wt.%): 1.6 C, 4.8 Cr, 2.0 Mo, 5.0 V, 105 W, 8.0 Co and balance Fe) has been examined using 3D-atom probe technique. By the depth profiling of the time to flight mass spectrometer and position sensitive recording, cylindrical volumes of 10-15 nm in diameter and up to 40 nm in depth have been probed and characterized. The depth profiling measurements of the samples show generally a very homogeneous structure which was expected by the powder metallurgical processing of the material. Different morphologies of the precipitates were recorded. Besides the needle shaped precipitates with an extend up to 20 nm and thickness of few atomic layers, platelets and spherical particles are observed as well. The species which can be assigned to the precipitates appear to some extend as MC molecules in the mass histogram, while the leading constituents in this MC are Mo, V and Cr. Beside distinct particles agglomerations like one-dimensional atomic chains of the alloy components are also observed in the 3D reconstructions of the tool steel matrix.

Visualizing projected Climate Changes - the CMIP5 Multi-Model Ensemble

NASA Astrophysics Data System (ADS)

Böttinger, Michael; Eyring, Veronika; Lauer, Axel; Meier-Fleischer, Karin

2017-04-01

Large ensembles add an additional dimension to climate model simulations. Internal variability of the climate system can be assessed for example by multiple climate model simulations with small variations in the initial conditions or by analyzing the spread in large ensembles made by multiple climate models under common protocols. This spread is often used as a measure of uncertainty in climate projections. In the context of the fifth phase of the WCRP's Coupled Model Intercomparison Project (CMIP5), more than 40 different coupled climate models were employed to carry out a coordinated set of experiments. Time series of the development of integral quantities such as the global mean temperature change for all models visualize the spread in the multi-model ensemble. A similar approach can be applied to 2D-visualizations of projected climate changes such as latitude-longitude maps showing the multi-model mean of the ensemble by adding a graphical representation of the uncertainty information. This has been demonstrated for example with static figures in chapter 12 of the last IPCC report (AR5) using different so-called stippling and hatching techniques. In this work, we focus on animated visualizations of multi-model ensemble climate projections carried out within CMIP5 as a way of communicating climate change results to the scientific community as well as to the public. We take a closer look at measures of robustness or uncertainty used in recent publications suitable for animated visualizations. Specifically, we use the ESMValTool [1] to process and prepare the CMIP5 multi-model data in combination with standard visualization tools such as NCL and the commercial 3D visualization software Avizo to create the animations. We compare different visualization techniques such as height fields or shading with transparency for creating animated visualization of ensemble mean changes in temperature and precipitation including corresponding robustness measures. [1] Eyring, V., Righi, M., Lauer, A., Evaldsson, M., Wenzel, S., Jones, C., Anav, A., Andrews, O., Cionni, I., Davin, E. L., Deser, C., Ehbrecht, C., Friedlingstein, P., Gleckler, P., Gottschaldt, K.-D., Hagemann, S., Juckes, M., Kindermann, S., Krasting, J., Kunert, D., Levine, R., Loew, A., Mäkelä, J., Martin, G., Mason, E., Phillips, A. S., Read, S., Rio, C., Roehrig, R., Senftleben, D., Sterl, A., van Ulft, L. H., Walton, J., Wang, S., and Williams, K. D.: ESMValTool (v1.0) - a community diagnostic and performance metrics tool for routine evaluation of Earth system models in CMIP, Geosci. Model Dev., 9, 1747-1802, doi:10.5194/gmd-9-1747-2016, 2016.

3D Graphics Through the Internet: A "Shoot-Out"

NASA Technical Reports Server (NTRS)

Watson, Val; Lasinski, T. A. (Technical Monitor)

1995-01-01

3D graphics through the Internet needs to move beyond the current lowest common denominator of pre-computed movies, which consume bandwidth and are non-interactive. Panelists will demonstrate and compare 3D graphical tools for accessing, analyzing, and collaborating on information through the Internet and World-wide web. The "shoot-out" will illustrate which tools are likely to be the best for the various types of information, including dynamic scientific data, 3-D objects, and virtual environments. The goal of the panel is to encourage more effective use of the Internet by encouraging suppliers and users of information to adopt the next generation of graphical tools.

Web-based interactive 2D/3D medical image processing and visualization software.

PubMed

Mahmoudi, Seyyed Ehsan; Akhondi-Asl, Alireza; Rahmani, Roohollah; Faghih-Roohi, Shahrooz; Taimouri, Vahid; Sabouri, Ahmad; Soltanian-Zadeh, Hamid

2010-05-01

There are many medical image processing software tools available for research and diagnosis purposes. However, most of these tools are available only as local applications. This limits the accessibility of the software to a specific machine, and thus the data and processing power of that application are not available to other workstations. Further, there are operating system and processing power limitations which prevent such applications from running on every type of workstation. By developing web-based tools, it is possible for users to access the medical image processing functionalities wherever the internet is available. In this paper, we introduce a pure web-based, interactive, extendable, 2D and 3D medical image processing and visualization application that requires no client installation. Our software uses a four-layered design consisting of an algorithm layer, web-user-interface layer, server communication layer, and wrapper layer. To compete with extendibility of the current local medical image processing software, each layer is highly independent of other layers. A wide range of medical image preprocessing, registration, and segmentation methods are implemented using open source libraries. Desktop-like user interaction is provided by using AJAX technology in the web-user-interface. For the visualization functionality of the software, the VRML standard is used to provide 3D features over the web. Integration of these technologies has allowed implementation of our purely web-based software with high functionality without requiring powerful computational resources in the client side. The user-interface is designed such that the users can select appropriate parameters for practical research and clinical studies. Copyright (c) 2009 Elsevier Ireland Ltd. All rights reserved.

3D treatment planning systems.

PubMed

Saw, Cheng B; Li, Sicong

2018-01-01

Three-dimensional (3D) treatment planning systems have evolved and become crucial components of modern radiation therapy. The systems are computer-aided designing or planning softwares that speed up the treatment planning processes to arrive at the best dose plans for the patients undergoing radiation therapy. Furthermore, the systems provide new technology to solve problems that would not have been considered without the use of computers such as conformal radiation therapy (CRT), intensity-modulated radiation therapy (IMRT), and volumetric modulated arc therapy (VMAT). The 3D treatment planning systems vary amongst the vendors and also the dose delivery systems they are designed to support. As such these systems have different planning tools to generate the treatment plans and convert the treatment plans into executable instructions that can be implemented by the dose delivery systems. The rapid advancements in computer technology and accelerators have facilitated constant upgrades and the introduction of different and unique dose delivery systems than the traditional C-arm type medical linear accelerators. The focus of this special issue is to gather relevant 3D treatment planning systems for the radiation oncology community to keep abreast of technology advancement by assess the planning tools available as well as those unique "tricks or tips" used to support the different dose delivery systems. Copyright © 2018 American Association of Medical Dosimetrists. Published by Elsevier Inc. All rights reserved.

YieldStar based reticle 3D measurements and its application

NASA Astrophysics Data System (ADS)

Vaenkatesan, Vidya; Finders, Jo; ten Berge, Peter; Plug, Reinder; Sijben, Anko; Schellekens, Twan; Dillen, Harm; Pocobiej, Wojciech; Jorge, Vasco G.; van Dijck, Jurgen

2016-09-01

YieldStar (YS) is an established ASML-built scatterometer that is capable of measuring wafer Critical Dimension (CD), Overlay and Focus. In a recent work, the application range of YS was extended to measure 3D CD patterns on a reticle (pattern CD, height, Side Wall Angle-SWA). The primary motivation for this study came from imaging studies that indicated a need for measuring and controlling reticle 3D topography. CD scanning electron microscope (CD-SEM), Atomic force microscope (AFM), 3D multiple detector SEM (3D-SEM) are the preferred tools for reticle metrology. While these tools serve the industry well, the current research to the impact of reticle 3D involves extensive costs, logistic challenges and increased reticle lead time. YS provides an attractive alternative as it can measure pattern CD, SWA and height in a single measurement and at high throughput. This work demonstrates the capability of YS as a reticle metrology tool.

3D-Printed specimens as a valuable tool in anatomy education: A pilot study.

PubMed

Garas, Monique; Vaccarezza, Mauro; Newland, George; McVay-Doornbusch, Kylie; Hasani, Jamila

2018-06-06

Three-dimensional (3D) printing is a modern technique of creating 3D-printed models that allows reproduction of human structures from MRI and CT scans via fusion of multiple layers of resin materials. To assess feasibility of this innovative resource as anatomy educational tool, we conducted a preliminary study on Curtin University undergraduate students to investigate the use of 3D models for anatomy learning as a main goal, to assess the effectiveness of different specimen types during the sessions and personally preferred anatomy learning tools among students as secondary aim. The study consisted of a pre-test, exposure to test (anatomical test) and post-test survey. During pre-test, all participants (both without prior experience and experienced groups) were given a brief introduction on laboratory safety and study procedure thus participants were exposed to 3D, wet and plastinated specimens of the heart, shoulder and thigh to identify the pinned structures (anatomical test). Then, participants were provided a post-test survey containing five questions. In total, 23 participants completed the anatomical test and post-test survey. A larger number of participants (85%) achieved right answers for 3D models compared to wet and plastinated materials, 74% of population selected 3D models as the most usable tool for identification of pinned structures and 45% chose 3D models as their preferred method of anatomy learning. This preliminary small-size study affirms the feasibility of 3D-printed models as a valuable asset in anatomy learning and shows their capability to be used adjacent to cadaveric materials and other widely used tools in anatomy education. Copyright © 2018 Elsevier GmbH. All rights reserved.

3-D interactive visualisation tools for Hi spectral line imaging

NASA Astrophysics Data System (ADS)

van der Hulst, J. M.; Punzo, D.; Roerdink, J. B. T. M.

2017-06-01

Upcoming HI surveys will deliver such large datasets that automated processing using the full 3-D information to find and characterize HI objects is unavoidable. Full 3-D visualization is an essential tool for enabling qualitative and quantitative inspection and analysis of the 3-D data, which is often complex in nature. Here we present SlicerAstro, an open-source extension of 3DSlicer, a multi-platform open source software package for visualization and medical image processing, which we developed for the inspection and analysis of HI spectral line data. We describe its initial capabilities, including 3-D filtering, 3-D selection and comparative modelling.

3D DOSY-TROSY to determine the translational diffusion coefficient of large protein complexes.

PubMed

Didenko, Tatiana; Boelens, Rolf; Rüdiger, Stefan G D

2011-01-01

The translational diffusion coefficient is a sensitive parameter to probe conformational changes in proteins and protein-protein interactions. Pulsed-field gradient NMR spectroscopy allows one to measure the translational diffusion with high accuracy. Two-dimensional (2D) heteronuclear NMR spectroscopy combined with diffusion-ordered spectroscopy (DOSY) provides improved resolution and therefore selectivity when compared with a conventional 1D readout. Here, we show that a combination of selective isotope labelling, 2D ¹H-¹³C methyl-TROSY (transverse relaxation-optimised spectroscopy) and DOSY allows one to study diffusion properties of large protein complexes. We propose that a 3D DOSY-heteronuclear multiple quantum coherence (HMQC) pulse sequence, that uses the TROSY effect of the HMQC sequence for ¹³C methyl-labelled proteins, is highly suitable for measuring the diffusion coefficient of large proteins. We used the 20 kDa co-chaperone p23 as model system to test this 3D DOSY-TROSY technique under various conditions. We determined the diffusion coefficient of p23 in viscous solutions, mimicking large complexes of up to 200 kDa. We found the experimental data to be in excellent agreement with theoretical predictions. To demonstrate the use for complex formation, we applied this technique to record the formation of a complex of p23 with the molecular chaperone Hsp90, which is around 200 kDa. We anticipate that 3D DOSY-TROSY will be a useful tool to study conformational changes in large protein complexes.

Tracking Cognitive Decline in Amnestic Mild Cognitive Impairment and Early-Stage Alzheimer Dementia: Mini-Mental State Examination versus Neuropsychological Battery.

PubMed

Kim, Joonho; Na, Han Kyu; Byun, Justin; Shin, Jiwon; Kim, Sungsoo; Lee, Byung Hwa; Na, Duk L

2017-01-01

Although the Mini-Mental State Examination (MMSE), Clinical Dementia Rating-Sum of Boxes (CDR-SOB), and neuropsychological batteries are widely used for evaluating cognitive function, it remains elusive which instrument best reflects the longitudinal disease progression in amnestic mild cognitive impairment (aMCI) and probable Alzheimer disease (AD). We investigated whether changes in these three instruments over time correlate with loss of cortical gray matter volume (cGMV). We retrospectively investigated 204 patients (aMCI, n = 114; AD, n = 90) who had undergone MMSE, CDR-SOB, the dementia version of the Seoul Neuropsychological Screening Battery (SNSB-D), and 3-dimensional T1-weighted magnetic resonance images at least twice. We investigated the partial correlation between annual decline in test scores and percent change of cGMV. In aMCI patients, changes in the SNSB-D total score (r = 0.340, p < 0.001) and CDR-SOB (r = 0.222, p = 0.020), but not MMSE, showed a correlation with cGMV loss, with the SNSB-D total score showing the strongest correlation. In AD patients, decline in all three test scores correlated significantly with cGMV loss, with MMSE exhibiting the strongest correlation (r = 0.464, p < 0.001). In aMCI patients, neuropsychological battery, though time-consuming, was the most adequate tool in tracking disease progression. In AD patients, however, MMSE may be the most effective longitudinal monitoring tool when considering cost-effectiveness. © 2017 S. Karger AG, Basel.

Metamesh, Version 1.0

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

Staley, Martin

Metamesh is a general-purpose C++ library for creating "mesh" data structures from smaller parts. That is, rather than providing a traditional "mesh format," as many libraries do, or a GUI for building meshes, Metamesh provides tools by which the mesh structures themselves can be built. Consider that a mesh in up to three dimensions can contain nodes (0d entities), edges (1d), faces (2d), and cells (3d). Edges are typically defined from two nodes. Faces can be defined from nodes or edges; and cells from nodes, edges, or faces. Someone might also wish to allow for general faces or cells, ormore » for only a specific variant - say, triangular faces and tetrahedral cells. Moreover, a mesh can have the same or a lesser dimension than that of its enclosing space. In 3d, say, one could have a full 3d mesh, a 2d "sheet" mesh without cells, a 1d "string" mesh with neither faces nor cells, or even a 1d "point cloud." And, aside from the mesh structure itself, additional data might be wanted: velocities at nodes, say, or fluxes across faces, or an average density in each cell. Metamesh supports all of this, through C++ generics and template metaprogramming techniques. Users fit Metamesh constructs together to define a mesh layout, and Metamesh then automatically provides the newly constructed mesh with functionality. Metamesh also provides facilities for spinning, extruding, visualizing, and performing I/O of whatever meshes a user builds.« less

The application of digital medical 3D printing technology on tumor operation

NASA Astrophysics Data System (ADS)

Chen, Jimin; Jiang, Yijian; Li, Yangsheng

2016-04-01

Digital medical 3D printing technology is a new hi-tech which combines traditional medical and digital design, computer science, bio technology and 3D print technology. At the present time there are four levels application: The printed 3D model is the first and simple application. The surgery makes use of the model to plan the processing before operation. The second is customized operation tools such as implant guide. It helps doctor to operate with special tools rather than the normal medical tools. The third level application of 3D printing in medical area is to print artificial bones or teeth to implant into human body. The big challenge is the fourth level which is to print organs with 3D printing technology. In this paper we introduced an application of 3D printing technology in tumor operation. We use 3D printing to print guide for invasion operation. Puncture needles were guided by printed guide in face tumors operation. It is concluded that this new type guide is dominantly advantageous.

Growth and characterization of different human rhinovirus C types in three-dimensional human airway epithelia reconstituted in vitro

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

Tapparel, Caroline, E-mail: Caroline.Tapparel@hcuge.ch; Sobo, Komla; Constant, Samuel

New molecular diagnostic tools have recently allowed the discovery of human rhinovirus species C (HRV-C) that may be overrepresented in children with lower respiratory tract complications. Unlike HRV-A and HRV-B, HRV-C cannot be propagated in conventional immortalized cell lines and their biological properties have been difficult to study. Recent studies have described the successful amplification of HRV-C15, HRV-C11, and HRV-C41 in sinus mucosal organ cultures and in fully differentiated human airway epithelial cells. Consistent with these studies, we report that a panel of clinical HRV-C specimens including HRV-C2, HRV-C7, HRV-C12, HRV-C15, and HRV-C29 types were all capable of mediating productivemore » infection in reconstituted 3D human primary upper airway epithelial tissues and that the virions enter and exit preferentially through the apical surface. Similar to HRV-A and HRV-B, our data support the acid sensitivity of HRV-C. We observed also that the optimum temperature requirement during HRV-C growth may be type-dependent. - Highlights: • A 3D human upper airway epithelia reconstituted in vitro supports HRV-C growth. • HRV-Cs enter and exit preferentially at the apical side of this ALI culture system. • HRV-Cs are acid sensitive. • Temperature sensitivity may be type-dependent for HRV-Cs.« less

Preparation of a Trp-BODIPY fluorogenic amino acid to label peptides for enhanced live-cell fluorescence imaging.

PubMed

Mendive-Tapia, Lorena; Subiros-Funosas, Ramon; Zhao, Can; Albericio, Fernando; Read, Nick D; Lavilla, Rodolfo; Vendrell, Marc

2017-08-01

Fluorescent peptides are valuable tools for live-cell imaging because of the high specificity of peptide sequences for their biomolecular targets. When preparing fluorescent versions of peptides, labels must be introduced at appropriate positions in the sequences to provide suitable reporters while avoiding any impairment of the molecular recognition properties of the peptides. This protocol describes the preparation of the tryptophan (Trp)-based fluorogenic amino acid Fmoc-Trp(C 2 -BODIPY)-OH and its incorporation into peptides for live-cell fluorescence imaging-an approach that is applicable to most peptide sequences. Fmoc-Trp(C 2 -BODIPY)-OH contains a BODIPY (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) fluorogenic core, which works as an environmentally sensitive fluorophore, showing high fluorescence in lipophilic conditions. It is attached to Trp via a spacer-free C-C linkage, resulting in a labeled amino acid that can mimic the molecular interactions of Trp, enabling wash-free imaging. This protocol covers the chemical synthesis of the fluorogenic amino acid Fmoc-Trp(C 2 -BODIPY)-OH (3-4 d), the preparation of the labeled antimicrobial peptide BODIPY-cPAF26 by solid-phase synthesis (6-7 d) and its spectral and biological characterization as a live-cell imaging probe for different fungal pathogens. As an example, we include a procedure for using BODIPY-cPAF26 for wash-free imaging of fungal pathogens, including real-time visualization of Aspergillus fumigatus (5 d for culturing, 1-2 d for imaging).

Monoclonal and anti-idiotypic anti-EBV/C3d receptor antibodies detect two binding sites, one for EBV and one for C3d on glycoprotein 140, the EBV/C3dR, expressed on human B lymphocytes.

PubMed

Barel, M; Fiandino, A; Delcayre, A X; Lyamani, F; Frade, R

1988-09-01

Glycoprotein (gp) 140, the EBV/C3dR of B lymphocytes, is a membrane site involved in human cell regulation. To analyze the specificities of the binding sites for EBV and for C3d on the gp 140 molecule, two distinct approaches were used. First, anti-EBV/C3dR mAb were prepared against highly purified EBV/C3dR. Nine anti-EBV/C3dR mAb were obtained. Four of these anti-EBV/C3dR mAb inhibited C3d binding but not EBV binding on gp 140, whereas four others exerted an inverse effect. These differences could not be due to differences in isotype, antibody concentration, affinity constant, and number of molecules bound on cell surface, as these parameters were identical for the nine used mAb. Second, polyclonal anti-idiotypic antibodies (Ab2) were prepared against F(ab)'2 fragments of polyclonal anti-EBV/C3dR (Ab1). Ab2 recognized the variable portion of Ab1 as controlled by immunoblotting experiments. Ab2, which did not react with the cell surface, inhibited Ab1 binding on Raji cells. Ab2 mimicked the EBV/C3dR by its properties to bind to particle-bound C3d and EBV, preventing their binding on Raji cell surface. C3d binding specificities contained in Ab2 were isolated by affinity chromatography on C3b/C3bi-Sepharose. These specificities, being the internal image of C3d binding site of EBV/C3dR, reacted with Ab1 and inhibited particle-bound C3d binding on Raji cells but did not react with EBV. Taken together, these data support strongly that gp 140, the EBV/C3dR, carried two distinct binding sites, one for EBV and one for C3d.

Virtual Exploration of the Ring Systems Chemical Universe.

PubMed

Visini, Ricardo; Arús-Pous, Josep; Awale, Mahendra; Reymond, Jean-Louis

2017-11-27

Here, we explore the chemical space of all virtually possible organic molecules focusing on ring systems, which represent the cyclic cores of organic molecules obtained by removing all acyclic bonds and converting all remaining atoms to carbon. This approach circumvents the combinatorial explosion encountered when enumerating the molecules themselves. We report the chemical universe database GDB4c containing 916 130 ring systems up to four saturated or aromatic rings and maximum ring size of 14 atoms and GDB4c3D containing the corresponding 6 555 929 stereoisomers. Almost all (98.6%) of these ring systems are unknown and represent chiral 3D-shaped macrocycles containing small rings and quaternary centers reminiscent of polycyclic natural products. We envision that GDB4c can serve to select new ring systems from which to design analogs of such natural products. The database is available for download at www.gdb.unibe.ch together with interactive visualization and search tools as a resource for molecular design.

a Combined Molecular Dynamics and NMR Spectroscopic Protocol for the Conformational Analysis of Oligosaccharides.

NASA Astrophysics Data System (ADS)

Varma, Vikram

A combined experimental and theoretical protocol for the conformational analysis of oligosaccharides is presented. Three disaccharides, methyl alpha - scD-mannopyranosyl-(1 to 3)-alpha- scD-mannopyranoside, methyl beta- scD-galactopyranosyl-(1 to 4)-beta- scD-glucopyranoside, and propyl beta- scD-2-acetamido -2-deoxy glucopyranosyl-(1 to 3)- alpha- scL-rhamnopyranoside, are used to evaluate a protocol for conformational analysis that makes use of molecular dynamics calculations with the CHARMM force field. Dynamics trajectories computed in vacuo and in water are used to calculate time-averaged NMR parameters such as spin-lattice relaxation times (T_1 ), Nuclear Overhauser Enhancements (NOE), and heteronuclear spin-spin coupling constants (^3J _{rm CH}). The calculated NMR parameters are then compared to experimental values and used to evaluate the computational procedure. The energetically accessible conformations are effectively sampled by the simulations. The method has been extended to the conformational analysis of higher-order oligosaccharides corresponding to the cell-wall polysaccharide of the Streptococcus Group A, and the Shigella flexneri Y O-antigen. The Streptococcus Group A cell-wall polysaccharide is comprised of a backbone of rhamnopyranosyl units connected by alternating alpha- scL-(1 to 3) and alpha- scL -(1 to 2) linkages, to which are attached N-acetyl-beta- scD-glucosamine ( beta- scD-GlcpNAc) residues at the 3 positions of the rhamnose backbone.rm A&rm B^'qquad A^'& rm Bqquad Acr[{-alpha}{-}L{-}Rha {it p}{-}(1to2){-alpha }{-}L{-}Rha{it p} {-}(1to3){-alpha}{ -}L{-}Rha{it p}-(1to2) -alpha-L-Rha{it p}{-}(1 to3){-alpha}{-}L{- }Rha{it p}{-}cr&uparrow(1 to3)&uparrow(1to3)crbeta {-}D{-}&rm Glc{it p }NAcqquadbeta{-}D{-}& rm Glc{it p}NAccr&rm C ^'&rm C] A branched trisaccharide (A^' -(C)B), a tetrasaccharide (A^' -(C)B-A), a pentasaccharide (C^' -B^'-A ^'-(C)B), and two hexasaccharides (C^'-B^ '-A^' -(C)B-A) and (A-(C^')B ^'-A^' -(C)B), have been chosen for study. The Shigella flexneri Y O-antigen is a linear polysaccharide that is composed of rhamnose units linked alpha- scL-(1 to 3) and alpha- scL-(1 to 2), interspersed by N-acetyl-beta - scD-glucosamine (beta- scD -GlcpNAc) to form a periodic repeating unit ABCD. &rm A&rm B&rm C&rm Dcr [{-alpha}{-}L {-}Rha{it p}-(1to2){ -alpha}{-}L{-}Rha{it p}{-}(1to3){-alpha} {-}L{-}Rha{it p}{ -}(1to3){-}beta{-}D {-}Glc{it p}NAc{-}(1 to2){-}]_{it n}A heptasaccharide corresponding to the fragment (ABCDA^'B ^'C^' ) of the Shigella flexneri Y polysaccharide has been investigated. The conformational properties of all of the oligosaccharides have been studied using molecular dynamics simulations. Interproton distances derived from ROESY spectra are used to determine the starting conformations of the oligosaccharides used in the dynamics calculations, and dynamics simulations are computed with proton pairs constrained to the ROESY -derived distances, as well as with the constraints removed. These dynamics trajectories are used to calculate ROESY buildup curves with CROSREL, a program that treats cross relaxation by means of a full matrix relaxation approach. The calculated buildup curves compare favorably with the experimental buildup curves. The study demonstrates that molecular dynamics, in conjunction with NMR spectroscopy, can be a useful tool in the understanding of the conformational behavior of oligosaccharides in solution. The results provide a model for antigen topology that can be used to infer some of the critical features of antibody-antigen interactions.

A study of phase defect measurement on EUV mask by multiple detectors CD-SEM

NASA Astrophysics Data System (ADS)

Yonekura, Isao; Hakii, Hidemitsu; Morisaki, Shinya; Murakawa, Tsutomu; Shida, Soichi; Kuribara, Masayuki; Iwai, Toshimichi; Matsumoto, Jun; Nakamura, Takayuki

2013-06-01

We have studied MVM (Multi Vision Metrology) -SEM® E3630 to measure 3D shape of defects. The four detectors (Detector A, B, C and D) are independently set up in symmetry for the primary electron beam axis. Signal processing of four direction images enables not only 2D (width) measurement but also 3D (height) measurement. At last PMJ, we have investigated the relation between the E3630's signal of programmed defect on MoSi-HT and defect height measured by AFM (Atomic Force Microscope). It was confirmed that height of integral profile by this tool is correlated with AFM. It was tested that E3630 has capability of observing multilayer defect on EUV. We have investigated correlation with AFM of width and depth or height of multilayer defect. As the result of observing programmed defects, it was confirmed that measurement result by E3630 is well correlated with AFM. And the function of 3D view image enables to show nm order defect.

Comparison of biotyping methods as alternative identification tools to molecular typing of pathogenic Cryptococcus species in sub-Saharan Africa

PubMed Central

Nyazika, Tinashe K.; Robertson, Valerie J.; Nherera, Brenda; Mapondera, Prichard T.; Meis, Jacques F.; Hagen, Ferry

2015-01-01

Summary Cryptococcal meningitis is the leading fungal infection and AIDS defining opportunistic illness in patients with late stage HIV infection, particularly in South-East Asia and sub-Saharan Africa. Given the high mortality, clinical differences and the extensive ecological niche of Cryptococcus neoformans and Cryptococcus gattii species complexes, there is need for laboratories in sub-Sahara African countries to adopt new and alternative reliable diagnostic algorithms that rapidly identify and distinguish these species. We biotyped 74 and then amplified fragment length polymorphism (AFLP) genotyped 66 Cryptococcus isolates from a cohort of patients with HIV-associated cryptococcal meningitis. Cryptococcus gattii sensu lato was isolated at a prevalence of 16.7% (n = 11/66) and C. neoformans sensu stricto was responsible for 83.3% (n = 55/66) of the infections. l-Canavanine glycine bromothymol blue, yeast-carbon-base-d-proline-d-tryptophan and creatinine dextrose bromothymol blue thymine were able to distinguish pathogenic C. gattii sensu lato from C. neoformans sensu stricto species when compared with amplified fragment length polymorphism genotyping. This study demonstrates high C. gattii sensu lato prevalence in Zimbabwe. In addition, biotyping methods can be used as alternative diagnostic tools to molecular typing in resource-limited areas for differentiating pathogenic Cryptococcus species. PMID:26661484

[Real time 3D echocardiography

NASA Technical Reports Server (NTRS)

Bauer, F.; Shiota, T.; Thomas, J. D.

2001-01-01

Three-dimensional representation of the heart is an old concern. Usually, 3D reconstruction of the cardiac mass is made by successive acquisition of 2D sections, the spatial localisation and orientation of which require complex guiding systems. More recently, the concept of volumetric acquisition has been introduced. A matricial emitter-receiver probe complex with parallel data processing provides instantaneous of a pyramidal 64 degrees x 64 degrees volume. The image is restituted in real time and is composed of 3 planes (planes B and C) which can be displaced in all spatial directions at any time during acquisition. The flexibility of this system of acquisition allows volume and mass measurement with greater accuracy and reproducibility, limiting inter-observer variability. Free navigation of the planes of investigation allows reconstruction for qualitative and quantitative analysis of valvular heart disease and other pathologies. Although real time 3D echocardiography is ready for clinical usage, some improvements are still necessary to improve its conviviality. Then real time 3D echocardiography could be the essential tool for understanding, diagnosis and management of patients.

Mechanism-Based FE Simulation of Tool Wear in Diamond Drilling of SiCp/Al Composites

PubMed Central

Xiang, Junfeng; Pang, Siqin; Xie, Lijing; Gao, Feinong; Hu, Xin; Yi, Jie; Hu, Fang

2018-01-01

The aim of this work is to analyze the micro mechanisms underlying the wear of macroscale tools during diamond machining of SiCp/Al6063 composites and to develop the mechanism-based diamond wear model in relation to the dominant wear behaviors. During drilling, high volume fraction SiCp/Al6063 composites containing Cu, the dominant wear mechanisms of diamond tool involve thermodynamically activated physicochemical wear due to diamond-graphite transformation catalyzed by Cu in air atmosphere and mechanically driven abrasive wear due to high-frequency scrape of hard SiC reinforcement on tool surface. An analytical diamond wear model, coupling Usui abrasive wear model and Arrhenius extended graphitization wear model was proposed and implemented through a user-defined subroutine for tool wear estimates. Tool wear estimate in diamond drilling of SiCp/Al6063 composites was achieved by incorporating the combined abrasive-chemical tool wear subroutine into the coupled thermomechanical FE model of 3D drilling. The developed drilling FE model for reproducing diamond tool wear was validated for feasibility and reliability by comparing numerically simulated tool wear morphology and experimentally observed results after drilling a hole using brazed polycrystalline diamond (PCD) and chemical vapor deposition (CVD) diamond coated tools. A fairly good agreement of experimental and simulated results in cutting forces, chip and tool wear morphologies demonstrates that the developed 3D drilling FE model, combined with a subroutine for diamond tool wear estimate can provide a more accurate analysis not only in cutting forces and chip shape but also in tool wear behavior during drilling SiCp/Al6063 composites. Once validated and calibrated, the developed diamond tool wear model in conjunction with other machining FE models can be easily extended to the investigation of tool wear evolution with various diamond tool geometries and other machining processes in cutting different workpiece materials. PMID:29414839

Open source software integrated into data services of Japanese planetary explorations

NASA Astrophysics Data System (ADS)

Yamamoto, Y.; Ishihara, Y.; Otake, H.; Imai, K.; Masuda, K.

2015-12-01

Scientific data obtained by Japanese scientific satellites and lunar and planetary explorations are archived in DARTS (Data ARchives and Transmission System). DARTS provides the data with a simple method such as HTTP directory listing for long-term preservation while DARTS tries to provide rich web applications for ease of access with modern web technologies based on open source software. This presentation showcases availability of open source software through our services. KADIAS is a web-based application to search, analyze, and obtain scientific data measured by SELENE(Kaguya), a Japanese lunar orbiter. KADIAS uses OpenLayers to display maps distributed from Web Map Service (WMS). As a WMS server, open source software MapServer is adopted. KAGUYA 3D GIS (KAGUYA 3D Moon NAVI) provides a virtual globe for the SELENE's data. The main purpose of this application is public outreach. NASA World Wind Java SDK is used to develop. C3 (Cross-Cutting Comparisons) is a tool to compare data from various observations and simulations. It uses Highcharts to draw graphs on web browsers. Flow is a tool to simulate a Field-Of-View of an instrument onboard a spacecraft. This tool itself is open source software developed by JAXA/ISAS, and the license is BSD 3-Caluse License. SPICE Toolkit is essential to compile FLOW. SPICE Toolkit is also open source software developed by NASA/JPL, and the website distributes many spacecrafts' data. Nowadays, open source software is an indispensable tool to integrate DARTS services.

Shape: A 3D Modeling Tool for Astrophysics.

PubMed

Steffen, Wolfgang; Koning, Nicholas; Wenger, Stephan; Morisset, Christophe; Magnor, Marcus

2011-04-01

We present a flexible interactive 3D morpho-kinematical modeling application for astrophysics. Compared to other systems, our application reduces the restrictions on the physical assumptions, data type, and amount that is required for a reconstruction of an object's morphology. It is one of the first publicly available tools to apply interactive graphics to astrophysical modeling. The tool allows astrophysicists to provide a priori knowledge about the object by interactively defining 3D structural elements. By direct comparison of model prediction with observational data, model parameters can then be automatically optimized to fit the observation. The tool has already been successfully used in a number of astrophysical research projects.

FPV: fast protein visualization using Java 3D.

PubMed

Can, Tolga; Wang, Yujun; Wang, Yuan-Fang; Su, Jianwen

2003-05-22

Many tools have been developed to visualize protein structures. Tools that have been based on Java 3D((TM)) are compatible among different systems and they can be run remotely through web browsers. However, using Java 3D for visualization has some performance issues with it. The primary concerns about molecular visualization tools based on Java 3D are in their being slow in terms of interaction speed and in their inability to load large molecules. This behavior is especially apparent when the number of atoms to be displayed is huge, or when several proteins are to be displayed simultaneously for comparison. In this paper we present techniques for organizing a Java 3D scene graph to tackle these problems. We have developed a protein visualization system based on Java 3D and these techniques. We demonstrate the effectiveness of the proposed method by comparing the visualization component of our system with two other Java 3D based molecular visualization tools. In particular, for van der Waals display mode, with the efficient organization of the scene graph, we could achieve up to eight times improvement in rendering speed and could load molecules three times as large as the previous systems could. EPV is freely available with source code at the following URL: http://www.cs.ucsb.edu/~tcan/fpv/

Trans3D: a free tool for dynamical visualization of EEG activity transmission in the brain.

PubMed

Blinowski, Grzegorz; Kamiński, Maciej; Wawer, Dariusz

2014-08-01

The problem of functional connectivity in the brain is in the focus of attention nowadays, since it is crucial for understanding information processing in the brain. A large repertoire of measures of connectivity have been devised, some of them being capable of estimating time-varying directed connectivity. Hence, there is a need for a dedicated software tool for visualizing the propagation of electrical activity in the brain. To this aim, the Trans3D application was developed. It is an open access tool based on widely available libraries and supporting both Windows XP/Vista/7(™), Linux and Mac environments. Trans3D can create animations of activity propagation between electrodes/sensors, which can be placed by the user on the scalp/cortex of a 3D model of the head. Various interactive graphic functions for manipulating and visualizing components of the 3D model and input data are available. An application of the Trans3D tool has helped to elucidate the dynamics of the phenomena of information processing in motor and cognitive tasks, which otherwise would have been very difficult to observe. Trans3D is available at: http://www.eeg.pl/. Copyright © 2014 Elsevier Ltd. All rights reserved.

48 CFR 225.7001 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Mooring Chain. (c) “End product” is defined in the clause at 252.225-7012, Preference for Certain Domestic Commodities. (d) Hand or measuring tools means those tools listed in Federal supply classifications 51 and 52...

48 CFR 225.7001 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Mooring Chain. (c) “End product” is defined in the clause at 252.225-7012, Preference for Certain Domestic Commodities. (d) Hand or measuring tools means those tools listed in Federal supply classifications 51 and 52...

48 CFR 225.7001 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Mooring Chain. (c) “End product” is defined in the clause at 252.225-7012, Preference for Certain Domestic Commodities. (d) Hand or measuring tools means those tools listed in Federal supply classifications 51 and 52...

48 CFR 225.7001 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Mooring Chain. (c) “End product” is defined in the clause at 252.225-7012, Preference for Certain Domestic Commodities. (d) Hand or measuring tools means those tools listed in Federal supply classifications 51 and 52...

48 CFR 225.7001 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Mooring Chain. (c) “End product” is defined in the clause at 252.225-7012, Preference for Certain Domestic Commodities. (d) Hand or measuring tools means those tools listed in Federal supply classifications 51 and 52...

iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D

PubMed Central

Liluashvili, Vaja; Kalayci, Selim; Fluder, Eugene; Wilson, Manda; Gabow, Aaron

2017-01-01

Abstract Visualizations of biomolecular networks assist in systems-level data exploration in many cellular processes. Data generated from high-throughput experiments increasingly inform these networks, yet current tools do not adequately scale with concomitant increase in their size and complexity. We present an open source software platform, interactome-CAVE (iCAVE), for visualizing large and complex biomolecular interaction networks in 3D. Users can explore networks (i) in 3D using a desktop, (ii) in stereoscopic 3D using 3D-vision glasses and a desktop, or (iii) in immersive 3D within a CAVE environment. iCAVE introduces 3D extensions of known 2D network layout, clustering, and edge-bundling algorithms, as well as new 3D network layout algorithms. Furthermore, users can simultaneously query several built-in databases within iCAVE for network generation or visualize their own networks (e.g., disease, drug, protein, metabolite). iCAVE has modular structure that allows rapid development by addition of algorithms, datasets, or features without affecting other parts of the code. Overall, iCAVE is the first freely available open source tool that enables 3D (optionally stereoscopic or immersive) visualizations of complex, dense, or multi-layered biomolecular networks. While primarily designed for researchers utilizing biomolecular networks, iCAVE can assist researchers in any field. PMID:28814063

iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D.

PubMed

Liluashvili, Vaja; Kalayci, Selim; Fluder, Eugene; Wilson, Manda; Gabow, Aaron; Gümüs, Zeynep H

2017-08-01

Visualizations of biomolecular networks assist in systems-level data exploration in many cellular processes. Data generated from high-throughput experiments increasingly inform these networks, yet current tools do not adequately scale with concomitant increase in their size and complexity. We present an open source software platform, interactome-CAVE (iCAVE), for visualizing large and complex biomolecular interaction networks in 3D. Users can explore networks (i) in 3D using a desktop, (ii) in stereoscopic 3D using 3D-vision glasses and a desktop, or (iii) in immersive 3D within a CAVE environment. iCAVE introduces 3D extensions of known 2D network layout, clustering, and edge-bundling algorithms, as well as new 3D network layout algorithms. Furthermore, users can simultaneously query several built-in databases within iCAVE for network generation or visualize their own networks (e.g., disease, drug, protein, metabolite). iCAVE has modular structure that allows rapid development by addition of algorithms, datasets, or features without affecting other parts of the code. Overall, iCAVE is the first freely available open source tool that enables 3D (optionally stereoscopic or immersive) visualizations of complex, dense, or multi-layered biomolecular networks. While primarily designed for researchers utilizing biomolecular networks, iCAVE can assist researchers in any field. © The Authors 2017. Published by Oxford University Press.

Conducting polymer scaffolds for electrical control of cellular functions (Conference Presentation)

NASA Astrophysics Data System (ADS)

Inal, Sahika; Wan, Alwin M.; Williams, Tiffany V.; Giannelis, Emmanuel P.; Fischbach-Teschl, Claudia; Gourdon, Delphine; Owens, Róisín. M.; Malliaras, George G.

2016-09-01

Considering the limited physiological relevance of 2D cell culture experiments, significant effort was devoted to the development of materials that could more accurately recreate the in vivo cellular microenvironment, and support 3D cell cultures in vitro. (1) One such class of materials is conducting polymers, which are promising due to their compliant mechanical properties, compatibility with biological systems, mixed electrical and ionic conductivity, and ability to form porous structures. (2) In this work, we report the fabrication of a single component, macroporous scaffold made from poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) via an ice-templating method. (3) PEDOT:PSS scaffolds offer tunable pore size, morphology and shape through facile changes in preparation conditions, and are capable of supporting 3D cell cultures due to their biocompatibility and tissue-like elasticity. Moreover, these materials are functional: they exhibit excellent electrochemical switching behavior and significantly lower impedance compared to films. Their electrochemical activity enables their use in the active channel of a state of the art diagnostic tool in the field of bioelectronics, i.e., the organic electrochemical transistor (OECT). The inclusion of cells within the porous architecture affects the impedance of the electrically-conducting polymer network and, thus, may be used as a method to quantify cell growth. The adhesion and pro-angiogenic secretions of mouse fibroblasts cultured within the scaffolds can be controlled by switching the electrochemical state of the polymer prior to cell-seeding. In summary, these smart materials hold promise not only as extracellular matrix-mimicking structures for cell culture, but also as high-performance bioelectronic tools for diagnostic and signaling applications. References [1] M. Holzwarth, P. X. Ma, Journal of Materials Chemistry, 21, 10243-10251 (2011). [2] L. H. Jimison, J. Rivnay, R. M. Owens, in Organic Electronics, Wiley-VCH Verlag GmbH and Co. KGaA, 27-6 (2013). [3] A. M.-D. Wan, S. Inal, T. Williams et al. Journal of Materials Chemistry B, DOI: 10.1039/C5TB00390C (2015).

Quantitative analyses of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy.

PubMed

Schmid, Volker J; Cremer, Marion; Cremer, Thomas

2017-07-01

Recent advancements of super-resolved fluorescence microscopy have revolutionized microscopic studies of cells, including the exceedingly complex structural organization of cell nuclei in space and time. In this paper we describe and discuss tools for (semi-) automated, quantitative 3D analyses of the spatial nuclear organization. These tools allow the quantitative assessment of highly resolved different chromatin compaction levels in individual cell nuclei, which reflect functionally different regions or sub-compartments of the 3D nuclear landscape, and measurements of absolute distances between sites of different chromatin compaction. In addition, these tools allow 3D mapping of specific DNA/RNA sequences and nuclear proteins relative to the 3D chromatin compaction maps and comparisons of multiple cell nuclei. The tools are available in the free and open source R packages nucim and bioimagetools. We discuss the use of masks for the segmentation of nuclei and the use of DNA stains, such as DAPI, as a proxy for local differences in chromatin compaction. We further discuss the limitations of 3D maps of the nuclear landscape as well as problems of the biological interpretation of such data. Copyright © 2017 Elsevier Inc. All rights reserved.

Cocaine locomotor activation, sensitization and place preference in six inbred strains of mice

PubMed Central

2011-01-01

Background The expanding set of genomics tools available for inbred mouse strains has renewed interest in phenotyping larger sets of strains. The present study aims to explore phenotypic variability among six commonly-used inbred mouse strains to both the rewarding and locomotor stimulating effects of cocaine in a place conditioning task, including several strains or substrains that have not yet been characterized for some or all of these behaviors. Methods C57BL/6J (B6), BALB/cJ (BALB), C3H/HeJ (C3H), DBA/2J (D2), FVB/NJ (FVB) and 129S1/SvImJ (129) mice were tested for conditioned place preference to 20 mg/kg cocaine. Results Place preference was observed in most strains with the exception of D2 and 129. All strains showed a marked increase in locomotor activity in response to cocaine. In BALB mice, however, locomotor activation was context-dependent. Locomotor sensitization to repeated exposure to cocaine was most significant in 129 and D2 mice but was absent in FVB mice. Conclusions Genetic correlations suggest that no significant correlation between conditioned place preference, acute locomotor activation, and locomotor sensitization exists among these strains indicating that separate mechanisms underlie the psychomotor and rewarding effects of cocaine. PMID:21806802

3D bioprinting of neural stem cell-laden thermoresponsive biodegradable polyurethane hydrogel and potential in central nervous system repair.

PubMed

Hsieh, Fu-Yu; Lin, Hsin-Hua; Hsu, Shan-Hui

2015-12-01

The 3D bioprinting technology serves as a powerful tool for building tissue in the field of tissue engineering. Traditional 3D printing methods involve the use of heat, toxic organic solvents, or toxic photoinitiators for fabrication of synthetic scaffolds. In this study, two thermoresponsive water-based biodegradable polyurethane dispersions (PU1 and PU2) were synthesized which may form gel near 37 °C without any crosslinker. The stiffness of the hydrogel could be easily fine-tuned by the solid content of the dispersion. Neural stem cells (NSCs) were embedded into the polyurethane dispersions before gelation. The dispersions containing NSCs were subsequently printed and maintained at 37 °C. The NSCs in 25-30% PU2 hydrogels (∼680-2400 Pa) had excellent proliferation and differentiation but not in 25-30% PU1 hydrogels. Moreover, NSC-laden 25-30% PU2 hydrogels injected into the zebrafish embryo neural injury model could rescue the function of impaired nervous system. However, NSC-laden 25-30% PU1 hydrogels only showed a minor repair effect in the zebrafish model. In addition, the function of adult zebrafish with traumatic brain injury was rescued after implantation of the 3D-printed NSC-laden 25% PU2 constructs. Therefore, the newly developed 3D bioprinting technique involving NSCs embedded in the thermoresponsive biodegradable polyurethane ink offers new possibilities for future applications of 3D bioprinting in neural tissue engineering. Copyright © 2015 Elsevier Ltd. All rights reserved.

The anatomy of E-Learning tools: Does software usability influence learning outcomes?

PubMed

Van Nuland, Sonya E; Rogers, Kem A

2016-07-08

Reductions in laboratory hours have increased the popularity of commercial anatomy e-learning tools. It is critical to understand how the functionality of such tools can influence the mental effort required during the learning process, also known as cognitive load. Using dual-task methodology, two anatomical e-learning tools were examined to determine the effect of their design on cognitive load during two joint learning exercises. A.D.A.M. Interactive Anatomy is a simplistic, two-dimensional tool that presents like a textbook, whereas Netter's 3D Interactive Anatomy has a more complex three-dimensional usability that allows structures to be rotated. It was hypothesized that longer reaction times on an observation task would be associated with the more complex anatomical software (Netter's 3D Interactive Anatomy), indicating a higher cognitive load imposed by the anatomy software, which would result in lower post-test scores. Undergraduate anatomy students from Western University, Canada (n = 70) were assessed using a baseline knowledge test, Stroop observation task response times (a measure of cognitive load), mental rotation test scores, and an anatomy post-test. Results showed that reaction times and post-test outcomes were similar for both tools, whereas mental rotation test scores were positively correlated with post-test values when students used Netter's 3D Interactive Anatomy (P = 0.007), but not when they used A.D.A.M. Interactive Anatomy. This suggests that a simple e-learning tool, such as A.D.A.M. Interactive Anatomy, is as effective as more complicated tools, such as Netter's 3D Interactive Anatomy, and does not academically disadvantage those with poor spatial ability. Anat Sci Educ 9: 378-390. © 2015 American Association of Anatomists. © 2015 American Association of Anatomists.

Developing an After Action Review System for a 3D Interactive Training Simulation Using XML

DTIC Science & Technology

2004-03-01

Implementation. Addison Wesley © 1999 ISBN 0-201-32557-8 [2] H. M. Deitel and P. J. Deitel , Deitel and Associates Inc.(2001). C++ How to Program 3rd...and how can this technique help the trainer and the trainee? They both now have a common useful tool to discern what happened during the simulation...participants who acted incorrectly but rather to spot any wrong decisions or actions, and analyze why they were wrong, what the consequences were, and how

Structural specificity of Rn nuclease I as probed on yeast tRNA(Phe) and tRNA(Asp).

PubMed Central

Przykorska, A; el Adlouni, C; Keith, G; Szarkowski, J W; Dirheimer, G

1992-01-01

A single-strand-specific nuclease from rye germ (Rn nuclease I) was characterized as a tool for secondary and tertiary structure investigation of RNAs. To test the procedure, yeast tRNA(Phe) and tRNA(Asp) for which the tertiary structures are known, as well as the 3'-half of tRNA(Asp) were used as substrates. In tRNA(Phe) the nuclease introduced main primary cuts at positions U33 and A35 of the anticodon loop and G18 and G19 of the D loop. No primary cuts were observed within the double stranded stems. In tRNA(Asp) the main cuts occurred at positions U33, G34, U35, C36 of the anticodon loop and G18 and C20:1 positions in the D loop. No cuts were observed in the T loop in intact tRNA(Asp) but strong primary cleavages occurred at positions psi 55, C56, A57 within that loop in the absence of the tertiary interactions between T and D loops (use of 3'-half tRNA(Asp)). These results show that Rn nuclease I is specific for exposed single-stranded regions. Images PMID:1542562

Neural Network Prediction of New Aircraft Design Coefficients

NASA Technical Reports Server (NTRS)

Norgaard, Magnus; Jorgensen, Charles C.; Ross, James C.

1997-01-01

This paper discusses a neural network tool for more effective aircraft design evaluations during wind tunnel tests. Using a hybrid neural network optimization method, we have produced fast and reliable predictions of aerodynamical coefficients, found optimal flap settings, and flap schedules. For validation, the tool was tested on a 55% scale model of the USAF/NASA Subsonic High Alpha Research Concept aircraft (SHARC). Four different networks were trained to predict coefficients of lift, drag, moment of inertia, and lift drag ratio (C(sub L), C(sub D), C(sub M), and L/D) from angle of attack and flap settings. The latter network was then used to determine an overall optimal flap setting and for finding optimal flap schedules.

Lipid transfer proteins from fruit: cloning, expression and quantification.

PubMed

Zuidmeer, Laurian; van Leeuwen, W Astrid; Budde, Ilona Kleine; Cornelissen, Jessica; Bulder, Ingrid; Rafalska, Ilona; Besolí, Noèlia Telléz; Akkerdaas, Jaap H; Asero, Riccardo; Fernandez Rivas, Montserrat; Rivas, Montserrat Fernandez; Gonzalez Mancebo, Eloina; Mancebo, Eloina Gonzalez; van Ree, Ronald

2005-08-01

Lipid transfer proteins (LTP) are stable, potentially life-threatening allergens in fruits and many other vegetable foods. The aim of this study was to clone and express recombinant apple LTP (Mal d 3), as has previously been done for peach LTP (Pru p 3) and set up quantitative tests for measuring fruit LTPs. cDNA for Mal d 3 and Pru p 3 was cloned, expressed in the yeast Pichia pastoris and the resulting proteins were purified via cation exchange chromatography. The immune reactivity of rMal d 3 was compared to nMal d 3 by RAST (inhibition), immunoblotting and basophil histamine release testing. To obtain monoclonal and monospecific polyclonal antibodies, mice and rabbits were immunized with purified nMal d 3. The deduced amino acid sequence of Mal d 3 was identical to the published sequence, Pru p 3 differed at two positions (S9A and S76H). The rMal d 3 had an IgE-binding potency and biological activity close to its natural counterpart. One sandwich ELISA selectively detecting apple LTP and another cross-reactive with cherry, nectarine and hazelnut LTP were developed. In addition, a competitive RIA was developed with polyclonal rabbit antiserum and labeled nMal d 3. rMal d 3 (as shown before for rPru p 3) may be a useful tool for application in component-resolved diagnosis of food allergy. Assays for the measurement of LTP will increase the traceability of this potentially dangerous allergen. Copyright 2005 S. Karger AG, Basel.

Hybrid Scenario Development Methodology and Tool: An Arctic-Oriented Scenario Example

DTIC Science & Technology

2011-07-01

T E N D S T A T E = S C E N A R I O T R I G G E R P O I N T SECURITY(INC DEFENCE) LEGAL ENVIRONMENTAL...SECURITY(INC DEFENCE) S C E N A R I O D E V E L O P M E N T E N D S T A T E = S C E N A R I O T R I G G E R P O I N T

Three-dimensional evidence network plot system: covariate imbalances and effects in network meta-analysis explored using a new software tool.

PubMed

Batson, Sarah; Score, Robert; Sutton, Alex J

2017-06-01

The aim of the study was to develop the three-dimensional (3D) evidence network plot system-a novel web-based interactive 3D tool to facilitate the visualization and exploration of covariate distributions and imbalances across evidence networks for network meta-analysis (NMA). We developed the 3D evidence network plot system within an AngularJS environment using a third party JavaScript library (Three.js) to create the 3D element of the application. Data used to enable the creation of the 3D element for a particular topic are inputted via a Microsoft Excel template spreadsheet that has been specifically formatted to hold these data. We display and discuss the findings of applying the tool to two NMA examples considering multiple covariates. These two examples have been previously identified as having potentially important covariate effects and allow us to document the various features of the tool while illustrating how it can be used. The 3D evidence network plot system provides an immediate, intuitive, and accessible way to assess the similarity and differences between the values of covariates for individual studies within and between each treatment contrast in an evidence network. In this way, differences between the studies, which may invalidate the usual assumptions of an NMA, can be identified for further scrutiny. Hence, the tool facilitates NMA feasibility/validity assessments and aids in the interpretation of NMA results. The 3D evidence network plot system is the first tool designed specifically to visualize covariate distributions and imbalances across evidence networks in 3D. This will be of primary interest to systematic review and meta-analysis researchers and, more generally, those assessing the validity and robustness of an NMA to inform reimbursement decisions. Copyright © 2017 Elsevier Inc. All rights reserved.

Enzyme and Cancer Cell Selectivity of Nanoparticles: Inhibition of 3D Metastatic Phenotype and Experimental Melanoma by Zinc Oxide.

PubMed

DeLong, Robert K; Mitchell, Jennifer A; Morris, R Tyler; Comer, Jeffrey; Hurst, Miranda N; Ghosh, Kartik; Wanekaya, Adam; Mudge, Miranda; Schaeffer, Ashley; Washington, Laurie L; Risor-Marhanka, Azure; Thomas, Spencer; Marroquin, Shanna; Lekey, Amber; Smith, Joshua J; Garrad, Richard; Aryal, Santosh; Abdelhakiem, Mohamed; Glaspell, Garry P

2017-02-01

Biomedical applications for metal and metal oxide nanoparticles are rapidly increasing. Here their functional impact on two well-characterized model enzymes, Luciferase (Luc) or β-galactosidase (β-Gal) was quantitatively compared. Nickel oxide nanoparticle (NiO-NP) activated β-Gal (>400% control) and boron carbide nanoparticle (B4C-NP) inhibited Luc(<10% control), whereas zinc oxide (ZnO-NP) and cobalt oxide (Co3O4-NP) activated β-Gal to a lesser extent and magnesium oxide (MgO) moderately inhibited both enzymes. Melanoma specific killing was in the order; ZnO > B4C ≥ Cu > MgO > Co3O4 > Fe2O3 > NiO, ZnO-NP inhibiting B16F10 and A375 cells as well as ERK enzyme (>90%) and several other cancer-associated kinases (AKT, CREB, p70S6K). ZnO-NP or nanobelt (NB) serve as photoluminescence (PL) cell labels and inhibit 3-D multi-cellular tumor spheroid (MCTS) growth and were tested in a mouse melanoma model. These results demonstrate nanoparticle and enzyme specific biochemical activity and suggest their utility as new tools to explore the important model metastatic foci 3-D environment and their chemotherapeutic potential.

[Case-control study on methods of limb length control in hip arthroplasty].

PubMed

Zhang, Yang-yang; Zuo, Jian-lin; Gao, Zhong-li

2016-02-01

To introduce a new measuring tool for measuring postoperative limb length exactly, and to provide a convenient and effective method to control limb length after total hip replacement. From January 2013 to September 2014, 102 patients undergoing primary unilateral hip replacement were divided into two groups: experimental group and control group. There were 51 patients in the experimental group, including 25 males and 26 females, ranging in age from 37 to 92 years old, with an average of 60.41 years old. The patients in experimental group were treated with new method to control limb length. Other 51 patients in the control group, including 27 males and 24 females, ranging in age from 35 to 87 years old, with an average of 61.00 years old. The patients in the control group were treated with normal methods such as shuck test or limb touching. All the patients were operated by the same experienced surgeon. In the experimental group,total hip arthroplasties (THA) were performed on 35 patients with avascular necrosis of the femoral head or femoral neck fracture, and 16 patients were treated with hemiarthroplasty (HA). In the control group, 38 patients received THA and 13 patients received HA. On the anterior-posterior X-ray radiograph, several indexes were measured as follows: the distance of bilateral femoral offset (a), the height from tip of great trochanter to the rotation center of the femoral head (b) and the vertical distance between the top of the minor trochanter and the two tear drops line (c). The leg length discrepancy can be assessed with three parameters as follows: d1, the absolute value of the difference between the bilateral a values; d2, the difference between the bilateral b values; d3, the difference between the bilateral c values. The SPSS 21.0 was applied for the statistical analysis. In the experimental and control groups, d1 were 4.49 mm and 7.32 mm (P = 0.013); d2 were 2.37 mm and 4.32 mm (P = 0.033); d3 were 3.32 mm and 6.08 mm (P = 0.031). The values of d1, d2 and d3 in the experimental group were significant smaller than those in the control group. The new measuring tool and method can be used to control the limb length and offset effectively during operation.

Coastal Online Analysis and Synthesis Tool 2.0 (COAST)

NASA Technical Reports Server (NTRS)

Brown, Richard B.; Navard, Andrew R.; Nguyen, Beth T.

2009-01-01

The Coastal Online Assessment and Synthesis Tool (COAST) 3D geobrowser has been developed to integrate disparate coastal datasets from NASA and other sources into a desktop tool that provides new data visualization and analysis capabilities for coastal researchers, managers, and residents. It is built upon the widely used NASA-developed open source World Wind geobrowser from NASA Ames (Patrick Hogan et al.) .Net and C# version is used for development. It is leveraged off of World Wind community shared code samples and COAST 2.0 enhancement direction is based on Coastal science community feedback and needs assessment (GOMA). The main objective is to empower the user to bring more user-meaningful data into multi-layered, multi-temporal spatial context.

Condition Based Maintenance Technology Impacts Study for the Military Land Environment

DTIC Science & Technology

2014-08-01

3a, 2g 3b,3m,3j,3e,3d,3f,3a,3c,3i 3c,3d,3h,3n 3d,3h 3e,3k,3i 3f,3h UNCLASSIFIED DSTO-RR-0404 UNCLASSIFIED 158 3g ,3c 3h,4b 3i,3m,3j,CBM...3e -> 3k 3i Egress of 2: 3n -> 3h 4b Egress of 2: 3k -> 3j 5c Egress of 2: 4d -> 3g 3c Egress of 1: 3a -> 2g Egress of 1: 1b -> 2g Egress...Ingress+Egress of 8: 2d 3b 3g 4d 4f -> 3c -> 3d 3h 3n Ingress+Egress of 7: 1b 2e 3a -> 2g -> 3b 2e 2c 2f Ingress+Egress of 7: 2a 2d 6b 6c -> 2b -> 3a

Identifying areas under potential risk of illegal construction and demolition waste dumping using GIS tools.

PubMed

Seror, Nissim; Portnov, Boris A

2018-05-01

Construction and demolition (C&D) waste, dumped illegally in ravines and open areas, contaminates soil and can cause underground water pollution and forests fires. Yet, effective monitoring of illegal C&D waste dumping and enforcing legislation against the offenders are often a difficult task due to the large size of geographic areas that need to be monitored, and limited human and financial resources available to environmental law enforcement agencies. In this study, we use Geographic Information System (GIS) tools and geo-statistical modelling to identify the areas under potentially elevated risk of illegal C&D waste dumping in the Haifa district of Israel. As our analysis shows, locational factors, significantly associated with the accumulated amount of waste in the existing illegal C&D waste sites, include: distance to the nearest main road, depth of the ravine present at the site (p<0.01), and forest proximity (p<0.05). Using the model incorporating these locational parameters, we mapped the areas under the elevated risk of illegal C&D waste dumping for future monitoring. As we suggest, the proposed approach may be useful for environmental law enforcement authorities, by helping them to focus on specific sites for inspection, save resources, and act against the offenders more efficiently. Copyright © 2018 Elsevier Ltd. All rights reserved.

3D printing of patient-specific anatomy: A tool to improve patient consent and enhance imaging interpretation by trainees.

PubMed

Liew, Yaoren; Beveridge, Erin; Demetriades, Andreas K; Hughes, Mark A

2015-01-01

We report the use of three-dimensional or 3D printed, patient-specific anatomy as a tool to improve informed patient consent and patient understanding in a case of posterior lumbar fixation. Next, we discuss its utility as an educational tool to enhance imaging interpretation by neurosurgery trainees.

A Roadmap for using Agile Development in a Traditional System

NASA Technical Reports Server (NTRS)

Streiffert, Barbara; Starbird, Thomas

2006-01-01

I. Ensemble Development Group: a) Produces activity planning software for in spacecraft; b) Built on Eclipse Rich Client Platform (open source development and runtime software); c) Funded by multiple sources including the Mars Technology Program; d) Incorporated the use of Agile Development. II. Next Generation Uplink Planning System: a) Researches the Activity Planning and Sequencing Subsystem for Mars Science Laboratory (APSS); b) APSS includes Ensemble, Activity Modeling, Constraint Checking, Command Editing and Sequencing tools plus other uplink generation utilities; c) Funded by the Mars Technology Program; d) Integrates all of the tools for APSS.

Automated UAV-based mapping for airborne reconnaissance and video exploitation

NASA Astrophysics Data System (ADS)

Se, Stephen; Firoozfam, Pezhman; Goldstein, Norman; Wu, Linda; Dutkiewicz, Melanie; Pace, Paul; Naud, J. L. Pierre

2009-05-01

Airborne surveillance and reconnaissance are essential for successful military missions. Such capabilities are critical for force protection, situational awareness, mission planning, damage assessment and others. UAVs gather huge amount of video data but it is extremely labour-intensive for operators to analyse hours and hours of received data. At MDA, we have developed a suite of tools towards automated video exploitation including calibration, visualization, change detection and 3D reconstruction. The on-going work is to improve the robustness of these tools and automate the process as much as possible. Our calibration tool extracts and matches tie-points in the video frames incrementally to recover the camera calibration and poses, which are then refined by bundle adjustment. Our visualization tool stabilizes the video, expands its field-of-view and creates a geo-referenced mosaic from the video frames. It is important to identify anomalies in a scene, which may include detecting any improvised explosive devices (IED). However, it is tedious and difficult to compare video clips to look for differences manually. Our change detection tool allows the user to load two video clips taken from two passes at different times and flags any changes between them. 3D models are useful for situational awareness, as it is easier to understand the scene by visualizing it in 3D. Our 3D reconstruction tool creates calibrated photo-realistic 3D models from video clips taken from different viewpoints, using both semi-automated and automated approaches. The resulting 3D models also allow distance measurements and line-of- sight analysis.

U.S. Geological Survey: A synopsis of Three-dimensional Modeling

USGS Publications Warehouse

Jacobsen, Linda J.; Glynn, Pierre D.; Phelps, Geoff A.; Orndorff, Randall C.; Bawden, Gerald W.; Grauch, V.J.S.

2011-01-01

The U.S. Geological Survey (USGS) is a multidisciplinary agency that provides assessments of natural resources (geological, hydrological, biological), the disturbances that affect those resources, and the disturbances that affect the built environment, natural landscapes, and human society. Until now, USGS map products have been generated and distributed primarily as 2-D maps, occasionally providing cross sections or overlays, but rarely allowing the ability to characterize and understand 3-D systems, how they change over time (4-D), and how they interact. And yet, technological advances in monitoring natural resources and the environment, the ever-increasing diversity of information needed for holistic assessments, and the intrinsic 3-D/4-D nature of the information obtained increases our need to generate, verify, analyze, interpret, confirm, store, and distribute its scientific information and products using 3-D/4-D visualization, analysis, modeling tools, and information frameworks. Today, USGS scientists use 3-D/4-D tools to (1) visualize and interpret geological information, (2) verify the data, and (3) verify their interpretations and models. 3-D/4-D visualization can be a powerful quality control tool in the analysis of large, multidimensional data sets. USGS scientists use 3-D/4-D technology for 3-D surface (i.e., 2.5-D) visualization as well as for 3-D volumetric analyses. Examples of geological mapping in 3-D include characterization of the subsurface for resource assessments, such as aquifer characterization in the central United States, and for input into process models, such as seismic hazards in the western United States.

MR thermometry characterization of a hyperthermia ultrasound array designed using the k-space computational method

PubMed Central

Al-Bataineh, Osama M; Collins, Christopher M; Park, Eun-Joo; Lee, Hotaik; Smith, Nadine Barrie

2006-01-01

Background Ultrasound induced hyperthermia is a useful adjuvant to radiation therapy in the treatment of prostate cancer. A uniform thermal dose (43°C for 30 minutes) is required within the targeted cancerous volume for effective therapy. This requires specific ultrasound phased array design and appropriate thermometry method. Inhomogeneous, acoustical, three-dimensional (3D) prostate models and economical computational methods provide necessary tools to predict the appropriate shape of hyperthermia phased arrays for better focusing. This research utilizes the k-space computational method and a 3D human prostate model to design an intracavitary ultrasound probe for hyperthermia treatment of prostate cancer. Evaluation of the probe includes ex vivo and in vivo controlled hyperthermia experiments using the noninvasive magnetic resonance imaging (MRI) thermometry. Methods A 3D acoustical prostate model was created using photographic data from the Visible Human Project®. The k-space computational method was used on this coarse grid and inhomogeneous tissue model to simulate the steady state pressure wavefield of the designed phased array using the linear acoustic wave equation. To ensure the uniformity and spread of the pressure in the length of the array, and the focusing capability in the width of the array, the equally-sized elements of the 4 × 20 elements phased array were 1 × 14 mm. A probe was constructed according to the design in simulation using lead zerconate titanate (PZT-8) ceramic and a Delrin® plastic housing. Noninvasive MRI thermometry and a switching feedback controller were used to accomplish ex vivo and in vivo hyperthermia evaluations of the probe. Results Both exposimetry and k-space simulation results demonstrated acceptable agreement within 9%. With a desired temperature plateau of 43.0°C, ex vivo and in vivo controlled hyperthermia experiments showed that the MRI temperature at the steady state was 42.9 ± 0.38°C and 43.1 ± 0.80°C, respectively, for 20 minutes of heating. Conclusion Unlike conventional computational methods, the k-space method provides a powerful tool to predict pressure wavefield in large scale, 3D, inhomogeneous and coarse grid tissue models. Noninvasive MRI thermometry supports the efficacy of this probe and the feedback controller in an in vivo hyperthermia treatment of canine prostate. PMID:17064421

MR thermometry characterization of a hyperthermia ultrasound array designed using the k-space computational method.

PubMed

Al-Bataineh, Osama M; Collins, Christopher M; Park, Eun-Joo; Lee, Hotaik; Smith, Nadine Barrie

2006-10-25

Ultrasound induced hyperthermia is a useful adjuvant to radiation therapy in the treatment of prostate cancer. A uniform thermal dose (43 degrees C for 30 minutes) is required within the targeted cancerous volume for effective therapy. This requires specific ultrasound phased array design and appropriate thermometry method. Inhomogeneous, acoustical, three-dimensional (3D) prostate models and economical computational methods provide necessary tools to predict the appropriate shape of hyperthermia phased arrays for better focusing. This research utilizes the k-space computational method and a 3D human prostate model to design an intracavitary ultrasound probe for hyperthermia treatment of prostate cancer. Evaluation of the probe includes ex vivo and in vivo controlled hyperthermia experiments using the noninvasive magnetic resonance imaging (MRI) thermometry. A 3D acoustical prostate model was created using photographic data from the Visible Human Project. The k-space computational method was used on this coarse grid and inhomogeneous tissue model to simulate the steady state pressure wavefield of the designed phased array using the linear acoustic wave equation. To ensure the uniformity and spread of the pressure in the length of the array, and the focusing capability in the width of the array, the equally-sized elements of the 4 x 20 elements phased array were 1 x 14 mm. A probe was constructed according to the design in simulation using lead zerconate titanate (PZT-8) ceramic and a Delrin plastic housing. Noninvasive MRI thermometry and a switching feedback controller were used to accomplish ex vivo and in vivo hyperthermia evaluations of the probe. Both exposimetry and k-space simulation results demonstrated acceptable agreement within 9%. With a desired temperature plateau of 43.0 degrees C, ex vivo and in vivo controlled hyperthermia experiments showed that the MRI temperature at the steady state was 42.9 +/- 0.38 degrees C and 43.1 +/- 0.80 degrees C, respectively, for 20 minutes of heating. Unlike conventional computational methods, the k-space method provides a powerful tool to predict pressure wavefield in large scale, 3D, inhomogeneous and coarse grid tissue models. Noninvasive MRI thermometry supports the efficacy of this probe and the feedback controller in an in vivo hyperthermia treatment of canine prostate.

Digital immunohistochemistry wizard: image analysis-assisted stereology tool to produce reference data set for calibration and quality control.

PubMed

Plancoulaine, Benoît; Laurinaviciene, Aida; Meskauskas, Raimundas; Baltrusaityte, Indra; Besusparis, Justinas; Herlin, Paulette; Laurinavicius, Arvydas

2014-01-01

Digital image analysis (DIA) enables better reproducibility of immunohistochemistry (IHC) studies. Nevertheless, accuracy of the DIA methods needs to be ensured, demanding production of reference data sets. We have reported on methodology to calibrate DIA for Ki67 IHC in breast cancer tissue based on reference data obtained by stereology grid count. To produce the reference data more efficiently, we propose digital IHC wizard generating initial cell marks to be verified by experts. Digital images of proliferation marker Ki67 IHC from 158 patients (one tissue microarray spot per patient) with an invasive ductal carcinoma of the breast were used. Manual data (mD) were obtained by marking Ki67-positive and negative tumour cells, using a stereological method for 2D object enumeration. DIA was used as an initial step in stereology grid count to generate the digital data (dD) marks by Aperio Genie and Nuclear algorithms. The dD were collected into XML files from the DIA markup images and overlaid on the original spots along with the stereology grid. The expert correction of the dD marks resulted in corrected data (cD). The percentages of Ki67 positive tumour cells per spot in the mD, dD, and cD sets were compared by single linear regression analysis. Efficiency of cD production was estimated based on manual editing effort. The percentage of Ki67-positive tumor cells was in very good agreement in the mD, dD, and cD sets: regression of cD from dD (R2=0.92) reflects the impact of the expert editing the dD as well as accuracy of the DIA used; regression of the cD from the mD (R2=0.94) represents the consistency of the DIA-assisted ground truth (cD) with the manual procedure. Nevertheless, the accuracy of detection of individual tumour cells was much lower: in average, 18 and 219 marks per spot were edited due to the Genie and Nuclear algorithm errors, respectively. The DIA-assisted cD production in our experiment saved approximately 2/3 of manual marking. Digital IHC wizard enabled DIA-assisted stereology to produce reference data in a consistent and efficient way. It can provide quality control measure for appraising accuracy of the DIA steps.

Digital immunohistochemistry wizard: image analysis-assisted stereology tool to produce reference data set for calibration and quality control

PubMed Central

2014-01-01

Background Digital image analysis (DIA) enables better reproducibility of immunohistochemistry (IHC) studies. Nevertheless, accuracy of the DIA methods needs to be ensured, demanding production of reference data sets. We have reported on methodology to calibrate DIA for Ki67 IHC in breast cancer tissue based on reference data obtained by stereology grid count. To produce the reference data more efficiently, we propose digital IHC wizard generating initial cell marks to be verified by experts. Methods Digital images of proliferation marker Ki67 IHC from 158 patients (one tissue microarray spot per patient) with an invasive ductal carcinoma of the breast were used. Manual data (mD) were obtained by marking Ki67-positive and negative tumour cells, using a stereological method for 2D object enumeration. DIA was used as an initial step in stereology grid count to generate the digital data (dD) marks by Aperio Genie and Nuclear algorithms. The dD were collected into XML files from the DIA markup images and overlaid on the original spots along with the stereology grid. The expert correction of the dD marks resulted in corrected data (cD). The percentages of Ki67 positive tumour cells per spot in the mD, dD, and cD sets were compared by single linear regression analysis. Efficiency of cD production was estimated based on manual editing effort. Results The percentage of Ki67-positive tumor cells was in very good agreement in the mD, dD, and cD sets: regression of cD from dD (R2=0.92) reflects the impact of the expert editing the dD as well as accuracy of the DIA used; regression of the cD from the mD (R2=0.94) represents the consistency of the DIA-assisted ground truth (cD) with the manual procedure. Nevertheless, the accuracy of detection of individual tumour cells was much lower: in average, 18 and 219 marks per spot were edited due to the Genie and Nuclear algorithm errors, respectively. The DIA-assisted cD production in our experiment saved approximately 2/3 of manual marking. Conclusions Digital IHC wizard enabled DIA-assisted stereology to produce reference data in a consistent and efficient way. It can provide quality control measure for appraising accuracy of the DIA steps. PMID:25565221

A graphic user interface for efficient 3D photo-reconstruction based on free software

NASA Astrophysics Data System (ADS)

Castillo, Carlos; James, Michael; Gómez, Jose A.

2015-04-01

Recently, different studies have stressed the applicability of 3D photo-reconstruction based on Structure from Motion algorithms in a wide range of geoscience applications. For the purpose of image photo-reconstruction, a number of commercial and freely available software packages have been developed (e.g. Agisoft Photoscan, VisualSFM). The workflow involves typically different stages such as image matching, sparse and dense photo-reconstruction, point cloud filtering and georeferencing. For approaches using open and free software, each of these stages usually require different applications. In this communication, we present an easy-to-use graphic user interface (GUI) developed in Matlab® code as a tool for efficient 3D photo-reconstruction making use of powerful existing software: VisualSFM (Wu, 2015) for photo-reconstruction and CloudCompare (Girardeau-Montaut, 2015) for point cloud processing. The GUI performs as a manager of configurations and algorithms, taking advantage of the command line modes of existing software, which allows an intuitive and automated processing workflow for the geoscience user. The GUI includes several additional features: a) a routine for significantly reducing the duration of the image matching operation, normally the most time consuming stage; b) graphical outputs for understanding the overall performance of the algorithm (e.g. camera connectivity, point cloud density); c) a number of useful options typically performed before and after the photo-reconstruction stage (e.g. removal of blurry images, image renaming, vegetation filtering); d) a manager of batch processing for the automated reconstruction of different image datasets. In this study we explore the advantages of this new tool by testing its performance using imagery collected in several soil erosion applications. References Girardeau-Montaut, D. 2015. CloudCompare documentation accessed at http://cloudcompare.org/ Wu, C. 2015. VisualSFM documentation access at http://ccwu.me/vsfm/doc.html#.

Evaluation of sticky traps for adult Aedes mosquitoes in Malaysia: a potential monitoring and surveillance tool for the efficacy of control strategies.

PubMed

Roslan, Muhammad Aidil; Ngui, Romano; Vythilingam, Indra; Sulaiman, Wan Yusoff Wan

2017-12-01

The present study compared the performance of sticky traps in order to identify the most effective and practical trap for capturing Aedes aegypti and Aedes albopictus mosquitoes. Three phases were conducted in the study, with Phase 1 evaluating the five prototypes (Models A, B, C, D, and E) of sticky trap release-and-recapture using two groups of mosquito release numbers (five and 50) that were released in each replicate. Similarly, Phase 2 compared the performance between Model E and the classical ovitrap that had been modified (sticky ovitrap), using five and 50 mosquito release numbers. Further assessment of both traps was carried out in Phase 3, in which both traps were installed in nine sampling grids. Results from Phase 1 showed that Model E was the trap that recaptured higher numbers of mosquitoes when compared to Models A, B, C, and D. Further assessment between Model E and the modified sticky ovitrap (known as Model F) found that Model F outperformed Model E in both Phases 2 and 3. Thus, Model F was selected as the most effective and practical sticky trap, which could serve as an alternative tool for monitoring and controlling dengue vectors in Malaysia. © 2017 The Society for Vector Ecology.

Identification of copy number variations and translocations in cancer cells from Hi-C data.

PubMed

Chakraborty, Abhijit; Ay, Ferhat

2017-10-18

Eukaryotic chromosomes adapt a complex and highly dynamic three-dimensional (3D) structure, which profoundly affects different cellular functions and outcomes including changes in epigenetic landscape and in gene expression. Making the scenario even more complex, cancer cells harbor chromosomal abnormalities (e.g., copy number variations (CNVs) and translocations) altering their genomes both at the sequence level and at the level of 3D organization. High-throughput chromosome conformation capture techniques (e.g., Hi-C), which are originally developed for decoding the 3D structure of the chromatin, provide a great opportunity to simultaneously identify the locations of genomic rearrangements and to investigate the 3D genome organization in cancer cells. Even though Hi-C data has been used for validating known rearrangements, computational methods that can distinguish rearrangement signals from the inherent biases of Hi-C data and from the actual 3D conformation of chromatin, and can precisely detect rearrangement locations de novo have been missing. In this work, we characterize how intra and inter-chromosomal Hi-C contacts are distributed for normal and rearranged chromosomes to devise a new set of algorithms (i) to identify genomic segments that correspond to CNV regions such as amplifications and deletions (HiCnv), (Nurtdinov et al.) to call inter-chromosomal translocations and their boundaries (HiCtrans) from Hi-C experiments, and (iii) to simulate Hi-C data from genomes with desired rearrangements and abnormalities (AveSim) in order to select optimal parameters for and to benchmark the accuracy of our methods. Our results on 10 different cancer cell lines with Hi-C data show that we identify a total number of 105 amplifications and 45 deletions together with 90 translocations, whereas we identify virtually no such events for two karyotypically normal cell lines. Our CNV predictions correlate very well with whole genome sequencing (WGS) data among chromosomes with CNV events for a breast cancer cell line (r=0.89) and capture most of the CNVs we simulate using Avesim. For HiCtrans predictions, we report evidence from the literature for 30 out of 90 translocations for eight of our cancer cell lines. Furthermore, we show that our tools identify and correctly classify relatively understudied rearrangements such as double minutes (DMs) and homogeneously staining regions (HSRs). Considering the inherent limitations of existing techniques for karyotyping (i.e., missing balanced rearrangements and those near repetitive regions), the accurate identification of CNVs and translocations in a cost-effective and high-throughput setting is still a challenge. Our results show that the set of tools we develop effectively utilize moderately sequenced Hi-C libraries (100-300 million reads) to identify known and de novo chromosomal rearrangements/abnormalities in well-established cancer cell lines. With the decrease in required number of cells and the increase in attainable resolution, we believe that our framework will pave the way towards comprehensive mapping of genomic rearrangements in primary cells from cancer patients using Hi-C. CNV calling: https://github.com/ay-lab/HiCnvTranslocation calling: https://github.com/ay-lab/HiCtransHi-C simulation: https://github.com/ay-lab/AveSim. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

TH-CD-BRA-11: Implementation and Evaluation of a New 3D Dosimetry Protocol for Validating MRI Guided Radiation Therapy Treatments

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

Mein, S; Rankine, L; Department of Radiation Oncology, Washington University School of Medicine

Purpose: To develop, evaluate and apply a novel high-resolution 3D remote dosimetry protocol for validation of MRI guided radiation therapy treatments (MRIdian by ViewRay™). We demonstrate the first application of the protocol (including two small but required new correction terms) utilizing radiochromic 3D plastic PRESAGE™ with optical-CT readout. Methods: A detailed study of PRESAGE™ dosimeters (2kg) was conducted to investigate the temporal and spatial stability of radiation induced optical density change (ΔOD) over 8 days. Temporal stability was investigated on 3 dosimeters irradiated with four equally-spaced square 6MV fields delivering doses between 10cGy and 300cGy. Doses were imaged (read-out) bymore » optical-CT at multiple intervals. Spatial stability of ΔOD response was investigated on 3 other dosimeters irradiated uniformly with 15MV extended-SSD fields with doses of 15cGy, 30cGy and 60cGy. Temporal and spatial (radial) changes were investigated using CERR and MATLAB’s Curve Fitting Tool-box. A protocol was developed to extrapolate measured ΔOD readings at t=48hr (the typical shipment time in remote dosimetry) to time t=1hr. Results: All dosimeters were observed to gradually darken with time (<5% per day). Consistent intra-batch sensitivity (0.0930±0.002 ΔOD/cm/Gy) and linearity (R2=0.9996) was observed at t=1hr. A small radial effect (<3%) was observed, attributed to curing thermodynamics during manufacture. The refined remote dosimetry protocol (including polynomial correction terms for temporal and spatial effects, CT and CR) was then applied to independent dosimeters irradiated with MR-IGRT treatments. Excellent line profile agreement and 3D-gamma results for 3%/3mm, 10% threshold were observed, with an average passing rate 96.5%± 3.43%. Conclusion: A novel 3D remote dosimetry protocol is presented capable of validation of advanced radiation treatments (including MR-IGRT). The protocol uses 2kg radiochromic plastic dosimeters read-out by optical-CT within a week of treatment. The protocol requires small corrections for temporal and spatially-dependent behaviors observed between irradiation and readout.« less

Comparison of disease-specific quality of life tools in patients with chronic venous disease.

PubMed

Kuet, Mong-Loon; Lane, Tristan Ra; Anwar, Muzaffar A; Davies, Alun H

2014-12-01

This work was presented as a poster in the American Venous Forum 25th Annual Meeting; 28 February 2013; Phoenix, Arizona, USA. Quality of life (QoL) is an important outcome measure in the treatment for chronic venous disease. The Aberdeen Varicose Vein Questionnaire (AVVQ) and the ChronIc Venous Insufficiency quality of life Questionnaire (CIVIQ-14) are two validated disease-specific QoL questionnaires in current use. The aim of this study is to evaluate the relationship between the AVVQ and the CIVIQ-14 to enable better comparison between studies and to compare these disease-specific QoL tools with generic QoL and clinician-driven tools. Adults attending our institution for management of their varicose veins completed the AVVQ, CIVIQ-14 and EuroQol-5D (EQ-5D). Clinical data, CEAP classification and the Venous Clinical Severity Score (VCSS) were collected. The relationship between the AVVQ and CIVIQ-14 scores was analysed using Spearman's correlation. The AVVQ and CIVIQ-14 scores were also analysed with a generic QoL tool (EQ-5D) and a clinician-driven tool, the VCSS. One hundred patients, mean age 57.5 (44 males; 56 females), participated in the study. The median AVVQ score was 21.9 (range 0-74) and the median CIVIQ-14 score was 30 (range 0-89). A strong correlation was demonstrated between the AVVQ and CIVIQ-14 scores (r = 0.8; p < 0.0001). Strong correlation was maintained for patients with C1-3 disease (r = 0.7; p < 0.0001) and C4-6 disease (r = 0.8; p < 0.0001). The VCSS correlated strongly with the AVVQ and CIVIQ-14 scores (r = 0.7; p < 0.0001 and r = 0.7; p < 0.0001, respectively). Both the AVVQ and CIVIQ-14 scores correlated well with the EQ-5D score (r = -0.5; p < 0.0001 and r = -0.7; p < 0.0001, respectively). This study demonstrates that there is good correlation between two widely used varicose vein specific QoL tools (AVVQ and CIVIQ-14) across the whole spectrum of disease severity. Strong correlation exists between these disease-specific QoL tools and generic and clinician-driven tools. Our findings confirm valid comparisons between studies using either disease-specific QoL tool. © The Author(s) 2013 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Cancer Data and Statistics Tools

MedlinePlus

... Joseph Jacqueline W. Miller Mona Saraiya Judith Lee Smith Sherri L. Stewart Mary C. White Debra Younginer ... MD, MPH Simple Singh, MD, MPH Judith Lee Smith, PhD Sherri L. Stewart, PhD Eric Tai, MD, ...

Manufacture and evaluation of 3-dimensional printed sizing tools for use during intraoperative breast brachytherapy.

PubMed

Walker, Joshua M; Elliott, David A; Kubicky, Charlotte D; Thomas, Charles R; Naik, Arpana M

2016-01-01

Three-dimensional (3D) printing has emerged as a promising modality for the production of medical devices. Here we describe the design, production, and implementation of a series of sizing tools for use in an intraoperative breast brachytherapy program. These devices were produced using a commercially available low-cost 3D printer and software, and their implementation resulted in an immediate decrease in consumable costs without affecting the quality of care or the speed of delivery. This work illustrates the potential of 3D printing to revolutionize the field of medical devices, enabling physicians to rapidly develop and prototype novel tools.

Customised 3D Printing: An Innovative Training Tool for the Next Generation of Orbital Surgeons.

PubMed

Scawn, Richard L; Foster, Alex; Lee, Bradford W; Kikkawa, Don O; Korn, Bobby S

2015-01-01

Additive manufacturing or 3D printing is the process by which three dimensional data fields are translated into real-life physical representations. 3D printers create physical printouts using heated plastics in a layered fashion resulting in a three-dimensional object. We present a technique for creating customised, inexpensive 3D orbit models for use in orbital surgical training using 3D printing technology. These models allow trainee surgeons to perform 'wet-lab' orbital decompressions and simulate upcoming surgeries on orbital models that replicate a patient's bony anatomy. We believe this represents an innovative training tool for the next generation of orbital surgeons.

A Mechanistic Study of Wetting Superhydrophobic Porous 3D Meshes

PubMed Central

Yohe, Stefan T.; Freedman, Jonathan D.; Falde, Eric J.; Colson, Yolonda L.; Grinstaff, Mark W.

2014-01-01

Superhydrophobic, porous, 3D materials composed of poly( ε -caprolactone) (PCL) and the hydrophobic polymer dopant poly(glycerol monostearate-co- ε -caprolactone) (PGC-C18) are fabricated using the electrospinning technique. These 3D materials are distinct from 2D superhydrophobic surfaces, with maintenance of air at the surface as well as within the bulk of the material. These superhydrophobic materials float in water, and when held underwater and pressed, an air bubble is released and will rise to the surface. By changing the PGC-C18 doping concentration in the meshes and/or the fiber size from the micro- to nanoscale, the long-term stability of the entrapped air layer is controlled. The rate of water infiltration into the meshes, and the resulting displacement of the entrapped air, is quantitatively measured using X-ray computed tomography. The properties of the meshes are further probed using surfactants and solvents of different surface tensions. Finally, the application of hydraulic pressure is used to quantify the breakthrough pressure to wet the meshes. The tools for fabrication and analysis of these superhydrophobic materials as well as the ability to control the robustness of the entrapped air layer are highly desirable for a number of existing and emerging applications. PMID:25309305

Formation of Fused-Ring 2′-Deoxycytidine Adducts from 1-Chloro-3-buten-2-one, an in Vitro 1,3-Butadiene Metabolite, under in Vitro Physiological Conditions

PubMed Central

Sun, Liang; Pelah, Avishay; Zhang, Dong-Ping; Zhong, Yu-Fang; An, Jing; Yu, Ying-Xin; Zhang, Xin-Yu; Elfarra, Adnan A.

2013-01-01

1-Chloro-3-buten-2-one (CBO) is a potential metabolite of 1,3-butadiene (BD), a carcinogenic air pollutant. CBO is a bifunctional alkylating agent that readily reacts with glutathione (GSH) to form mono-GSH and di-GSH adducts. Recently, CBO and its precursor 1-chloro-2-hydroxy-3-butene (CHB) were found to be cytotoxic and genotoxic in human liver cells in culture with CBO being approximately 100-fold more potent than CHB. In the present study, CBO was shown to react readily with 2′-deoxycytidine (dC) under in vitro physiological conditions (pH 7.4, 37 °C) to form four dC adducts with the CBO moieties forming fused rings with the N3 and N4 atoms of dC. The four products were structurally characterized as 2-hydroxy-2-hydroxymethyl-7-(2-deoxy-β-D-erythro-pentofuranosyl)-1,2,3,4-tetrahy dro-6-oxo-6H,7H-pyrimido[1,6-a]pyrimidin-5-ium (dC-1 and dC-2, a pair of diastereomers), 4-chloromethyl-4-hydroxy-7-(2-deoxy-β-D-erythro-pentofuranosyl)-1,2,3,4-tetrahydr o-6-oxo-6H,7H-pyrimido[1,6-a]pyrimidin-5-ium (dC-3), and 2-chloromethyl-2-hydroxy-7-(2-deoxy-β-D-erythro-pentofuranosyl)-1,2,3,4-tetrahydr o-6-oxo-6H,7H-pyrimido[1,6-a]pyrimidin-5-ium (dC-4). Interestingly, dC-1 and dC-2 were stable under our experimental conditions (pH 7.4, 37 °C, 6 h) and existed in equilibrium as indicated by HPLC analysis, whereas dC-3 and dC-4 were labile with the half-lives being 3.0 ± 0.36 and 1.7 ± 0.06 h, respectively. Decomposition of dC-4 produced both dC-1 and dC-2, whereas acid hydrolysis of dC-1/dC-2 and dC-4 in 1 M HCl at 100 °C for 30 min yielded the deribosylated adducts dC-1H/dC-2H and dC-4H, respectively. Because fused-ring dC adducts of other chemicals are mutagenic, the characterized CBO-dC adducts could be mutagenic and play a role in the cytotoxicity and genotoxicity of CBO and its precursors, CHB and BD. The CBO-dC adducts may also be used as standards to characterize CBO-DNA adducts and to develop potential biomarkers for CBO formation in vivo. PMID:24020501

TU-C-BRE-11: 3D EPID-Based in Vivo Dosimetry: A Major Step Forward Towards Optimal Quality and Safety in Radiation Oncology Practice

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

Mijnheer, B; Mans, A; Olaciregui-Ruiz, I

Purpose: To develop a 3D in vivo dosimetry method that is able to substitute pre-treatment verification in an efficient way, and to terminate treatment delivery if the online measured 3D dose distribution deviates too much from the predicted dose distribution. Methods: A back-projection algorithm has been further developed and implemented to enable automatic 3D in vivo dose verification of IMRT/VMAT treatments using a-Si EPIDs. New software tools were clinically introduced to allow automated image acquisition, to periodically inspect the record-and-verify database, and to automatically run the EPID dosimetry software. The comparison of the EPID-reconstructed and planned dose distribution is donemore » offline to raise automatically alerts and to schedule actions when deviations are detected. Furthermore, a software package for online dose reconstruction was also developed. The RMS of the difference between the cumulative planned and reconstructed 3D dose distributions was used for triggering a halt of a linac. Results: The implementation of fully automated 3D EPID-based in vivo dosimetry was able to replace pre-treatment verification for more than 90% of the patient treatments. The process has been fully automated and integrated in our clinical workflow where over 3,500 IMRT/VMAT treatments are verified each year. By optimizing the dose reconstruction algorithm and the I/O performance, the delivered 3D dose distribution is verified in less than 200 ms per portal image, which includes the comparison between the reconstructed and planned dose distribution. In this way it was possible to generate a trigger that can stop the irradiation at less than 20 cGy after introducing large delivery errors. Conclusion: The automatic offline solution facilitated the large scale clinical implementation of 3D EPID-based in vivo dose verification of IMRT/VMAT treatments; the online approach has been successfully tested for various severe delivery errors.« less

Advances in X-ray Mapping for Characterization of Microstructures: Silicon Drift Detectors, Microcalorimeters, X-ray Spectrum Imaging, and Data Mining

NASA Astrophysics Data System (ADS)

Newbury, D. E.

2006-05-01

X-ray mapping, performed with the electron probe microanalyzer (EPMA) or scanning electron microscope/energy dispersive x-ray spectrometer (SEM/EDS), is one of the most popular modes of studying chemically heterogeneous microstructures [1]. Despite the maturity of the technique, now in its 50th anniversary year [2], recent remarkable advances in instrumentation and software will provide microanalysts with an even more effective and efficient microstructural characterization tool: (1) Increased x-ray mapping speed: The silicon drift detector (SDD) [3] is a new form of the familiar silicon EDS that uses the same detection physics but with a radically different design that outperforms the classic Si-EDS in nearly every way [4]: (1) the SDD operates requires only Peltier cooling to -20 oC to - 50 oC; (2) for a given detector active area, the SDD has superior resolution; (3) the SDD achieves the same resolution but with a peaking time that is 5 to 8 times faster; and (4) maximum output count rate (OCR) ranges from about 14 kHz at optimum resolution (134 eV at MnKa for a 50 mm2 area) to 500 kHz (217 eV). This OCR performance enables rapid x-ray mapping collection in the x-ray spectrum image (XSI) mode, in which a complete EDS spectrum (2048 10eV-channels) is captured at each pixel (e.g., 10 ms dwell with 1.3 ms overhead per pixel, or 185 seconds for a 128x128 pixel map). XSI collection captures all possible spectral information within the limits imposed by the spectrometer and the primary beam dose. (2) EDS with WDS resolution: The microcalorimeter EDS measures the temperature rise when a single x-ray photon is absorbed in a metal target [5]. Demonstrated resolution is 4.5 eV at Mn Ka for a broad energy range (0.2 - 10 keV) spectrometer and 2 eV (AlKa) for a low photon energy range (0.2 - 2.0 keV) version. The low energy spectrometer is sensitive to peak shape and position changes associated with chemical bonding, opening the possibility of EDS chemical-state mapping. (3) Data mining: In the XSI mode, data is captured at the rate of 100 Mbytes per XSI database or more. Efficient software tools have been developed that enable the analyst to quickly recognize major and minor constituent features in this datacube, and even to detect rare unexpected features that occur at only one pixel in a large map [6]. Advanced image cube data reduction can be achieved with tools based on statistical methods, such as principal component analysis, that quickly establishes correlations between different elements, such as distinct phases [7]. 1. Goldstein, J., Newbury, D., Joy, D., Lyman, C., Echlin, P., Lifshin, E., Sawyer, L., and Michael, J., Scanning Electron Microscopy and X-ray Microanalysis, 3rd edition (Kluwer Academic Plenum Press, New York, 2003). 2. Cosslett, E. and P. Duncumb, Nature, 177 (1956) 1172. 3. Struder, L., Fiorini, C., Gatti, E., Hartmann, R., Holl, P., Krause, N., Lechner, P., Longoni, A., Lutz, G., Kemmer, J., Meidinger, N., Popp, M., Soltau, H., and van Zanthier, C., High resolution non dispersive x-ray spectroscopy with state of the art silicon detectors, Mikrochim. Acta, Suppl, 15 (1998) 11 4. Newbury, D. SCANNING, 27 (2005) 227. 5. Wollman, D., Irwin, K., Hilton, G., Dulcie, L., Newbury, D., and Martinis, J., J. Micros. 188 (1997) 196. 6. Newbury, D. and Bright, D., SCANNING, 27 (2005) 15. 7. Kotula, P. Keenan, M., and Michael J., Micros. Microanal. 9 (2003) 1

gp140, the EBV/C3d receptor (CR2) of human B lymphocytes, is involved in cell-free phosphorylation of p120, a nuclear ribonucleoprotein.

PubMed

Delcayre, A X; Fiandino, A; Barel, M; Frade, R

1987-12-01

gp140, the EB/C3d receptor (EBV/C3dR; CR2), is a membrane site involved in human B cell regulation. Cross-linking of this receptor on the cell surface by its specific ligands led to the enhancement of B cell proliferation in synergy with T cell factors. In vitro activation of human peripheral B lymphocytes by cross-linking membrane immunoglobulins with anti-mu antibody induced EBV/C3dR phosphorylation. These studies were pursued by analyzing cell-free phosphorylation of EBV/C3dR isolated from Raji cell fractions, and immobilized on OKB7, a monoclonal anti-EBV/C3dR antibody. Three EBV/C3dR-related antigens which could be cell-free phosphorylated were detected: gp140, the EBV/C3dR, p130 and p120. gp140, the mature form of EBV/C3dR, was isolated from plasma membrane and from purified nuclei. p130 was identified as an intracellular intermediate of EBV/C3dR glycosylation, localized in low-density microsomes. Phosphoamino acid analysis of EBV/C3dR allowed the detection of phosphotyrosine and phosphoserine residues. These data suggest that EBV/C3dR could carry an autophosphorylation activity and could be associated to serine kinases. Using polyclonal anti-p120 antibody and anti-120 kDa nuclear ribonucleoprotein monoclonal antibody (mAb), p120 was identified as a nuclear ribonucleoprotein antigenically not related to EBV/C3dR. Detection of p120 on EBV/C3dR, immobilized on OKB7, was due to interactions between both antigens, instead of anti-EBV/C3dR mAb cross-reactivity with p120. Cell-free phosphorylation of p120 was under the control of EBV/C3dR. However, it is not yet established whether other nuclear or membrane components were involved in the control of p120 cell-free phosphorylation by EBV/C3dR. From the data presented herein, we propose that phosphorylation of a 120-kDa nuclear ribonucleoprotein by EBV/C3dR-associated kinases could represent a crucial step in in vivo regulation of human B cell activation.

Architecutres, Models, Algorithms, and Software Tools for Configurable Computing

DTIC Science & Technology

2000-03-06

and J.G. Nash. The gated interconnection network for dynamic programming. Plenum, 1988 . [18] Ju wook Jang, Heonchul Park, and Viktor K. Prasanna. A ...Sep. 1997. [2] C. Ebeling, D. C. Cronquist , P. Franklin and C. Fisher, "RaPiD - A configurable computing architecture for compute-intensive...ABSTRACT (Maximum 200 words) The Models, Algorithms, and Architectures for Reconfigurable Computing (MAARC) project developed a sound framework for

Attitude and Self-Efficacy Change: English Language Learning in Virtual Worlds

ERIC Educational Resources Information Center

Zheng, Dongping; Young, Michael F.; Brewer, Robert A.; Wagner, Manuela

2009-01-01

This study explored affective factors in learning English as a foreign language in a 3D game-like virtual world, Quest Atlantis (QA). Through the use of communication tools (e.g., chat, bulletin board, telegrams, and email), 3D avatars, and 2D webpage navigation tools in virtual space, nonnative English speakers (NNES) co-solved online…

Modeling and modification of medical 3D objects. The benefit of using a haptic modeling tool.

PubMed

Kling-Petersen, T; Rydmark, M

2000-01-01

The Computer Laboratory of the medical faculty in Goteborg (Mednet) has since the end of 1998 been one of a limited numbers of participants in the development of a new modeling tool together with SensAble Technologies Inc [http:¿www.sensable.com/]. The software called SensAble FreeForm was officially released at Siggraph September 1999. Briefly, the software mimics the modeling techniques traditionally used by clay artists. An imported model or a user defined block of "clay" can be modified using different tools such as a ball, square block, scrape etc via the use of a SensAble Technologies PHANToM haptic arm. The model will deform in 3D as a result of touching the "clay" with any selected tool and the amount of deformation is linear to the force applied. By getting instantaneous haptic as well as visual feedback, precise and intuitive changes are easily made. While SensAble FreeForm lacks several of the features normally associated with a 3D modeling program (such as text handling, application of surface and bumpmaps, high-end rendering engines, etc) it's strength lies in the ability to rapidly create non-geometric 3D models. For medical use, very few anatomically correct models are created from scratch. However, FreeForm features tools enable advanced modification of reconstructed or 3D scanned models. One of the main problems with 3D laserscanning of medical specimens is that the technique usually leaves holes or gaps in the dataset corresponding to areas in shadows such as orifices, deep grooves etc. By using FreeForms different tools, these defects are easily corrected and gaps are filled out. Similarly, traditional 3D reconstruction (based on serial sections etc) often shows artifacts as a result of the triangulation and/or tessellation processes. These artifacts usually manifest as unnatural ridges or uneven areas ("the accordion effect"). FreeForm contains a smoothing algorithm that enables the user to select an area to be modified and subsequently apply any given amount of smoothing to the object. While the final objects need to be exported for further 3D graphic manipulation, FreeForm addresses one of the most time consuming problems of 3D modeling: modification and creation of non-geometric 3D objects.

Correction tool for Active Shape Model based lumbar muscle segmentation.

PubMed

Valenzuela, Waldo; Ferguson, Stephen J; Ignasiak, Dominika; Diserens, Gaelle; Vermathen, Peter; Boesch, Chris; Reyes, Mauricio

2015-08-01

In the clinical environment, accuracy and speed of the image segmentation process plays a key role in the analysis of pathological regions. Despite advances in anatomic image segmentation, time-effective correction tools are commonly needed to improve segmentation results. Therefore, these tools must provide faster corrections with a low number of interactions, and a user-independent solution. In this work we present a new interactive correction method for correcting the image segmentation. Given an initial segmentation and the original image, our tool provides a 2D/3D environment, that enables 3D shape correction through simple 2D interactions. Our scheme is based on direct manipulation of free form deformation adapted to a 2D environment. This approach enables an intuitive and natural correction of 3D segmentation results. The developed method has been implemented into a software tool and has been evaluated for the task of lumbar muscle segmentation from Magnetic Resonance Images. Experimental results show that full segmentation correction could be performed within an average correction time of 6±4 minutes and an average of 68±37 number of interactions, while maintaining the quality of the final segmentation result within an average Dice coefficient of 0.92±0.03.

Comparison of four rapid diagnostic tests, ELISA, microscopy and PCR for the detection of Giardia lamblia, Cryptosporidium spp. and Entamoeba histolytica in feces.

PubMed

Van den Bossche, Dorien; Cnops, Lieselotte; Verschueren, Jacob; Van Esbroeck, Marjan

2015-03-01

Microscopy is the diagnostic reference standard for the detection of parasites, but it is labor-intensive and requires experience. Rapid diagnostic tests (RDTs) can provide an alternative to microscopy. RDTs from four different manufacturers were compared to enzyme-linked immunosorbent assay (ELISA), microscopy and/or parasite-specific real-time PCR: ImmunoCardSTAT!®CGE (Meridian Bioscience Inc., Cincinnati, Ohio, USA) (A), Crypto/Giardia Duo-Strip (Coris Bioconcepts, Gembloux, Belgium) (B), RIDA®QUICK Cryptosporidium/Giardia/Entamoeba Combi (R-BioPharm, Darmstadt, Germany) (C) and Giardia/Cryptosporidium Quik Chek (Techlab Inc., Blacksburg, Virginia, USA) (D). Thirty frozen samples were analyzed retrospectively. For Giardia lamblia (n=12) and Cryptosporidium (n=12) sensitivities ranged from 58% (B), over 83% (A, C) to 100% (D) and from 92% (B) to 100% (A, C, D), respectively. Specificity for both G. lamblia and Cryptosporidium was 100% for all RDT brands. Sensitivity for Entamoeba histolytica (n=5) was 100%, while specificity reached 80% (A) to 88% (C). In a prospective study, fresh samples were tested. For G. lamblia (n=30), sensitivity ranged from 66% (B), over 79% (A) and 83% (C) to 100% (D) and specificity varied between 94% (D) and 100% (A, B, C). For Cryptosporidium (n=3), sensitivity was 100% for all brands except (B) (67%) and specificities were 95% (A, B), 98% (C) and 100% (D). E. histolytica (n=1) was detected by both (A) and (C), while specificity was 81% and 87% respectively. RDTs can be a valuable tool when microscopic expertise is poor and in remote and outbreak settings where other techniques are often not available and rapid diagnosis is required. Copyright © 2015 Elsevier B.V. All rights reserved.

The mathematical and computer modeling of the worm tool shaping

NASA Astrophysics Data System (ADS)

Panchuk, K. L.; Lyashkov, A. A.; Ayusheev, T. V.

2017-06-01

Traditionally mathematical profiling of the worm tool is carried out on the first T. Olivier method, known in the theory of gear gearings, with receiving an intermediate surface of the making lath. It complicates process of profiling and its realization by means of computer 3D-modeling. The purpose of the work is the improvement of mathematical model of profiling and its realization based on the methods of 3D-modeling. Research problems are: receiving of the mathematical model of profiling which excludes the presence of the making lath in it; realization of the received model by means of frame and superficial modeling; development and approbation of technology of solid-state modeling for the solution of the problem of profiling. As the basic, the kinematic method of research of the mutually envelope surfaces is accepted. Computer research is executed by means of CAD based on the methods of 3D-modeling. We have developed mathematical model of profiling of the worm tool; frame, superficial and solid-state models of shaping of the mutually enveloping surfaces of the detail and the tool are received. The offered mathematical models and the technologies of 3D-modeling of shaping represent tools for theoretical and experimental profiling of the worm tool. The results of researches can be used at design of metal-cutting tools.

Chromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealing.

PubMed

Adhikari, Badri; Trieu, Tuan; Cheng, Jianlin

2016-11-07

Reconstructing three-dimensional structures of chromosomes is useful for visualizing their shapes in a cell and interpreting their function. In this work, we reconstruct chromosomal structures from Hi-C data by translating contact counts in Hi-C data into Euclidean distances between chromosomal regions and then satisfying these distances using a structure reconstruction method rigorously tested in the field of protein structure determination. We first evaluate the robustness of the overall reconstruction algorithm on noisy simulated data at various levels of noise by comparing with some of the state-of-the-art reconstruction methods. Then, using simulated data, we validate that Spearman's rank correlation coefficient between pairwise distances in the reconstructed chromosomal structures and the experimental chromosomal contact counts can be used to find optimum conversion rules for transforming interaction frequencies to wish distances. This strategy is then applied to real Hi-C data at chromosome level for optimal transformation of interaction frequencies to wish distances and for ranking and selecting structures. The chromosomal structures reconstructed from a real-world human Hi-C dataset by our method were validated by the known two-compartment feature of the human chromosome organization. We also show that our method is robust with respect to the change of the granularity of Hi-C data, and consistently produces similar structures at different chromosomal resolutions. Chromosome3D is a robust method of reconstructing chromosome three-dimensional models using distance restraints obtained from Hi-C interaction frequency data. It is available as a web application and as an open source tool at http://sysbio.rnet.missouri.edu/chromosome3d/ .

Decoupled 1D/3D analysis of a hydraulic valve

NASA Astrophysics Data System (ADS)

Mehring, Carsten; Zopeya, Ashok; Latham, Matt; Ihde, Thomas; Massie, Dan

2014-10-01

Analysis approaches during product development of fluid valves and other aircraft fluid delivery components vary greatly depending on the development stage. Traditionally, empirical or simplistic one-dimensional tools are being deployed during preliminary design, whereas detailed analysis such as CFD (Computational Fluid Dynamics) tools are used to refine a selected design during the detailed design stage. In recent years, combined 1D/3D co-simulation has been deployed specifically for system level simulations requiring an increased level of analysis detail for one or more components. The present paper presents a decoupled 1D/3D analysis approach where 3D CFD analysis results are utilized to enhance the fidelity of a dynamic 1D modelin context of an aircraft fuel valve.

Haemoglobin A1c as a screening tool for type 2 diabetes and prediabetes in populations of Swedish and Middle-East ancestry.

PubMed

Hellgren, Margareta; Hjörleifsdottir Steiner, Kristin; Bennet, Louise

2017-08-01

To explore and compare sensitivity and specificity for HbA1c ≥48mmol/mol as a predictor for type 2 diabetes mellitus (T2DM) in two populations with different ethnicity and to examine the predictive value of two levels of HbA1c (≥42mmol/mol, ≥39mmol/mol) for prediabetes in these populations. Four cohorts were examined with an oral glucose tolerance test. (1) The MEDIM Study (n=1991 individuals of Swedish and Iraqi ancestry); (2) The Skaraborg Project (n=1327 individuals of Swedish ancestry); (3) The 4-D study (n=424 individuals of Swedish, Iraqi and Turkish ancestry); (4) The Flemingsberg study (n=212 participants of Turkish ancestry). HbA1c ≥48mmol/mol had a sensitivity for T2DM of 31% and 25% respectively in individuals of Middle-East and Swedish ancestry. The positive and negative predictive value was high in both populations (70.3, 96.4 and 96.2, 97.6 respectively). Using HbA1c ≥42mmol/mol and ≥39mmol/mol as a predictor for prediabetes gave a sensitivity of 17% and 36% in individuals of Middle-East and 15% and 34% in individuals of Swedish ancestry. Even if HbA1c ≥48mmol/mol is a valuable diagnostic tool, it is a blunt and insensitive tool for screening and would exclude most people with T2DM, independent of ancestry and age. HbA1c is an inefficient way to detect individuals with prediabetes. Copyright © 2017 Primary Care Diabetes Europe. Published by Elsevier Ltd. All rights reserved.

Mixed-Linkage Glucan Oligosaccharides Produced by Automated Glycan Assembly Serve as Tools To Determine the Substrate Specificity of Lichenase.

PubMed

Dallabernardina, Pietro; Schuhmacher, Frank; Seeberger, Peter H; Pfrengle, Fabian

2017-03-02

The mixed-linkage (1→3),(1→4)-d-glucan (MLG) specific glycosyl hydrolase lichenase is an important biochemical tool for the structural characterization of MLGs. It holds potential for application in the brewery, animal feed, and biofuel industries. Several defined MLG oligosaccharides obtained by automated glycan assembly are used to analyze the substrate specificities of Bacillus subtilis lichenase. Two glucose building blocks (BBs), equipped with a temporary fluorenylmethyloxycarbonyl chloride (Fmoc) protecting group in the C-3 or C-4 position, served to assemble different oligosaccharides by using an automated oligosaccharide synthesizer. Light-induced cleavage of the glycan products from the solid support followed by global deprotection provided seven MLG oligosaccharides of different length and connectivity. After incubation of the MLG oligosaccharides with lichenase, the digestion products were analyzed by HPLC-MS. These digestion experiments provided insights into the enzyme's active site that is in line with other recent evidence suggesting that the substrate specificity of lichenases has to be reconsidered. These results demonstrate that synthetic MLG oligosaccharides are useful tools to analyze mixed-linkage β-glucanases. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Shadow-driven 4D haptic visualization.

PubMed

Zhang, Hui; Hanson, Andrew

2007-01-01

Just as we can work with two-dimensional floor plans to communicate 3D architectural design, we can exploit reduced-dimension shadows to manipulate the higher-dimensional objects generating the shadows. In particular, by taking advantage of physically reactive 3D shadow-space controllers, we can transform the task of interacting with 4D objects to a new level of physical reality. We begin with a teaching tool that uses 2D knot diagrams to manipulate the geometry of 3D mathematical knots via their projections; our unique 2D haptic interface allows the user to become familiar with sketching, editing, exploration, and manipulation of 3D knots rendered as projected imageson a 2D shadow space. By combining graphics and collision-sensing haptics, we can enhance the 2D shadow-driven editing protocol to successfully leverage 2D pen-and-paper or blackboard skills. Building on the reduced-dimension 2D editing tool for manipulating 3D shapes, we develop the natural analogy to produce a reduced-dimension 3D tool for manipulating 4D shapes. By physically modeling the correct properties of 4D surfaces, their bending forces, and their collisions in the 3D haptic controller interface, we can support full-featured physical exploration of 4D mathematical objects in a manner that is otherwise far beyond the experience accessible to human beings. As far as we are aware, this paper reports the first interactive system with force-feedback that provides "4D haptic visualization" permitting the user to model and interact with 4D cloth-like objects.

C3d enhanced DNA vaccination induced humoral immune response to glycoprotein C of pseudorabies virus

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

Tong Tiezhu; Provincial Key Laboratory of Preventive Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070; Fan Huiying

2006-09-08

Murine C3d were utilized to enhance immunogenicity of pseudorabies virus (PrV) gC DNA vaccination. Three copies of C3d and four copies of CR2-binding domain M28{sub 4} were fused, respectively, to truncated gC gene encoding soluble glycoprotein C (sgC) in pcDNA3.1. BALB/c mice were, respectively, immunized with recombinant plasmids, blank vector, and inactivated vaccine. The antibody ELISA titer for sgC-C3d{sub 3} DNA was 49-fold more than that for sgC DNA, and the neutralizing antibody obtained 8-fold rise. Protection of mice from death after lethal PrV (316 LD{sub 5}) challenge was augmented from 25% to 100%. Furthermore, C3d fusion increased Th2-biased immunemore » response by inducing IL-4 production. The IL-4 level for sgC-C3d{sub 3} DNA immunization approached that for the inactivated vaccine. Compared to C3d, M28 enhanced sgC DNA immunogenicity to a lesser extent. In conclusion, we demonstrated that murine C3d fusion significantly enhanced gC DNA immunity by directing Th1-biased to a balanced and more effective Th1/Th2 response.« less

Propel: Tools and Methods for Practical Source Code Model Checking

NASA Technical Reports Server (NTRS)

Mansouri-Samani, Massoud; Mehlitz, Peter; Markosian, Lawrence; OMalley, Owen; Martin, Dale; Moore, Lantz; Penix, John; Visser, Willem

2003-01-01

The work reported here is an overview and snapshot of a project to develop practical model checking tools for in-the-loop verification of NASA s mission-critical, multithreaded programs in Java and C++. Our strategy is to develop and evaluate both a design concept that enables the application of model checking technology to C++ and Java, and a model checking toolset for C++ and Java. The design concept and the associated model checking toolset is called Propel. It builds upon the Java PathFinder (JPF) tool, an explicit state model checker for Java applications developed by the Automated Software Engineering group at NASA Ames Research Center. The design concept that we are developing is Design for Verification (D4V). This is an adaption of existing best design practices that has the desired side-effect of enhancing verifiability by improving modularity and decreasing accidental complexity. D4V, we believe, enhances the applicability of a variety of V&V approaches; we are developing the concept in the context of model checking. The model checking toolset, Propel, is based on extending JPF to handle C++. Our principal tasks in developing the toolset are to build a translator from C++ to Java, productize JPF, and evaluate the toolset in the context of D4V. Through all these tasks we are testing Propel capabilities on customer applications.

3D Slicer as a tool for interactive brain tumor segmentation.

PubMed

Kikinis, Ron; Pieper, Steve

2011-01-01

User interaction is required for reliable segmentation of brain tumors in clinical practice and in clinical research. By incorporating current research tools, 3D Slicer provides a set of interactive, easy to use tools that can be efficiently used for this purpose. One of the modules of 3D Slicer is an interactive editor tool, which contains a variety of interactive segmentation effects. Use of these effects for fast and reproducible segmentation of a single glioblastoma from magnetic resonance imaging data is demonstrated. The innovation in this work lies not in the algorithm, but in the accessibility of the algorithm because of its integration into a software platform that is practical for research in a clinical setting.

3-D sprag ratcheting tool

NASA Technical Reports Server (NTRS)

Wade, Michael O. (Inventor); Poland, Jr., James W. (Inventor)

2003-01-01

A ratcheting device comprising a driver head assembly which includes at least two 3-D sprag elements positioned within a first groove within the driver head assembly such that at least one of the 3-D sprag elements may lockingly engage the driver head assembly and a mating hub assembly to allow for rotation of the hub assembly in one direction with respect to the driver head assembly. This arrangement allows the ratcheting tool to impart torque in either the clockwise or counterclockwise direction without having to first rotate the ratcheting tool in the direction opposite the direction in which the torque is applied. This arrangement also allows the ratcheting tool to impart torque in either the clockwise or counterclockwise direction while in the neutral position.

Computer-assisted template-guided custom-designed 3D-printed implant placement with custom-designed 3D-printed surgical tooling: an in-vitro proof of a novel concept.

PubMed

Anssari Moin, David; Derksen, Wiebe; Waars, Hugo; Hassan, Bassam; Wismeijer, Daniel

2017-05-01

The aim of this study was to introduce a new concept for computer-assisted template-guided placement of a custom 3D-designed/3D-printed implant with congruent custom 3D-designed/3D-printed surgical tooling and to test the feasibility and accuracy of this method in-vitro. One partially edentulous human mandibular cadaver was scanned with a cone-beam computed tomography (CBCT) system and intra-oral scan system. The 3D data of this cadaver were imported in specialized software and used to analyse the region of a missing tooth. Based on the functional and anatomical parameters, an individual implant with congruent surgical tooling and surgical guided template was designed and 3D-printed. The guided osteotomy was performed, and the custom implant inserted. To evaluate the planned implant position in comparison with the placed implant position, the mandible with implant was scanned again with the CBCT system and software matching was applied to measure the accuracy of the procedure. The angular deflection with the planned implant position was 0.40°. When comparing the 3D positions of the shoulder, there is a deviation of 0.72 mm resulting in an apical deviation of 0.72 mm. With the use of currently available technology, it is very well feasible to create in a virtual simulation a custom implant with congruent custom surgical tooling and to transfer this to a clinical setting. However, further research on multiple levels is needed to explore this novel approach. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

3D Slicer as an Image Computing Platform for the Quantitative Imaging Network

PubMed Central

Fedorov, Andriy; Beichel, Reinhard; Kalpathy-Cramer, Jayashree; Finet, Julien; Fillion-Robin, Jean-Christophe; Pujol, Sonia; Bauer, Christian; Jennings, Dominique; Fennessy, Fiona; Sonka, Milan; Buatti, John; Aylward, Stephen; Miller, James V.; Pieper, Steve; Kikinis, Ron

2012-01-01

Quantitative analysis has tremendous but mostly unrealized potential in healthcare to support objective and accurate interpretation of the clinical imaging. In 2008, the National Cancer Institute began building the Quantitative Imaging Network (QIN) initiative with the goal of advancing quantitative imaging in the context of personalized therapy and evaluation of treatment response. Computerized analysis is an important component contributing to reproducibility and efficiency of the quantitative imaging techniques. The success of quantitative imaging is contingent on robust analysis methods and software tools to bring these methods from bench to bedside. 3D Slicer is a free open source software application for medical image computing. As a clinical research tool, 3D Slicer is similar to a radiology workstation that supports versatile visualizations but also provides advanced functionality such as automated segmentation and registration for a variety of application domains. Unlike a typical radiology workstation, 3D Slicer is free and is not tied to specific hardware. As a programming platform, 3D Slicer facilitates translation and evaluation of the new quantitative methods by allowing the biomedical researcher to focus on the implementation of the algorithm, and providing abstractions for the common tasks of data communication, visualization and user interface development. Compared to other tools that provide aspects of this functionality, 3D Slicer is fully open source and can be readily extended and redistributed. In addition, 3D Slicer is designed to facilitate the development of new functionality in the form of 3D Slicer extensions. In this paper, we present an overview of 3D Slicer as a platform for prototyping, development and evaluation of image analysis tools for clinical research applications. To illustrate the utility of the platform in the scope of QIN, we discuss several use cases of 3D Slicer by the existing QIN teams, and we elaborate on the future directions that can further facilitate development and validation of imaging biomarkers using 3D Slicer. PMID:22770690

Computational Analysis of Material Flow During Friction Stir Welding of AA5059 Aluminum Alloys

DTIC Science & Technology

2011-01-01

tool material (AISI H13 tool steel ) is modeled as an isotropic linear-elastic material. Within the analysis, the effects of some of the FSW key process...threads/m; (b) tool 598 material = AISI H13 tool steel ; (c) workpiece material = 599 AA5059; (d) tool rotation speed = 500 rpm; (e) tool travel 600 speed...the strain-hardening term is augmented to take into account for the effect of dynamic recrystallization) while the FSW tool material (AISI H13

3D Flow Visualization Using Texture Advection

NASA Technical Reports Server (NTRS)

Kao, David; Zhang, Bing; Kim, Kwansik; Pang, Alex; Moran, Pat (Technical Monitor)

2001-01-01

Texture advection is an effective tool for animating and investigating 2D flows. In this paper, we discuss how this technique can be extended to 3D flows. In particular, we examine the use of 3D and 4D textures on 3D synthetic and computational fluid dynamics flow fields.

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.

Setup Instructions for the Applied Anomaly Detection Tool (AADT) Web Server

DTIC Science & Technology

2016-09-01

ARL-TR-7798 ● SEP 2016 US Army Research Laboratory Setup Instructions for the Applied Anomaly Detection Tool (AADT) Web Server...for the Applied Anomaly Detection Tool (AADT) Web Server by Christian D Schlesiger Computational and Information Sciences Directorate, ARL...SUBTITLE Setup Instructions for the Applied Anomaly Detection Tool (AADT) Web Server 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT

Stage Separation CFD Tool Development and Evaluation

NASA Technical Reports Server (NTRS)

Droege, Alan; Gomez, Reynaldo; Wang, Ten-See

2002-01-01

This viewgraph presentation evaluates CFD (Computational Fluid Dynamics) tools for solving stage separation problems. The demonstration and validation of the tools is for a second generation RLV (Reusable Launch Vehicle) stage separation. The flow solvers are: Cart3D; Overflow/Overflow-D; Unic.

Mapping of the bcl-2 oncogene on mouse chromosome 1.

PubMed

Mock, B A; Givol, D; D'Hoostelaere, L A; Huppi, K; Seldin, M F; Gurfinkel, N; Unger, T; Potter, M; Mushinski, J F

1988-01-01

Two bcl-2 alleles have been identified in inbred strains of mice by restriction fragment length polymorphism (RFLP). Analysis of a bcl-2 RFLP in a series of bilineal congenic strains (C.D2), developed as a tool for chromosomal mapping studies, revealed linkage of bcl-2 to the Idh-1/Pep-3 region of murine chromosome 1. The co-segregation of bcl-2 alleles with allelic forms of two other chromosome 1 loci, Ren-1,2 and Spna-1, in a set of back-cross progeny, positions bcl-2 7.8 cM centromeric from Ren-1,2.

Detection of Cutting Tool Wear using Statistical Analysis and Regression Model

NASA Astrophysics Data System (ADS)

Ghani, Jaharah A.; Rizal, Muhammad; Nuawi, Mohd Zaki; Haron, Che Hassan Che; Ramli, Rizauddin

2010-10-01

This study presents a new method for detecting the cutting tool wear based on the measured cutting force signals. A statistical-based method called Integrated Kurtosis-based Algorithm for Z-Filter technique, called I-kaz was used for developing a regression model and 3D graphic presentation of I-kaz 3D coefficient during machining process. The machining tests were carried out using a CNC turning machine Colchester Master Tornado T4 in dry cutting condition. A Kistler 9255B dynamometer was used to measure the cutting force signals, which were transmitted, analyzed, and displayed in the DasyLab software. Various force signals from machining operation were analyzed, and each has its own I-kaz 3D coefficient. This coefficient was examined and its relationship with flank wear lands (VB) was determined. A regression model was developed due to this relationship, and results of the regression model shows that the I-kaz 3D coefficient value decreases as tool wear increases. The result then is used for real time tool wear monitoring.

40 CFR Table 3 to Subpart Vvvv of... - MACT Model Point Value Formulas for Open Molding Operations 1

Code of Federal Regulations, 2010 CFR

2010-07-01

..., tooling resin a. Atomized 0.014 × (Resin HAP%)2.425 b. Atomized, plus vacuum bagging with roll-out 0.01185 × (Resin HAP%)2.425 c. Atomized, plus vacuum bagging without roll-out 0.00945 × (Resin HAP%)2.425 d. Nonatomized 0.014 × (Resin HAP%)2.275 e. Nonatomized, plus vaccum bagging with roll-out 0.0110 × (Resin HAP%)2...

Imaging dopamine D3 receptors in the human brain with positron emission tomography, [11C]PHNO, and a selective D3 receptor antagonist.

PubMed

Searle, Graham; Beaver, John D; Comley, Robert A; Bani, Massimo; Tziortzi, Andri; Slifstein, Mark; Mugnaini, Manolo; Griffante, Cristiana; Wilson, Alan A; Merlo-Pich, Emilio; Houle, Sylvain; Gunn, Roger; Rabiner, Eugenii A; Laruelle, Marc

2010-08-15

Dopamine D(3) receptors are involved in the pathophysiology of several neuropsychiatric conditions. [(11)C]-(+)-PHNO is a radiolabeled D(2) and D(3) agonist, suitable for imaging the agonist binding sites (denoted D(2HIGH) and D(3)) of these receptors with positron emission tomography (PET). PET studies in nonhuman primates documented that, in vivo, [(11)C]-(+)-PHNO displays a relative selectivity for D(3) compared with D(2HIGH) receptor sites and that the [(11)C]-(+)-PHNO signal is enriched in D(3) contribution compared with conventional ligands such as [(11)C] raclopride. To define the D(3) contribution (f(PHNO)(D3)) to [(11)C]-(+)-PHNO binding potential (BP(ND)) in healthy humans, 52 PET scans were obtained in 19 healthy volunteers at baseline and following oral administration of various doses of the selective D(3) receptor antagonist, GSK598809. The impact of GSK598809 on [(11)C]-(+)-PHNO was regionally selective. In dorsal regions of the striatum, GSK598809 did not significantly affect [(11)C]-(+)-PHNO BP(ND) (f(PHNO)(D3) approximately 0%). Conversely, in the substantia nigra, GSK598809 dose-dependently reduced [(11)C]-(+)-PHNO binding to nonspecific level (f(PHNO)(D3) approximately 100%). In ventral striatum (VST), globus pallidus and thalamus (THA), [(11)C]-(+)-PHNO BP(ND) was attributable to a combination of D(2HIGH) and D(3) receptor sites, with f(PHNO)(D3) of 26%, 67% and 46%, respectively. D(3) receptor binding potential (BP(ND)(D3)) was highest in globus pallidus (1.90) and substantial nigra (1.39), with lower levels in VST (.77) and THA (.18) and negligible levels in dorsal striatum. This study elucidated the pharmacologic nature of the [(11)C]-(+)-PHNO signal in healthy subjects and provided the first quantification of D(3) receptor availability with PET in the living human brain. Copyright 2010 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Developing and Evaluating the HRM Technique for Identifying Cytochrome P450 2D6 Polymorphisms.

PubMed

Lu, Hsiu-Chin; Chang, Ya-Sian; Chang, Chun-Chi; Lin, Ching-Hsiung; Chang, Jan-Gowth

2015-05-01

Cytochrome P450 2D6 is one of the important enzymes involved in the metabolism of many widely used drugs. Genetic polymorphisms of CYP2D6 can affect its activity. Therefore, an efficient method for identifying CYP2D6 polymorphisms is clinically important. We developed a high-resolution melting (HRM) analysis to investigate CYP2D6 polymorphisms. Genomic DNA was extracted from peripheral blood samples from 71 healthy individuals. All nine exons of the CYP2D6 gene were sequenced before screening by HRM analysis. This method can detect the most genotypes (*1, *2, *4, *10, *14, *21 *39, and *41) of CYP2D6 in Chinese. All samples were successfully genotyped. The four most common mutant CYP2D6 alleles (*1, *2, *10, and *41) can be genotyped. The single nucleotides polymorphism (SNP) frequencies of 100C > T (rs1065852), 1039C > T (rs1081003), 1661G > C (rs1058164), 2663G > A (rs28371722), 2850C > T (rs16947), 2988G > A (rs28371725), 3181A > G, and 4180G > C (rs1135840) were 58%, 61%, 73%, 1%, 13%, 3%, 1%, 73%, respectively. We identified 100% of all heterozygotes without any errors. The two homozygous genotypes (1661G > C and 4180G > C) can be distinguished by mixing with a known genotype sample to generate an artificial heterozygote for HRM analysis. Therefore, all samples could be identified using our HRM method, and the results of HRM analysis are identical to those obtained by sequencing. Our method achieved 100% sensitivity, specificity, positive prediction value and negative prediction value. HRM analysis is a nongel resolution method that is faster and less expensive than direct sequencing. Our study shows that it is an efficient tool for typing CYP2D6 polymorphisms. © 2014 Wiley Periodicals, Inc.

FT3D: three-dimensional Fourier analysis on small Unix workstations for electron microscopy and tomographic studies.

PubMed

Lanzavecchia, S; Bellon, P L; Tosoni, L

1993-12-01

FT3D is a self-contained package of tools for three-dimensional Fourier analysis, written in the C language for Unix workstations. It can evaluate direct transforms of three-dimensional real functions, inverse transforms, auto- and cross-correlations and spectra. The library has been developed to support three-dimensional reconstructions of biological structures from projections obtained in the electron microscope. This paper discusses some features of the library, which has been implemented in such a way as to profit from the resources of modern workstations. A table of elapsed times for jobs of different dimensions with different RAM buffers is reported for the particular hardware used in the authors' laboratory.

PLOT3D Export Tool for Tecplot

NASA Technical Reports Server (NTRS)

Alter, Stephen

2010-01-01

The PLOT3D export tool for Tecplot solves the problem of modified data being impossible to output for use by another computational science solver. The PLOT3D Exporter add-on enables the use of the most commonly available visualization tools to engineers for output of a standard format. The exportation of PLOT3D data from Tecplot has far reaching effects because it allows for grid and solution manipulation within a graphical user interface (GUI) that is easily customized with macro language-based and user-developed GUIs. The add-on also enables the use of Tecplot as an interpolation tool for solution conversion between different grids of different types. This one add-on enhances the functionality of Tecplot so significantly, it offers the ability to incorporate Tecplot into a general suite of tools for computational science applications as a 3D graphics engine for visualization of all data. Within the PLOT3D Export Add-on are several functions that enhance the operations and effectiveness of the add-on. Unlike Tecplot output functions, the PLOT3D Export Add-on enables the use of the zone selection dialog in Tecplot to choose which zones are to be written by offering three distinct options - output of active, inactive, or all zones (grid blocks). As the user modifies the zones to output with the zone selection dialog, the zones to be written are similarly updated. This enables the use of Tecplot to create multiple configurations of a geometry being analyzed. For example, if an aircraft is loaded with multiple deflections of flaps, by activating and deactivating different zones for a specific flap setting, new specific configurations of that aircraft can be easily generated by only writing out specific zones. Thus, if ten flap settings are loaded into Tecplot, the PLOT3D Export software can output ten different configurations, one for each flap setting.

Histologic evaluation of post-implantation immediate C4d deposition in 13 intestinal grafts: correlation with cell-based crossmatching, cold ischemia time, and preservation injury.

PubMed

López-García, P; Calvo Pulido, J; Colina, F; Ballestin Carcavilla, C; Jiménez-Romero, C; Martinez González, M A; Ibarrola de Andrés, C; López-Alonso, G; Cambra Molero, F; Justo Alonso, I; Moreno-González, E

2014-01-01

C4d deposits are predictive of humoral rejection in kidney and heart transplantation. The aim of this study was to identify C4d deposit patterns in intestinal mucosa of the grafts on biopsy specimens obtained immediately after implantation and to detect if it could be a valuable tool to predict humoral or acute rejection. A second objective was to search for a statistically significant relationship between positive C4d deposition and other collected variables. Thirteen immediately post-transplantation mucosal graft biopsy specimens, formalin fixed, underwent immunohistochemical stain for C4d deposits. Diffuse intense staining of capillary endothelium was considered positive and absent, focal or weak stains as negative. Preservation injury grade and cold ischemia times were registered for each case. Donor-specific preformed antibodies were detected by complement dependent cytotoxicity serologic technique (crossmatching). Another 19 endoscopic follow-up biopsy specimens from days 2 to 6 were also evaluated. Statistical studies were made using the index of correlation ρ (Spearman's test). Diffuse intense C4d deposits were observed in 2 grafts, focal and weak in 5, and completely negative in 6. The mean cold ischemia time was 327 ± 101 minutes. Two cases showed diffuse positive deposits, 1 had a positive crossmatch and the cold ischemia time was 360 minutes whereas the other had not preformed antibodies and its cold ischemia time was 475 minutes. Humoral or acute rejection was not observed in follow-up mucosal biopsy specimens. There was no statistically significant relationship between the C4d deposition, cold ischemia time, crossmatching results, and preservation injury degree. In conclusion, C4d deposition was not a helpful tool for diagnosis of humoral rejection and prediction of acute rejection during the early post-transplantation period. Copyright © 2014 Elsevier Inc. All rights reserved.

TetrUSS Capabilities for S and C Applications

NASA Technical Reports Server (NTRS)

Frink, Neal T.; Parikh, Paresh

2004-01-01

TetrUSS is a suite of loosely coupled computational fluid dynamics software that is packaged into a complete flow analysis system. The system components consist of tools for geometry setup, grid generation, flow solution, visualization, and various utilities tools. Development began in 1990 and it has evolved into a proven and stable system for Euler and Navier-Stokes analysis and design of unconventional configurations. It is 1) well developed and validated, 2) has a broad base of support, and 3) is presently is a workhorse code because of the level of confidence that has been established through wide use. The entire system can now run on linux or mac architectures. In the following slides, I will highlight more of the features of the VGRID and USM3D codes.

MSX-3D: a tool to validate 3D protein models using mass spectrometry.

PubMed

Heymann, Michaël; Paramelle, David; Subra, Gilles; Forest, Eric; Martinez, Jean; Geourjon, Christophe; Deléage, Gilbert

2008-12-01

The technique of chemical cross-linking followed by mass spectrometry has proven to bring valuable information about the protein structure and interactions between proteic subunits. It is an effective and efficient way to experimentally investigate some aspects of a protein structure when NMR and X-ray crystallography data are lacking. We introduce MSX-3D, a tool specifically geared to validate protein models using mass spectrometry. In addition to classical peptides identifications, it allows an interactive 3D visualization of the distance constraints derived from a cross-linking experiment. Freely available at http://proteomics-pbil.ibcp.fr

Reuse Tools to Support ADA Instantiation Construction

DTIC Science & Technology

1990-06-01

assests Figure 3- 1 Research Summary-Gaining a New Perspective Working definitions of several relevant and driving terms are now in order: A software part...Report DTIC E -ECTE 0CT 3 01990 CIN: C02087KV000100 E LI I JUNE 1990 DISTP ’[ -lease; Ar:T7 ,’,7",;, 7 ’ rlue REPORT DOCUMENTATION PAGE 1 0 Puic .paftV bu...AftqW1o. Vh == to toe Otim ItNamn a. Maneralut w4d BudgP No0ton4 DC 208 1 . AGENCY USE ONLY (L"" BWk) 2. REPORT DATE 3. REPORT TYPE AND DATES COVERED

Satellite Vulnerability to Space Debris- An Improved 3D Risk Assessment Methodology

NASA Astrophysics Data System (ADS)

Grassi, Lilith; Destefanis, Roberto; Tiboldo, Francesca; Donath, Therese; Winterboer, Arne; Evand, Leanne; Janovsky, Rolf; Kempf, Scott; Rudolph, Martin; Schafer, Frank; Gelhaus, Johannes

2013-08-01

The work described in the present paper, performed as a part of the PÇ-ROTECT project, presents an enhanced method to evaluate satellite vulnerability to micrometeoroids and orbital debris (MMOD), using the ESABASE2/Debris tool (developed under ESA contract). Starting from the estimation of induced failures on spacecraft (S/C) components and from the computation of lethal impacts (with an energy leading to the loss of the satellite), and considering the equipment redundancies and interactions between components, the debris-induced S/C functional impairment is assessed. The developed methodology, illustrated through its application to a case study satellite, includes the capability to estimate the number of failures on internal components, overcoming the limitations of current tools which do not allow propagating the debris cloud inside the S/C. The ballistic limit of internal equipment behind a sandwich panel structure is evaluated through the implementation of the Schäfer Ryan Lambert (SRL) Ballistic Limit Equation (BLE).

Tracking and Quantifying Developmental Processes in C. elegans Using Open-source Tools.

PubMed

Dutta, Priyanka; Lehmann, Christina; Odedra, Devang; Singh, Deepika; Pohl, Christian

2015-12-16

Quantitatively capturing developmental processes is crucial to derive mechanistic models and key to identify and describe mutant phenotypes. Here protocols are presented for preparing embryos and adult C. elegans animals for short- and long-term time-lapse microscopy and methods for tracking and quantification of developmental processes. The methods presented are all based on C. elegans strains available from the Caenorhabditis Genetics Center and on open-source software that can be easily implemented in any laboratory independently of the microscopy system used. A reconstruction of a 3D cell-shape model using the modelling software IMOD, manual tracking of fluorescently-labeled subcellular structures using the multi-purpose image analysis program Endrov, and an analysis of cortical contractile flow using PIVlab (Time-Resolved Digital Particle Image Velocimetry Tool for MATLAB) are shown. It is discussed how these methods can also be deployed to quantitatively capture other developmental processes in different models, e.g., cell tracking and lineage tracing, tracking of vesicle flow.

Tool wear of (Ti, Al) N-coated polycrystalline cubic boron nitride compact in cutting of hardened steel

NASA Astrophysics Data System (ADS)

Wada, Tadahiro; Hanyu, Hiroyuki

2017-11-01

Polycrystalline cubic boron nitride compact (cBN) is effective tool material for cutting hardened steel. In addition to coated high speed steel and coated cemented carbide that has long been used for cutting materials, more recently, coated cBN has also been used. In this study, to verify the effectiveness of the (Ti,Al)N-coated cBN, which is formed on the substrate of cBN by the physical vapor deposition method, the hardened steel was turned with the (Ti,Al)N-coated cBN tool at a cutting speed of 3.33, 5.00 m/s, a feed rate of 0.3 mm/rev and a depth of cut of 0.1 mm. Furthermore, the uncoated cBN, which was the substrate of the (Ti,Al)N-coated, was also used. The tool wear of the cBN tools was experimentally investigated. The following results were obtained: (1) The contact area between the rake face and the chip of the (Ti,.Al)N-coated cBN tool was smaller than that of the uncoated cBN tool. (2) The tool wear of the (Ti,Al)N-coated cBN was smaller than that of uncoated cBN. (3) The wear progress of the (Ti,Al)N-coated cBN with the main element phase of the TiCN-Al, was slower than that of the (Ti,Al)N-coated cBN with the main element phase of the TiN-Al. (4) In the case of the high cutting speed of 5.00 m/s, the tool wear of the (Ti,Al)N-coated cBN was also smaller than that of uncoated cBN. The above results clarify that the (Ti,Al)N-coated cBN can be used as a tool material in high feed cutting of hardened steel.

Prediction of conserved sites and domains in glycoproteins B, C and D of herpes viruses.

PubMed

Rasheed, Muhammad Asif; Ansari, Abdur Rahman; Ihsan, Awais; Navid, Muhammad Tariq; Ur-Rehman, Shahid; Raza, Sohail

2018-03-01

Glycoprotein B (gB), C (gC) and D (gD) of herpes simplex virus are implicated in virus adsorption and penetration. The gB, gC and gD are glycoproteins for different processes of virus binding and attachment to the host cells. Moreover, their expression is necessary and sufficient to induce cell fusion in the absence of other glycoproteins. Egress of herpes simplex virus (HSV) and other herpes viruses from cells involves extensive modification of cellular membranes and sequential envelopment, de-envelopment and re-envelopment steps. Viral glycoproteins are important in these processes, and frequently two or more glycoproteins can largely suffice in any step. Hence, we target the 3 important glycoproteins (B, C and D) of eight different herpes viruses of different species. These species include human (HSV1 and 2), bovine (BHV1), equine (EHV1 and 4), chicken (ILT1 and MDV2) and pig (PRV1). By applying different bioinformatics tools, we highlighted the conserved sites in these glycoproteins which might be most significant regarding attachment and infection of the viruses. Moreover the conserved domains in these glycoproteins are also highlighted. From this study, we will able to analyze the role of different viral glycoproteins of different species during herpes virus adsorption and penetration. Moreover, this study will help to construct the antivirals that target the glycoproteins of different herpes viruses. Copyright © 2018 Elsevier Ltd. All rights reserved.

TH-AB-202-03: A Novel Tool for Computing Deliverable Doses in Dynamic MLC Tracking Treatments

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

Fast, M; Kamerling, C; Menten, M

2016-06-15

Purpose: In tracked dynamic multi-leaf collimator (MLC) treatments, segments are continuously adapted to the target centroid motion in beams-eye-view. On-the-fly segment adaptation, however, potentially induces dosimetric errors due to the finite MLC leaf width and non-rigid target motion. In this study, we outline a novel tool for computing the 4d dose of lung SBRT plans delivered with MLC tracking. Methods: The following automated workflow was developed: A) centroid tracking, where the initial segments are morphed to each 4dCT phase based on the beams-eye-view GTV shift (followed by a dose calculation on each phase); B) re-optimized tracking, in which all morphedmore » initial plans from (A) are further optimised (“warm-started”) in each 4dCT phase using the initial optimisation parameters but phase-specific volume definitions. Finally, both dose sets are accumulated to the reference phase using deformable image registration. Initial plans were generated according to the RTOG-1021 guideline (54Gy, 3-Fx, equidistant 9-beam IMRT) on the peak-exhale (reference) phase of a phase-binned 4dCT. Treatment planning and delivery simulations were performed in RayStation (research v4.6) using our in-house segment-morphing algorithm, which directly links to RayStation through a native C++ interface. Results: Computing the tracking plans and 4d dose distributions via the in-house interface takes 5 and 8 minutes respectively for centroid and re-optimized tracking. For a sample lung SBRT patient with 14mm peak-to-peak motion in sup-inf direction, mainly perpendicular leaf motion (0-collimator) resulted in small dose changes for PTV-D95 (−13cGy) and GTV-D98 (+18cGy) for the centroid tracking case compared to the initial plan. Modest reductions of OAR doses (e.g. spinal cord D2: −11cGy) were achieved in the idealized tracking case. Conclusion: This study presents an automated “1-click” workflow for computing deliverable MLC tracking doses in RayStation. Adding a non-deliverable re-optimized tracking scenario is expected to help quantify plan robustness for more challenging patients with anatomy deformations. We acknowledge support of the MLC tracking research from Elekta AB. MFF is supported by Cancer Research UK under Programme C33589/A19908. Research at ICR is also supported by Cancer Research UK under Programme C33589/A19727 and NHS funding to the NIHR Biomedical Research Centre at RMH and ICR.« less

WE-D-BRA-04: Online 3D EPID-Based Dose Verification for Optimum Patient Safety

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

Spreeuw, H; Rozendaal, R; Olaciregui-Ruiz, I

2015-06-15

Purpose: To develop an online 3D dose verification tool based on EPID transit dosimetry to ensure optimum patient safety in radiotherapy treatments. Methods: A new software package was developed which processes EPID portal images online using a back-projection algorithm for the 3D dose reconstruction. The package processes portal images faster than the acquisition rate of the portal imager (∼ 2.5 fps). After a portal image is acquired, the software seeks for “hot spots” in the reconstructed 3D dose distribution. A hot spot is in this study defined as a 4 cm{sup 3} cube where the average cumulative reconstructed dose exceedsmore » the average total planned dose by at least 20% and 50 cGy. If a hot spot is detected, an alert is generated resulting in a linac halt. The software has been tested by irradiating an Alderson phantom after introducing various types of serious delivery errors. Results: In our first experiment the Alderson phantom was irradiated with two arcs from a 6 MV VMAT H&N treatment having a large leaf position error or a large monitor unit error. For both arcs and both errors the linac was halted before dose delivery was completed. When no error was introduced, the linac was not halted. The complete processing of a single portal frame, including hot spot detection, takes about 220 ms on a dual hexacore Intel Xeon 25 X5650 CPU at 2.66 GHz. Conclusion: A prototype online 3D dose verification tool using portal imaging has been developed and successfully tested for various kinds of gross delivery errors. The detection of hot spots was proven to be effective for the timely detection of these errors. Current work is focused on hot spot detection criteria for various treatment sites and the introduction of a clinical pilot program with online verification of hypo-fractionated (lung) treatments.« less

Reproducing the internal and external anatomy of fossil bones: Two new automatic digital tools.

PubMed

Profico, Antonio; Schlager, Stefan; Valoriani, Veronica; Buzi, Costantino; Melchionna, Marina; Veneziano, Alessio; Raia, Pasquale; Moggi-Cecchi, Jacopo; Manzi, Giorgio

2018-04-21

We present two new automatic tools, developed under the R environment, to reproduce the internal and external structures of bony elements. The first method, Computer-Aided Laser Scanner Emulator (CA-LSE), provides the reconstruction of the external portions of a 3D mesh by simulating the action of a laser scanner. The second method, Automatic Segmentation Tool for 3D objects (AST-3D), performs the digital reconstruction of anatomical cavities. We present the application of CA-LSE and AST-3D methods to different anatomical remains, highly variable in terms of shape, size and structure: a modern human skull, a malleus bone, and a Neanderthal deciduous tooth. Both methods are developed in the R environment and embedded in the packages "Arothron" and "Morpho," where both the codes and the data are fully available. The application of CA-LSE and AST-3D allows the isolation and manipulation of the internal and external components of the 3D virtual representation of complex bony elements. In particular, we present the output of the four case studies: a complete modern human endocast and the right maxillary sinus, the dental pulp of the Neanderthal tooth and the inner network of blood vessels of the malleus. Both methods demonstrated to be much faster, cheaper, and more accurate than other conventional approaches. The tools we presented are available as add-ons in existing software within the R platform. Because of ease of application, and unrestrained availability of the methods proposed, these tools can be widely used by paleoanthropologists, paleontologists and anatomists. © 2018 Wiley Periodicals, Inc.

Impact of tool wear on cross wedge rolling process stability and on product quality

NASA Astrophysics Data System (ADS)

Gutierrez, Catalina; Langlois, Laurent; Baudouin, Cyrille; Bigot, Régis; Fremeaux, Eric

2017-10-01

Cross wedge rolling (CWR) is a metal forming process used in the automotive industry. One of its applications is in the manufacturing process of connecting rods. CWR transforms a cylindrical billet into a complex axisymmetrical shape with an accurate distribution of material. This preform is forged into shape in a forging die. In order to improve CWR tool lifecycle and product quality it is essential to understand tool wear evolution and the physical phenomena that change on the CWR process due to the resulting geometry of the tool when undergoing tool wear. In order to understand CWR tool wear behavior, numerical simulations are necessary. Nevertheless, if the simulations are performed with the CAD geometry of the tool, results are limited. To solve this difficulty, two numerical simulations with FORGE® were performed using the real geometry of the tools (both up and lower roll) at two different states: (1) before starting lifecycle and (2) end of lifecycle. The tools were 3D measured with ATOS triple scan by GOM® using optical 3D measuring techniques. The result was a high-resolution point cloud of the entire geometry of the tool. Each 3D point cloud was digitalized and converted into a STL format. The geometry of the tools in a STL format was input for the 3D simulations. Both simulations were compared. Defects of products obtained in simulation were compared to main defects of products found industrially. Two main defects are: (a) surface defects on the preform that are not fixed in the die forging operation; and (b) Preform bent (no longer straight), with two possible impacts: on the one hand that the robot cannot grab it to take it to the forging stage; on the other hand, an unfilled section in the forging operation.

Virtual tool mark generation for efficient striation analysis in forensic science

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

Ekstrand, Laura

In 2009, a National Academy of Sciences report called for investigation into the scienti c basis behind tool mark comparisons (National Academy of Sciences, 2009). Answering this call, Chumbley et al. (2010) attempted to prove or disprove the hypothesis that tool marks are unique to a single tool. They developed a statistical algorithm that could, in most cases, discern matching and non-matching tool marks made at di erent angles by sequentially numbered screwdriver tips. Moreover, in the cases where the algorithm misinterpreted a pair of marks, an experienced forensics examiner could discern the correct outcome. While this research served tomore » con rm the basic assumptions behind tool mark analysis, it also suggested that statistical analysis software could help to reduce the examiner's workload. This led to a new tool mark analysis approach, introduced in this thesis, that relies on 3D scans of screwdriver tip and marked plate surfaces at the micrometer scale from an optical microscope. These scans are carefully cleaned to remove noise from the data acquisition process and assigned a coordinate system that mathematically de nes angles and twists in a natural way. The marking process is then simulated by using a 3D graphics software package to impart rotations to the tip and take the projection of the tip's geometry in the direction of tool travel. The edge of this projection, retrieved from the 3D graphics software, becomes a virtual tool mark. Using this method, virtual marks are made at increments of 5 and compared to a scan of the evidence mark. The previously developed statistical package from Chumbley et al. (2010) performs the comparison, comparing the similarity of the geometry of both marks to the similarity that would occur due to random chance. The resulting statistical measure of the likelihood of the match informs the examiner of the angle of the best matching virtual mark, allowing the examiner to focus his/her mark analysis on a smaller range of angles. Preliminary results are quite promising. In a study with both sides of 6 screwdriver tips and 34 corresponding marks, the method distinguished known matches from known non-matches with zero false positive matches and only two matches mistaken for non-matches. For matches, it could predict the correct marking angle within 5-10 . Moreover, on a standard desktop computer, the virtual marking software is capable of cleaning 3D tip and plate scans in minutes and producing a virtual mark and comparing it to a real mark in seconds. These results support several of the professional conclusions of the tool mark analysis com- munity, including the idea that marks produced by the same tool only match if they are made at similar angles. The method also displays the potential to automate part of the comparison process, freeing the examiner to focus on other tasks, which is important in busy, backlogged crime labs. Finally, the method o ers the unique chance to directly link an evidence mark to the tool that produced it while reducing potential damage to the evidence.« less

3D Extended Logging for Geothermal Resources: Field Trials with the Geo-Bilt System

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

Mallan, R; Wilt, M; Kirkendall, B

2002-05-29

Geo-BILT (Geothermal Borehole Induction Logging Tool) is an extended induction logging tool designed for 3D resistivity imaging around a single borehole. The tool was developed for deployment in high temperature geothermal wells under a joint program funded by the California Energy Commission, Electromagnetic Instruments (EMI) and the U.S. Department of Energy. EM1 was responsible for tool design and manufacture, and numerical modeling efforts were being addressed at Lawrence Livermore Laboratory (LLNL) and other contractors. The field deployment was done by EM1 and LLNL. The tool operates at frequencies from 2 to 42 kHz, and its design features a series ofmore » three-component magnetic sensors offset at 2 and 5 meters from a three-component magnetic source. The combined package makes it possible to do 3D resistivity imaging, deep into the formation, from a single well. The manufacture and testing of the tool was completed in spring of 2001, and the initial deployment of Geo-BILT occurred in May 2001 at the Lost Hills oil field in southern California at leases operated by Chevron USA. This site was chosen for the initial field test because of the favorable geological conditions and the availability of a number of wells suitable for tool deployment. The second deployment occurred in April 2002 at the Dixie Valley geothermal field, operated by Caithness Power LLC, in central Nevada. This constituted the first test in a high temperature environment. The Chevron site features a fiberglass-cased observation well in the vicinity of a water injector. The injected water, which is used for pressure maintenance and for secondary sweep of the heavy oil formation, has a much lower resistivity than the oil bearing formation. This, in addition to the non-uniform flow of this water, creates a 3D resistivity structure, which is analogous to conditions produced from flowing fractures adjacent to geothermal boreholes. Therefore, it is an excellent site for testing the 3D capability of the tool in a low risk environment. The Dixie Valley site offered an environment where the tool could locate near-well fractures associated with steam development. The Lost Hills field measurements yielded a data set suitable for 3D imaging. The Geo-BLT data corresponded to existing conventional logging data and showed clear indications, in several depth intervals, of near-well 3D structure. Subsequent 3D inversion of these data produced a model consistent with non-planar water flow in specific layers. The Dixie Valley measurements identified structures associated with dike intrusions and water inflow at particular depths. Preliminary analysis suggests these structures are steeply dipping, which is consistent with the geology.« less

Virtual Solar System Project: Building Understanding through Model Building.

ERIC Educational Resources Information Center

Barab, Sasha A.; Hay, Kenneth E.; Barnett, Michael; Keating, Thomas

2000-01-01

Describes an introductory astronomy course for undergraduate students in which students use three-dimensional (3-D) modeling tools to model the solar system and develop rich understandings of astronomical phenomena. Indicates that 3-D modeling can be used effectively in regular undergraduate university courses as a tool to develop understandings…

Analysis of chronic aortic regurgitation by 2D and 3D echocardiography and cardiac MRI

PubMed Central

Stoebe, Stephan; Metze, Michael; Jurisch, Daniel; Tayal, Bhupendar; Solty, Kilian; Laufs, Ulrich; Pfeiffer, Dietrich; Hagendorff, Andreas

2018-01-01

Purpose The study compares the feasibility of the quantitative volumetric and semi-quantitative approach for quantification of chronic aortic regurgitation (AR) using different imaging modalities. Methods Left ventricular (LV) volumes, regurgitant volumes (RVol) and regurgitant fractions (RF) were assessed retrospectively by 2D, 3D echocardiography and cMRI in 55 chronic AR patients. Semi-quantitative parameters were assessed by 2D echocardiography. Results 22 (40%) patients had mild, 25 (46%) moderate and 8 (14%) severe AR. The quantitative volumetric approach was feasible using 2D, 3D echocardiography and cMRI, whereas the feasibility of semi-quantitative parameters varied considerably. LV volume (LVEDV, LVESV, SVtot) analyses showed good correlations between the different imaging modalities, although significantly increased LV volumes were assessed by cMRI. RVol was significantly different between 2D/3D echocardiography and 2D echocardiography/cMRI but was not significantly different between 3D echocardiography/cMRI. RF was not statistically different between 2D echocardiography/cMRI and 3D echocardiography/cMRI showing poor correlations (r < 0.5) between the different imaging modalities. For AR grading by RF, moderate agreement was observed between 2D/3D echocardiography and 2D echocardiography/cMRI and good agreement was observed between 3D echocardiography/cMRI. Conclusion Semi-quantitative parameters are difficult to determine by 2D echocardiography in clinical routine. The quantitative volumetric RF assessment seems to be feasible and can be discussed as an alternative approach in chronic AR. However, RVol and RF did not correlate well between the different imaging modalities. The best agreement for grading of AR severity by RF was observed between 3D echocardiography and cMRI. LV volumes can be verified by different approaches and different imaging modalities. PMID:29519957

Polymer physics predicts the effects of structural variants on chromatin architecture.

PubMed

Bianco, Simona; Lupiáñez, Darío G; Chiariello, Andrea M; Annunziatella, Carlo; Kraft, Katerina; Schöpflin, Robert; Wittler, Lars; Andrey, Guillaume; Vingron, Martin; Pombo, Ana; Mundlos, Stefan; Nicodemi, Mario

2018-05-01

Structural variants (SVs) can result in changes in gene expression due to abnormal chromatin folding and cause disease. However, the prediction of such effects remains a challenge. Here we present a polymer-physics-based approach (PRISMR) to model 3D chromatin folding and to predict enhancer-promoter contacts. PRISMR predicts higher-order chromatin structure from genome-wide chromosome conformation capture (Hi-C) data. Using the EPHA4 locus as a model, the effects of pathogenic SVs are predicted in silico and compared to Hi-C data generated from mouse limb buds and patient-derived fibroblasts. PRISMR deconvolves the folding complexity of the EPHA4 locus and identifies SV-induced ectopic contacts and alterations of 3D genome organization in homozygous or heterozygous states. We show that SVs can reconfigure topologically associating domains, thereby producing extensive rewiring of regulatory interactions and causing disease by gene misexpression. PRISMR can be used to predict interactions in silico, thereby providing a tool for analyzing the disease-causing potential of SVs.

Spatial Point Pattern Analysis of Neurons Using Ripley's K-Function in 3D

PubMed Central

Jafari-Mamaghani, Mehrdad; Andersson, Mikael; Krieger, Patrik

2010-01-01

The aim of this paper is to apply a non-parametric statistical tool, Ripley's K-function, to analyze the 3-dimensional distribution of pyramidal neurons. Ripley's K-function is a widely used tool in spatial point pattern analysis. There are several approaches in 2D domains in which this function is executed and analyzed. Drawing consistent inferences on the underlying 3D point pattern distributions in various applications is of great importance as the acquisition of 3D biological data now poses lesser of a challenge due to technological progress. As of now, most of the applications of Ripley's K-function in 3D domains do not focus on the phenomenon of edge correction, which is discussed thoroughly in this paper. The main goal is to extend the theoretical and practical utilization of Ripley's K-function and corresponding tests based on bootstrap resampling from 2D to 3D domains. PMID:20577588

Rapid reconstruction of 3D neuronal morphology from light microscopy images with augmented rayburst sampling.

PubMed

Ming, Xing; Li, Anan; Wu, Jingpeng; Yan, Cheng; Ding, Wenxiang; Gong, Hui; Zeng, Shaoqun; Liu, Qian

2013-01-01

Digital reconstruction of three-dimensional (3D) neuronal morphology from light microscopy images provides a powerful technique for analysis of neural circuits. It is time-consuming to manually perform this process. Thus, efficient computer-assisted approaches are preferable. In this paper, we present an innovative method for the tracing and reconstruction of 3D neuronal morphology from light microscopy images. The method uses a prediction and refinement strategy that is based on exploration of local neuron structural features. We extended the rayburst sampling algorithm to a marching fashion, which starts from a single or a few seed points and marches recursively forward along neurite branches to trace and reconstruct the whole tree-like structure. A local radius-related but size-independent hemispherical sampling was used to predict the neurite centerline and detect branches. Iterative rayburst sampling was performed in the orthogonal plane, to refine the centerline location and to estimate the local radius. We implemented the method in a cooperative 3D interactive visualization-assisted system named flNeuronTool. The source code in C++ and the binaries are freely available at http://sourceforge.net/projects/flneurontool/. We validated and evaluated the proposed method using synthetic data and real datasets from the Digital Reconstruction of Axonal and Dendritic Morphology (DIADEM) challenge. Then, flNeuronTool was applied to mouse brain images acquired with the Micro-Optical Sectioning Tomography (MOST) system, to reconstruct single neurons and local neural circuits. The results showed that the system achieves a reasonable balance between fast speed and acceptable accuracy, which is promising for interactive applications in neuronal image analysis.

Cryosurgery Planning Using Bubble Packing in 3D

PubMed Central

Tanaka, Daigo; Shimada, Kenji; Rossi, Michael R.; Rabin, Yoed

2008-01-01

As part of an ongoing project to develop automated tools for cryosurgery planning, the current study focuses on the development of a 3D bubble packing method. A proof-of-concept for the new method is demonstrated on five prostate models, reconstructed from ultrasound images. The new method is a modification of an established method in 2D. Ellipsoidal bubbles are packed in the volume of the prostate in the current study; such bubbles can be viewed as a first-order approximation of a frozen region around a single cryoprobe. When all cryoprobes are inserted to the same depth, optimum planning was found to occur at about 60% of the length of the prostate (measured from its apex), which leads to cooling of approximately 75% of the prostate volume below a specific temperature threshold of −22°C. Bubble packing has the potential to dramatically reduce the run time for automated planning. PMID:17963095

Cryosurgery planning using bubble packing in 3D.

PubMed

Tanaka, Daigo; Shimada, Kenji; Rossi, Michael R; Rabin, Yoed

2008-04-01

As part of an ongoing project to develop automated tools for cryosurgery planning, the current study focuses on the development of a 3D bubble packing method. A proof-of-concept for the new method is demonstrated on five prostate models, reconstructed from ultrasound images. The new method is a modification of an established method in 2D. Ellipsoidal bubbles are packed in the volume of the prostate in the current study; such bubbles can be viewed as a first-order approximation of a frozen region around a single cryoprobe. When all cryoprobes are inserted to the same depth, optimum planning was found to occur at about 60% of the length of the prostate (measured from its apex), which leads to cooling of approximately 75% of the prostate volume below a specific temperature threshold of - 22 degrees C. Bubble packing has the potential to dramatically reduce the run time for automated planning.

Scientific Visualization Made Easy for the Scientist

NASA Astrophysics Data System (ADS)

Westerhoff, M.; Henderson, B.

2002-12-01

amirar is an application program used in creating 3D visualizations and geometric models of 3D image data sets from various application areas, e.g. medicine, biology, biochemistry, chemistry, physics, and engineering. It has demonstrated significant adoption in the market place since becoming commercially available in 2000. The rapid adoption has expanded the features being requested by the user base and broadened the scope of the amira product offering. The amira product offering includes amira Standard, amiraDevT, used to extend the product capabilities by users, amiraMolT, used for molecular visualization, amiraDeconvT, used to improve quality of image data, and amiraVRT, used in immersive VR environments. amira allows the user to construct a visualization tailored to his or her needs without requiring any programming knowledge. It also allows 3D objects to be represented as grids suitable for numerical simulations, notably as triangular surfaces and volumetric tetrahedral grids. The amira application also provides methods to generate such grids from voxel data representing an image volume, and it includes a general-purpose interactive 3D viewer. amiraDev provides an application-programming interface (API) that allows the user to add new components by C++ programming. amira supports many import formats including a 'raw' format allowing immediate access to your native uniform data sets. amira uses the power and speed of the OpenGLr and Open InventorT graphics libraries and 3D graphics accelerators to allow you to access over 145 modules, enabling you to process, probe, analyze and visualize your data. The amiraMolT extension adds powerful tools for molecular visualization to the existing amira platform. amiraMolT contains support for standard molecular file formats, tools for visualization and analysis of static molecules as well as molecular trajectories (time series). amiraDeconv adds tools for the deconvolution of 3D microscopic images. Deconvolution is the process of increasing image quality and resolution by computationally compensating artifacts of the recording process. amiraDeconv supports 3D wide field microscopy as well as 3D confocal microscopy. It offers both non-blind and blind image deconvolution algorithms. Non-blind deconvolution uses an individual measured point spread function, while non-blind algorithms work on the basis of only a few recording parameters (like numerical aperture or zoom factor). amiraVR is a specialized and extended version of the amira visualization system which is dedicated for use in immersive installations, such as large-screen stereoscopic projections, CAVEr or Holobenchr systems. Among others, it supports multi-threaded multi-pipe rendering, head-tracking, advanced 3D interaction concepts, and 3D menus allowing interaction with any amira object in the same way as on the desktop. With its unique set of features, amiraVR represents both a VR (Virtual Reality) ready application for scientific and medical visualization in immersive environments, and a development platform that allows building VR applications.

Broadband Dielectric Spectroscopy of Ruddlesden-Popper Srn+1TinO3n+1 (n = 1,2,3) Thin Films

DTIC Science & Technology

2009-01-29

permittivity, strontium compounds N. D. Orloff, W. Tian, C. J. Fennie , C. H. Lee, D. Gu, J. Mateu, X. X. Xi, K. M. Rabe, D. G. Schlom, I. Takeuchi, J...of Ruddlesden–Popper Srn+1TinO3n+1 (n = 1,2,3) thin films N. D. Orloff, W. Tian, C. J. Fennie , C. H. Lee, D. Gu et al. Citation: Appl. Phys. Lett... Fennie ,4 C. H. Lee,3,5 D. Gu,2 J. Mateu,6 X. X. Xi,5 K. M. Rabe,7 D. G. Schlom,3 I. Takeuchi,1 and J. C. Booth2 1Department of Materials Science and

The solvent at antigen-binding site regulated C3d-CR2 interactions through the C-terminal tail of C3d at different ion strengths: insights from molecular dynamics simulation.

PubMed

Zhang, Yan; Guo, Jingjing; Li, Lanlan; Liu, Xuewei; Yao, Xiaojun; Liu, Huanxiang

2016-10-01

The interactions of complement receptor 2 (CR2) and the degradation fragment C3d of complement component C3 play important links between the innate and adaptive immune systems. Due to the importance of C3d-CR2 interaction in the design of vaccines and inhibitors, a number of studies have been performed to investigate C3d-CR2 interaction. Many studies have indicated C3d-CR2 interactions are ionic strength-dependent. To investigate the molecular mechanism of C3d-CR2 interaction and the origin of effects of ionic strength, molecular dynamics simulations for C3d-CR2 complex together with the energetic and structural analysis were performed. Our results revealed the increased interactions between charged protein and ions weaken C3d-CR2 association, as ionic strengths increase. Moreover, ion strengths have similar effects on antigen-binding site and CR2 binding site. Meanwhile, Ala17 and Gln20 will transform between the activated and non-activated states mediated by His133 and Glu135 at different ion strengths. Our results reveal the origins of the effects of ionic strengths on C3d-CR2 interactions are due to the changes of water, ion occupancies and distributions. This study uncovers the origin of the effect of ionic strength on C3d-CR2 interaction and deepens the understanding of the molecular mechanism of their interaction, which is valuable for the design of vaccines and small molecule inhibitors. Copyright © 2016 Elsevier B.V. All rights reserved.

Interactive graphic editing tools in bioluminescent imaging simulation

NASA Astrophysics Data System (ADS)

Li, Hui; Tian, Jie; Luo, Jie; Wang, Ge; Cong, Wenxiang

2005-04-01

It is a challenging task to accurately describe complicated biological tissues and bioluminescent sources in bioluminescent imaging simulation. Several graphic editing tools have been developed to efficiently model each part of the bioluminescent simulation environment and to interactively correct or improve the initial models of anatomical structures or bioluminescent sources. There are two major types of graphic editing tools: non-interactive tools and interactive tools. Geometric building blocks (i.e. regular geometric graphics and superquadrics) are applied as non-interactive tools. To a certain extent, complicated anatomical structures and bioluminescent sources can be approximately modeled by combining a sufficient large number of geometric building blocks with Boolean operators. However, those models are too simple to describe the local features and fine changes in 2D/3D irregular contours. Therefore, interactive graphic editing tools have been developed to facilitate the local modifications of any initial surface model. With initial models composed of geometric building blocks, interactive spline mode is applied to conveniently perform dragging and compressing operations on 2D/3D local surface of biological tissues and bioluminescent sources inside the region/volume of interest. Several applications of the interactive graphic editing tools will be presented in this article.

Three dimensional Lagrangian structures in the Antarctic Polar Vortex.

NASA Astrophysics Data System (ADS)

Mancho, Ana M.; Garcia-Garrido, Victor J.; Curbelo, Jezabel; Niang, Coumba; Mechoso, Carlos R.; Wiggins, Stephen

2017-04-01

Dynamical systems theory has supported the description of transport processes in fluid dynamics. For understanding trajectory patterns in chaotic advection the geometrical approach by Poincaré seeks for spatial structures that separate regions corresponding to qualitatively different types of trajectories. These structures have been referred to as Lagrangian Coherent Structures (LCS), which typically in geophysical flows are well described under the approach of incompressible 2D flows. Different tools have been used to visualize LCS. In this presentation we use Lagrangian Descriptors [1,2,3,4] (function M) for visualizing 3D Lagrangian structures in the atmosphere, in particular in the Antarctic Polar Vortex. The function M is computed in a fully 3D incompressible flow obtained from data provided by the European Centre for Medium-Range Weather Forecast and it is represented in 2D surfaces. We discuss the findings during the final warming that took place in the spring of 1979 [5]. This research is supported by MINECO grant MTM2014-56392-R. Support is acknowledged also from CSIC grant COOPB20265, U.S. NSF grant AGS-1245069 and ONR grant No. N00014- 01-1-0769. C. Niang acknowledges Fundacion Mujeres por Africa and ICMAT Severo Ochoa project SEV-2011-0087 for financial support. [1] C. Mendoza, A. M. Mancho. The hidden geometry of ocean flows. Physical Review Letters 105 (2010), 3, 038501-1-038501-4. [2] A. M. Mancho, S. Wiggins, J. Curbelo, C. Mendoza. Lagrangian Descriptors: A Method for Revealing Phase Space Structures of General Time Dependent Dynamical Systems. Communications in Nonlinear Science and Numerical Simulation. 18 (2013) 3530-3557. [3] C. Lopesino, F. Balibrea-Iniesta, S. Wiggins and A. M. Mancho. Lagrangian descriptors for two dimensional, area preserving autonomous and nonautonomous maps. Communications in Nonlinear Science and Numerical Simulations, 27 (2015) (1-3), 40-51. [4] C. Lopesino, F. Balibrea-Iniesta, V. J. García-Garrido, S. Wiggins, and A. M. Mancho, A. M. A theoretical framework for lagrangian descriptors. International Journal of Bifurcation and Chaos (2017) to appear. [5] The three-dimensional Lagrangian geometry of the Antarctic Polar Vortex circulation. Preprint.

A systematic review of 3-D printing in cardiovascular and cerebrovascular diseases

PubMed Central

Sun, Zhonghua; Lee, Shen-Yuan

2017-01-01

Objective: The application of 3-D printing has been increasingly used in medicine, with research showing many applications in cardiovascular disease. This systematic review analyzes those studies published about the applications of 3-D printed, patient-specific models in cardiovascular and cerebrovascular diseases. Methods: A search of PubMed/Medline and Scopus databases was performed to identify studies investigating the 3-D printing in cardiovascular and cerebrovascular diseases. Only studies based on patient’s medical images were eligible for review, while reports on in vitro phantom or review articles were excluded. Results: A total of 48 studies met selection criteria for inclusion in the review. A range of patient-specific 3-D printed models of different cardiovascular and cerebrovascular diseases were generated in these studies with most of them being developed using cardiac CT and MRI data, less commonly with 3-D invasive angiographic or echocardiographic images. The review of these studies showed high accuracy of 3-D printed, patient-specific models to represent complex anatomy of the cardiovascular and cerebrovascular system and depict various abnormalities, especially congenital heart diseases and valvular pathologies. Further, 3-D printing can serve as a useful education tool for both parents and clinicians, and a valuable tool for pre-surgical planning and simulation. Conclusion: This systematic review shows that 3-D printed models based on medical imaging modalities can accurately replicate complex anatomical structures and pathologies of the cardiovascular and cerebrovascular system. 3-D printing is a useful tool for both education and surgical planning in these diseases. PMID:28430115

28 CFR 50.10 - Policy regarding obtaining information from, or records of, members of the news media; and...

Code of Federal Regulations, 2014 CFR

2014-07-01

... views the use of certain law enforcement tools, including subpoenas, court orders issued pursuant to 18... court orders issued pursuant to 18 U.S.C. 2703(d) or 3123, in particular, may be used, after... use of a subpoena, court order issued pursuant to 18 U.S.C. 2703(d) or 3123, or warrant to obtain from...

Microscopic transport model animation visualisation on KML base

NASA Astrophysics Data System (ADS)

Yatskiv, I.; Savrasovs, M.

2012-10-01

By reading classical literature devoted to the simulation theory it could be found that one of the greatest possibilities of simulation is the ability to present processes inside the system by animation. This gives to the simulation model additional value during presentation of simulation results for the public and authorities who are not familiar enough with simulation. That is why most of universal and specialised simulation tools have the ability to construct 2D and 3D representation of the model. Usually the development of such representation could take much time and there must be put a lot forces into creating an adequate 3D representation of the model. For long years such well-known microscopic traffic flow simulation software tools as VISSIM, AIMSUN and PARAMICS have had a possibility to produce 2D and 3D animation. But creation of realistic 3D model of the place where traffic flows are simulated, even in these professional software tools it is a hard and time consuming action. The goal of this paper is to describe the concepts of use the existing on-line geographical information systems for visualisation of animation produced by simulation software. For demonstration purposes the following technologies and tools have been used: PTV VISION VISSIM, KML and Google Earth.

Reorganization of equivalence classes: effects of preliminary training and meaningful stimuli.

PubMed

Arntzen, Erik; Nartey, Richard K; Fields, Lanny

2018-05-01

In Condition 1, adults learned the baseline relations for the three equivalence classes A1-B1-C1-D1-E1, A2-B2-C2-D2-E2, and A3-B3-C3-D3-E3. Classes contained abstract shapes in the ABS and four preliminary training groups. Each class in the PIC group contained one picture and four abstract shapes. Before class formation for four other groups, preliminary training involved establishing identity (CC) or arbitrary (CX) relations either with or without a delay. Without preliminary training, classes formed with low and high likelihoods in the ABS and PIC groups, respectively. Preliminary training with no delay produced modest increases in class formation, while preliminary training with delay produced large increases in class formation. Condition 2 replicated Condition 1 but with training of reassigned BC and CD relations that linked C from one class to B and D from another class: B1-C2, B2-C3, B3-C1, C2-D1, C3-D2, and C1-D3. Subsequent tests assessed the emergence of the reorganized classes A1-B1-C2-D1-E1, A2-B2-C3-D2-E2, and A3-B3-C1-D3-E3. All preliminary training procedures increased likelihood of forming the reorganized classes to the level seen in the PIC group. Greater gains were produced by preliminary training with no delays than with delays. Test performances also showed how preliminary training influenced baseline acquisition speed and participant-defined relations. © 2018 Society for the Experimental Analysis of Behavior.

Survey of Network Visualization Tools

DTIC Science & Technology

2007-12-01

Dimensionality • 2D Comments: Deployment Type: • Components for tool building • Standalone Tool OS: • Windows Extensibility • ActiveX ...Visual Basic Comments: Interoperability Daisy is fully compliant with Microsoft’s ActiveX , therefore, other Windows based programs can...other functions that improve analytic decision making. Available in ActiveX , C++, Java, and .NET editions. • Tom Sawyer Visualization: Enables you to

Models of anxiety: responses of mice to novelty and open spaces in a 3D maze.

PubMed

Ennaceur, A; Michalikova, S; van Rensburg, R; Chazot, P L

2006-11-01

The present report describes the emotional responses of different strains of mice to exposure to a novel open space model of anxiety using a 3D spatial navigation task. The 3D maze is modification of the radial maze with flexible arms that can be raised above or lowered below the horizontal level of a central platform. To access the arms animals need to cross a bridge linking the arms to the central platform. In this model, mice are exposed to novelty in an unfamiliar open space setting with no safe alternative. Fear from novelty is compounded with the need to explore. The drive to escape and the drive to approach are intermingled making this open space model radically different from the current models of anxiety which provide animals with the choice between safe and anxiogenic spaces. In a series of experiments, we examined the behaviour of different groups of mice from C57, C3H, CD1 and Balb/c strains. In the first experiment, different groups of C57 mice were tested in one of the three arms configurations. In the second experiment, C57 mice were compared to C3H mice. In the third experiment, C57 mice were compared to CD1 and Balb/c mice in the raised arm configuration over three successive sessions. In the fourth experiment, we examined the behaviour of C57 mice in the lowered arm configuration with an open and an enclosed central. In the final experiment, we examined the difference between C57 and C3H mice of both genders. Using several spatio-temporal parameters of the transition responses between central platform, bridges and arms, we have been able to show consistent results demonstrating significant differences between C57 and C3H mice, and between Balb/c and both C57 and CD1 mice. C3H appear more anxious than C57 mice, and Balb/c mice seem more anxious than C57 and CD1 mice. We also observed significant differences between sexes in C3H mice but not in C57 mice. C3H male mice appear more anxious than C3H female mice and than both C57 male and female mice. In the lowered arm configuration with an enclosed central platform, C57 mice took longer time to make a first entry to an arm, made more visits to bridges before first entry to an arm and required longer time between re-entries to arms, spent longer time on the central platform and shorter time on arms compared to mice in the other arm configurations. They also made frequent entries to the centre and bridges compared to mice in the lowered arm with an open central platform. These results demonstrate not only the sensitivity of the parameters of the test but also the consistencies and concordances of the results which make this 3D maze a valuable new tool in the study of the underlying neural mechanisms of anxiety responses in addition to learning and memory, and in assessing the effects of potential anxiolytic drugs. In this report we examine methodological issues related to the design of animal behavioural paradigms and question the value and the construct validity of the current models of human anxiety.

TomoEED: Fast Edge-Enhancing Denoising of Tomographic Volumes.

PubMed

Moreno, J J; Martínez-Sánchez, A; Martínez, J A; Garzón, E M; Fernández, J J

2018-05-29

TomoEED is an optimized software tool for fast feature-preserving noise filtering of large 3D tomographic volumes on CPUs and GPUs. The tool is based on the anisotropic nonlinear diffusion method. It has been developed with special emphasis in the reduction of the computational demands by using different strategies, from the algorithmic to the high performance computing perspectives. TomoEED manages to filter large volumes in a matter of minutes in standard computers. TomoEED has been developed in C. It is available for Linux platforms at http://www.cnb.csic.es/%7ejjfernandez/tomoeed. gmartin@ual.es, JJ.Fernandez@csic.es. Supplementary data are available at Bioinformatics online.

S3D: An interactive surface grid generation tool

NASA Technical Reports Server (NTRS)

Luh, Raymond Ching-Chung; Pierce, Lawrence E.; Yip, David

1992-01-01

S3D, an interactive software tool for surface grid generation, is described. S3D provides the means with which a geometry definition based either on a discretized curve set or a rectangular set can be quickly processed towards the generation of a surface grid for computational fluid dynamics (CFD) applications. This is made possible as a result of implementing commonly encountered surface gridding tasks in an environment with a highly efficient and user friendly graphical interface. Some of the more advanced features of S3D include surface-surface intersections, optimized surface domain decomposition and recomposition, and automated propagation of edge distributions to surrounding grids.

Identification and restoration in 3D fluorescence microscopy

NASA Astrophysics Data System (ADS)

Dieterlen, Alain; Xu, Chengqi; Haeberle, Olivier; Hueber, Nicolas; Malfara, R.; Colicchio, B.; Jacquey, Serge

2004-06-01

3-D optical fluorescent microscopy becomes now an efficient tool for volumic investigation of living biological samples. The 3-D data can be acquired by Optical Sectioning Microscopy which is performed by axial stepping of the object versus the objective. For any instrument, each recorded image can be described by a convolution equation between the original object and the Point Spread Function (PSF) of the acquisition system. To assess performance and ensure the data reproducibility, as for any 3-D quantitative analysis, the system indentification is mandatory. The PSF explains the properties of the image acquisition system; it can be computed or acquired experimentally. Statistical tools and Zernike moments are shown appropriate and complementary to describe a 3-D system PSF and to quantify the variation of the PSF as function of the optical parameters. Some critical experimental parameters can be identified with these tools. This is helpful for biologist to define an aquisition protocol optimizing the use of the system. Reduction of out-of-focus light is the task of 3-D microscopy; it is carried out computationally by deconvolution process. Pre-filtering the images improves the stability of deconvolution results, now less dependent on the regularization parameter; this helps the biologists to use restoration process.

Advancements to Visualization Control System (VCS, part of UV-CDAT), a Visualization Package Designed for Climate Scientists

NASA Astrophysics Data System (ADS)

Lipsa, D.; Chaudhary, A.; Williams, D. N.; Doutriaux, C.; Jhaveri, S.

2017-12-01

Climate Data Analysis Tools (UV-CDAT, https://uvcdat.llnl.gov) is a data analysis and visualization software package developed at Lawrence Livermore National Laboratory and designed for climate scientists. Core components of UV-CDAT include: 1) Community Data Management System (CDMS) which provides I/O support and a data model for climate data;2) CDAT Utilities (GenUtil) that processes data using spatial and temporal averaging and statistic functions; and 3) Visualization Control System (VCS) for interactive visualization of the data. VCS is a Python visualization package primarily built for climate scientists, however, because of its generality and breadth of functionality, it can be a useful tool to other scientific applications. VCS provides 1D, 2D and 3D visualization functions such as scatter plot and line graphs for 1d data, boxfill, meshfill, isofill, isoline for 2d scalar data, vector glyphs and streamlines for 2d vector data and 3d_scalar and 3d_vector for 3d data. Specifically for climate data our plotting routines include projections, Skew-T plots and Taylor diagrams. While VCS provided a user-friendly API, the previous implementation of VCS relied on slow performing vector graphics (Cairo) backend which is suitable for smaller dataset and non-interactive graphics. LLNL and Kitware team has added a new backend to VCS that uses the Visualization Toolkit (VTK) as its visualization backend. VTK is one of the most popular open source, multi-platform scientific visualization library written in C++. Its use of OpenGL and pipeline processing architecture results in a high performant VCS library. Its multitude of available data formats and visualization algorithms results in easy adoption of new visualization methods and new data formats in VCS. In this presentation, we describe recent contributions to VCS that includes new visualization plots, continuous integration testing using Conda and CircleCI, tutorials and examples using Jupyter notebooks as well as upgrades that we are planning in the near future which will improve its ease of use and reliability and extend its capabilities.

Seismic Pulse Broadening Associated with Fracture Damage Caused by Explosions in Crystalline Rock

DTIC Science & Technology

1989-08-30

1/ 3 ’)I 3/ 2 -C2(() - 1 +) 3D °2/ 3 D 1 - D 1/ - (I -C, X) 1+ 2/3)-)o _ I C4)L( oj and for loading at constant a3 43 D 02𔃽 (D )?/3 31 (28) where S...U3, 103-112. Von Karman, T. (1911). Festigkeitswversuche unter allseiRgim druck , Z. Ver. Dt. Ing., 51, 1749-1757. Wawersik, W.R., and C. Fairhurst

NASAL-Geom, a free upper respiratory tract 3D model reconstruction software

NASA Astrophysics Data System (ADS)

Cercos-Pita, J. L.; Cal, I. R.; Duque, D.; de Moreta, G. Sanjuán

2018-02-01

The tool NASAL-Geom, a free upper respiratory tract 3D model reconstruction software, is here described. As a free software, researchers and professionals are welcome to obtain, analyze, improve and redistribute it, potentially increasing the rate of development, and reducing at the same time ethical conflicts regarding medical applications which cannot be analyzed. Additionally, the tool has been optimized for the specific task of reading upper respiratory tract Computerized Tomography scans, and producing 3D geometries. The reconstruction process is divided into three stages: preprocessing (including Metal Artifact Reduction, noise removal, and feature enhancement), segmentation (where the nasal cavity is identified), and 3D geometry reconstruction. The tool has been automatized (i.e. no human intervention is required) a critical feature to avoid bias in the reconstructed geometries. The applied methodology is discussed, as well as the program robustness and precision.

Monodeuterated Methane, an Isotopic Tool To Assess Biological Methane Metabolism Rates

PubMed Central

Steele, Joshua A.; Ziebis, Wiebke; Scheller, Silvan; Case, David; Reynard, Linda M.; Orphan, Victoria J.

2017-01-01

ABSTRACT Biological methane oxidation is a globally relevant process that mediates the flux of an important greenhouse gas through both aerobic and anaerobic metabolic pathways. However, measuring these metabolic rates presents many obstacles, from logistical barriers to regulatory hurdles and poor precision. Here we present a new approach for investigating microbial methane metabolism based on hydrogen atom dynamics, which is complementary to carbon-focused assessments of methanotrophy. The method uses monodeuterated methane (CH3D) as a metabolic substrate, quantifying the aqueous D/H ratio over time using off-axis integrated cavity output spectroscopy. This approach represents a nontoxic, comparatively rapid, and straightforward approach that supplements existing radiotopic and stable carbon isotopic methods; by probing hydrogen atoms, it offers an additional dimension for examining rates and pathways of methane metabolism. We provide direct comparisons between the CH3D procedure and the well-established 14CH4 radiotracer method for several methanotrophic systems, including type I and II aerobic methanotroph cultures and methane-seep sediment slurries and carbonate rocks under anoxic and oxic incubation conditions. In all applications tested, methane consumption values calculated via the CH3D method were directly and consistently proportional to 14C radiolabel-derived methane oxidation rates. We also employed this method in a nontraditional experimental setup, using flexible, gas-impermeable bags to investigate the role of pressure on seep sediment methane oxidation rates. Results revealed an 80% increase over atmospheric pressure in methanotrophic rates the equivalent of ~900-m water depth, highlighting the importance of this parameter on methane metabolism and exhibiting the flexibility of the newly described method. IMPORTANCE Microbial methane consumption is a critical component of the global carbon cycle, with wide-ranging implications for climate regulation and hydrocarbon exploitation. Nonetheless, quantifying methane metabolism typically involves logistically challenging methods and/or specialized equipment; these impediments have limited our understanding of methane fluxes and reservoirs in natural systems, making effective management difficult. Here, we offer an easily implementable, precise method using monodeuterated methane (CH3D) that advances three specific aims. First, it allows users to directly compare methane consumption rates between different experimental treatments of the same inoculum. Second, by empirically linking the CH3D procedure with the well-established 14C radiocarbon approach, we determine absolute scaling factors that facilitate rate measurements for several aerobic and anaerobic systems of interest. Third, CH3D represents a helpful tool in evaluating the relationship between methane activation and full oxidation in methanotrophic metabolisms. The procedural advantages, consistency, and novel research questions enabled by the CH3D method should prove useful in a wide range of culture-based and environmental microbial systems to further elucidate methane metabolism dynamics. PMID:28861523

Monodeuterated Methane, an Isotopic Tool To Assess Biological Methane Metabolism Rates.

PubMed

Marlow, Jeffrey J; Steele, Joshua A; Ziebis, Wiebke; Scheller, Silvan; Case, David; Reynard, Linda M; Orphan, Victoria J

2017-01-01

Biological methane oxidation is a globally relevant process that mediates the flux of an important greenhouse gas through both aerobic and anaerobic metabolic pathways. However, measuring these metabolic rates presents many obstacles, from logistical barriers to regulatory hurdles and poor precision. Here we present a new approach for investigating microbial methane metabolism based on hydrogen atom dynamics, which is complementary to carbon-focused assessments of methanotrophy. The method uses monodeuterated methane (CH 3 D) as a metabolic substrate, quantifying the aqueous D/H ratio over time using off-axis integrated cavity output spectroscopy. This approach represents a nontoxic, comparatively rapid, and straightforward approach that supplements existing radiotopic and stable carbon isotopic methods; by probing hydrogen atoms, it offers an additional dimension for examining rates and pathways of methane metabolism. We provide direct comparisons between the CH 3 D procedure and the well-established 14 CH 4 radiotracer method for several methanotrophic systems, including type I and II aerobic methanotroph cultures and methane-seep sediment slurries and carbonate rocks under anoxic and oxic incubation conditions. In all applications tested, methane consumption values calculated via the CH 3 D method were directly and consistently proportional to 14 C radiolabel-derived methane oxidation rates. We also employed this method in a nontraditional experimental setup, using flexible, gas-impermeable bags to investigate the role of pressure on seep sediment methane oxidation rates. Results revealed an 80% increase over atmospheric pressure in methanotrophic rates the equivalent of ~900-m water depth, highlighting the importance of this parameter on methane metabolism and exhibiting the flexibility of the newly described method. IMPORTANCE Microbial methane consumption is a critical component of the global carbon cycle, with wide-ranging implications for climate regulation and hydrocarbon exploitation. Nonetheless, quantifying methane metabolism typically involves logistically challenging methods and/or specialized equipment; these impediments have limited our understanding of methane fluxes and reservoirs in natural systems, making effective management difficult. Here, we offer an easily implementable, precise method using monodeuterated methane (CH 3 D) that advances three specific aims. First, it allows users to directly compare methane consumption rates between different experimental treatments of the same inoculum. Second, by empirically linking the CH 3 D procedure with the well-established 14 C radiocarbon approach, we determine absolute scaling factors that facilitate rate measurements for several aerobic and anaerobic systems of interest. Third, CH 3 D represents a helpful tool in evaluating the relationship between methane activation and full oxidation in methanotrophic metabolisms. The procedural advantages, consistency, and novel research questions enabled by the CH 3 D method should prove useful in a wide range of culture-based and environmental microbial systems to further elucidate methane metabolism dynamics.

bioWeb3D: an online webGL 3D data visualisation tool.

PubMed

Pettit, Jean-Baptiste; Marioni, John C

2013-06-07

Data visualization is critical for interpreting biological data. However, in practice it can prove to be a bottleneck for non trained researchers; this is especially true for three dimensional (3D) data representation. Whilst existing software can provide all necessary functionalities to represent and manipulate biological 3D datasets, very few are easily accessible (browser based), cross platform and accessible to non-expert users. An online HTML5/WebGL based 3D visualisation tool has been developed to allow biologists to quickly and easily view interactive and customizable three dimensional representations of their data along with multiple layers of information. Using the WebGL library Three.js written in Javascript, bioWeb3D allows the simultaneous visualisation of multiple large datasets inputted via a simple JSON, XML or CSV file, which can be read and analysed locally thanks to HTML5 capabilities. Using basic 3D representation techniques in a technologically innovative context, we provide a program that is not intended to compete with professional 3D representation software, but that instead enables a quick and intuitive representation of reasonably large 3D datasets.

TRITIUM-LABELED COMPOUNDS VII. ISOTOPE EFFECTS IN THE OXIDATION OF d- MANNITOLS-C$sup 14$ AND d-MANNITOLS-t TO d-FRUCTOSES

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

Sniegoski, L.T.; Frush, H.L.; Isbell, H.S.

1961-09-01

D-Mannitols, labeled either with carbon-14 at C1, C2, or C3, or with tritium attached to C1, C2, or C3, were prepared. After oxidation by Acetobacter suboxydans, the distribution of radioactivity in each of the resulting labeled D- fructoses was determined. Labeled D-mannitol is unique among the hexitols in that it may be oxidized by A. suboxydans in either the labeled or the unlabeled part of the molecule. Except in the oxidation of D-mannitol-2-t, the competing reactions result in the formation of a mixture of D-fructoses, each having radioactivity in one of two different positions. Hence, the isotope effect, k*/ k,more » (where k* and k are, respectively, the rate constants for oxidation in the labeled and in the unlabeled part of the labeled emannitol molecule) is the ratio of the activities at the two positions of the product, D-fructose. The following isotope effects were found for the bacterial oxidation of labeled D-mannitols: for D-mannitol-2-C/sup 14/, k*/k = 0.93; for Dmannitol-2-t, k*/k = 0.23; and for D-mannitol-3-t, k*/k = 0.70. For D-mannitols labeled at other positions, no isotope effect was detected, since k*/k was unity. The large isotope effect for D-mannitol-2-t is indicative of rupture of the C2-H bond in the rate determining process. It is suggested that the secondary isotope effect for tritium at C3 indicates hyperconjugation of the C3 hydrogen atom in the activated enzyme-- substrate complex; the lack of such effect for tritium at C1 may be due to unfavorable steric conditions for hyperconjugation of the C1 hydrogen atoms in the complex. The following substances were prepared and their isotopic distributions determined: D-fructose1,6-C/sup 14/ and D-fructose-1,6-t (from 1- labeled D-mannitols); D-fructose-2,5-C/sup 14/ and D-fructose-5-t (from 2-labeled e-mannitols); and D-fructose-3,4-C/sup 14/ and D-fructose-3,4-t (from 3-labeled D- mannitols). A procedure, employing D-fructose-1,6-C/sup 14/ as an internal standard, was devised for the analysis of D-fructose-3,4-t. (auth)« less

Exercise decreases the risk of metabolic syndrome in elderly females.

PubMed

Kemmler, Wolfgang; Von Stengel, Simon; Engelke, Klaus; Kalender, Willi A

2009-02-01

To determine the effect of exercise based on a multiple purpose, high-intensity philosophy on parameters of metabolic syndrome (MetS) in older females with the MetS. Thirty-two women (68.7 +/- 3.4 yr) with the MetS according to the International Diabetes Federation (IDF) took part in the exercise training (EG), and 33 females (69.5 +/- 4.3 yr) also with MetS served as control group (CG). Beside the diagnostic tools of the MetS (waist circumference, triglycerides, HDL-C, blood pressure, and glucose), corresponding anthropometric parameters, total cholesterol, and high-sensitivity C-reactive protein (hsCRP) were determined. After 12 months of exercise, significant effects were observed for total body fat [EG: -1287 g vs CG: +484 g; P = 0.001; confidence interval (CI) = -2787 to -744 g], trunk fat (-1070 vs -203 g; P = 0.005; CI = -1460 to -274 g), hip circumference (-2.1 vs +1.0 cm; P = 0.001; CI = -4.8 to -1.3 cm), triglycerides: (-24.1 vs -0.3 mg dL(-1); P = 0.021; CI = -43.9 to -3.7 mg dL(-1)), total cholesterol: (-19.8 vs +0.2 mg dL(-1); P = 0.008; CI = -34.6 to -5.5 mg dL(-1)), and HDL-C: (+3.8 vs -0.2 mg dL(-1); P = 0.036; CI = 0.3 to 7.6 mg dL(-1)). Waist circumference slightly decreased in both groups (EG: -0.7% vs CG: -0.6%; P = 0.94). Resting systolic (-7.1 vs -6.4 mm Hg; P = 0.84) and diastolic (-8.0 vs -+9.8 mm Hg; P = 0.39) blood pressure significantly decreased in both groups. Changes of glucose and hsCRP did not significantly vary between groups (glucose: +0.7 vs +1.0 mg dL(-1), P = 0.88; hsCRP: -0.68 vs -0.50 mg L(-1), P = 0.36). The number of criteria of the MetS significantly decreased in the EG (4.13-3.66) and slightly decreased in the CG (4.12-3.97); however, significant time group interactions were not observed (P = 0.15; CI = -0.74 to 0.12). Our multipurpose exercise program significantly affects most parameters of the MetS in elderly women.

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

DNA vaccines expressing soluble CD4-envelope proteins fused to C3d elicit cross-reactive neutralizing antibodies to HIV-1.

PubMed

Bower, Joseph F; Green, Thomas D; Ross, Ted M

2004-10-25

DNA vaccines expressing the envelope (Env) of the human immunodeficiency virus type 1 (HIV-1) have been relatively ineffective at generating high-titer, long-lasting, neutralizing antibodies in a variety of animal models. In this study, DNA vaccines were constructed to express a fusion protein of the soluble human CD4 (sCD4) and the gp120 subunit of the HIV-1 envelope. To enhance the immunogenicity of the expressed fusion protein, three copies of the murine C3d (mC3d3) were added to the carboxyl terminus of the complex. Monoclonal antibodies that recognize CD4-induced epitopes on gp120 efficiently bound to sCD4-gp120 or sCD4-gp120-mC3d3. In addition, both sCD4-gp120 and sCD4-gp120-mC3d3 bound to cells expressing appropriate coreceptors in the absence of cell surface hCD4. Mice (BALB/c) vaccinated with DNA vaccines expressing either gp120-mC3d3 or sCD4-gp120-mC3d3 elicited antibodies that neutralized homologous virus infection. However, the use of sCD4-gp120-mC3d3-DNA elicited the highest titers of neutralizing antibodies that persisted after depletion of anti-hCD4 antibodies. Interestingly, only mice vaccinated with DNA expressing sCD4-gp120-mC3d3 had antibodies that elicited cross-protective neutralizing antibodies. The fusion of sCD4 to the HIV-1 envelope exposes neutralizing epitopes that elicit broad protective immunity when the fusion complex is coupled with the molecular adjuvant, C3d.

Design and Implementation of a new Autonomous Sensor Fish to Support Advanced Hydropower Development

DOE PAGES

Deng, Zhiqun; Lu, Jun; Myjak, Mitchell J.; ...

2014-11-04

Acceleration in development of additional conventional hydropower requires tools and methods to perform laboratory and in-field validation of turbine performance and fish passage claims. The new-generation Sensor Fish has been developed with more capabilities to accommodate a wider range of users over a wider range of turbine designs and operating environments. It provides in situ measurements of three dimensional (3D) accelerations, 3D rotational velocities, 3D orientation, pressure, and temperature at a sampling frequency of 2048 Hz. It also has an automatic floatation system and built-in radio frequency transmitter for recovery. The relative errors of the pressure, acceleration and rotational velocitymore » were within ±2%, ±5%, and ±5%, respectively. The accuracy of orientation was within ±4° and accuracy of temperature was ±2°C. It is being deployed to evaluate the biological effects of turbines or other hydraulic structures in several countries.« less

3-D Printing as an Effective Educational Tool for MEMS Design and Fabrication

ERIC Educational Resources Information Center

Dahle, Reena; Rasel, Rafiul

2016-01-01

This paper presents a series of course modules developed as a high-impact and cost-effective learning tool for modeling and simulating the microfabrication process and design of microelectromechanical systems (MEMS) devices using three-dimensional (3-D) printing. Microfabrication technology is an established fabrication technique for small and…

Multiwalled carbon nanotubes and dispersed nanodiamond novel hybrids: Microscopic structure evolution, physical properties, and radiation resilience

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

Gupta, S.; Farmer, J.

2011-01-01

We report the structure and physical properties of novel hybrids of multiwalled carbon nanotubes (MWCNTs) and ultradispersed diamond (UDD) forming nanocomposite ensemble that were subjected to 50, 100, and 10{sup 3} kGy gamma ray doses and characterized using various analytical tools to investigate hierarchical defects evolution. This work is prompted by recent work on single-walled CNTs and UDD ensemble [Gupta et al., J. Appl. Phys. 107, 104308 (2010)] where radiation-induced microscopic defects seem to be stabilized by UDD. The present experiments show similar effects where these hybrids display only a minimal structural modification under the maximum dose. Quantitative analyses ofmore » multiwavelength Raman spectra revealed lattice defects induced by irradiation assessed through the variation in prominent D, G, and 2D bands. A minimal change in the position of D, G, and 2D bands and a marginal increase in intensity of the defect-induced double resonant Raman scattered D and 2D bands are some of the implications suggesting the radiation coupling. The in-plane correlation length (L{sub a}) was also determined following Tunistra-Koenig relation from the ratio of D to G band (I{sub D}/I{sub G}) besides microscopic stress. However, we also suggest the following taking into account of intrinsic defects of the constituents: (a) charge transfer arising at the interface due to the difference in electronegativity of MWCNT C sp{sup 2} and UDD core (C sp{sup 3}) leading to phonon and electron energy renormalization; (b) misorientation of C sp{sup 2} at the interface of MWCNT and UDD shell (C sp{sup 2}) resulting in structural disorder; (c) softening or violation of the q{approx}0 selection rule leading to D band broadening and a minimal change in G band intensity; and (d) normalized intensity of D and G bands with 2D band help to distinguish defect-induced double resonance phenomena. The MWCNT when combined with nanodiamond showed a slight decrease in their conductance further affected by irradiation pointing at relatively good interfacial contact. Furthermore, owing to high thermal and electrical conductivity properties, they can facilitate potentially efficient heat-transfer applications and some results deduced using Nielsen's model is provided.« less

Improvement of electrical resistivity tomography for leachate injection monitoring.

PubMed

Clément, R; Descloitres, M; Günther, T; Oxarango, L; Morra, C; Laurent, J-P; Gourc, J-P

2010-03-01

Leachate recirculation is a key process in the scope of operating municipal waste landfills as bioreactors, which aims to increase the moisture content to optimize the biodegradation in landfills. Given that liquid flows exhibit a complex behaviour in very heterogeneous porous media, in situ monitoring methods are required. Surface time-lapse electrical resistivity tomography (ERT) is usually proposed. Using numerical modelling with typical 2D and 3D injection plume patterns and 2D and 3D inversion codes, we show that wrong changes of resistivity can be calculated at depth if standard parameters are used for time-lapse ERT inversion. Major artefacts typically exhibit significant increases of resistivity (more than +30%) which can be misinterpreted as gas migration within the waste. In order to eliminate these artefacts, we tested an advanced time-lapse ERT procedure that includes (i) two advanced inversion tools and (ii) two alternative array geometries. The first advanced tool uses invariant regions in the model. The second advanced tool uses an inversion with a "minimum length" constraint. The alternative arrays focus on (i) a pole-dipole array (2D case), and (ii) a star array (3D case). The results show that these two advanced inversion tools and the two alternative arrays remove almost completely the artefacts within +/-5% both for 2D and 3D situations. As a field application, time-lapse ERT is applied using the star array during a 3D leachate injection in a non-hazardous municipal waste landfill. To evaluate the robustness of the two advanced tools, a synthetic model including both true decrease and increase of resistivity is built. The advanced time-lapse ERT procedure eliminates unwanted artefacts, while keeping a satisfactory image of true resistivity variations. This study demonstrates that significant and robust improvements can be obtained for time-lapse ERT monitoring of leachate recirculation in waste landfills. Copyright 2009 Elsevier Ltd. All rights reserved.

Improvement of electrical resistivity tomography for leachate injection monitoring

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

Clement, R., E-mail: remi.clement@hmg.inpg.f; Descloitres, M.; Guenther, T., E-mail: Thomas.Guenther@liag-hannover.d

2010-03-15

Leachate recirculation is a key process in the scope of operating municipal waste landfills as bioreactors, which aims to increase the moisture content to optimize the biodegradation in landfills. Given that liquid flows exhibit a complex behaviour in very heterogeneous porous media, in situ monitoring methods are required. Surface time-lapse electrical resistivity tomography (ERT) is usually proposed. Using numerical modelling with typical 2D and 3D injection plume patterns and 2D and 3D inversion codes, we show that wrong changes of resistivity can be calculated at depth if standard parameters are used for time-lapse ERT inversion. Major artefacts typically exhibit significantmore » increases of resistivity (more than +30%) which can be misinterpreted as gas migration within the waste. In order to eliminate these artefacts, we tested an advanced time-lapse ERT procedure that includes (i) two advanced inversion tools and (ii) two alternative array geometries. The first advanced tool uses invariant regions in the model. The second advanced tool uses an inversion with a 'minimum length' constraint. The alternative arrays focus on (i) a pole-dipole array (2D case), and (ii) a star array (3D case). The results show that these two advanced inversion tools and the two alternative arrays remove almost completely the artefacts within +/-5% both for 2D and 3D situations. As a field application, time-lapse ERT is applied using the star array during a 3D leachate injection in a non-hazardous municipal waste landfill. To evaluate the robustness of the two advanced tools, a synthetic model including both true decrease and increase of resistivity is built. The advanced time-lapse ERT procedure eliminates unwanted artefacts, while keeping a satisfactory image of true resistivity variations. This study demonstrates that significant and robust improvements can be obtained for time-lapse ERT monitoring of leachate recirculation in waste landfills.« less

BINDING OF SOLUBLE IMMUNE COMPLEXES TO HUMAN LYMPHOBLASTOID CELLS

PubMed Central

Theofilopoulos, Argyrios N.; Dixon, Frank J.; Bokisch, Viktor A.

1974-01-01

In the present work we studied the expression of membrane-bound Ig (MBIg) as well as receptors for IgG Fc and complement on nine human lymphoblastoid cell lines. When MBIg and receptors for IgG Fc were compared, four categories of cell lines could be distinguished: (a) cell lines having both MBIg and receptors for IgG Fc, (b) cell lines having MBIg but lacking receptors for IgG Fc, (c) cell lines lacking MBIg but having receptors for IgG Fc, and (d) cell lines lacking both MBIg and receptors for IgG Fc. Two types of receptors for complement could be detected on the cell lines studied, one for C3-C3b and one for C3d. When sensitized red cells carrying C3b or C3d were used for rosette tests, three categories of cell lines could be distinguished: (a) cell lines having receptors for C3b and C3d, (b) cell lines having receptors only for C3d and (c) cell lines lacking both receptors. However, when a more sensitive immunofluorescent method was used instead of the rosette technique, it was found that cell lines unable to form rosettes with EAC1423bhu were able to bind soluble C3 or C3b which indicated the presence of these receptors on the cell surface. Inhibition experiments showed that receptors for C3-C3b and receptors for C3d are distinct and that receptors for C3-C3b and C3d are different from receptors for IgG Fc. A cell line (Raji) without MBIg but with receptors for IgG Fc, C3-C3b, and C3d was selected for use in studying the binding mechanism of soluble immune complexes to cell surface membrane. Aggregated human gamma globulin was used in place of immune complexes. Immune complexes containing complement bind to Raji cells only via receptors for complement, namely receptors for C3-C3b and C3d. Binding of immune complexes containing complement to cells is much greater than that of complexes without complement. Immune complexes bound to cells via receptors for complement can be partially released from the cell surface by addition of normal human serum as well as isolated human C3 or C3b. We postulate that such release is due to competition of immune complex bound C3b and free C3 or C3b for the receptors on Raji cells. PMID:4139225

Visualizing Science Dissections in 3D: Contextualizing Student Responses to Multidimensional Learning Materials in Science Dissections

NASA Astrophysics Data System (ADS)

Walker, Robin Annette

A series of dissection tasks was developed in this mixed-methods study of student self-explanations of their learning using actual and virtual multidimensional science dissections and visuo-spatial instruction. Thirty-five seventh-grade students from a science classroom (N = 20 Female/15 Male, Age =13 years) were assigned to three dissection environments instructing them to: (a) construct static paper designs of frogs, (b) perform active dissections with formaldehyde specimens, and (c) engage with interactive 3D frog visualizations and virtual simulations. This multi-methods analysis of student engagement with anchored dissection materials found learning gains on labeling exercises and lab assessments among most students. Data revealed that students who correctly utilized multimedia text and diagrams, individually and collaboratively, manipulated 3D tools more effectively and were better able to self-explain and complete their dissection work. Student questionnaire responses corroborated that they preferred learning how to dissect a frog using 3D multimedia instruction. The data were used to discuss the impact of 3D technologies, programs, and activities on student learning, spatial reasoning, and their interest in science. Implications were drawn regarding how to best integrate 3D visualizations into science curricula as innovative learning options for students, as instructional alternatives for teachers, and as mandated dissection choices for those who object to physical dissections in schools.

40 CFR 1065.720 - Liquefied petroleum gas.

Code of Federal Regulations, 2010 CFR

2010-07-01

..., C3H8 Minimum, 0.85 m3/m3 ASTM D2163-05. Vapor pressure at 38 °C Maximum, 1400 kPa ASTM D1267-02 or 2598-022. Volatility residue (evaporated temperature, 35 °C) Maximum, −38 °C ASTM D1837-02a. Butanes Maximum, 0.05 m3/m3 ASTM D2163-05. Butenes Maximum, 0.02 m3/m3 ASTM D2163-05. Pentenes and heavier Maximum...

Preclinical validation and imaging of Wnt-induced repair in human 3D lung tissue cultures.

PubMed

Uhl, Franziska E; Vierkotten, Sarah; Wagner, Darcy E; Burgstaller, Gerald; Costa, Rita; Koch, Ina; Lindner, Michael; Meiners, Silke; Eickelberg, Oliver; Königshoff, Melanie

2015-10-01

Chronic obstructive pulmonary disease (COPD) is characterised by a progressive loss of lung tissue. Inducing repair processes within the adult diseased lung is of major interest and Wnt/β-catenin signalling represents a promising target for lung repair. However, the translation of novel therapeutic targets from model systems into clinical use remains a major challenge.We generated murine and patient-derived three-dimensional (3D) ex vivo lung tissue cultures (LTCs), which closely mimic the 3D lung microenvironment in vivo. Using two well-known glycogen synthase kinase-3β inhibitors, lithium chloride (LiCl) and CHIR 99021 (CT), we determined Wnt/β-catenin-driven lung repair processes in high spatiotemporal resolution using quantitative PCR, Western blotting, ELISA, (immuno)histological assessment, and four-dimensional confocal live tissue imaging.Viable 3D-LTCs exhibited preserved lung structure and function for up to 5 days. We demonstrate successful Wnt/β-catenin signal activation in murine and patient-derived 3D-LTCs from COPD patients. Wnt/β-catenin signalling led to increased alveolar epithelial cell marker expression, decreased matrix metalloproteinase-12 expression, as well as altered macrophage activity and elastin remodelling. Importantly, induction of surfactant protein C significantly correlated with disease stage (per cent predicted forced expiratory volume in 1 s) in patient-derived 3D-LTCs.Patient-derived 3D-LTCs represent a valuable tool to analyse potential targets and drugs for lung repair. Enhanced Wnt/β-catenin signalling attenuated pathological features of patient-derived COPD 3D-LTCs. Copyright ©ERS 2015.

Novel 3D Approach to Flare Modeling via Interactive IDL Widget Tools

NASA Astrophysics Data System (ADS)

Nita, G. M.; Fleishman, G. D.; Gary, D. E.; Kuznetsov, A.; Kontar, E. P.

2011-12-01

Currently, and soon-to-be, available sophisticated 3D models of particle acceleration and transport in solar flares require a new level of user-friendly visualization and analysis tools allowing quick and easy adjustment of the model parameters and computation of realistic radiation patterns (images, spectra, polarization, etc). We report the current state of the art of these tools in development, already proved to be highly efficient for the direct flare modeling. We present an interactive IDL widget application intended to provide a flexible tool that allows the user to generate spatially resolved radio and X-ray spectra. The object-based architecture of this application provides full interaction with imported 3D magnetic field models (e.g., from an extrapolation) that may be embedded in a global coronal model. Various tools provided allow users to explore the magnetic connectivity of the model by generating magnetic field lines originating in user-specified volume positions. Such lines may serve as reference lines for creating magnetic flux tubes, which are further populated with user-defined analytical thermal/non thermal particle distribution models. By default, the application integrates IDL callable DLL and Shared libraries containing fast GS emission codes developed in FORTRAN and C++ and soft and hard X-ray codes developed in IDL. However, the interactive interface allows interchanging these default libraries with any user-defined IDL or external callable codes designed to solve the radiation transfer equation in the same or other wavelength ranges of interest. To illustrate the tool capacity and generality, we present a step-by-step real-time computation of microwave and X-ray images from realistic magnetic structures obtained from a magnetic field extrapolation preceding a real event, and compare them with the actual imaging data obtained by NORH and RHESSI instruments. We discuss further anticipated developments of the tools needed to accommodate temporal evolution of the magnetic field structure and/or fast electron population implied by the electron acceleration and transport. This work was supported in part by NSF grants AGS-0961867, AST-0908344, and NASA grants NNX10AF27G and NNX11AB49G to New Jersey Institute of Technology, by a UK STFC rolling grant, STFC/PPARC Advanced Fellowship, and the Leverhulme Trust, UK. Financial support by the European Commission through the SOLAIRE and HESPE Networks is gratefully acknowledged.

Effect of human patient plasma ex vivo treatment on gene expression and progenitor cell activation of primary human liver cells in multi-compartment 3D perfusion bioreactors for extra-corporeal liver support.

PubMed

Schmelzer, Eva; Mutig, Kerim; Schrade, Petra; Bachmann, Sebastian; Gerlach, Jörg C; Zeilinger, Katrin

2009-07-01

Cultivation of primary human liver cells in innovative 3D perfusion multi-compartment capillary membrane bioreactors using decentralized mass exchange and integral oxygenation provides in vitro conditions close to the physiologic environment in vivo. While a few scale-up bioreactors were used clinically, inoculated liver progenitors in these bioreactors were not investigated. Therefore, we characterized regenerative processes and expression patterns of auto- and paracrine mediators involved in liver regeneration in bioreactors after patient treatment. Primary human liver cells containing parenchymal and non-parenchymal cells co-cultivated in bioreactors were used for clinical extra-corporeal liver support to bridge to liver transplantation. 3D tissue re-structuring in bioreactors was studied; expression of proteins and genes related to regenerative processes and hepatic progenitors was analyzed. Formation of multiple bile ductular networks and colonies of putative progenitors were observed within parenchymal cell aggregates. HGF was detected in scattered cells located close to vascular-like structures, expression of HGFA and c-Met was assigned to biliary cells and hepatocytes. Increased expression of genes associated to hepatic progenitors was detected following clinical application. The results confirm auto- and paracrine interactions between co-cultured cells in the bioreactor. The 3D bioreactor provides a valuable tool to study mechanisms of progenitor activation and hepatic regeneration ex vivo under patient plasma treatment. (c) 2009 Wiley Periodicals, Inc.

Pneumococcal polysaccharides complexed with C3d bind to human B lymphocytes via complement receptor type 2.

PubMed Central

Griffioen, A W; Rijkers, G T; Janssens-Korpela, P; Zegers, B J

1991-01-01

The immunoregulatory function of the complement system has been the focus of many investigations. In particular, fragments of complement factor C3 have been shown to play a role in B-lymphocyte activation and proliferation, lymphokine production, and the generation of in vitro antibody production. Purified pneumococcal polysaccharides (PS) can induce direct activation of C3 via the alternative pathway. Using sera of C1q-deficient patients and healthy subjects, we demonstrated that C3d, a split product of C3 that is generated after degradation of iC3b, can be bound to PS antigens. The binding of C3d to PS can occur in the absence of specific antibodies. Subsequently, we showed that PS complexed with C3d can be recognized by complement receptor type 2 that is expressed on B cells. Treatment of B cells with a monoclonal antibody recognizing the C3d-binding site of complement receptor type 2 reduces the binding of PS-C3d to the cells. In addition, we showed that PS4 complexed with C3d exerted an increased immunogenicity compared with free PS4. Our results show that the complement system plays a role in the activation of PS-specific B cells, carrying membrane receptors for C3d. Consequently, the complement system plays a regulatory role in the antibody response to T-cell-independent type 2 antigens such as PS. PMID:1826897

Anti-Rh(c), "little c," isoimmunization: the role of rHuEpo in preventing late anemia.

PubMed

Zuppa, Antonio A; Cardiello, Valentina; Alighieri, Giovanni; Cota, Francesco; D'Antuono, Annamaria; Riccardi, Riccardo; Catenazzi, Piero; Romagnoli, Costantino

2013-08-01

The overall prevalence of non-Rh-D isoimmunization seems to lie between 0.15% and 1.1%. Anti-Rh(c) alloimmunization, "little c," occurs in 0.07% of pregnancies and shows a quite broad clinical presentation. Late anemia is a frequent problem occurring in the setting of isoimmunization. It occurs more frequently after intrauterine blood transfusions or exsanguinotransfusion, and it can be thought as a hyporegenerative anemia. The authors describe the use of human recombinant erythropoietin in preventing late anemia in a case of anti-Rh(c) isoimmunization. The use of human recombinant erythropoietin is a valid tool for preventing late-onset anemia due to either anti-Rh-D or non-anti-Rh-D isoimmunization.

Enabling Real-Time Volume Rendering of Functional Magnetic Resonance Imaging on an iOS Device.

PubMed

Holub, Joseph; Winer, Eliot

2017-12-01

Powerful non-invasive imaging technologies like computed tomography (CT), ultrasound, and magnetic resonance imaging (MRI) are used daily by medical professionals to diagnose and treat patients. While 2D slice viewers have long been the standard, many tools allowing 3D representations of digital medical data are now available. The newest imaging advancement, functional MRI (fMRI) technology, has changed medical imaging from viewing static to dynamic physiology (4D) over time, particularly to study brain activity. Add this to the rapid adoption of mobile devices for everyday work and the need to visualize fMRI data on tablets or smartphones arises. However, there are few mobile tools available to visualize 3D MRI data, let alone 4D fMRI data. Building volume rendering tools on mobile devices to visualize 3D and 4D medical data is challenging given the limited computational power of the devices. This paper describes research that explored the feasibility of performing real-time 3D and 4D volume raycasting on a tablet device. The prototype application was tested on a 9.7" iPad Pro using two different fMRI datasets of brain activity. The results show that mobile raycasting is able to achieve between 20 and 40 frames per second for traditional 3D datasets, depending on the sampling interval, and up to 9 frames per second for 4D data. While the prototype application did not always achieve true real-time interaction, these results clearly demonstrated that visualizing 3D and 4D digital medical data is feasible with a properly constructed software framework.

Thermodynamics of triple helix formation: spectrophotometric studies on the d(A)10.2d(T)10 and d(C+3T4C+3).d(G3A4G3).d(C3T4C3) triple helices.

PubMed Central

Pilch, D S; Brousseau, R; Shafer, R H

1990-01-01

We have stabilized the d(A)10.2d(T)10 and d(C+LT4C+3).d(G3A4G3).d(C3T4C3) triple helices with either NaCl or MgCl2 at pH 5.5. UV mixing curves demonstrate a 1:2 stoichiometry of purine to pyrimidine strands under the appropriate conditions of pH and ionic strength. Circular dichroic titrations suggest a possible sequence-independent spectral signature for triplex formation. Thermal denaturation profiles indicate the initial loss of the third strand followed by dissociation of the underlying duplex with increasing temperature. Depending on the base sequence and ionic conditions, the binding affinity of the third strand for the duplex at 25 degrees C is two to five orders of magnitude lower than that of the two strands forming the duplex. Thermodynamic parameters for triplex formation were determined for both sequences in the presence of 50 mM MgCl2 and/or 2.0 M NaCl. Hoogsteen base pairs are 0.22-0.64 kcal/mole less stable than Watson-Crick base pairs, depending on ionic conditions and base composition. C+.G and T.A Hoogsteen base pairs appear to have similar stability in the presence of Mg2+ ions at low pH. PMID:2216768

The molecular adjuvant mC3d enhances the immunogenicity of FimA from type I fimbriae of Salmonella enterica serovar Enteritidis.

PubMed

Musa, Hassan-Hussein; Zhang, Wei-Juan; Lv, Jing; Duan, Xiao-Li; Yang, Yang; Zhu, Chun-Hong; Li, Hui-Fang; Chen, Kuan-Wei; Meng, Xia; Zhu, Guo-Qiang

2014-02-01

The fimbriae of Salmonella enterica serovar Enteritidis are used for colonization and invasion into host cells, and have drawn considerable interest because fimbriae can serve as potential immunogens against many pathogenic bacteria that colonize on epithelial surfaces. The purpose of the study is to use a molecular adjuvant, C3d, to enhance the immunogenicity of FimA proteins against Salmonella enterica serovar Enteritidis. FimA of type I fimbriae from Salmonella enteritidis and FimA with one copy of mC3d, two copies of mC3d2 and three copies of mC3d3 were cloned into the expression vector pCold-TF. Soluble fusion proteins of FimA with different copy of mC3d were induced by IPTG and expressed into Escherichia coli BL21 (DE3). Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) showed that the recombinant proteins from pCold-TF-fimA, TF-fimA-mC3d, TF-fimA-mC3d2, TF-fimA-mC3d3 were 70 kDa, 100 kDa, 130 kDa and 160 kDa, respectively. The fusion protein was recognized by rabbit anti-fimbriae polyclonal antibodies, and then visualized by goat anti-rabbit polyclonal antibodies with a chrome appearance by enzyme-subtract interaction. The recombinant proteins were purified by Ni-TED (tris-carboxymethyl ethylene diamine), immobilized metal ion affinity chromatography (IMAC). Balb/c mice were subcutaneously immunized with the purified proteins and the immune response was monitored by an enzyme-linked immunosorbent assay (ELISA) for FimA-specific antibody. The immunized mice were challenged with a 10-fold LD50 dose (i.e., 100 CFU) of Salmonella enterica serovar Enteritidis standard strain (SD-2) 1 week after the second immunization. The immunized mice with the fusion proteins FimA-mC3d2 and FimA-mC3d3 had increased levels of ELISA titer of antibody that were 2 and 4 logs, respectively, more immunogenic than the TF-FimA protein alone. The challenge results showed that immune protection rate in the mice immunized with 10 μg of FimA, FimA-mC3d2, and FimA-mC3d3 were 50%, 75% and 100%, respectively. We conclude that mC3d can be expressed in a prokaryotic vector and enhance the immune response of the recombinant protein. FimA-mC3d3 is potentially a subunit vaccine against S. enterica serovar Enteritidis infection. Copyright © 2012. Published by Elsevier B.V.

Epithelial innervation of human cornea: a three-dimensional study using confocal laser scanning fluorescence microscopy.

PubMed

Guthoff, Rudolf F; Wienss, Holger; Hahnel, Christian; Wree, Andreas

2005-07-01

Evaluation of a new method to visualize distribution and morphology of human corneal nerves (Adelta- and C-fibers) by means of fluorescence staining, confocal laser scanning microscopy, and 3-dimensional (3D) reconstruction. Trephinates of corneas with a diagnosis of Fuchs corneal dystrophy were sliced into layers of 200 microm thickness using a Draeger microkeratome (Storz, Germany). The anterior lamella was stained with the Life/Dead-Kit (Molecular Probes Inc.), examined by the confocal laser scanning microscope "Odyssey XL," step size between 0.5 and 1 microm, and optical sections were digitally 3D-reconstructed. Immediate staining of explanted corneas by the Life/Dead-Kit gave a complete picture of the nerves in the central human cornea. Thin nerves running parallel to the Bowman layer in the subepithelial plexus perforate the Bowman layer orthogonally through tube-like structures. Passing the Bowman layer, Adelta- and C-fibers can be clearly distinguished by fiber diameter, and, while running in the basal epithelial plexus, by their spatial arrangement. Adelta-fibers run straight and parallel to the Bowman layer underneath the basal cell layer. C-fibers, after a short run parallel to the Bowman layer, send off multiple branches penetrating epithelial cell layers orthogonally, ending blindly in invaginations of the superficial cells. In contrast to C-fibers, Adelta-fibers show characteristic bulbous formations when kinking into the basal epithelial plexus. Ex-vivo fluorescence staining of the cornea and 3D reconstructions of confocal scans provide a fast and easily reproducible tool to visualize nerves of the anterior living cornea at high resolution. This may help to clarify gross variations of nerve fiber patterns under various clinical and experimental conditions.

Synthesis, characterization and computational study of the newly synthetized sulfonamide molecule

NASA Astrophysics Data System (ADS)

Murthy, P. Krishna; Suneetha, V.; Armaković, Stevan; Armaković, Sanja J.; Suchetan, P. A.; Giri, L.; Rao, R. Sreenivasa

2018-02-01

A new compound N-(2,5-dimethyl-4-nitrophenyl)-4-methylbenzenesulfonamide (NDMPMBS) has been derived from 2,5-dimethyl-4-nitroaniline and 4-methylbenzene-1-sulfonyl chloride. Structure was characterized by SCXRD studies and spectroscopic tools. Compound crystallized in the monoclinic crystal system with P21/c space group a = 10.0549, b = 18.967, c = 8.3087, β = 103.18 and Z = 4. Type and nature of intermolecular interaction in crystal state investigated by 3D-Hirshfeld surface and 2D-finger print plots revealed that title compound stabilized by several interactions. The structural and electronic properties of title compound have been calculated at DFT/B3LYP/6-311G++(d,p) level of theory. Computationally obtained spectral data was compared with experimental results, showing excellent mutual agreement. Assignment of each vibrational wave number was done on the basis of potential energy distribution (PED). Investigation of local reactivity descriptors encompassed visualization of molecular electrostatic potential (MEP) and average local ionization energy (ALIE) surfaces, visualization of Fukui functions, natural bond order (NBO) analysis, bond dissociation energies for hydrogen abstraction (H-BDE) and radial distribution functions (RDF) after molecular dynamics (MD) simulations. MD simulations were also used in order to investigate interaction of NDMPMBS molecule with 1WKR and 3ETT proteins protein.

An Examination of Target Tracking in the Antisubmarine Warfare Systems Evaluation Tool (ASSET)

DTIC Science & Technology

1991-09-01

fnCorC- Ingi Ing?)))) WX CY) Calt) (dlat2 Ccosl.±sp lat2 C) (if 0- C. diet dIng? 0.0001) (proqa (if (- flag 0) (proqa (if f- ding 0) (proqa (if (c latl...x Y)) (if (or C brg 90) Cbzg 2101) fsetq rnq C- cat? dIng)) Csetq tag (abs C/ diet Cco&Lisp brgC C C Csetq rng tC 60.1077 rng)) (list rag brgC C;let...Xdus i .X KetO : 0 yea 0 0 vi : .- (-2ln(md(I ))) cod 2rad(l ( i +Xd ye n .- (-2.n(rd(I)))n 2- rnd(I ) +Ydis n ,Vet V .xp -aA 4A,- - .k .H- it .- vx

Quantification of Dynamic Morphological Drug Responses in 3D Organotypic Cell Cultures by Automated Image Analysis

PubMed Central

Härmä, Ville; Schukov, Hannu-Pekka; Happonen, Antti; Ahonen, Ilmari; Virtanen, Johannes; Siitari, Harri; Åkerfelt, Malin; Lötjönen, Jyrki; Nees, Matthias

2014-01-01

Glandular epithelial cells differentiate into complex multicellular or acinar structures, when embedded in three-dimensional (3D) extracellular matrix. The spectrum of different multicellular morphologies formed in 3D is a sensitive indicator for the differentiation potential of normal, non-transformed cells compared to different stages of malignant progression. In addition, single cells or cell aggregates may actively invade the matrix, utilizing epithelial, mesenchymal or mixed modes of motility. Dynamic phenotypic changes involved in 3D tumor cell invasion are sensitive to specific small-molecule inhibitors that target the actin cytoskeleton. We have used a panel of inhibitors to demonstrate the power of automated image analysis as a phenotypic or morphometric readout in cell-based assays. We introduce a streamlined stand-alone software solution that supports large-scale high-content screens, based on complex and organotypic cultures. AMIDA (Automated Morphometric Image Data Analysis) allows quantitative measurements of large numbers of images and structures, with a multitude of different spheroid shapes, sizes, and textures. AMIDA supports an automated workflow, and can be combined with quality control and statistical tools for data interpretation and visualization. We have used a representative panel of 12 prostate and breast cancer lines that display a broad spectrum of different spheroid morphologies and modes of invasion, challenged by a library of 19 direct or indirect modulators of the actin cytoskeleton which induce systematic changes in spheroid morphology and differentiation versus invasion. These results were independently validated by 2D proliferation, apoptosis and cell motility assays. We identified three drugs that primarily attenuated the invasion and formation of invasive processes in 3D, without affecting proliferation or apoptosis. Two of these compounds block Rac signalling, one affects cellular cAMP/cGMP accumulation. Our approach supports the growing needs for user-friendly, straightforward solutions that facilitate large-scale, cell-based 3D assays in basic research, drug discovery, and target validation. PMID:24810913

Physics-Based Design Tools for Lightweight Ceramic Composite Turbine Components with Durable Microstructures

NASA Technical Reports Server (NTRS)

DiCarlo, James A.

2011-01-01

Under the Supersonics Project of the NASA Fundamental Aeronautics Program, modeling and experimental efforts are underway to develop generic physics-based tools to better implement lightweight ceramic matrix composites into supersonic engine components and to assure sufficient durability for these components in the engine environment. These activities, which have a crosscutting aspect for other areas of the Fundamental Aero program, are focusing primarily on improving the multi-directional design strength and rupture strength of high-performance SiC/SiC composites by advanced fiber architecture design. This presentation discusses progress in tool development with particular focus on the use of 2.5D-woven architectures and state-of-the-art constituents for a generic un-cooled SiC/SiC low-pressure turbine blade.

Stereoscopic display of 3D models for design visualization

NASA Astrophysics Data System (ADS)

Gilson, Kevin J.

2006-02-01

Advances in display technology and 3D design visualization applications have made real-time stereoscopic visualization of architectural and engineering projects a reality. Parsons Brinkerhoff (PB) is a transportation consulting firm that has used digital visualization tools from their inception and has helped pioneer the application of those tools to large scale infrastructure projects. PB is one of the first Architecture/Engineering/Construction (AEC) firms to implement a CAVE- an immersive presentation environment that includes stereoscopic rear-projection capability. The firm also employs a portable stereoscopic front-projection system, and shutter-glass systems for smaller groups. PB is using commercial real-time 3D applications in combination with traditional 3D modeling programs to visualize and present large AEC projects to planners, clients and decision makers in stereo. These presentations create more immersive and spatially realistic presentations of the proposed designs. This paper will present the basic display tools and applications, and the 3D modeling techniques PB is using to produce interactive stereoscopic content. The paper will discuss several architectural and engineering design visualizations we have produced.

SU-E-T-29: A Web Application for GPU-Based Monte Carlo IMRT/VMAT QA with Delivered Dose Verification

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

Folkerts, M; University of California, San Diego, La Jolla, CA; Graves, Y

Purpose: To enable an existing web application for GPU-based Monte Carlo (MC) 3D dosimetry quality assurance (QA) to compute “delivered dose” from linac logfile data. Methods: We added significant features to an IMRT/VMAT QA web application which is based on existing technologies (HTML5, Python, and Django). This tool interfaces with python, c-code libraries, and command line-based GPU applications to perform a MC-based IMRT/VMAT QA. The web app automates many complicated aspects of interfacing clinical DICOM and logfile data with cutting-edge GPU software to run a MC dose calculation. The resultant web app is powerful, easy to use, and is ablemore » to re-compute both plan dose (from DICOM data) and delivered dose (from logfile data). Both dynalog and trajectorylog file formats are supported. Users upload zipped DICOM RP, CT, and RD data and set the expected statistic uncertainty for the MC dose calculation. A 3D gamma index map, 3D dose distribution, gamma histogram, dosimetric statistics, and DVH curves are displayed to the user. Additional the user may upload the delivery logfile data from the linac to compute a 'delivered dose' calculation and corresponding gamma tests. A comprehensive PDF QA report summarizing the results can also be downloaded. Results: We successfully improved a web app for a GPU-based QA tool that consists of logfile parcing, fluence map generation, CT image processing, GPU based MC dose calculation, gamma index calculation, and DVH calculation. The result is an IMRT and VMAT QA tool that conducts an independent dose calculation for a given treatment plan and delivery log file. The system takes both DICOM data and logfile data to compute plan dose and delivered dose respectively. Conclusion: We sucessfully improved a GPU-based MC QA tool to allow for logfile dose calculation. The high efficiency and accessibility will greatly facilitate IMRT and VMAT QA.« less

United States Air Force Summer Research Program 1991. Summer Faculty Research Program (SFRP) Reports. Volume 4. Rome Laboratory, Arnold Engineering Development Center, F. J. Seiler Research Laboratory

DTIC Science & Technology

1992-01-09

Herschfelder, J. 0., C . F. Curtis, and R. B. Bird, "Molecular Theory of Gases and Liquids", John Willey and Sons, New York, (1954), Chs. 7 and 8. 12...AL iryLt’ AND SLOTME 5- FUIING NUERS 1991 Sumn~er FAculty Resezrzi! ?ro-rz~ (SFBZF) Volne 2SbV0d. 4 F496202-4:4#- C -CO076 MtrGary_ Soore ___________ 7...Engineering Tools for Parallel Software Development Dr. John Antonio 2 (Report Not Available at this Time) Dr. Abdul Aziz Bhatti 3 A Taxonomy for

Conductivity as a Tool for Evaluating the Homogeneity of Sintered Discs of Transition Metal Oxides.

DTIC Science & Technology

1981-02-18

KERSHAW. B KHVZAI H LEIVA, K DWIGHT N00014 77 C 0387 UNCLASSIFIED T-13 L SECURITY CLASSIFICAThON OF TIIS PAI’E 1 -,, k . -’nerl REOTDNAG’" IREAD...Kershaw, B . Khazai, H. Leiva, K . Dwight and A. Wold Prepared for Publication in the Materials Research Bulletin Brown University Department of...Sintered Discs of Transition.0 PERFORMNGOR¢.REPORT NUMBER M e t a l O x i d e s e • " ! t P’b . ’ 1 R P T N K -w h f Y l N I4 -7 7 -C-1 3 8 Ro~ershaw; Ba

Retinoic Acid Therapy Resistance Progresses from Unilineage to Bilineage in HL-60 Leukemic Blasts

PubMed Central

Jensen, Holly A.; Bunaciu, Rodica P.; Ibabao, Christopher N.; Myers, Rebecca; Varner, Jeffrey D.; Yen, Andrew

2014-01-01

Emergent resistance can be progressive and driven by global signaling aberrations. All-trans retinoic acid (RA) is the standard therapeutic agent for acute promyelocytic leukemia, but 10–20% of patients are not responsive, and initially responsive patients relapse and develop retinoic acid resistance. The patient-derived, lineage-bipotent acute myeloblastic leukemia (FAB M2) HL-60 cell line is a potent tool for characterizing differentiation-induction therapy responsiveness and resistance in t(15;17)-negative cells. Wild-type (WT) HL-60 cells undergo RA-induced granulocytic differentiation, or monocytic differentiation in response to 1,25-dihydroxyvitamin D3 (D3). Two sequentially emergent RA-resistant HL-60 cell lines, R38+ and R38-, distinguishable by RA-inducible CD38 expression, do not arrest in G1/G0 and fail to upregulate CD11b and the myeloid-associated signaling factors Vav1, c-Cbl, Lyn, Fgr, and c-Raf after RA treatment. Here, we show that the R38+ and R38- HL-60 cell lines display a progressive reduced response to D3-induced differentiation therapy. Exploiting the biphasic dynamic of induced HL-60 differentiation, we examined if resistance-related defects occurred during the first 24 h (the early or “precommitment” phase) or subsequently (the late or “lineage-commitment” phase). HL-60 were treated with RA or D3 for 24 h, washed and retreated with either the same, different, or no differentiation agent. Using flow cytometry, D3 was able to induce CD38, CD11b and CD14 expression, and G1/G0 arrest when present during the lineage-commitment stage in R38+ cells, and to a lesser degree in R38- cells. Clustering analysis of cytometry and quantified Western blot data indicated that WT, R38+ and R38- HL-60 cells exhibited decreasing correlation between phenotypic markers and signaling factor expression. Thus differentiation induction therapy resistance can develop in stages, with initial partial RA resistance and moderate vitamin D3 responsiveness (unilineage maturation block), followed by bilineage maturation block and progressive signaling defects, notably the reduced expression of Vav1, Fgr, and c-Raf. PMID:24922062

Electrostatic contributions drive the interaction between Staphylococcus aureus protein Efb-C and its complement target C3d.

PubMed

Haspel, Nurit; Ricklin, Daniel; Geisbrecht, Brian V; Kavraki, Lydia E; Lambris, John D

2008-11-01

The C3-inhibitory domain of Staphylococcus aureus extracellular fibrinogen-binding protein (Efb-C) defines a novel three-helix bundle motif that regulates complement activation. Previous crystallographic studies of Efb-C bound to its cognate subdomain of human C3 (C3d) identified Arg-131 and Asn-138 of Efb-C as key residues for its activity. In order to characterize more completely the physical and chemical driving forces behind this important interaction, we employed in this study a combination of structural, biophysical, and computational methods to analyze the interaction of C3d with Efb-C and the single-point mutants R131A and N138A. Our results show that while these mutations do not drastically affect the structure of the Efb-C/C3d recognition complex, they have significant adverse effects on both the thermodynamic and kinetic profiles of the resulting complexes. We also characterized other key interactions along the Efb-C/C3d binding interface and found an intricate network of salt bridges and hydrogen bonds that anchor Efb-C to C3d, resulting in its potent complement inhibitory properties.

Natural 13C abundance: a tool to trace the incorporation of dung-derived carbon into soil particle-size fractions.

PubMed

Amelung, W; Bol, R; Friedrich, C

1999-01-01

During the decay of 13C enriched dung patches, the; delta 13C signal of surface soil (1-5 cm) increased with a temporary maximum after 42 d. To understand the underlying processes, we investigated the incorporation of dung-derived C into soil particle-size fractions. Dung, collected from beef steers fed on maize (delta 13C = -15.36/1000) or ryegrass (delta 13C = -25.67/1000), was applied in circular patches to a C3 pasture at North Wyke, UK. Triplicates were sampled from surface soil (1-5 cm) at 14, 28, 42, and 70 d after application, pooled, separated into fine (< 0.2 micron) and coarse clay (0.2-2 microns), silt plus fine sand (2-250 microns), and coarse sand (250-2000 microns), and analyzed for total C, N, and delta 13C. As particle-size diameter decreased, the C/N ratios decreased and delta 13C values increased at all plots due to increasing microbial alteration of soil organic matter. After dung application, ca. 60% of dung-derived C in soil was recovered in the 0.2-250 microns fractions during the whole experiment. The proportion of dung-derived C in the fine clay peaked 42 d after dung application, coinciding with the delta 13C maximum in the bulk soil and the maximum leaching rate measured in lysimeters at this time in another study at the same sites. The percentage of dung-derived C as particulate C in the coarse sand fraction increased until the end of the experiment. We conclude that incorporation of C into soil from decomposing dung patches involved both temporary sorption of leached dung C to < 0.2 micron fractions and continuous accumulation of particulate C (> 250 microns).

Metabolism of 20-Hydroxyvitamin D3 and 20,23-Dihydroxyvitamin D3 by Rat and Human CYP24A1

PubMed Central

Tieu, Elaine W.; Li, Wei; Chen, Jianjun; Kim, Tae-Kang; Ma, Dejian; Slominski, Andrzej T.; Tuckey, Robert C.

2015-01-01

CYP11A1 hydroxylates vitamin D3 producing 20S-hydroxyvitamin D3 [20(OH)D3] and 20S,23-dihydroxyvitamin D3 [20,23(OH)2D3] as the major and most characterized metabolites. Both display immuno-regulatory and anti-cancer properties while being non-calcemic. A previous study indicated 20(OH)D3 can be metabolized by rat CYP24A1 to products including 20S,24-dihydroxyvitamin D3 [20,24(OH)2D3] and 20S,25-dihydroxyvitamin D3, with both producing greater inhibition of melanoma colony formation than 20(OH)D3. The aim of this study was to characterize the ability of rat and human CYP24A1 to metabolize 20(OH)D3 and 20,23(OH)2D3. Both isoforms metabolized 20(OH)D3 to the same dihydroxyvitamin D species with no secondary metabolites being observed. Hydroxylation at C24 produced both enantiomers of 20,24(OH)2D3. For rat CYP24A1 the preferred initial site of hydroxylation was at C24 whereas the human enzyme preferred C25. 20,23(OH)2D3 was initially metabolized to 20S,23,24-trihydroxyvitamin D3 and 20S,23,25-trihydroxyvitamin D3 by rat and human CYP24A1 as determined by NMR, with both isoforms showing a preference for initial hydroxylation at C25. CYP24A1 was able to further oxidize these metabolites in a series of reactions which included the cleavage of C23-C24 bond, as indicated by high resolution mass spectrometry of the products, analogous to the catabolism of 1,25(OH)2D3 via the C24-oxidation pathway. Similar catalytic efficiencies were observed for the metabolism of 20(OH)D3 and 20,23(OH)2D3 by human CYP24A1 and were lower than for the metabolism of 1,25(OH)2D3. We conclude that rat and human CYP24A1 metabolizes 20(OH)D3 producing only dihydroxyvitamin D3 species as products which retain biological activity, whereas 20,23(OH)2D3 undergoes multiple oxidations which include cleavage of the side chain. PMID:25727742

Collaborative Aerial-Drawing System for Supporting Co-Creative Communication

NASA Astrophysics Data System (ADS)

Osaki, Akihiro; Taniguchi, Hiroyuki; Miwa, Yoshiyuki

This paper describes the collaborative augmented reality (AR) system with which multiple users can handwrite 3D lines in the air simultaneously and manipulate the lines directly in the real world. In addition, we propose a new technique for co-creative communication utilizing the 3D drawing activity. Up to now, the various 3D user interfaces have been proposed. Although most of them aim to solve the specific problems in the virtual environments, the possibility of the 3D drawing expression has not been explored yet. Accordingly, we paid special attention to the interaction with the real objects in daily life, and considered to manipulate real objects and 3D lines without any distinctions by the same action. The developed AR system consists of a stereoscopic head-mounted display, a drawing tool, 6DOF sensors measuring three-dimensional position and Euler angles, and the 3D user interface, which enables to push, grasp and pitch 3D lines directly by use of the drawing tool. Additionally users can pick up desired color from either a landscape or a virtual line through the direct interaction with this tool. For sharing 3D lines among multiple users at the same place, the distributed-type AR system has been developed that mutually sends and receives drawn data between systems. With the developed system, users can proceed to design jointly in the real space through arranging each 3D drawing by direct manipulation. Moreover, a new application to the entertainment has become possible to play sports like catch, fencing match, or the like.

A Guide for Industrial Mobilization

DTIC Science & Technology

1989-03-01

packages; and cient, increased production controls may be needed. These actions include: i. Releasing machine tool trigger or- ders and increasing buys...710). the Department of Defense to maintain facili- 4. The National Defense Act authorizes: ties, machine tools , production equipment, and skilled...Defense Industrial Reserve Act pro- Room 3876, U.S. Departm nt of Commerce vides for the reserve of machine tools and other Washington, D.C. 20230 or

Building a Genetic Manipulation Tool Box for Orchid Biology: Identification of Constitutive Promoters and Application of CRISPR/Cas9 in the Orchid, Dendrobium officinale

PubMed Central

Kui, Ling; Chen, Haitao; Zhang, Weixiong; He, Simei; Xiong, Zijun; Zhang, Yesheng; Yan, Liang; Zhong, Chaofang; He, Fengmei; Chen, Junwen; Zeng, Peng; Zhang, Guanghui; Yang, Shengchao; Dong, Yang; Wang, Wen; Cai, Jing

2017-01-01

Orchidaceae is the second largest family of flowering plants, which is highly valued for its ornamental purposes and medicinal uses. Dendrobium officinale is a special orchid species that can grow without seed vernalization. Because the whole-genome sequence of D. officinale is publicly available, this species is poised to become a convenient research model for the evolutionary, developmental, and genetic studies of Orchidaceae. Despite these advantages, the methods of genetic manipulation are poorly developed in D. officinale. In this study, based on the previously developed Agrobacterium-mediated gene transformation system, we identified several highly efficient promoters for exogenous gene expression and successfully applied the CRISPR/Cas9 system for editing endogenous genes in the genome of D. officinale. These two basic techniques contribute to the genetic manipulation toolbox of Orchidaceae. The pCambia-1301-35SN vector containing the CaMV 35S promoter and the β-glucuronidase (GUS) and Superfolder green fluorescence protein (SG) as reporter genes were introduced into the plant tissues by the Agrobacterium-mediated transformation system. Fluorescence emission from the transformed plants confirmed the successful transcription and translation of SG genes into functional proteins. We compared the GUS activity under different promoters including four commonly used promoters (MtHP, CVMV, MMV and PCISV) with CaMV 35S promoter and found that MMV, CVMV, and PCISV were as effective as the 35S promoter. Furthermore, we applied the CRISPR/Cas9-mediated genome editing system successfully in D. officinale. By selecting five target genes (C3H, C4H, 4CL, CCR, and IRX) in the lignocellulose biosynthesis pathway, we showed that, for a given target, this system can generate edits (insertions, deletions, or substitutions) at a rate of 10 to 100%. These results showed that our two genetic manipulation tools can efficiently express exogenous genes and edit endogenous genes in D. officinale. These efficient research tools will not only help create novel D. officinale varieties, but will also facilitate the molecular genetic investigation of orchid biology. PMID:28127299

Building a Genetic Manipulation Tool Box for Orchid Biology: Identification of Constitutive Promoters and Application of CRISPR/Cas9 in the Orchid, Dendrobium officinale.

PubMed

Kui, Ling; Chen, Haitao; Zhang, Weixiong; He, Simei; Xiong, Zijun; Zhang, Yesheng; Yan, Liang; Zhong, Chaofang; He, Fengmei; Chen, Junwen; Zeng, Peng; Zhang, Guanghui; Yang, Shengchao; Dong, Yang; Wang, Wen; Cai, Jing

2016-01-01

Orchidaceae is the second largest family of flowering plants, which is highly valued for its ornamental purposes and medicinal uses. Dendrobium officinale is a special orchid species that can grow without seed vernalization. Because the whole-genome sequence of D. officinale is publicly available, this species is poised to become a convenient research model for the evolutionary, developmental, and genetic studies of Orchidaceae. Despite these advantages, the methods of genetic manipulation are poorly developed in D. officinale . In this study, based on the previously developed Agrobacterium -mediated gene transformation system, we identified several highly efficient promoters for exogenous gene expression and successfully applied the CRISPR/Cas9 system for editing endogenous genes in the genome of D. officinale . These two basic techniques contribute to the genetic manipulation toolbox of Orchidaceae. The pCambia-1301-35SN vector containing the CaMV 35S promoter and the β-glucuronidase ( GUS ) and Superfolder green fluorescence protein (SG) as reporter genes were introduced into the plant tissues by the Agrobacterium -mediated transformation system. Fluorescence emission from the transformed plants confirmed the successful transcription and translation of SG genes into functional proteins. We compared the GUS activity under different promoters including four commonly used promoters (MtHP, CVMV, MMV and PCISV) with CaMV 35S promoter and found that MMV, CVMV, and PCISV were as effective as the 35S promoter. Furthermore, we applied the CRISPR/Cas9-mediated genome editing system successfully in D. officinale . By selecting five target genes ( C3H, C4H, 4CL, CCR, and IRX ) in the lignocellulose biosynthesis pathway, we showed that, for a given target, this system can generate edits (insertions, deletions, or substitutions) at a rate of 10 to 100%. These results showed that our two genetic manipulation tools can efficiently express exogenous genes and edit endogenous genes in D. officinale . These efficient research tools will not only help create novel D. officinale varieties, but will also facilitate the molecular genetic investigation of orchid biology.

Evaluation of an interactive science publishing tool: toward enabling three-dimensional analysis of medical images.

PubMed

Rinewalt, Daniel; Williams, Betsy W; Reeves, Anthony P; Shah, Palmi; Hong, Edward; Mulshine, James L

2015-03-01

Higher resolution medical imaging platforms are rapidly emerging, but there is a challenge in applying these tools in a clinically meaningful way. The purpose of the current study was to evaluate a novel three-dimensional (3D) software imaging environment, known as interactive science publishing (ISP), in appraising 3D computed tomography images and to compare this approach with traditional planar (2D) imaging in a series of lung cancer cases. Twenty-four physician volunteers at different levels of training across multiple specialties were recruited to evaluate eight lung cancer-related clinical vignettes. The volunteers were asked to compare the performance of traditional 2D versus the ISP 3D imaging in assessing different visualization environments for diagnostic and measurement processes and to further evaluate the ISP tool in terms of general satisfaction, usability, and probable applicability. Volunteers were satisfied with both imaging methods; however, the 3D environment had significantly higher ratings. Measurement performance was comparable using both traditional 2D and 3D image evaluation. Physicians not trained in 2D measurement approaches versus those with such training demonstrated better performance with ISP and preferred working in the ISP environment. Recent postgraduates with only modest self-administered training performed equally well on 3D and 2D cases. This suggests that the 3D environment has no reduction in accuracy over the conventional 2D approach, while providing the advantage of a digital environment for cross-disciplinary interaction for shared problem solving. Exploration of more effective, efficient, self-directed training could potentially result in further improvement in image evaluation proficiency and potentially decrease training costs. Copyright © 2015. Published by Elsevier Inc.

Specificity of monoclonal antibodies to strains of Dickeya sp. that cause bacterial heart rot of pineapple.

PubMed

Peckham, Gabriel D; Kaneshiro, Wendy S; Luu, Van; Berestecky, John M; Alvarez, Anne M

2010-10-01

During a severe outbreak of bacterial heart rot that occurred in pineapple plantations on Oahu, Hawaii, in 2003 and years following, 43 bacterial strains were isolated from diseased plants or irrigation water and identified as Erwinia chrysanthemi (now Dickeya sp.) by phenotypic, molecular, and pathogenicity assays. Rep-PCR fingerprint patterns grouped strains from pineapple plants and irrigation water into five genotypes (A-E) that differed from representatives of other Dickeya species, Pectobacterium carotovorum and other enteric saprophytes isolated from pineapple. Monoclonal antibodies produced following immunization of mice with virulent type C Dickeya sp. showed only two specificities. MAb Pine-1 (2D11G1, IgG1 with kappa light chain) reacted to all 43 pineapple/water strains and some reference strains (D. dianthicola, D. chrysanthemi, D. paradisiaca, some D. dadantii, and uncharacterized Dickeya sp.) but did not react to reference strains of D. dieffenbachiae, D. zeae, or one of the two Malaysian pineapple strains. MAb Pine-2 (2A7F2, IgG3 with kappa light chain) reacted to all type B, C, and D strains but not to any A or E strains or any reference strains except Dickeya sp. isolated from Malaysian pineapple. Pathogenicity tests showed that type C strains were more aggressive than type A strains when inoculated during cool months. Therefore, MAb Pine-2 distinguishes the more virulent type C strains from less virulent type A pineapple strains and type E water strains. MAbs with these two specificities enable development of rapid diagnostic tests that will distinguish the systemic heart rot pathogen from opportunistic bacteria associated with rotted tissues. Use of the two MAbs in field assays also permits the monitoring of a known subpopulation and provides additional decision tools for disease containment and management practices.

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters

PubMed Central

Ono, Keiichiro; Demchak, Barry; Ideker, Trey

2014-01-01

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape to popular JavaScript library readable formats. In addition, we implemented template web applications for browser-based interactive network visualization that can be used as basis for complex data visualization applications for bioinformatics research. Example web applications created with these tools demonstrate how Cytoscape works in modern data visualization workflows built with traditional desktop tools and emerging web-based technologies. This interactivity enables researchers more flexibility than with static images, thereby greatly improving the quality of insights researchers can gain from them. PMID:25520778

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters.

PubMed

Ono, Keiichiro; Demchak, Barry; Ideker, Trey

2014-01-01

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape to popular JavaScript library readable formats. In addition, we implemented template web applications for browser-based interactive network visualization that can be used as basis for complex data visualization applications for bioinformatics research. Example web applications created with these tools demonstrate how Cytoscape works in modern data visualization workflows built with traditional desktop tools and emerging web-based technologies. This interactivity enables researchers more flexibility than with static images, thereby greatly improving the quality of insights researchers can gain from them.

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

Lichtscheidl, Alejandro G.; Janicke, Michael T.; Scott, Brian L.

The synthesis and full characterization, including Nuclear Magnetic Resonance (NMR) data ( 1H, 13C{ 1H} and 119Sn{ 1H}), for a series of Me 3SnX (X = O-2,6-tBu 2C 6H 3 (1), (Me 3Sn)N(2,6- iPr 2C 6H 3) (3), NH-2,4,6- tBu 3C 6H 2 (4), N(SiMe 3) 2 (5), NEt 2, C 5Me 5 (6), Cl, Br, I, and SnMe 3) compounds in benzene-d 6, toluene-d 8, dichloromethane-d 2, chloroform-d 1, acetonitrile-d 3, and tetrahydrofuran-d 8 are reported. The X-ray crystal structures of Me 3Sn(O-2,6- tBu 2C 6H 3) (1), Me 3Sn(O-2,6- iPr 2C 6H 3) (2), and (Me 3Sn)(NH-2,4,6- tBumore » 3C 6H 2) (4) are also presented. As a result, these compiled data complement existing literature data and ease the characterization of these compounds by routine NMR experiments.« less

Freeform manufacturing of a microoptical lens array on a steep curved substrate by use of a voice coil fast tool servo.

PubMed

Scheiding, Sebastian; Yi, Allen Y; Gebhardt, Andreas; Li, Lei; Risse, Stefan; Eberhardt, Ramona; Tünnermann, Andreas

2011-11-21

We report what is to our knowledge the first approach to diamond turn microoptical lens array on a steep curved substrate by use of a voice coil fast tool servo. In recent years ultraprecision machining has been employed to manufacture accurate optical components with 3D structure for beam shaping, imaging and nonimaging applications. As a result, geometries that are difficult or impossible to manufacture using lithographic techniques might be fabricated using small diamond tools with well defined cutting edges. These 3D structures show no rotational symmetry, but rather high frequency asymmetric features thus can be treated as freeform geometries. To transfer the 3D surface data with the high frequency freeform features into a numerical control code for machining, the commonly piecewise differentiable surfaces are represented as a cloud of individual points. Based on this numeric data, the tool radius correction is calculated to account for the cutting-edge geometry. Discontinuities of the cutting tool locations due to abrupt slope changes on the substrate surface are bridged using cubic spline interpolation.When superimposed with the trajectory of the rotationally symmetric substrate the complete microoptical geometry in 3D space is established. Details of the fabrication process and performance evaluation are described. © 2011 Optical Society of America

Can 3D Gamified Simulations Be Valid Vocational Training Tools for Persons with Intellectual Disability? An Experiment Based on a Real-life Situation.

PubMed

von Barnekow, Ariel; Bonet-Codina, Núria; Tost, Dani

2017-03-23

To investigate if 3D gamified simulations can be valid vocational training tools for persons with intellectual disability. A 3D gamified simulation composed by a set of training tasks for cleaning in hostelry was developed in collaboration with professionals of a real hostel and pedagogues of a special needs school. The learning objectives focus on the acquisition of vocabulary skills, work procedures, social abilities and risk prevention. Several accessibility features were developed to make the tasks easy to do from a technological point-of-view. A pilot experiment was conducted to test the pedagogical efficacy of this tool on intellectually disabled workers and students. User scores in the gamified simulation follow a curve of increasing progression. When confronted with reality, they recognized the scenario and tried to reproduce what they had learned in the simulation. Finally, they were interested in the tool, they showed a strong feeling of immersion and engagement, and they reported having fun. On the basis of this experiment we believe that 3D gamified simulations can be efficient tools to train social and professional skills of persons with intellectual disabilities contributing thus to foster their social inclusion through work.

Diamond in 3-D

NASA Image and Video Library

2004-08-20

This 3-D, microscopic imager mosaic of a target area on a rock called Diamond Jenness was taken after NASA Mars Exploration Rover Opportunity ground into the surface with its rock abrasion tool for a second time. 3D glasses are necessary.

Rapid fabrication of detachable three-dimensional tissues by layering of cell sheets with heating centrifuge.

PubMed

Haraguchi, Yuji; Kagawa, Yuki; Hasegawa, Akiyuki; Kubo, Hirotsugu; Shimizu, Tatsuya

2018-01-18

Confluent cultured cells on a temperature-responsive culture dish can be harvested as an intact cell sheet by decreasing temperature below 32°C. A three-dimensional (3-D) tissue can be fabricated by the layering of cell sheets. A resulting 3-D multilayered cell sheet-tissue on a temperature-responsive culture dish can be also harvested without any damage by only temperature decreasing. For shortening the fabrication time of the 3-D multilayered constructs, we attempted to layer cell sheets on a temperature-responsive culture dish with centrifugation. However, when a cell sheet was attached to the culture surface with a conventional centrifuge at 22-23°C, the cell sheet hardly adhere to the surface due to its noncell adhesiveness. Therefore, in this study, we have developed a heating centrifuge. In centrifugation (55g) at 36-37°C, the cell sheet adhered tightly within 5 min to the dish without significant cell damage. Additionally, centrifugation accelerated the cell sheet-layering process. The heating centrifugation shortened the fabrication time by one-fifth compared to a multilayer tissue fabrication without centrifugation. Furthermore, the multilayered constructs were finally detached from the dishes by decreasing temperature. This rapid tissue-fabrication method will be used as a valuable tool in the field of tissue engineering and regenerative therapy. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 2018. © 2018 American Institute of Chemical Engineers.

Harnessing the power of emerging petascale platforms

NASA Astrophysics Data System (ADS)

Mellor-Crummey, John

2007-07-01

As part of the US Department of Energy's Scientific Discovery through Advanced Computing (SciDAC-2) program, science teams are tackling problems that require computational simulation and modeling at the petascale. A grand challenge for computer science is to develop software technology that makes it easier to harness the power of these systems to aid scientific discovery. As part of its activities, the SciDAC-2 Center for Scalable Application Development Software (CScADS) is building open source software tools to support efficient scientific computing on the emerging leadership-class platforms. In this paper, we describe two tools for performance analysis and tuning that are being developed as part of CScADS: a tool for analyzing scalability and performance, and a tool for optimizing loop nests for better node performance. We motivate these tools by showing how they apply to S3D, a turbulent combustion code under development at Sandia National Laboratory. For S3D, our node performance analysis tool helped uncover several performance bottlenecks. Using our loop nest optimization tool, we transformed S3D's most costly loop nest to reduce execution time by a factor of 2.94 for a processor working on a 503 domain.

3D Designing for Mathematical Learning

ERIC Educational Resources Information Center

Greenstein, Steven; Leszczynski, Eliza; Fernández, Eileen

2017-01-01

Inspired by the promise of new 3D technologies and the proposition that new tools make innovation possible, this article provides a case study of how a tool called Thirty6 was designed and used in classrooms by mathematics teachers in their own varied and invented ways. Unlike established manipulatives that are designed to support the learning of…

Web-Based Interactive 3D Visualization as a Tool for Improved Anatomy Learning

ERIC Educational Resources Information Center

Petersson, Helge; Sinkvist, David; Wang, Chunliang; Smedby, Orjan

2009-01-01

Despite a long tradition, conventional anatomy education based on dissection is declining. This study tested a new virtual reality (VR) technique for anatomy learning based on virtual contrast injection. The aim was to assess whether students value this new three-dimensional (3D) visualization method as a learning tool and what value they gain…

Annotation an effective device for student feedback: a critical review of the literature.

PubMed

Ball, Elaine C

2010-05-01

The paper examines hand-written annotation, its many features, difficulties and strengths as a feedback tool. It extends and clarifies what modest evidence is in the public domain and offers an evaluation of how to use annotation effectively in the support of student feedback [Marshall, C.M., 1998a. The Future of Annotation in a Digital (paper) World. Presented at the 35th Annual GLSLIS Clinic: Successes and Failures of Digital Libraries, June 20-24, University of Illinois at Urbana-Champaign, March 24, pp. 1-20; Marshall, C.M., 1998b. Toward an ecology of hypertext annotation. Hypertext. In: Proceedings of the Ninth ACM Conference on Hypertext and Hypermedia, June 20-24, Pittsburgh Pennsylvania, US, pp. 40-49; Wolfe, J.L., Nuewirth, C.M., 2001. From the margins to the centre: the future of annotation. Journal of Business and Technical Communication, 15(3), 333-371; Diyanni, R., 2002. One Hundred Great Essays. Addison-Wesley, New York; Wolfe, J.L., 2002. Marginal pedagogy: how annotated texts affect writing-from-source texts. Written Communication, 19(2), 297-333; Liu, K., 2006. Annotation as an index to critical writing. Urban Education, 41, 192-207; Feito, A., Donahue, P., 2008. Minding the gap annotation as preparation for discussion. Arts and Humanities in Higher Education, 7(3), 295-307; Ball, E., 2009. A participatory action research study on handwritten annotation feedback and its impact on staff and students. Systemic Practice and Action Research, 22(2), 111-124; Ball, E., Franks, H., McGrath, M., Leigh, J., 2009. Annotation is a valuable tool to enhance learning and assessment in student essays. Nurse Education Today, 29(3), 284-291]. Although a significant number of studies examine annotation, this is largely related to on-line tools and computer mediated communication and not hand-written annotation as comment, phrase or sign written on the student essay to provide critique. Little systematic research has been conducted to consider how this latter form of annotation influences student learning and assessment or, indeed, helps tutors to employ better annotative practices [Juwah, C., Macfarlane-Dick, D., Matthew, B., Nicol, D., Ross, D., Smith, B., 2004. Enhancing student learning through effective formative feedback. The Higher Education Academy, 1-40; Jewitt, C., Kress, G., 2005. English in classrooms: only write down what you need to know: annotation for what? English in Education, 39(1), 5-18]. There is little evidence on ways to heighten students' self-awareness when their essays are returned with annotated feedback [Storch, N., Tapper, J., 1997. Student annotations: what NNS and NS university students say about their own writing. Journal of Second Language Writing, 6(3), 245-265]. The literature review clarifies forms of annotation as feedback practice and offers a summary of the challenges and usefulness of annotation. Copyright 2009. Published by Elsevier Ltd.

Cultural Resources Intensive Survey and Testing of Mississippi River Levee Berms, Crittenden and Desha Counties, Arkansas and Mississippi, Scott, Cape Girardeau and Pemiscot Counties, Missouri Item R-618 Knowlton; Desha County, Arkansas.

DTIC Science & Technology

1983-11-01

grave goods such as copper beads, pipes, raw, rare materials, and conch shells from the Gulf are common (Haag 1971:18). The Hopewellilan concept of...WILMSEN, E. N. 1970 Lithic Analysis and Cultural Inference: A Paleo-Indian Case. Anthropological Papers of the University of Arizona 16. 1973...ground celt of black porphyry (Figure C-3:d). It shows some chipping along one longitudinal side. This tool is 10 centimeters in length, 3.5 centimeters

Experiences with the MANA simulation tool

DTIC Science & Technology

2006-08-01

ALERT and FAVS simulations. Also, agents in these simulations needed to conduct careful formation fighting while following established CF doctrine...simulations auraient dû pouvoir se déplacer en formation , suivant la doctrine établie des Forces canadiennes. Cependant, des comportements d’une...29 Annex C – Alternative approach to inter-squad coordination of retreat.................................. 32 List of acronyms

Cost and time-effective method for multi-scale measures of rugosity, fractal dimension, and vector dispersion from coral reef 3D models

PubMed Central

Dey, S.

2017-01-01

We present a method to construct and analyse 3D models of underwater scenes using a single cost-effective camera on a standard laptop with (a) free or low-cost software, (b) no computer programming ability, and (c) minimal man hours for both filming and analysis. This study focuses on four key structural complexity metrics: point-to-point distances, linear rugosity (R), fractal dimension (D), and vector dispersion (1/k). We present the first assessment of accuracy and precision of structure-from-motion (SfM) 3D models from an uncalibrated GoPro™ camera at a small scale (4 m2) and show that they can provide meaningful, ecologically relevant results. Models had root mean square errors of 1.48 cm in X-Y and 1.35 in Z, and accuracies of 86.8% (R), 99.6% (D at scales 30–60 cm), 93.6% (D at scales 1–5 cm), and 86.9 (1/k). Values of R were compared to in-situ chain-and-tape measurements, while values of D and 1/k were compared with ground truths from 3D printed objects modelled underwater. All metrics varied less than 3% between independently rendered models. We thereby improve and rigorously validate a tool for ecologists to non-invasively quantify coral reef structural complexity with a variety of multi-scale metrics. PMID:28406937

Assessing metal contamination from construction and demolition (C&D) waste used to infill wetlands: using Deroceras reticulatum (Mollusca: Gastropoda).

PubMed

Staunton, John A; Mc Donnell, Rory J; Gormally, Michael J; Williams, Chris D; Henry, Tiernan; Morrison, Liam

2014-11-01

Large quantities of construction and demolition waste (C&D) are produced globally every year, with little known about potential environmental impacts. In the present study, the slug, Deroceras reticulatum (Mollusca: Gastropoda) was used as the first biomonitor of metals (Ag, As, Ba, Cd, Co, Cr, Cu, Mn, Mo, Ni, Pb, Sb, Se, Ti, Tl, V and Zn) on wetlands post infilling with construction and demolition (C&D) waste. The bioaccumulation of As, Ba, Cd, Co, Sb, Se and Tl were found to be significantly elevated in slugs collected on C&D waste when compared to unimproved pastures (control sites), while Mo, Se and Sr had significantly higher concentrations in slugs collected on C&D waste when compared to known contaminated sites (mining locations), indicating the potential hazardous nature of C&D waste to biota. Identifying exact sources for these metals within the waste can be problematic, due to its heterogenic nature. Biomonitors are a useful tool for future monitoring and impact studies, facilitating policy makers and regulations in other countries regarding C&D waste infill. In addition, improving separation of C&D waste to allow increased reuse and recycling is likely to be effective in reducing the volume of waste being used as infill, subsequently decreasing potential metal contamination.

After Action Review Tools for Dismounted Soldier Systems

DTIC Science & Technology

2008-06-01

Social Sciences A Directorate of the Department of the Army Deputy Chief of Staff, G1 Authorized and approved for distribution: BARBARA A. BLACK, Ph.D...began to improve both the quantity and quality of food supplies. However, the greatest change came in April with the arrival of Friedrich Wilhelm von...Management during training. 41 DATE: TA *IMMM27 lwba:4 MR TES Casftsa MwaWr SYSTM STATUS: RUNNING Training Elements in View 3 Pre Opicwlg p Post OPS C u S Q

Synthetic Lectins: New Tools for Detection and Management of Prostate Cancer

DTIC Science & Technology

2015-08-01

development of a prostate cancer diagnostic. AIM 1 describes a library based approach for the discovery of SLs targeting CAGs. AIM 2 describes biochemical...help with fluorescence polarization. This work was supported by funds provided from NIH COBRE grant P20RR17698.Notes and references 1 D. H. Dube and C...R. Bertozzi, Nat. Rev. Drug Discovery , 2005, 4, 477–488. 2 V. Harmat and G. Naray-Szabo, Croat. Chim. Acta, 2009, 82, 277– 282. 3 J. J. Lavigne and

Synthetic Lectins: New Tools for Detection and Management of Prostate Cancer

DTIC Science & Technology

2014-08-01

diagnostic. AIM 1 describes a library based approach for the discovery of SLs targeting CAGs. AIM 2 describes biochemical and biophysical...Obianyo for their help with fluorescence polarization. This work was supported by funds provided from NIH COBRE grant P20RR17698.Notes and references...1 D. H. Dube and C. R. Bertozzi, Nat. Rev. Drug Discovery , 2005, 4, 477–488. 2 V. Harmat and G. Naray-Szabo, Croat. Chim. Acta, 2009, 82, 277– 282. 3

Space transfer vehicle concepts and requirements study. Volume 3: Program cost estimates. Book 2: WBS and dictionary

NASA Technical Reports Server (NTRS)

Peffley, A. F.

1991-01-01

This document describes the products and services to be developed, tested, produced, and operated for the Space Transfer Vehicle (STV) Program. The Work Breakdown Structure (WBS) and WBS Dictionary are program management tools used to catalog, account by task, and summarize work packages of a space system program. The products or services to be delivered or accomplished during the STV C/D phase are the primary focus of this work breakdown structure document.

Novel mutations in the CDKL5 gene in complex genotypes associated with West syndrome with variable phenotype: First description of somatic mosaic state.

PubMed

Jdila, Marwa Ben; Issa, Abir Ben; Khabou, Boudour; Rhouma, Bochra Ben; Kamoun, Fatma; Ammar-Keskes, Leila; Triki, Chahnez; Fakhfakh, Faiza

2017-10-01

West syndrome is a rare epileptic encephalopathy of early infancy, characterized by epileptic spasms, hypsarrhythmia, and psychomotor retardation beginning in the first year of life. The present study reports the clinical, molecular and bioinformatic investigation in the three studied West patients. The results revealed a complex genotype with more than one mutation in each patient including the known mutations c.1910C>G (P2, P3); c.2372A>C in P3 and c.2395C>G in P1 and novel variants including c.616G>A, shared by the three patients P1, P2 and P3; c.1403G>C shared by P2 and P3 and c.2288A>G in patient P1. All the mutations were at somatic mosaic state and were de novo in the patients except ones (c.2372A>C). To our knowledge; the somatic mosaic state is described for the first time in patients with West syndrome. Five identified mutations were located in the C-terminal domain of the protein, while the novel mutation (c.616G>A) was in the catalytic domain. Bioinformatic tools predicted that this latter is the most pathogenic substitution affecting 3D protein structure and the secondary mRNA structure. Complex genotype composed of different combinations of mutations in each patient seems to be related to the phenotype variability. Copyright © 2017. Published by Elsevier B.V.

Bone density assessment for evaluation of gender differences in cervical vertebral maturation: A computed tomography study.

PubMed

Usha, K; Baskaranarayanan, Balashanmugam; Nagarajan, D; Selvarani, R; Vijjaykanth, M

2016-10-01

The cervical vertebral maturation (CVM) method is a vital tool for assessing the biological maturation of the orthodontic patient to evaluate the amount of mandibular bone growth left. To assess and visualize the cervical vertebral morphology (bone density) of orthodontic patients of the age group 9,16,27 years. Twenty four subjects with age group of 9,16,27 who were randomly selected and subjected to 3d tomographic study to estimate the biological age of the orthodontic patients by analyzing c1 c2 and c3 vertebrae. The results showed that bone density of males is lesser than females in 9 and 16 years, whereas they have more bone density than females in 27 years. The study provides qualitative method of assessing the biological age of the patient by using images of cervical vertebrae by three dimensional approach. Hence it can be useful for orthodontic diagnosis and treatment plan.

Planets and Life

NASA Astrophysics Data System (ADS)

Sullivan, Woodruff T., III; Baross, John

2007-09-01

Foreword; Preface; Contributors; Prologue; Part I. History: 1. History of astrobiological ideas W. T. Sullivan and D. Carney; 2. From exobiology to astrobiology S. J. Dick; Part II. The Physical Stage: 3. Formation of Earth-like habitable planets D. E. Brownlee and M. Kress; 4. Planetary atmospheres and life D. Catling and J. F. Kasting; Part III. The Origin of Life on Earth: 5. Does 'life' have a definition? C.E. Cleland and C. F. Chyba; 6. Origin of life: crucial issues R. Shapiro; 7. Origin of proteins and nucleic acids A. Ricardo and S. A. Benner; 8. The roots of metabolism G.D. Cody and J. H. Scott; 9. Origin of cellular life D. W. Deamer; Part IV. Life on Earth: 10. Evolution: a defining feature of life J. A. Baross; 11. Evolution of metabolism and early microbial communities J. A. Leigh, D. A. Stahl and J. T. Staley; 12. The earliest records of life on Earth R. Buick; 13. The origin and diversification of eukaryotes M. L. Sogin, D. J. Patterson and A. McArthur; 14. Limits of carbon life on Earth and elsewhere J. A. Baross, J. Huber and M. Schrenk; 15. Life in ice J. W. Deming and H. Eicken; 16. The evolution and diversification of life S. Awramik and K. J. McNamara; 17. Mass extinctions P. D. Ward; Part V. Potentially Habitable Worlds: 18. Mars B. M. Jakosky, F. Westall and A. Brack; 19. Europa C. F. Chyba and C. B. Phillips; 20. Titan J. I. Lunine and B. Rizk; 21. Extrasolar planets P. Butler; Part VI. Searching for Extraterrestrial Life: 22. How to search for life on other worlds C. P. McKay; 23. Instruments and strategies for detecting extraterrestrial life P. G. Conrad; 24. Societial and ethical concerns M. S. Race; 25. Planetary protection J. D. Rummel; 26. Searching for extraterrestrial intelligence J. C. Tarter; 27. Alien biochemistries P. D. Ward and S. A. Benner; Part VII. Future of the Field: 28. Disciplinary and educational opportunities L. Wells, J. Armstrong and J. Huber; Epilogue C. F. Chyba; Appendixes: A. Units and usages; B. Planetary properties; C. The geological time scale S. Awramik and K. J. McNamara; D. Astrobiological destinations on planet Earth J. Harnmeijer; E. Micro*scope web tool D. J. Patterson and M. L. Sogin; Index.

Application of cell co-culture system to study fat and muscle cells.

PubMed

Pandurangan, Muthuraman; Hwang, Inho

2014-09-01

Animal cell culture is a highly complex process, in which cells are grown under specific conditions. The growth and development of these cells is a highly unnatural process in vitro condition. Cells are removed from animal tissues and artificially cultured in various culture vessels. Vitamins, minerals, and serum growth factors are supplied to maintain cell viability. Obtaining result homogeneity of in vitro and in vivo experiments is rare, because their structure and function are different. Living tissues have highly ordered complex architecture and are three-dimensional (3D) in structure. The interaction between adjacent cell types is quite distinct from the in vitro cell culture, which is usually two-dimensional (2D). Co-culture systems are studied to analyze the interactions between the two different cell types. The muscle and fat co-culture system is useful in addressing several questions related to muscle modeling, muscle degeneration, apoptosis, and muscle regeneration. Co-culture of C2C12 and 3T3-L1 cells could be a useful diagnostic tool to understand the muscle and fat formation in animals. Even though, co-culture systems have certain limitations, they provide a more realistic 3D view and information than the individual cell culture system. It is suggested that co-culture systems are useful in evaluating the intercellular communication and composition of two different cell types.

Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

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

Tjong, Harianto; Li, Wenyuan; Kalhor, Reza

Conformation capture technologies (e.g., Hi-C) chart physical interactions between chromatin regions on a genome-wide scale. However, the structural variability of the genome between cells poses a great challenge to interpreting ensemble-averaged Hi-C data, particularly for long-range and interchromosomal interactions. Here, we present a probabilistic approach for deconvoluting Hi-C data into a model population of distinct diploid 3D genome structures, which facilitates the detection of chromatin interactions likely to co-occur in individual cells. Here, our approach incorporates the stochastic nature of chromosome conformations and allows a detailed analysis of alternative chromatin structure states. For example, we predict and experimentally confirm themore » presence of large centromere clusters with distinct chromosome compositions varying between individual cells. The stability of these clusters varies greatly with their chromosome identities. We show that these chromosome-specific clusters can play a key role in the overall chromosome positioning in the nucleus and stabilizing specific chromatin interactions. By explicitly considering genome structural variability, our population-based method provides an important tool for revealing novel insights into the key factors shaping the spatial genome organization.« less

Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

DOE PAGES

Tjong, Harianto; Li, Wenyuan; Kalhor, Reza; ...

2016-03-07

Conformation capture technologies (e.g., Hi-C) chart physical interactions between chromatin regions on a genome-wide scale. However, the structural variability of the genome between cells poses a great challenge to interpreting ensemble-averaged Hi-C data, particularly for long-range and interchromosomal interactions. Here, we present a probabilistic approach for deconvoluting Hi-C data into a model population of distinct diploid 3D genome structures, which facilitates the detection of chromatin interactions likely to co-occur in individual cells. Here, our approach incorporates the stochastic nature of chromosome conformations and allows a detailed analysis of alternative chromatin structure states. For example, we predict and experimentally confirm themore » presence of large centromere clusters with distinct chromosome compositions varying between individual cells. The stability of these clusters varies greatly with their chromosome identities. We show that these chromosome-specific clusters can play a key role in the overall chromosome positioning in the nucleus and stabilizing specific chromatin interactions. By explicitly considering genome structural variability, our population-based method provides an important tool for revealing novel insights into the key factors shaping the spatial genome organization.« less

A Lower Temperature FDM 3D Printing for the Manufacture of Patient-Specific Immediate Release Tablets.

PubMed

Okwuosa, Tochukwu C; Stefaniak, Dominika; Arafat, Basel; Isreb, Abdullah; Wan, Ka-Wai; Alhnan, Mohamed A

2016-11-01

The fabrication of ready-to-use immediate release tablets via 3D printing provides a powerful tool to on-demand individualization of dosage form. This work aims to adapt a widely used pharmaceutical grade polymer, polyvinylpyrrolidone (PVP), for instant on-demand production of immediate release tablets via FDM 3D printing. Dipyridamole or theophylline loaded filaments were produced via processing a physical mixture of API (10%) and PVP in the presence of plasticizer through hot-melt extrusion (HME). Computer software was utilized to design a caplet-shaped tablet. The surface morphology of the printed tablet was assessed using scanning electron microscopy (SEM). The physical form of the drugs and its integrity following an FDM 3D printing were assessed using x-ray powder diffractometry (XRPD), thermal analysis and HPLC. In vitro drug release studies for all 3D printed tablets were conducted in a USP II dissolution apparatus. Bridging 3D printing process with HME in the presence of a thermostable filler, talc, enabled the fabrication of immediate release tablets at temperatures as low as 110°C. The integrity of two model drugs was maintained following HME and FDM 3D printing. XRPD indicated that a portion of the loaded theophylline remained crystalline in the tablet. The fabricated tablets demonstrated excellent mechanical properties, acceptable in-batch variability and an immediate in vitro release pattern. Combining the advantages of PVP as an impeding polymer with FDM 3D printing at low temperatures, this approach holds a potential in expanding the spectrum of drugs that could be used in FDM 3D printing for on demand manufacturing of individualised dosage forms.

30 CFR 902.15 - Approval of Alaska regulatory program amendments.

Code of Federal Regulations, 2011 CFR

2011-07-01

...), .185(a)(3), (4), (5), .207(c)(5)(C), .213(g), (h), .323(a) through (d), .325(b), (c), (d)(1), (2), (3...), .349(2)(A), .353(a)(1), (2), (3), .371(d)(1) through (4), .373(b), (c), (d), .375(b), (e) through (h...), .491(a), (1), (6), (7), (8), (c)(4) through (8), (e), (f), .901(e), .907(c) through (h), (j). December...

30 CFR 902.15 - Approval of Alaska regulatory program amendments.

Code of Federal Regulations, 2010 CFR

2010-07-01

...), .185(a)(3), (4), (5), .207(c)(5)(C), .213(g), (h), .323(a) through (d), .325(b), (c), (d)(1), (2), (3...), .349(2)(A), .353(a)(1), (2), (3), .371(d)(1) through (4), .373(b), (c), (d), .375(b), (e) through (h...), .491(a), (1), (6), (7), (8), (c)(4) through (8), (e), (f), .901(e), .907(c) through (h), (j). December...

29 CFR 1926.959 - Lineman's body belts, safety straps, and lanyards.

Code of Federal Regulations, 2010 CFR

2010-07-01

... tool pockets. On shifting D belts, this measurement for pocket tabs shall be taken when the D ring section is centered. (3) A maximum of four (4) tool loops shall be so situated on the body belt that four... of tool loops, and any other attachments. (4) Suitable copper, steel, or equivalent liners shall be...

The role of 3-D interactive visualization in blind surveys of H I in galaxies

NASA Astrophysics Data System (ADS)

Punzo, D.; van der Hulst, J. M.; Roerdink, J. B. T. M.; Oosterloo, T. A.; Ramatsoku, M.; Verheijen, M. A. W.

2015-09-01

Upcoming H I surveys will deliver large datasets, and automated processing using the full 3-D information (two positional dimensions and one spectral dimension) to find and characterize H I objects is imperative. In this context, visualization is an essential tool for enabling qualitative and quantitative human control on an automated source finding and analysis pipeline. We discuss how Visual Analytics, the combination of automated data processing and human reasoning, creativity and intuition, supported by interactive visualization, enables flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities helping the discovery and analysis of subtle structures in the 3-D domain. The requirements for a fully interactive visualization tool are: coupled 1-D/2-D/3-D visualization, quantitative and comparative capabilities, combined with supervised semi-automated analysis. Moreover, the source code must have the following characteristics for enabling collaborative work: open, modular, well documented, and well maintained. We review four state of-the-art, 3-D visualization packages assessing their capabilities and feasibility for use in the case of 3-D astronomical data.

19F and 13C NMR studies of polyol metabolism in freeze-tolerant pupae of Hyalophora cecropia.

PubMed

Podlasek, C A; Serianni, A S

1994-01-28

Sorbitol biosynthesis and regulation in freeze tolerant pupae of Hyalophora cecropia have been investigated as a function of temperature by 19F and 13C nuclear magnetic resonance (NMR) spectroscopy using several 13C-labeled and/or fluorine-substituted carbohydrates. 3-Deoxy-3-fluoro-D-glucose (3DFG) was metabolized to 3-deoxy-3-fluoro-D-sorbitol (3DFS), 3-deoxy-3-fluoro-D-fructose (3DFF), and 3-deoxy-3-fluoro-D-gluconic acid (3DFGA), indicating that the enzymes required for sorbitol biosynthesis and metabolism are active in H. cecropia at warm (22 degrees C) and cold (4 and -10 degrees C) temperatures. Two additional metabolites were produced when pupae were injected with either 3DFG, 3DFS, 3DFF, or 3-deoxy-3-fluoro-D-mannose (3DFM). One of these was identified as 3-deoxy-3-fluoro-D-mannitol (3DFML) by 13C NMR using [1-13C]3DFM and [1-13C]3DFG as metabolic probes. H. cecropia pupae injected with D-glucose labeled with 13C at C-1, C-2, or C-3 and subsequently analyzed by 13C NMR clearly demonstrated the ability to generate sorbitol and fructose. In contrast, gas chromatography/mass spectrometric analysis of hemolymph failed to detect sorbitol in pupae reared under natural conditions (i.e. in the absence of injected enriched sugars). Thus, although H. cecropia pupae have the enzymic machinery to biosynthesize sorbitol, they do not appear to accumulate high steady-state concentrations of this polyol over the temperature range studied. The specificity of the enzymes involved in alditol biosynthesis in H. cecropia was examined by 13C NMR with a wide range of aldoses enriched with 13C at C-1. Pupae were capable of converting these sugars to their corresponding [1-13C]alditols, indicating that nonspecific dehydrogenase(s), in addition to aldose reductase, is(are) involved in polyol biosynthesis in H. cecropia pupae.

Parametric study of STOL short-haul transport engine cycles and operational techniques to minimize community noise impact

NASA Technical Reports Server (NTRS)

1974-01-01

The effect of aircraft operational techniques in the terminal area on community noise impact of future short haul aircraft was investigated. Aircraft equipped with mechanical flap (MF) and aircraft with externally blown flap (EBF) were used to study the noise impact at four U.S. airports. The four airports were: (1) Hanscom Field (Boston), (2) Washington National (D.C.), (3) Midway (Chicago) and (4) Orange County (California). With the exception of Washington National (D.C.), the study showed that a reduction of approximately 40 percent in the number of people highly annoyed can be obtained by using the recommended operational techniques. The evaluation procedures and methodology developed in the study represent an advance in acoustical state-of-the-art and provide an effective and useful tool for determining aircraft noise impact on the airport community.

VizieR Online Data Catalog: Slug analysis of star clusters in NGC 628 & 7793 (Krumholz+, 2015)

NASA Astrophysics Data System (ADS)

Krumholz, M. R.; Adamo, A.; Fumagalli, M.; Wofford, A.; Calzetti, D.; Lee, J. C.; Whitmore, B. C.; Bright, S. N.; Grasha, K.; Gouliermis, D. A.; Kim, H.; Nair, P.; Ryon, J. E.; Smith, L. J.; Thilker, D.; Ubeda, L.; Zackrisson, E.

2016-02-01

In this paper we use slug, the Stochastically Lighting Up Galaxies code (da Silva et al. 2012ApJ...745..145D, 2014MNRAS.444.3275D; Krumholz et al. 2015MNRAS.452.1447K), and its post-processing tool for analysis of star cluster properties, cluster_slug, to analyze an initial sample of clusters from the LEGUS (Calzetti et al. 2015AJ....149...51C). A description of the steps required to produce final cluster catalogs of the Legacy Extragalactic UV Survey (LEGUS) targets can be found in Calzetti et al. (2015AJ....149...51C), and in A. Adamo et al. (2015, in preparation). LEGUS is an HST Cycle 21 Treasury program that is imaging 50 nearby galaxies in five broadbands with the WFC3/UVIS, from the NUV to the I band. (1 data file).

30 CFR 946.25 - Approval of Virginia abandoned mine land reclamation plan amendments.

Code of Federal Regulations, 2010 CFR

2010-07-01

..., 1987 November 13, 1987 VR 480-03-19.884.13(c) (2), (5), (6), (7), (d)(1), (2); Establish emergency... CFR 884.13(a), (b), (c)(1), (c)(2), (c)(3), (c)(4), (c)(5), (c)(6), (c)(7), (d)(1), (d)(2), (d)(3), (d... Division of Mined Land Reclamation, P.O. Drawer 900, Big Stone Gap, Virginia 24219, or (2) Office of...

Web3DMol: interactive protein structure visualization based on WebGL.

PubMed

Shi, Maoxiang; Gao, Juntao; Zhang, Michael Q

2017-07-03

A growing number of web-based databases and tools for protein research are being developed. There is now a widespread need for visualization tools to present the three-dimensional (3D) structure of proteins in web browsers. Here, we introduce our 3D modeling program-Web3DMol-a web application focusing on protein structure visualization in modern web browsers. Users submit a PDB identification code or select a PDB archive from their local disk, and Web3DMol will display and allow interactive manipulation of the 3D structure. Featured functions, such as sequence plot, fragment segmentation, measure tool and meta-information display, are offered for users to gain a better understanding of protein structure. Easy-to-use APIs are available for developers to reuse and extend Web3DMol. Web3DMol can be freely accessed at http://web3dmol.duapp.com/, and the source code is distributed under the MIT license. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Critical evaluation of reverse engineering tool Imagix 4D!

PubMed

Yadav, Rashmi; Patel, Ravindra; Kothari, Abhay

2016-01-01

The comprehension of legacy codes is difficult to understand. Various commercial reengineering tools are available that have unique working styles, and are equipped with their inherent capabilities and shortcomings. The focus of the available tools is in visualizing static behavior not the dynamic one. Therefore, it is difficult for people who work in software product maintenance, code understanding reengineering/reverse engineering. Consequently, the need for a comprehensive reengineering/reverse engineering tool arises. We found the usage of Imagix 4D to be good as it generates the maximum pictorial representations in the form of flow charts, flow graphs, class diagrams, metrics and, to a partial extent, dynamic visualizations. We evaluated Imagix 4D with the help of a case study involving a few samples of source code. The behavior of the tool was analyzed on multiple small codes and a large code gcc C parser. Large code evaluation was performed to uncover dead code, unstructured code, and the effect of not including required files at preprocessing level. The utility of Imagix 4D to prepare decision density and complexity metrics for a large code was found to be useful in getting to know how much reengineering is required. At the outset, Imagix 4D offered limitations in dynamic visualizations, flow chart separation (large code) and parsing loops. The outcome of evaluation will eventually help in upgrading Imagix 4D and posed a need of full featured tools in the area of software reengineering/reverse engineering. It will also help the research community, especially those who are interested in the realm of software reengineering tool building.

JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases.

PubMed

Feng, Guangjie; Burton, Nick; Hill, Bill; Davidson, Duncan; Kerwin, Janet; Scott, Mark; Lindsay, Susan; Baldock, Richard

2005-03-09

Many three-dimensional (3D) images are routinely collected in biomedical research and a number of digital atlases with associated anatomical and other information have been published. A number of tools are available for viewing this data ranging from commercial visualization packages to freely available, typically system architecture dependent, solutions. Here we discuss an atlas viewer implemented to run on any workstation using the architecture neutral Java programming language. We report the development of a freely available Java based viewer for 3D image data, descibe the structure and functionality of the viewer and how automated tools can be developed to manage the Java Native Interface code. The viewer allows arbitrary re-sectioning of the data and interactive browsing through the volume. With appropriately formatted data, for example as provided for the Electronic Atlas of the Developing Human Brain, a 3D surface view and anatomical browsing is available. The interface is developed in Java with Java3D providing the 3D rendering. For efficiency the image data is manipulated using the Woolz image-processing library provided as a dynamically linked module for each machine architecture. We conclude that Java provides an appropriate environment for efficient development of these tools and techniques exist to allow computationally efficient image-processing libraries to be integrated relatively easily.

Filling gaps in cultural heritage documentation by 3D photography

NASA Astrophysics Data System (ADS)

Schuhr, W.; Lee, J. D.

2015-08-01

This contribution promotes 3D photography as an important tool to obtain objective object information. Keeping mainly in mind World Heritage documentation as well as Heritage protection, it is another intention of this paper, to stimulate the interest in applications of 3D photography for professionals as well as for amateurs. In addition this is also an activity report of the international CIPA task group 3. The main part of this paper starts with "Digging the treasure of existing international 3D photography". This does not only belong to tangible but also to intangible Cultural Heritage. 3D photography clearly supports the recording, the visualization, the preservation and the restoration of architectural and archaeological objects. Therefore the use of 3D photography in C.H. should increase on an international level. The presented samples in 3D represent a voluminous, almost partly "forgotten treasure" of international archives for 3D photography. The next chapter is on "Promoting new 3D photography in Cultural Heritage". Though 3D photographs are a well-established basic photographic and photogrammetric tool, even suited to provide "near real" documentation, they are still a matter of research and improvement. Beside the use of 3D cameras even single lenses cameras are very much suited for photographic 3D documentation purposes in Cultural Heritage. Currently at the Faculty of Civil Engineering of the University of Applied Sciences Magdeburg-Stendal, low altitude aerial photography is exposed from a maximum height of 13m, using a hand hold carbon telescope rod. The use of this "huge selfie stick" is also an (international) recommendation, to expose high resolution 3D photography of monuments under expedition conditions. In addition to the carbon rod recently a captive balloon and a hexacopter UAV- platform is in use, mainly to take better synoptically (extremely low altitude, ground truth) aerial photography. Additional experiments with respect to "easy geometry" and to multistage concepts of 3D photographs in Cultural Heritage just started. Furthermore a revised list of the 3D visualization principles, claiming completeness, has been carried out. Beside others in an outlook *It is highly recommended, to list every historical and current stereo view with relevance to Cultural Heritage in a global Monument Information System (MIS), like in google earth. *3D photographs seem to be very suited, to complete and/or at least partly to replace manual archaeological sketches. In this concern the still underestimated 3D effect will be demonstrated, which even allows, e.g., the spatial perception of extremely small scratches etc... *A consequent dealing with 3D Technology even seems to indicate, currently we experience the beginning of a new age of "real 3DPC- screens", which at least could add or even partly replace the conventional 2D screens. Here the spatial visualization is verified without glasses in an all-around vitreous body. In this respect nowadays widespread lasered crystals showing monuments are identified as "Early Bird" 3D products, which, due to low resolution and contrast and due to lack of color, currently might even remember to the status of the invention of photography by Niepce (1827), but seem to promise a great future also in 3D Cultural Heritage documentation. *Last not least 3D printers more and more seem to conquer the IT-market, obviously showing an international competition.

26 CFR 1.355-6 - Recognition of gain on certain distributions of stock or securities in controlled corporation.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., unless otherwise stated, assume that P, S, T, X, Y, N, HC, D, D1, D2, D3, and C are corporations, A and B... and D2, D1 and D2 each owns 50 percent of the stock of D3, and D3 owns all of the stock of C. Within... the stock of D1, D2, D3, and C on the date A purchases the T stock under the attribution rules of...

DNA vaccines expressing soluble CD4-envelope proteins fused to C3d elicit cross-reactive neutralizing antibodies to HIV-1

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

Bower, Joseph F.; Green, Thomas D.; Ross, Ted M.

2004-10-25

DNA vaccines expressing the envelope (Env) of the human immunodeficiency virus type 1 (HIV-1) have been relatively ineffective at generating high-titer, long-lasting, neutralizing antibodies in a variety of animal models. In this study, DNA vaccines were constructed to express a fusion protein of the soluble human CD4 (sCD4) and the gp120 subunit of the HIV-1 envelope. To enhance the immunogenicity of the expressed fusion protein, three copies of the murine C3d (mC3d{sub 3}) were added to the carboxyl terminus of the complex. Monoclonal antibodies that recognize CD4-induced epitopes on gp120 efficiently bound to sCD4-gp120 or sCD4-gp120-mC3d{sub 3}. In addition, bothmore » sCD4-gp120 and sCD4-gp120-mC3d{sub 3} bound to cells expressing appropriate coreceptors in the absence of cell surface hCD4. Mice (BALB/c) vaccinated with DNA vaccines expressing either gp120-mC3d{sub 3} or sCD4-gp120-mC3d{sub 3} elicited antibodies that neutralized homologous virus infection. However, the use of sCD4-gp120-mC3d{sub 3}-DNA elicited the highest titers of neutralizing antibodies that persisted after depletion of anti-hCD4 antibodies. Interestingly, only mice vaccinated with DNA expressing sCD4-gp120-mC3d{sub 3} had antibodies that elicited cross-protective neutralizing antibodies. The fusion of sCD4 to the HIV-1 envelope exposes neutralizing epitopes that elicit broad protective immunity when the fusion complex is coupled with the molecular adjuvant, C3d.« less

Three-dimensional tool radius compensation for multi-axis peripheral milling

NASA Astrophysics Data System (ADS)

Chen, Youdong; Wang, Tianmiao

2013-05-01

Few function about 3D tool radius compensation is applied to generating executable motion control commands in the existing computer numerical control (CNC) systems. Once the tool radius is changed, especially in the case of tool size changing with tool wear in machining, a new NC program has to be recreated. A generic 3D tool radius compensation method for multi-axis peripheral milling in CNC systems is presented. The offset path is calculated by offsetting the tool path along the direction of the offset vector with a given distance. The offset vector is perpendicular to both the tangent vector of the tool path and the orientation vector of the tool axis relative to the workpiece. The orientation vector equations of the tool axis relative to the workpiece are obtained through homogeneous coordinate transformation matrix and forward kinematics of generalized kinematics model of multi-axis machine tools. To avoid cutting into the corner formed by the two adjacent tool paths, the coordinates of offset path at the intersection point have been calculated according to the transition type that is determined by the angle between the two tool path tangent vectors at the corner. Through the verification by the solid cutting simulation software VERICUT® with different tool radiuses on a table-tilting type five-axis machine tool, and by the real machining experiment of machining a soup spoon on a five-axis machine tool with the developed CNC system, the effectiveness of the proposed 3D tool radius compensation method is confirmed. The proposed compensation method can be suitable for all kinds of three- to five-axis machine tools as a general form.

Effects of D-glucose upon D-fructose metabolism in rat hepatocytes: A 13C NMR study.

PubMed

Malaisse, W J; Ladrière, L; Verbruggen, I; Willem, R

2002-12-01

Isolated hepatocytes from fed rats were exposed for 120 min to D-glucose (10 mM) and either D-[1-13C]fructose, D-[2-13C]fructose or D-[6-13C]fructose (also 10 mM) in the presence of D2O. The identification and quantification of 13C-enriched D-fructose and its metabolites (D-glucose, L-lactate, L-alanine) in the incubation medium and the measurement of their deuterated isotopomers indicated, by comparison with a prior study conducted in the absence of exogenous D-glucose, that the major effects of the aldohexose were to increase the recovery of 13C-enriched D-fructose, decrease the production of 13C-enriched D-glucose, restrict the deuteration of the 13C-enriched isotopomers of D-glucose to those generated by cells exposed to D-[2-13C]fructose, and to accentuate the lesser deuteration of the C, (as compared to C5) of 13C-enriched D-glucose derived from D-[2-13C]fructose. The ratio between C2-deuterated and C2-hydrogenated L-lactate, as well as the relative amounts of the CH3-, CH2D-, CHD, and CD3- isotopomers of 13C-enriched L-lactate were not significantly different, however, in the absence or presence of exogenous D-glucose. These findings indicate that exogenous D-glucose suppressed the deuteration of the C1 of D-[I-13C]glucose generated by hepatocytes exposed to D-[1-13C]fructose or D-[6-13C]fructose, as otherwise attributable, in part at least, to gluconeogenesis from fructose-derived [3-13C]pyruvate, and apparently favoured the phosphorylation of D-fructose by hexokinase isoenzymes, probably through stimulation of D-fructose phosphorylation by glucokinase.

bioWeb3D: an online webGL 3D data visualisation tool

PubMed Central

2013-01-01

Background Data visualization is critical for interpreting biological data. However, in practice it can prove to be a bottleneck for non trained researchers; this is especially true for three dimensional (3D) data representation. Whilst existing software can provide all necessary functionalities to represent and manipulate biological 3D datasets, very few are easily accessible (browser based), cross platform and accessible to non-expert users. Results An online HTML5/WebGL based 3D visualisation tool has been developed to allow biologists to quickly and easily view interactive and customizable three dimensional representations of their data along with multiple layers of information. Using the WebGL library Three.js written in Javascript, bioWeb3D allows the simultaneous visualisation of multiple large datasets inputted via a simple JSON, XML or CSV file, which can be read and analysed locally thanks to HTML5 capabilities. Conclusions Using basic 3D representation techniques in a technologically innovative context, we provide a program that is not intended to compete with professional 3D representation software, but that instead enables a quick and intuitive representation of reasonably large 3D datasets. PMID:23758781

Development of a patient positioning error compensation tool for Korea Heavy-Ion Medical Accelerator Treatment Center

NASA Astrophysics Data System (ADS)

Kim, Min-Joo; Suh, Tae-Suk; Cho, Woong; Jung, Won-Gyun

2015-07-01

In this study, a potential validation tool for compensating for the patient positioning error was developed by using 2D/3D and 3D/3D image registration. For 2D/3D registration, digitallyreconstructed radiography (DRR) and three-dimensional computed tomography (3D-CT) images were applied. The ray-casting algorithm is the most straightforward method for generating DRR, so we adopted the traditional ray-casting method, which finds the intersections of a ray with all objects, voxels of the 3D-CT volume in the scene. The similarity between the extracted DRR and the orthogonal image was measured by using a normalized mutual information method. Two orthogonal images were acquired from a Cyber-knife system from the anterior-posterior (AP) and right lateral (RL) views. The 3D-CT and the two orthogonal images of an anthropomorphic phantom and of the head and neck of a cancer patient were used in this study. For 3D/3D registration, planning CT and in-room CT images were applied. After registration, the translation and the rotation factors were calculated to position a couch to be movable in six dimensions. Registration accuracies and average errors of 2.12 mm ± 0.50 mm for transformations and 1.23 ° ± 0.40 ° for rotations were acquired by using 2D/3D registration with the anthropomorphic Alderson-Rando phantom. In addition, registration accuracies and average errors of 0.90 mm ± 0.30 mm for transformations and 1.00 ° ± 0.2 ° for rotations were acquired by using CT image sets. We demonstrated that this validation tool could compensate for patient positioning errors. In addition, this research could be a fundamental step in compensating for patient positioning errors at the Korea Heavy-ion Medical Accelerator Treatment Center.

Electrostatic Steering Accelerates C3d:CR2 Association.

PubMed

Mohan, Rohith R; Huber, Gary A; Morikis, Dimitrios

2016-08-25

Electrostatic effects are ubiquitous in protein interactions and are found to be pervasive in the complement system as well. The interaction between complement fragment C3d and complement receptor 2 (CR2) has evolved to become a link between innate and adaptive immunity. Electrostatic interactions have been suggested to be the driving factor for the association of the C3d:CR2 complex. In this study, we investigate the effects of ionic strength and mutagenesis on the association of C3d:CR2 through Brownian dynamics simulations. We demonstrate that the formation of the C3d:CR2 complex is ionic strength-dependent, suggesting the presence of long-range electrostatic steering that accelerates the complex formation. Electrostatic steering occurs through the interaction of an acidic surface patch in C3d and the positively charged CR2 and is supported by the effects of mutations within the acidic patch of C3d that slow or diminish association. Our data are in agreement with previous experimental mutagenesis and binding studies and computational studies. Although the C3d acidic patch may be locally destabilizing because of unfavorable Coulombic interactions of like charges, it contributes to the acceleration of association. Therefore, acceleration of function through electrostatic steering takes precedence to stability. The site of interaction between C3d and CR2 has been the target for delivery of CR2-bound nanoparticle, antibody, and small molecule biomarkers, as well as potential therapeutics. A detailed knowledge of the physicochemical basis of C3d:CR2 association may be necessary to accelerate biomarker and drug discovery efforts.

Evaluation of 3D Gamma index calculation implemented in two commercial dosimetry systems

NASA Astrophysics Data System (ADS)

Xing, Aitang; Arumugam, Sankar; Deshpande, Shrikant; George, Armia; Vial, Philip; Holloway, Lois; Goozee, Gary

2015-01-01

3D Gamma index is one of the metrics which have been widely used for clinical routine patient specific quality assurance for IMRT, Tomotherapy and VMAT. The algorithms for calculating the 3D Gamma index using global and local methods implemented in two software tools: PTW- VeriSoft® as a part of OCTIVIUS 4D dosimeter systems and 3DVHTM from Sun Nuclear were assessed. The Gamma index calculated by the two systems was compared with manual calculated for one data set. The Gamma pass rate calculated by the two systems was compared using 3%/3mm, 2%/2mm, 3%/2mm and 2%/3mm for two additional data sets. The Gamma indexes calculated by the two systems were accurate, but Gamma pass rates calculated by the two software tools for same data set with the same dose threshold were different due to the different interpolation of raw dose data by the two systems and different implementation of Gamma index calculation and other modules in the two software tools. The mean difference was -1.3%±3.38 (1SD) with a maximum difference of 11.7%.

Inhibitor design strategy based on an enzyme structural flexibility: a case of bacterial MurD ligase.

PubMed

Perdih, Andrej; Hrast, Martina; Barreteau, Hélène; Gobec, Stanislav; Wolber, Gerhard; Solmajer, Tom

2014-05-27

Increasing bacterial resistance to available antibiotics stimulated the discovery of novel efficacious antibacterial agents. The biosynthesis of the bacterial peptidoglycan, where the MurD enzyme is involved in the intracellular phase of the UDP-MurNAc-pentapeptide formation, represents a collection of highly selective targets for novel antibacterial drug design. In our previous computational studies, the C-terminal domain motion of the MurD ligase was investigated using Targeted Molecular Dynamic (TMD) simulation and the Off-Path Simulation (OPS) technique. In this study, we present a drug design strategy using multiple protein structures for the identification of novel MurD ligase inhibitors. Our main focus was the ATP-binding site of the MurD enzyme. In the first stage, three MurD protein conformations were selected based on the obtained OPS/TMD data as the initial criterion. Subsequently, a two-stage virtual screening approach was utilized combining derived structure-based pharmacophores with molecular docking calculations. Selected compounds were then assayed in the established enzyme binding assays, and compound 3 from the aminothiazole class was discovered to act as a dual MurC/MurD inhibitor in the micomolar range. A steady-state kinetic study was performed on the MurD enzyme to provide further information about the mechanistic aspects of its inhibition. In the final stage, all used conformations of the MurD enzyme with compound 3 were simulated in classical molecular dynamics (MD) simulations providing atomistic insights of the experimental results. Overall, the study depicts several challenges that need to be addressed when trying to hit a flexible moving target such as the presently studied bacterial MurD enzyme and show the possibilities of how computational tools can be proficiently used at all stages of the drug discovery process.

Orbit Transfer Rocket Engine Technology Program

DTIC Science & Technology

1993-10-15

3 TASK D - ADVANCED ENGINE STUDY .............................................. 5 Phase I (D.1, D.2 and D. 3 ...34 High Velocity Ratio Diffusing Crossovers (1.2) .............................. 41 Soft Wear Ring Seals (B. 3 and B.5...67 Combustor Coolant Channel Selection (C.2) .................................. 77 Combustor Caloriniiter Experiments (C. 3 , C.A

Ice-Accretion Test Results for Three Large-Scale Swept-Wing Models in the NASA Icing Research Tunnel

NASA Technical Reports Server (NTRS)

Broeren, Andy P.; Potapczuk, Mark G.; Lee, Sam; Malone, Adam M.; Paul, Benard P., Jr.; Woodard, Brian S.

2016-01-01

Icing simulation tools and computational fluid dynamics codes are reaching levels of maturity such that they are being proposed by manufacturers for use in certification of aircraft for flight in icing conditions with increasingly less reliance on natural-icing flight testing and icing-wind-tunnel testing. Sufficient high-quality data to evaluate the performance of these tools is not currently available. The objective of this work was to generate a database of ice-accretion geometry that can be used for development and validation of icing simulation tools as well as for aerodynamic testing. Three large-scale swept wing models were built and tested at the NASA Glenn Icing Research Tunnel (IRT). The models represented the Inboard (20% semispan), Midspan (64% semispan) and Outboard stations (83% semispan) of a wing based upon a 65% scale version of the Common Research Model (CRM). The IRT models utilized a hybrid design that maintained the full-scale leading-edge geometry with a truncated afterbody and flap. The models were instrumented with surface pressure taps in order to acquire sufficient aerodynamic data to verify the hybrid model design capability to simulate the full-scale wing section. A series of ice-accretion tests were conducted over a range of total temperatures from -23.8 deg C to -1.4 deg C with all other conditions held constant. The results showed the changing ice-accretion morphology from rime ice at the colder temperatures to highly 3-D scallop ice in the range of -11.2 deg C to -6.3 deg C. Warmer temperatures generated highly 3-D ice accretion with glaze ice characteristics. The results indicated that the general scallop ice morphology was similar for all three models. Icing results were documented for limited parametric variations in angle of attack, drop size and cloud liquid-water content (LWC). The effect of velocity on ice accretion was documented for the Midspan and Outboard models for a limited number of test cases. The data suggest that there are morphological characteristics of glaze and scallop ice accretion on these swept-wing models that are dependent upon the velocity. This work has resulted in a large database of ice-accretion geometry on large-scale, swept-wing models.

PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination.

PubMed

Lee, Woonghee; Stark, Jaime L; Markley, John L

2014-11-01

Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727-1728. doi: 10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nuclear Overhauser data sets ((13)C- and/or (15)N-NOESY). The output is a set of assigned NOEs and 3D structural models for the protein. Ponderosa Analyzer supports the visualization, validation, and refinement of the results from Ponderosa Server. These tools enable semi-automated NMR-based structure determination of proteins in a rapid and robust fashion. We present examples showing the use of PONDEROSA-C/S in solving structures of four proteins: two that enable comparison with the original PONDEROSA package, and two from the Critical Assessment of automated Structure Determination by NMR (Rosato et al. in Nat Methods 6:625-626. doi: 10.1038/nmeth0909-625 , 2009) competition. The software package can be downloaded freely in binary format from http://pine.nmrfam.wisc.edu/download_packages.html. Registered users of the National Magnetic Resonance Facility at Madison can submit jobs to the PONDEROSA-C/S server at http://ponderosa.nmrfam.wisc.edu, where instructions, tutorials, and instructions can be found. Structures are normally returned within 1-2 days.

IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data

PubMed Central

Kaas, Quentin; Ruiz, Manuel; Lefranc, Marie-Paule

2004-01-01

IMGT/3Dstructure-DB and IMGT/Structural-Query are a novel 3D structure database and a new tool for immunological proteins. They are part of IMGT, the international ImMunoGenetics information system®, a high-quality integrated knowledge resource specializing in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) and related proteins of the immune system (RPI) of human and other vertebrate species, which consists of databases, Web resources and interactive on-line tools. IMGT/3Dstructure-DB data are described according to the IMGT Scientific chart rules based on the IMGT-ONTOLOGY concepts. IMGT/3Dstructure-DB provides IMGT gene and allele identification of IG, TR and MHC proteins with known 3D structures, domain delimitations, amino acid positions according to the IMGT unique numbering and renumbered coordinate flat files. Moreover IMGT/3Dstructure-DB provides 2D graphical representations (or Collier de Perles) and results of contact analysis. The IMGT/StructuralQuery tool allows search of this database based on specific structural characteristics. IMGT/3Dstructure-DB and IMGT/StructuralQuery are freely available at http://imgt.cines.fr. PMID:14681396

Developing a 300C Analog Tool for EGS

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

Normann, Randy

2015-03-23

This paper covers the development of a 300°C geothermal well monitoring tool for supporting future EGS (enhanced geothermal systems) power production. This is the first of 3 tools planed. This is an analog tool designed for monitoring well pressure and temperature. There is discussion on 3 different circuit topologies and the development of the supporting surface electronics and software. There is information on testing electronic circuits and component. One of the major components is the cable used to connect the analog tool to the surface.

Interactive 3D visualization for theoretical virtual observatories

NASA Astrophysics Data System (ADS)

Dykes, T.; Hassan, A.; Gheller, C.; Croton, D.; Krokos, M.

2018-06-01

Virtual observatories (VOs) are online hubs of scientific knowledge. They encompass a collection of platforms dedicated to the storage and dissemination of astronomical data, from simple data archives to e-research platforms offering advanced tools for data exploration and analysis. Whilst the more mature platforms within VOs primarily serve the observational community, there are also services fulfilling a similar role for theoretical data. Scientific visualization can be an effective tool for analysis and exploration of data sets made accessible through web platforms for theoretical data, which often contain spatial dimensions and properties inherently suitable for visualization via e.g. mock imaging in 2D or volume rendering in 3D. We analyse the current state of 3D visualization for big theoretical astronomical data sets through scientific web portals and virtual observatory services. We discuss some of the challenges for interactive 3D visualization and how it can augment the workflow of users in a virtual observatory context. Finally we showcase a lightweight client-server visualization tool for particle-based data sets, allowing quantitative visualization via data filtering, highlighting two example use cases within the Theoretical Astrophysical Observatory.

Evaluation of the 3d Urban Modelling Capabilities in Geographical Information Systems

NASA Astrophysics Data System (ADS)

Dogru, A. O.; Seker, D. Z.

2010-12-01

Geographical Information System (GIS) Technology, which provides successful solutions to basic spatial problems, is currently widely used in 3 dimensional (3D) modeling of physical reality with its developing visualization tools. The modeling of large and complicated phenomenon is a challenging problem in terms of computer graphics currently in use. However, it is possible to visualize that phenomenon in 3D by using computer systems. 3D models are used in developing computer games, military training, urban planning, tourism and etc. The use of 3D models for planning and management of urban areas is very popular issue of city administrations. In this context, 3D City models are produced and used for various purposes. However the requirements of the models vary depending on the type and scope of the application. While a high level visualization, where photorealistic visualization techniques are widely used, is required for touristy and recreational purposes, an abstract visualization of the physical reality is generally sufficient for the communication of the thematic information. The visual variables, which are the principle components of cartographic visualization, such as: color, shape, pattern, orientation, size, position, and saturation are used for communicating the thematic information. These kinds of 3D city models are called as abstract models. Standardization of technologies used for 3D modeling is now available by the use of CityGML. CityGML implements several novel concepts to support interoperability, consistency and functionality. For example it supports different Levels-of-Detail (LoD), which may arise from independent data collection processes and are used for efficient visualization and efficient data analysis. In one CityGML data set, the same object may be represented in different LoD simultaneously, enabling the analysis and visualization of the same object with regard to different degrees of resolution. Furthermore, two CityGML data sets containing the same object in different LoD may be combined and integrated. In this study GIS tools used for 3D modeling issues were examined. In this context, the availability of the GIS tools for obtaining different LoDs of CityGML standard. Additionally a 3D GIS application that covers a small part of the city of Istanbul was implemented for communicating the thematic information rather than photorealistic visualization by using 3D model. An abstract model was created by using a commercial GIS software modeling tools and the results of the implementation were also presented in the study.

1α,25(OH)2-Vitamin D3 Inhibits C2C12 Cell Differentiation by Activating c-Src and ERK1/2.

PubMed

Wang, Zhonghua; Jiang, Aijun; Mei, Jingwei; Zhang, Xinyan

2018-05-01

The steroid hormone 1α,25(OH)2-vitamin D3 (1,25-D3) induced some biological responses through activation of MAPK cascades in various cell types. It seems that 1,25-D3 plays different roles at different stages of proliferating, differentiating, and differentiated C2C12 cells. We wanted to detect the effect of 1,25-D3 on myogenic differentiation and the role of ERK1/2 in differentiating stage induced by 2% horse serum with 1,25-D3. In this study, cells were induced to differentiate with 2% horse serum until the 7th day (with addition of 1,25-D3 every two days). The protein level of MHC (myosin heavy chain) and phosphorylation level of Src and ERK1/2 were determined with western blot. U0126 (MEK inhibitor) and PP2 (Src specific inhibitor) were used to confirm the relationship between 1,25-D3, MHC, Src, and ERK1/2. 1,25-D3 inhibited differentiation of C2C12 cells and fusion of myotubes by phosphorylating and activating Src and ERK1/2. Phosphorylation of ERK1/2 was inhibited, not only by U0126 but also by PP2 (a Src specific inhibitor) which led to the promotion of differentiation of C2C12 cells; however, U0126 did not inhibit Src phosphorylation. These results suggested that 1,25-D3 possibly inhibited C2C12 differentiation through Src and ERK1/2, and Src played an upstream role in this signaling pathway.

L3.PHI.CTF.P10.02-rev2 Coupling of Subchannel T/H (CTF) and CRUD Chemistry (MAMBA1D)

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

Salko, Robert K.; Palmtag, Scott; Collins, Benjamin S.

2015-05-15

The purpose of this milestone is to create a preliminary capability for modeling light water reactor (LWR) thermal-hydraulic (T/H) and CRUD growth using the CTF subchannel code and the subgrid version of the MAMBA CRUD chemistry code, MAMBA1D. In part, this is a follow-on to Milestone L3.PHI.VCS.P9.01, which is documented in Report CASL-U-2014-0188-000, titled "Development of CTF Capability for Modeling Reactor Operating Cycles with Crud Growth". As the title suggests, the previous milestone set up a framework for modeling reactor operation cycles with CTF. The framework also facilitated coupling to a CRUD chemistry capability for modeling CRUD growth throughout themore » reactor operating cycle. To demonstrate the capability, a simple CRUD \\surrogate" tool was developed and coupled to CTF; however, it was noted that CRUD growth predictions by the surrogate were not considered realistic. This milestone builds on L3.PHI.VCS.P9.01 by replacing this simple surrogate tool with the more advanced MAMBA1D CRUD chemistry code. Completing this task involves addressing unresolved tasks from Milestone L3.PHI.VCS.P9.01, setting up an interface to MAMBA1D, and extracting new T/H information from CTF that was not previously required in the simple surrogate tool. Speci c challenges encountered during this milestone include (1) treatment of the CRUD erosion model, which requires local turbulent kinetic energy (TKE) (a value that CTF does not calculate) and (2) treatment of the MAMBA1D CRUD chimney boiling model in the CTF rod heat transfer solution. To demonstrate this new T/H, CRUD modeling capability, two sets of simulations were performed: (1) an 18 month cycle simulation of a quarter symmetry model of Watts Bar and (2) a simulation of Assemblies G69 and G70 from Seabrook Cycle 5. The Watts Bar simulation is merely a demonstration of the capability. The simulation of the Seabrook cycle, which had experienced CRUD-related fuel rod failures, had actual CRUD-scrape data to compare with results. As results show, the initial CTF/MAMBA1D-predicted CRUD thicknesses were about half of their expected values, so further investigation will be required for this simulation.« less

Solar Energy.

DTIC Science & Technology

1980-04-01

r G 2 W to* L- .0 -- >0m0 L tox >- td . U74o m Et -t C V).--01- MU a#CO Cmto (D 3- 4h - ’- ; %14 4 , c o ’ow ft 000 -- -t4ME’toL0S:Oj- D- C - L 1: 0) d...I- C M-D w 0A--DC C 0 c c 0 :3 -DmC tD 4)Oft- (A OU .l C). 4A LDQC4--U-- M*; U.;O 0 fu ,0 4 a> U W, GD >. 0 D GDI GDO; )D Co C U ODDDL MG (n 4 In 41...r4C4 󈧭 u 41 C, a, -300c’- 41..𔃼 : WC WA 140U Zm L: 1 >. O X424.a 0 L E -0 0) z’ a- W - 3uV ’oC o w mc C-1 (000 40 02 .D Ga cr > -4 II -, 0r0 OC L

Hyperfine excitation of C2H and C2D by para-H2

NASA Astrophysics Data System (ADS)

Dumouchel, Fabien; Lique, François; Spielfiedel, Annie; Feautrier, Nicole

2017-10-01

The [C2H]/[C2D] abundance ratio is a useful tool to explore the physical and chemical conditions of cold molecular clouds. Hence, an accurate determination of both the C2H and C2D abundances is of fundamental interest. Due to the low density of the interstellar medium, the population of the energy levels of the molecules is not at local thermodynamical equilibrium. Thus, the accurate modelling of the emission spectra requires the calculation of collisional rate coefficients with the most abundant interstellar species. Hence, we provide rate coefficients for the hyperfine excitation of C2H and C2D by para-H2(j=0), the most abundant collisional partner in cold molecular clouds. State-to-state rate coefficients between the lowest levels were computed for temperatures ranging from 5 to 80 K. For both isotopologues, the Δj = ΔF propensity rule is observed. The comparison between C2H and C2D rate coefficients shows that differences by up to a factor of two exist, mainly for Δj = ΔN = 1 transitions. The new rate coefficients will significantly help in the interpretation of recent observed spectra.

High School Students' Forming 3D Objects Using Technological and Non-Technological Tools

ERIC Educational Resources Information Center

Okumus, Samet; Hollebrands, Karen

2016-01-01

We analyzed the ways in which two high school students formed 3D objects from the rotation of 2D figures. The students participated in a task-based interview using paper-and-pencil, manipulatives, and Cabri 3D. The results indicated that they had difficulty using paper-and-pencil to rotate 2D figures to form 3D objects. Their difficulty stemmed…

Luminogenic cytochrome P450 assays.

PubMed

Cali, James J; Ma, Dongping; Sobol, Mary; Simpson, Daniel J; Frackman, Susan; Good, Troy D; Daily, William J; Liu, David

2006-08-01

Luminogenic cytochrome P450 (CYP) assays couple CYP enzyme activity to firefly luciferase luminescence in a technology called P450-Glo(TM) (Promega). Luminogenic substrates are used in assays of human CYP1A1, -1A2, -1B1, -2C8, -2C9, -2C19, -2D6, -2J2, -3A4, -3A7, -4A11, -4F3B, -4F12 and -19. The assays detect dose-dependent CYP inhibition by test compounds against recombinant CYP enzymes or liver microsomes. Induction or inhibition of CYP activities in cultured hepatocytes is measured in a nonlytic approach that leaves cells intact for additional analysis. Luminogenic CYP assays offer advantages of speed and safety over HPLC and radiochemical-based methods. Compared with fluorogenic methods the approach offers advantages of improved sensitivity and decreased interference between optical properties of test compound and CYP substrate. These homogenous assays are sensitive and robust tools for high-throughput CYP screening in early drug discovery.

Exploratory Climate Data Visualization and Analysis Using DV3D and UVCDAT

NASA Technical Reports Server (NTRS)

Maxwell, Thomas

2012-01-01

Earth system scientists are being inundated by an explosion of data generated by ever-increasing resolution in both global models and remote sensors. Advanced tools for accessing, analyzing, and visualizing very large and complex climate data are required to maintain rapid progress in Earth system research. To meet this need, NASA, in collaboration with the Ultra-scale Visualization Climate Data Analysis Tools (UVCOAT) consortium, is developing exploratory climate data analysis and visualization tools which provide data analysis capabilities for the Earth System Grid (ESG). This paper describes DV3D, a UV-COAT package that enables exploratory analysis of climate simulation and observation datasets. OV3D provides user-friendly interfaces for visualization and analysis of climate data at a level appropriate for scientists. It features workflow inte rfaces, interactive 40 data exploration, hyperwall and stereo visualization, automated provenance generation, and parallel task execution. DV30's integration with CDAT's climate data management system (COMS) and other climate data analysis tools provides a wide range of high performance climate data analysis operations. DV3D expands the scientists' toolbox by incorporating a suite of rich new exploratory visualization and analysis methods for addressing the complexity of climate datasets.

3D Voronoi grid dedicated software for modeling gas migration in deep layered sedimentary formations with TOUGH2-TMGAS

NASA Astrophysics Data System (ADS)

Bonduà, Stefano; Battistelli, Alfredo; Berry, Paolo; Bortolotti, Villiam; Consonni, Alberto; Cormio, Carlo; Geloni, Claudio; Vasini, Ester Maria

2017-11-01

As is known, a full three-dimensional (3D) unstructured grid permits a great degree of flexibility when performing accurate numerical reservoir simulations. However, when the Integral Finite Difference Method (IFDM) is used for spatial discretization, constraints (arising from the required orthogonality between the segment connecting the blocks nodes and the interface area between blocks) pose difficulties in the creation of grids with irregular shaped blocks. The full 3D Voronoi approach guarantees the respect of IFDM constraints and allows generation of grids conforming to geological formations and structural objects and at the same time higher grid resolution in volumes of interest. In this work, we present dedicated pre- and post-processing gridding software tools for the TOUGH family of numerical reservoir simulators, developed by the Geothermal Research Group of the DICAM Department, University of Bologna. VORO2MESH is a new software coded in C++, based on the voro++ library, allowing computation of the 3D Voronoi tessellation for a given domain and the creation of a ready to use TOUGH2 MESH file. If a set of geological surfaces is available, the software can directly generate the set of Voronoi seed points used for tessellation. In order to reduce the number of connections and so to decrease computation time, VORO2MESH can produce a mixed grid with regular blocks (orthogonal prisms) and irregular blocks (polyhedron Voronoi blocks) at the point of contact between different geological formations. In order to visualize 3D Voronoi grids together with the results of numerical simulations, the functionality of the TOUGH2Viewer post-processor has been extended. We describe an application of VORO2MESH and TOUGH2Viewer to validate the two tools. The case study deals with the simulation of the migration of gases in deep layered sedimentary formations at basin scale using TOUGH2-TMGAS. A comparison between the simulation performances of unstructured and structured grids is presented.

RockFall analyst: A GIS extension for three-dimensional and spatially distributed rockfall hazard modeling

NASA Astrophysics Data System (ADS)

Lan, Hengxing; Derek Martin, C.; Lim, C. H.

2007-02-01

Geographic information system (GIS) modeling is used in combination with three-dimensional (3D) rockfall process modeling to assess rockfall hazards. A GIS extension, RockFall Analyst (RA), which is capable of effectively handling large amounts of geospatial information relative to rockfall behaviors, has been developed in ArcGIS using ArcObjects and C#. The 3D rockfall model considers dynamic processes on a cell plane basis. It uses inputs of distributed parameters in terms of raster and polygon features created in GIS. Two major components are included in RA: particle-based rockfall process modeling and geostatistics-based rockfall raster modeling. Rockfall process simulation results, 3D rockfall trajectories and their velocity features either for point seeders or polyline seeders are stored in 3D shape files. Distributed raster modeling, based on 3D rockfall trajectories and a spatial geostatistical technique, represents the distribution of spatial frequency, the flying and/or bouncing height, and the kinetic energy of falling rocks. A distribution of rockfall hazard can be created by taking these rockfall characteristics into account. A barrier analysis tool is also provided in RA to aid barrier design. An application of these modeling techniques to a case study is provided. The RA has been tested in ArcGIS 8.2, 8.3, 9.0 and 9.1.

Stereoscopic applications for design visualization

NASA Astrophysics Data System (ADS)

Gilson, Kevin J.

2007-02-01

Advances in display technology and 3D design visualization applications have made real-time stereoscopic visualization of architectural and engineering projects a reality. Parsons Brinkerhoff (PB) is a transportation consulting firm that has used digital visualization tools from their inception and has helped pioneer the application of those tools to large scale infrastructure projects. PB is one of the first Architecture/Engineering/Construction (AEC) firms to implement a CAVE- an immersive presentation environment that includes stereoscopic rear-projection capability. The firm also employs a portable stereoscopic front-projection system, and shutter-glass systems for smaller groups. PB is using commercial real-time 3D applications in combination with traditional 3D modeling programs to visualize and present large AEC projects to planners, clients and decision makers in stereo. These presentations create more immersive and spatially realistic presentations of the proposed designs. This paper will present the basic display tools and applications, and the 3D modeling techniques PB is using to produce interactive stereoscopic content. The paper will discuss several architectural and engineering design visualizations we have produced.

Logistics of Behavior Screenings: How and Why Do We Conduct Behavior Screenings at Our School?

ERIC Educational Resources Information Center

Oakes, Wendy Peia; Lane, Kathleen Lynne; Cox, Meredith Lucille; Messenger, Mallory

2014-01-01

In this article, the authors provide an overview of behavior screening tools available, including free and commercially available options. Next, the authors offer step-by-step procedures for (a) selecting, (b) scheduling, (c) preparing, (d) administering, and (e) scoring and interpreting behaviors screening tools. The authors conclude with…

Upholding Accessibility Standards When Selecting Tech Tools

ERIC Educational Resources Information Center

Whetstone, Kimarie W.

2017-01-01

Research-supported guidelines to assist faculty with finding and evaluating online course tools and media that are accessible to learners taking online college courses in the United States are not generally available. The recent refresh to Section 508 of the Rehabilitation Act of 1973, as amended (29 U.S.C. § 794(d)) provides justification for…

Geometric modeling of hepatic arteries in 3D ultrasound with unsupervised MRA fusion during liver interventions.

PubMed

Gérard, Maxime; Michaud, François; Bigot, Alexandre; Tang, An; Soulez, Gilles; Kadoury, Samuel

2017-06-01

Modulating the chemotherapy injection rate with regard to blood flow velocities in the tumor-feeding arteries during intra-arterial therapies may help improve liver tumor targeting while decreasing systemic exposure. These velocities can be obtained noninvasively using Doppler ultrasound (US). However, small vessels situated in the liver are difficult to identify and follow in US. We propose a multimodal fusion approach that non-rigidly registers a 3D geometric mesh model of the hepatic arteries obtained from preoperative MR angiography (MRA) acquisitions with intra-operative 3D US imaging. The proposed fusion tool integrates 3 imaging modalities: an arterial MRA, a portal phase MRA and an intra-operative 3D US. Preoperatively, the arterial phase MRA is used to generate a 3D model of the hepatic arteries, which is then non-rigidly co-registered with the portal phase MRA. Once the intra-operative 3D US is acquired, we register it with the portal MRA using a vessel-based rigid initialization followed by a non-rigid registration using an image-based metric based on linear correlation of linear combination. Using the combined non-rigid transformation matrices, the 3D mesh model is fused with the 3D US. 3D US and multi-phase MRA images acquired from 10 porcine models were used to test the performance of the proposed fusion tool. Unimodal registration of the MRA phases yielded a target registration error (TRE) of [Formula: see text] mm. Initial rigid alignment of the portal MRA and 3D US yielded a mean TRE of [Formula: see text] mm, which was significantly reduced to [Formula: see text] mm ([Formula: see text]) after affine image-based registration. The following deformable registration step allowed for further decrease of the mean TRE to [Formula: see text] mm. The proposed tool could facilitate visualization and localization of these vessels when using 3D US intra-operatively for either intravascular or percutaneous interventions to avoid vessel perforation.

Sc2C2@D3h(14246)-C74: A Missing Piece of the Clusterfullerene Puzzle.

PubMed

Wang, Yaofeng; Tang, Qiangqiang; Feng, Lai; Chen, Ning

2017-02-20

Clusterfullerenes with variable carbon cages have been extensively studied in recent years. However, despite all these efforts, C 74 cage-based clusterfullerene remains a missing piece of the puzzle. Herein, we show that single-crystal X-ray crystallographic analysis unambiguously assigns the previously reported dimetallofullerene Sc 2 @C 76 to a novel carbide clusterfullerene, Sc 2 C 2 @D 3h (14246)-C 74 , the first experimentally proven clusterfullerene with a C 74 cage. In addition, Sc 2 C 2 @D 3h (14246)-C 74 was charaterized by mass spectrometry, ultraviolet-visible-near-infrared absorption spectroscopy, 45 Sc nuclear magnetic resonance, and cyclic voltammetry. Comparative studies of the motion of the carbide cluster in Sc 2 C 2 @D 3h (14246)-C 74 and Sc 2 C 2 @C 2n (n = 40-44) revealed that a combination of factors, involving both the shape and size of the cage, is crucial in dictating the cluster motion. Moreover, structural studies of D 3h (14246)-C 74 revealed that it can be easily converted to C s (10528)-C 72 and T d (19151)-C 76 cages via C 2 desertion/insertion and Stone-Wales transformation. This suggests that D 3h (14246)-C 74 might play an important role in the growth pathway of clusterfullerenes.

D-MATRIX: a web tool for constructing weight matrix of conserved DNA motifs.

PubMed

Sen, Naresh; Mishra, Manoj; Khan, Feroz; Meena, Abha; Sharma, Ashok

2009-07-27

Despite considerable efforts to date, DNA motif prediction in whole genome remains a challenge for researchers. Currently the genome wide motif prediction tools required either direct pattern sequence (for single motif) or weight matrix (for multiple motifs). Although there are known motif pattern databases and tools for genome level prediction but no tool for weight matrix construction. Considering this, we developed a D-MATRIX tool which predicts the different types of weight matrix based on user defined aligned motif sequence set and motif width. For retrieval of known motif sequences user can access the commonly used databases such as TFD, RegulonDB, DBTBS, Transfac. D-MATRIX program uses a simple statistical approach for weight matrix construction, which can be converted into different file formats according to user requirement. It provides the possibility to identify the conserved motifs in the co-regulated genes or whole genome. As example, we successfully constructed the weight matrix of LexA transcription factor binding site with the help of known sos-box cis-regulatory elements in Deinococcus radiodurans genome. The algorithm is implemented in C-Sharp and wrapped in ASP.Net to maintain a user friendly web interface. D-MATRIX tool is accessible through the CIMAP domain network. http://203.190.147.116/dmatrix/

6-Oxocytidine a novel protonated C-base analogue for stable triple helix formation.

PubMed Central

Berressem, R; Engels, J W

1995-01-01

2'-O-Methyl-3'-O-phosphoramidite building blocks of 6-oxocytidine 6 and its 5-methyl derivative 7, respectively, were synthesized and incorporated via phosphoramidite chemistry in 15 mer oligodeoxynucleotides [d(T72T7), S2; d(T73T7), S3] to obtain potential Py.Pu.Py triplex forming homopyrimidine strands. UV thermal denaturation studies and CD spectroscopy of 1:1 mixtures of these oligomers and a 21 mer target duplex [d(C3A7GA7C3)-d(G3T7CT7G3), D1] with a complementary purine tract showed a nearly pH-independent (6.0-8.0) triple helix formation with melting temperatures of 21-19 degrees C and 18.5-17.5 degrees C, respectively (buffer system: 50 mM sodium cacodylate, 100 mM NaCl, 20 mM MgCl2). In contrast, with the corresponding 15mer deoxy-C-containing oligonucleotide [d(T(7)1T7), S1] triplex formation was observed only below pH 6.6. Specificity for the recognition of Watson-Crick GC-base pairs was observed by pairing the modified C-bases of the 15mers with all other possible Watson-Crick-base compositions in the target duplex [d(C3A7XA7C3)-d(G3T7YT7G3), X = A,C,T; Y = T,G,A, D2-4]. Additionally, the Watson-Crick-pairing of the modified oligomers S2 and S3 was studied. PMID:7567457

6-Oxocytidine a novel protonated C-base analogue for stable triple helix formation.

PubMed

Berressem, R; Engels, J W

1995-09-11

2'-O-Methyl-3'-O-phosphoramidite building blocks of 6-oxocytidine 6 and its 5-methyl derivative 7, respectively, were synthesized and incorporated via phosphoramidite chemistry in 15 mer oligodeoxynucleotides [d(T72T7), S2; d(T73T7), S3] to obtain potential Py.Pu.Py triplex forming homopyrimidine strands. UV thermal denaturation studies and CD spectroscopy of 1:1 mixtures of these oligomers and a 21 mer target duplex [d(C3A7GA7C3)-d(G3T7CT7G3), D1] with a complementary purine tract showed a nearly pH-independent (6.0-8.0) triple helix formation with melting temperatures of 21-19 degrees C and 18.5-17.5 degrees C, respectively (buffer system: 50 mM sodium cacodylate, 100 mM NaCl, 20 mM MgCl2). In contrast, with the corresponding 15mer deoxy-C-containing oligonucleotide [d(T(7)1T7), S1] triplex formation was observed only below pH 6.6. Specificity for the recognition of Watson-Crick GC-base pairs was observed by pairing the modified C-bases of the 15mers with all other possible Watson-Crick-base compositions in the target duplex [d(C3A7XA7C3)-d(G3T7YT7G3), X = A,C,T; Y = T,G,A, D2-4]. Additionally, the Watson-Crick-pairing of the modified oligomers S2 and S3 was studied.

Quantitative analysis of diffusion tensor orientation: theoretical framework.

PubMed

Wu, Yu-Chien; Field, Aaron S; Chung, Moo K; Badie, Benham; Alexander, Andrew L

2004-11-01

Diffusion-tensor MRI (DT-MRI) yields information about the magnitude, anisotropy, and orientation of water diffusion of brain tissues. Although white matter tractography and eigenvector color maps provide visually appealing displays of white matter tract organization, they do not easily lend themselves to quantitative and statistical analysis. In this study, a set of visual and quantitative tools for the investigation of tensor orientations in the human brain was developed. Visual tools included rose diagrams, which are spherical coordinate histograms of the major eigenvector directions, and 3D scatterplots of the major eigenvector angles. A scatter matrix of major eigenvector directions was used to describe the distribution of major eigenvectors in a defined anatomic region. A measure of eigenvector dispersion was developed to describe the degree of eigenvector coherence in the selected region. These tools were used to evaluate directional organization and the interhemispheric symmetry of DT-MRI data in five healthy human brains and two patients with infiltrative diseases of the white matter tracts. In normal anatomical white matter tracts, a high degree of directional coherence and interhemispheric symmetry was observed. The infiltrative diseases appeared to alter the eigenvector properties of affected white matter tracts, showing decreased eigenvector coherence and interhemispheric symmetry. This novel approach distills the rich, 3D information available from the diffusion tensor into a form that lends itself to quantitative analysis and statistical hypothesis testing. (c) 2004 Wiley-Liss, Inc.

Cloning and characterization of d-threonine aldolase from the green alga Chlamydomonas reinhardtii.

PubMed

Hirato, Yuki; Tokuhisa, Mayumi; Tanigawa, Minoru; Ashida, Hiroyuki; Tanaka, Hiroyuki; Nishimura, Katsushi

2017-03-01

d-Threonine aldolase (DTA) catalyzes the pyridoxal 5'-phosphate (PLP)-dependent interconversion of d-threonine and glycine plus acetaldehyde. The enzyme is a powerful tool for the stereospecific synthesis of various β-hydroxy amino acids in synthetic organic chemistry. In this study, DTA from the green alga Chlamydomonas reinhardtii was discovered and characterized, representing the first report to describe the existence of eukaryotic DTA. DTA was overexpressed in recombinant Escherichia coli BL21 (DE3) cells; the specific activity of the enzyme in the cell-free extract was 0.8 U/mg. The recombinant enzyme was purified to homogeneity by ammonium sulfate fractionation, DEAE-Sepharose, and Mono Q column chromatographies (purified enzyme 7.0 U/mg). For the cleavage reaction, the optimal temperature and pH were 70 °C and pH 8.4, respectively. The enzyme demonstrated 90% of residual activity at 50 °C for 1 h. The enzyme catalyzed the synthesis of d- and d-allo threonine from a mixture of glycine and acetaldehyde (the diastereomer excess of d-threonine was 18%). DTA was activated by several divalent metal ions, including manganese, and was inhibited by PLP enzyme inhibitors and metalloenzyme inhibitors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Science Opportunity Analyzer (SOA): Science Planning Made Simple

NASA Technical Reports Server (NTRS)

Streiffert, Barbara A.; Polanskey, Carol A.

2004-01-01

.For the first time at JPL, the Cassini mission to Saturn is using distributed science operations for developing their experiments. Remote scientists needed the ability to: a) Identify observation opportunities; b) Create accurate, detailed designs for their observations; c) Verify that their designs meet their objectives; d) Check their observations against project flight rules and constraints; e) Communicate their observations to other scientists. Many existing tools provide one or more of these functions, but Science Opportunity Analyzer (SOA) has been built to unify these tasks into a single application. Accurate: Utilizes JPL Navigation and Ancillary Information Facility (NAIF) SPICE* software tool kit - Provides high fidelity modeling. - Facilitates rapid adaptation to other flight projects. Portable: Available in Unix, Windows and Linux. Adaptable: Designed to be a multi-mission tool so it can be readily adapted to other flight projects. Implemented in Java, Java 3D and other innovative technologies. Conclusion: SOA is easy to use. It only requires 6 simple steps. SOA's ability to show the same accurate information in multiple ways (multiple visualization formats, data plots, listings and file output) is essential to meet the needs of a diverse, distributed science operations environment.

Calcium/vitamin D supplementation, serum 25-hydroxyvitamin D concentrations, and cholesterol profiles in the Women's Health Initiative calcium/vitamin D randomized trial.

PubMed

Schnatz, Peter F; Jiang, Xuezhi; Vila-Wright, Sharon; Aragaki, Aaron K; Nudy, Matthew; O'Sullivan, David M; Jackson, Rebecca; LeBlanc, Erin; Robinson, Jennifer G; Shikany, James M; Womack, Catherine R; Martin, Lisa W; Neuhouser, Marian L; Vitolins, Mara Z; Song, Yiqing; Kritchevsky, Stephen; Manson, JoAnn E

2014-08-01

The objective of this study was to evaluate whether increased serum 25-hydroxyvitamin D3 (25OHD3) concentrations, in response to calcium/vitamin D (CaD) supplementation, are associated with improved lipids in postmenopausal women. The parent trial was a double-blind, randomized, placebo-controlled, parallel-group trial designed to test the effects of CaD supplementation (1,000 mg of elemental calcium + 400 IU of vitamin D3 daily) versus placebo in postmenopausal women. Women from the general community, including multiple sites in the United States, were enrolled between 1993 and 1998. This cohort included 300 white, 200 African-American, and 100 Hispanic participants who were randomly selected from the Women's Health Initiative CaD trial. Serum 25OHD3 and lipid (fasting plasma triglycerides [TG], high-density lipoprotein cholesterol [HDL-C], and calculated low-density lipoprotein cholesterol [LDL-C]) levels were assessed before and after CaD randomization. There was a 38% increase in mean serum 25OHD3 concentrations after 2 years (95% CI, 1.29-1.47, P < 0.001) for women randomized to CaD (24.3 ng/mL postrandomization mean) compared with placebo (18.2 ng/mL). Women randomized to CaD had a 4.46-mg/dL mean decrease in LDL-C (P = 0.03). Higher concentrations of 25OHD3 were associated with higher HDL-C levels (P = 0.003), along with lower LDL-C and TG levels (P = 0.02 and P < 0.001, respectively). Supplemental CaD significantly increases 25OHD3 concentrations and decreases LDL-C. Women with higher 25OHD3 concentrations have more favorable lipid profiles, including increased HDL-C, lower LDL-C, and lower TG. These results support the hypothesis that higher concentrations of 25OHD3, in response to CaD supplementation, are associated with improved LDL-C.

Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses.

PubMed

Talukder, Shyamal K; Saha, Malay C

2017-01-01

Most important food and feed crops in the world belong to the C3 grass family. The future of food security is highly reliant on achieving genetic gains of those grasses. Conventional breeding methods have already reached a plateau for improving major crops. Genomics tools and resources have opened an avenue to explore genome-wide variability and make use of the variation for enhancing genetic gains in breeding programs. Major C3 annual cereal breeding programs are well equipped with genomic tools; however, genomic research of C3 cool-season perennial grasses is lagging behind. In this review, we discuss the currently available genomics tools and approaches useful for C3 cool-season perennial grass breeding. Along with a general review, we emphasize the discussion focusing on forage grasses that were considered orphan and have little or no genetic information available. Transcriptome sequencing and genotype-by-sequencing technology for genome-wide marker detection using next-generation sequencing (NGS) are very promising as genomics tools. Most C3 cool-season perennial grass members have no prior genetic information; thus NGS technology will enhance collinear study with other C3 model grasses like Brachypodium and rice. Transcriptomics data can be used for identification of functional genes and molecular markers, i.e., polymorphism markers and simple sequence repeats (SSRs). Genome-wide association study with NGS-based markers will facilitate marker identification for marker-assisted selection. With limited genetic information, genomic selection holds great promise to breeders for attaining maximum genetic gain of the cool-season C3 perennial grasses. Application of all these tools can ensure better genetic gains, reduce length of selection cycles, and facilitate cultivar development to meet the future demand for food and fodder.

40 CFR 86.513-2004 - Fuel and engine lubricant specifications.

Code of Federal Regulations, 2010 CFR

2010-07-01

... ASTM D 86-97 23.9—35.0 1 2. 10% point, °C ASTM D 86-97 48.9—57.2 3. 50% point, °C ASTM D 86-97 93.3—110.0 4. 90% point, °C ASTM D 86-97 148.9—162.8 5. End point, °C ASTM D 86-97 212.8 Hydrocarbon composition: 1. Olefins, volume % ASTM D 1319-98 10 maximum 2. Aromatics, volume % ASTM D 1319-98 35 maximum 3...

Influence of water stress on the carbon isotopic composition of modern plants: Implications for C4 plant appearance in Indian subcontinent

NASA Astrophysics Data System (ADS)

Basu, S.; Ghosh, S.; Sanyal, P.

2016-12-01

The carbon isotopic composition (d13C) of modern terrestrial plants (C3 and C4) provides the baseline to understand past vegetation composition, paleodietary changes and animal migration etc. Accuracy of past environment reconstruction is dependent on the end-member d13C values of plants which found to vary in regional scale. For instance, the d13C values of Indian C3 plants (d13CC3) are 1 to 2‰ more negative compared to global mean. As observed, most of the previous database is devoid of samples from tropical monsoon realm (like India) and the difference between global and regional mean may introduce errors in vegetation reconstruction. To constrain end-member d13CC3 value, published and newly generated results from wide range of mean annual precipitation (MAP: 1-11,700 mm) are compiled which is ca. 1.5 higher in sample size (n=2440) compared to previous database. Using logarithmic function, new relationship between d13C value and MAP (d13CC3 (‰) =20.1585(0.3061)-1.1276(0.0489)ln(MAP+700)) is proposed. The modeled mean d13CC3 value (-28.9‰) is close to average d13CC3 value for Indian plants (-29.1‰) and suggests the importance of vegetation from low-latitudinal tropical region in global compilation. It was observed that C3 plants, on a global scale, are less sensitive to wet climate relative to dry condition. This inference is in agreement with the paleoclimatic data from Indian subcontinent for the late Quaternary period. Despite well established correlation between d13CC3 value and MAP, previous investigation from Indian subcontinent used fixed end-member values to reconstruct past vegetation and total change in the d13C value of proxies was attributed to changes in relative abundance of C3 and C4 plants. Using region-specific mean d13C value of plants, after correcting for changing MAP and error propagation, existence of C4 before ca. 11 Ma plant is observed; earlier to previous reported timing.

OPMILL - MICRO COMPUTER PROGRAMMING ENVIRONMENT FOR CNC MILLING MACHINES THREE AXIS EQUATION PLOTTING CAPABILITIES

NASA Technical Reports Server (NTRS)

Ray, R. B.

1994-01-01

OPMILL is a computer operating system for a Kearney and Trecker milling machine that provides a fast and easy way to program machine part manufacture with an IBM compatible PC. The program gives the machinist an "equation plotter" feature which plots any set of equations that define axis moves (up to three axes simultaneously) and converts those equations to a machine milling program that will move a cutter along a defined path. Other supported functions include: drill with peck, bolt circle, tap, mill arc, quarter circle, circle, circle 2 pass, frame, frame 2 pass, rotary frame, pocket, loop and repeat, and copy blocks. The system includes a tool manager that can handle up to 25 tools and automatically adjusts tool length for each tool. It will display all tool information and stop the milling machine at the appropriate time. Information for the program is entered via a series of menus and compiled to the Kearney and Trecker format. The program can then be loaded into the milling machine, the tool path graphically displayed, and tool change information or the program in Kearney and Trecker format viewed. The program has a complete file handling utility that allows the user to load the program into memory from the hard disk, save the program to the disk with comments, view directories, merge a program on the disk with one in memory, save a portion of a program in memory, and change directories. OPMILL was developed on an IBM PS/2 running DOS 3.3 with 1 MB of RAM. OPMILL was written for an IBM PC or compatible 8088 or 80286 machine connected via an RS-232 port to a Kearney and Trecker Data Mill 700/C Control milling machine. It requires a "D:" drive (fixed-disk or virtual), a browse or text display utility, and an EGA or better display. Users wishing to modify and recompile the source code will also need Turbo BASIC, Turbo C, and Crescent Software's QuickPak for Turbo BASIC. IBM PC and IBM PS/2 are registered trademarks of International Business Machines. Turbo BASIC and Turbo C are trademarks of Borland International.

Uranyl Ion Complexes with Long-Chain Aliphatic α,ω-Dicarboxylates and 3d-Block Metal Counterions.

PubMed

Thuéry, Pierre; Harrowfield, Jack

2016-03-07

Twelve new complexes were obtained from reaction of uranyl ions with the aliphatic dicarboxylic acids HOOC-(CH2)n-2-COOH (H2Cn; n = 7-10 and 12) under solvo-hydrothermal conditions, in the presence of 3d-block metal ions (Mn(2+), Fe(3+), Co(2+), Ni(2+), and Cu(2+)) and 2,2'-bipyridine (bipy) or 1,10-phenanthroline (phen). In contrast to previously reported triple-stranded helicates obtained with C9(2-) and C12(2-), all these complexes crystallize as polymeric one-dimensional (1D) or two-dimensional (2D) species. [Fe(bipy)3][(UO2)2(C7)3]·3H2O (1), [Cu(phen)2]2[(UO2)3(C7)4(H2O)2]·2H2O (2), and [Cu(bipy)2]2[(UO2)2(C9)3] (6), in which the 3d cation was reduced in situ, are 1D ladderlike polymers displaying tetra- or hexanuclear rings, of sufficient width to encompass two counterions in 2 and 6. The three complexes [Co(phen)3][(UO2)3(C8)3(O)]·H2O (3), [Ni(phen)3][(UO2)3(C8)3(O)]·H2O (4) and [Co(phen)3][(UO2)3(C9)3(O)]·H2O (5) contain bis(μ3-oxo)-bridged tetranuclear secondary building units, and they crystallize as deeply furrowed 2D assemblies. Depending on the nature of the counterion, C10(2-) gives [Ni(bipy)3][(UO2)2(C10)3]·2H2O (7), a 2D network displaying elongated decanuclear rings containing the counterions, or [Mn(phen)3][(UO2)2(C10)3]·6H2O (8), [Co(phen)3][(UO2)2(C10)3]·7H2O (9), and [Ni(phen)3][(UO2)2(C10)3]·7H2O (10), which consist of 2D assemblies with honeycomb topology; the hexanuclear rings in 8-10 are chairlike and occupied by one counterion and two uranyl groups from neighboring layers. Two complexes of the ligand with the longest chain, C12(2-), are reported. [UO2(C12)(bipy)] (11) is a neutral 1D species in which bipy chelates the uranyl ion and plays an important role in the packing through π-stacking interactions. Two polymeric units, 1D and 2D, coexist in the complex [Ni(bipy)3][(UO2)2(C12)3][UO2(C12)(H2O)2]·H2O (12); the 2D network has the honeycomb topology, but the hexanuclear rings are markedly convoluted, with local features akin to those in helicates, and the counterions are embedded in intralayer cavities. Emission spectra measured in the solid state show in most cases various degrees of quenching, with intense and well-resolved uranyl emission being observed only for complexes 2 and 11.

Gray matter segmentation of the spinal cord with active contours in MR images.

PubMed

Datta, Esha; Papinutto, Nico; Schlaeger, Regina; Zhu, Alyssa; Carballido-Gamio, Julio; Henry, Roland G

2017-02-15

Fully or partially automated spinal cord gray matter segmentation techniques for spinal cord gray matter segmentation will allow for pivotal spinal cord gray matter measurements in the study of various neurological disorders. The objective of this work was multi-fold: (1) to develop a gray matter segmentation technique that uses registration methods with an existing delineation of the cord edge along with Morphological Geodesic Active Contour (MGAC) models; (2) to assess the accuracy and reproducibility of the newly developed technique on 2D PSIR T1 weighted images; (3) to test how the algorithm performs on different resolutions and other contrasts; (4) to demonstrate how the algorithm can be extended to 3D scans; and (5) to show the clinical potential for multiple sclerosis patients. The MGAC algorithm was developed using a publicly available implementation of a morphological geodesic active contour model and the spinal cord segmentation tool of the software Jim (Xinapse Systems) for initial estimate of the cord boundary. The MGAC algorithm was demonstrated on 2D PSIR images of the C2/C3 level with two different resolutions, 2D T2* weighted images of the C2/C3 level, and a 3D PSIR image. These images were acquired from 45 healthy controls and 58 multiple sclerosis patients selected for the absence of evident lesions at the C2/C3 level. Accuracy was assessed though visual assessment, Hausdorff distances, and Dice similarity coefficients. Reproducibility was assessed through interclass correlation coefficients. Validity was assessed through comparison of segmented gray matter areas in images with different resolution for both manual and MGAC segmentations. Between MGAC and manual segmentations in healthy controls, the mean Dice similarity coefficient was 0.88 (0.82-0.93) and the mean Hausdorff distance was 0.61 (0.46-0.76) mm. The interclass correlation coefficient from test and retest scans of healthy controls was 0.88. The percent change between the manual segmentations from high and low-resolution images was 25%, while the percent change between the MGAC segmentations from high and low resolution images was 13%. Between MGAC and manual segmentations in MS patients, the average Dice similarity coefficient was 0.86 (0.8-0.92) and the average Hausdorff distance was 0.83 (0.29-1.37) mm. We demonstrate that an automatic segmentation technique, based on a morphometric geodesic active contours algorithm, can provide accurate and precise spinal cord gray matter segmentations on 2D PSIR images. We have also shown how this automated technique can potentially be extended to other imaging protocols. Copyright © 2016 Elsevier Inc. All rights reserved.

Stereometric parameters change vs. Topographic Change Analysis (TCA) agreement in Heidelberg Retina Tomography III (HRT-3) early detection of clinical significant glaucoma progression.

PubMed

Dascalu, A M; Cherecheanu, A P; Stana, D; Voinea, L; Ciuluvica, R; Savlovschi, C; Serban, D

2014-01-01

to investigate the sensitivity and specificity of the stereometric parameters change analysis vs. Topographic Change Analysis in early detection of glaucoma progression. 81 patients with POAG were monitored for 4 years (GAT monthly, SAP at every 6 months, optic disc photographs and HRT3 yearly). The exclusion criteria were other optic disc or retinal pathology; topographic standard deviation (TSD>30; inter-test variation of reference height>25 μm. The criterion for structural progression was the following: at least 20 adjacent super-pixels with a clinically significant decrease in height (>5%). 16 patients of the total 81 presented structural progression on TCA. The most useful stereometric parameters for the early detection of glaucoma progression were the following: Rim Area change (sensitivity 100%, specificity 74.2% for a "cut-off " value of -0.05), C/D Area change (sensitivity 85.7%, specificity 71.5% for a "cut off " value of 0.02), C/D linear change (sensitivity 85.7%, specificity 71.5% for a "cut-off " value of 0.02), Rim Volume change (sensitivity 71.4%, specificity 88.8% for a "cut-off " value of -0.04). RNFL Thickness change (<0) was highly sensitive (82%), but less specific for glaucoma progression (45,2%). Changes of the other stereometric parameters have a limited diagnostic value for the early detection of glaucoma progression. TCA is a valuable tool for the assessment of the structural progression in glaucoma patients and its inter-test variability is low. On long-term, the quantitative analysis according to stereometric parameters change is also very important. The most relevant parameters to detect progression are RA, C/D Area, Linear C/D and RV.

MEMHDX: an interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets.

PubMed

Hourdel, Véronique; Volant, Stevenn; O'Brien, Darragh P; Chenal, Alexandre; Chamot-Rooke, Julia; Dillies, Marie-Agnès; Brier, Sébastien

2016-11-15

With the continued improvement of requisite mass spectrometers and UHPLC systems, Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) workflows are rapidly evolving towards the investigation of more challenging biological systems, including large protein complexes and membrane proteins. The analysis of such extensive systems results in very large HDX-MS datasets for which specific analysis tools are required to speed up data validation and interpretation. We introduce a web application and a new R-package named 'MEMHDX' to help users analyze, validate and visualize large HDX-MS datasets. MEMHDX is composed of two elements. A statistical tool aids in the validation of the results by applying a mixed-effects model for each peptide, in each experimental condition, and at each time point, taking into account the time dependency of the HDX reaction and number of independent replicates. Two adjusted P-values are generated per peptide, one for the 'Change in dynamics' and one for the 'Magnitude of ΔD', and are used to classify the data by means of a 'Logit' representation. A user-friendly interface developed with Shiny by RStudio facilitates the use of the package. This interactive tool allows the user to easily and rapidly validate, visualize and compare the relative deuterium incorporation on the amino acid sequence and 3D structure, providing both spatial and temporal information. MEMHDX is freely available as a web tool at the project home page http://memhdx.c3bi.pasteur.fr CONTACT: marie-agnes.dillies@pasteur.fr or sebastien.brier@pasteur.frSupplementary information: Supplementary data is available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Syntheses, structures, and 1H, 13C{ 1H} and 119Sn{ 1H} NMR chemical shifts of a family of trimethyltin alkoxide, amide, halide and cyclopentadienyl compounds

DOE PAGES

Lichtscheidl, Alejandro G.; Janicke, Michael T.; Scott, Brian L.; ...

2015-08-21

The synthesis and full characterization, including Nuclear Magnetic Resonance (NMR) data ( 1H, 13C{ 1H} and 119Sn{ 1H}), for a series of Me 3SnX (X = O-2,6-tBu 2C 6H 3 (1), (Me 3Sn)N(2,6- iPr 2C 6H 3) (3), NH-2,4,6- tBu 3C 6H 2 (4), N(SiMe 3) 2 (5), NEt 2, C 5Me 5 (6), Cl, Br, I, and SnMe 3) compounds in benzene-d 6, toluene-d 8, dichloromethane-d 2, chloroform-d 1, acetonitrile-d 3, and tetrahydrofuran-d 8 are reported. The X-ray crystal structures of Me 3Sn(O-2,6- tBu 2C 6H 3) (1), Me 3Sn(O-2,6- iPr 2C 6H 3) (2), and (Me 3Sn)(NH-2,4,6- tBumore » 3C 6H 2) (4) are also presented. As a result, these compiled data complement existing literature data and ease the characterization of these compounds by routine NMR experiments.« less

Synthesis, characterization and properties of uridine 5'-( -D-apio-D-furanosyl pyrophosphate).

PubMed

Kindel, P K; Watson, R R

1973-06-01

1. A method was developed for synthesizing UDP-apiose [uridine 5'-(alpha-d-apio-d-furanosyl pyrophosphate)] from UDP-glucuronic acid [uridine 5'-(alpha-d-glucopyranosyluronic acid pyrophosphate)] in 62% yield with the enzyme UDP-glucuronic acid cyclase. 2. UDP-apiose had the same mobility as uridine 5'-(alpha-d-xylopyranosyl pyrophosphate) when chromatographed on paper and when subjected to paper electrophoresis at pH5.8. When [(3)H]UDP-[U-(14)C]glucuronic acid was used as the substrate for UDP-glucuronic acid cyclase, the (3)H/(14)C ratio in the reaction product was that expected if d-apiose remained attached to the uridine. In separate experiments doubly labelled reaction product was: (a) hydrolysed at pH2 and 100 degrees C for 15min; (b) degraded at pH8.0 and 100 degrees C for 3min; (c) used as a substrate in the enzymic synthesis of [(14)C]apiin. In each type of experiment the reaction products were isolated and identified and were found to be those expected if [(3)H]UDP-[U-(14)C]apiose was the starting compound. 3. Chemical characterization established that the product containing d-[U-(14)C]apiose and phosphate formed on alkaline degradation of UDP-[U-(14)C]apiose was alpha-d-[U-(14)C]apio-d-furanosyl 1:2-cyclic phosphate. 4. Chemical characterization also established that the product containing d-[U-(14)C]apiose and phosphate formed on acid hydrolysis of alpha-d-[U-(14)C]apio-d-furanosyl 1:2-cyclic phosphate was d-[U-(14)C]apiose 2-phosphate. 5. The half-life periods for the degradation of UDP-[U-(14)C]apiose to alpha-d-[U-(14)C]apio-d-furanosyl 1:2-cyclic phosphate and UMP at pH8.0 and 80 degrees C, at pH8.0 and 25 degrees C and at pH8.0 and 4 degrees C were 31.6s, 97.2min and 16.5h respectively. The half-life period for the hydrolysis of UDP-[U-(14)C]-apiose to d-[U-(14)C]apiose and UDP at pH3.0 and 40 degrees C was 4.67min. After 20 days at pH6.2-6.6 and 4 degrees C, 17% of the starting UDP-[U-(14)C]apiose was degraded to alpha-d-[U-(14)C]apio-d-furanosyl 1:2-cyclic phosphate and UMP and 23% was hydrolysed to d-[U-(14)C]apiose and UDP. After 120 days at pH6.4 and -20 degrees C 2% of the starting UDP-[U-(14)C]apiose was degraded and 4% was hydrolysed.

Synthesis, characterization and properties of uridine 5′-(α-d-apio-d-furanosyl pyrophosphate)

PubMed Central

Kindel, Paul K.; Watson, Ronald R.

1973-01-01

1. A method was developed for synthesizing UDP-apiose [uridine 5′-(α-d-apio-d-furanosyl pyrophosphate)] from UDP-glucuronic acid [uridine 5′-(α-d-glucopyranosyluronic acid pyrophosphate)] in 62% yield with the enzyme UDP-glucuronic acid cyclase. 2. UDP-apiose had the same mobility as uridine 5′-(α-d-xylopyranosyl pyrophosphate) when chromatographed on paper and when subjected to paper electrophoresis at pH5.8. When [3H]UDP-[U-14C]glucuronic acid was used as the substrate for UDP-glucuronic acid cyclase, the 3H/14C ratio in the reaction product was that expected if d-apiose remained attached to the uridine. In separate experiments doubly labelled reaction product was: (a) hydrolysed at pH2 and 100°C for 15min; (b) degraded at pH8.0 and 100°C for 3min; (c) used as a substrate in the enzymic synthesis of [14C]apiin. In each type of experiment the reaction products were isolated and identified and were found to be those expected if [3H]UDP-[U-14C]apiose was the starting compound. 3. Chemical characterization established that the product containing d-[U-14C]apiose and phosphate formed on alkaline degradation of UDP-[U-14C]apiose was α-d-[U-14C]apio-d-furanosyl 1:2-cyclic phosphate. 4. Chemical characterization also established that the product containing d-[U-14C]apiose and phosphate formed on acid hydrolysis of α-d-[U-14C]apio-d-furanosyl 1:2-cyclic phosphate was d-[U-14C]apiose 2-phosphate. 5. The half-life periods for the degradation of UDP-[U-14C]apiose to α-d-[U-14C]apio-d-furanosyl 1:2-cyclic phosphate and UMP at pH8.0 and 80°C, at pH8.0 and 25°C and at pH8.0 and 4°C were 31.6s, 97.2min and 16.5h respectively. The half-life period for the hydrolysis of UDP-[U-14C]-apiose to d-[U-14C]apiose and UDP at pH3.0 and 40°C was 4.67min. After 20 days at pH6.2–6.6 and 4°C, 17% of the starting UDP-[U-14C]apiose was degraded to α-d-[U-14C]apio-d-furanosyl 1:2-cyclic phosphate and UMP and 23% was hydrolysed to d-[U-14C]apiose and UDP. After 120 days at pH6.4 and −20°C 2% of the starting UDP-[U-14C]apiose was degraded and 4% was hydrolysed. PMID:4723773

3D visualization of molecular structures in the MOGADOC database

NASA Astrophysics Data System (ADS)

Vogt, Natalja; Popov, Evgeny; Rudert, Rainer; Kramer, Rüdiger; Vogt, Jürgen

2010-08-01

The MOGADOC database (Molecular Gas-Phase Documentation) is a powerful tool to retrieve information about compounds which have been studied in the gas-phase by electron diffraction, microwave spectroscopy and molecular radio astronomy. Presently the database contains over 34,500 bibliographic references (from the beginning of each method) for about 10,000 inorganic, organic and organometallic compounds and structural data (bond lengths, bond angles, dihedral angles, etc.) for about 7800 compounds. Most of the implemented molecular structures are given in a three-dimensional (3D) presentation. To create or edit and visualize the 3D images of molecules, new tools (special editor and Java-based 3D applet) were developed. Molecular structures in internal coordinates were converted to those in Cartesian coordinates.

Towards a Decision Support Tool for 3d Visualisation: Application to Selectivity Purpose of Single Object in a 3d City Scene

NASA Astrophysics Data System (ADS)

Neuville, R.; Pouliot, J.; Poux, F.; Hallot, P.; De Rudder, L.; Billen, R.

2017-10-01

This paper deals with the establishment of a comprehensive methodological framework that defines 3D visualisation rules and its application in a decision support tool. Whilst the use of 3D models grows in many application fields, their visualisation remains challenging from the point of view of mapping and rendering aspects to be applied to suitability support the decision making process. Indeed, there exists a great number of 3D visualisation techniques but as far as we know, a decision support tool that facilitates the production of an efficient 3D visualisation is still missing. This is why a comprehensive methodological framework is proposed in order to build decision tables for specific data, tasks and contexts. Based on the second-order logic formalism, we define a set of functions and propositions among and between two collections of entities: on one hand static retinal variables (hue, size, shape…) and 3D environment parameters (directional lighting, shadow, haze…) and on the other hand their effect(s) regarding specific visual tasks. It enables to define 3D visualisation rules according to four categories: consequence, compatibility, potential incompatibility and incompatibility. In this paper, the application of the methodological framework is demonstrated for an urban visualisation at high density considering a specific set of entities. On the basis of our analysis and the results of many studies conducted in the 3D semiotics, which refers to the study of symbols and how they relay information, the truth values of propositions are determined. 3D visualisation rules are then extracted for the considered context and set of entities and are presented into a decision table with a colour coding. Finally, the decision table is implemented into a plugin developed with three.js, a cross-browser JavaScript library. The plugin consists of a sidebar and warning windows that help the designer in the use of a set of static retinal variables and 3D environment parameters.

Production of unnaturally linked chimeric proteins using a combination of sortase-catalyzed transpeptidation and click chemistry.

PubMed

Witte, Martin D; Theile, Christopher S; Wu, Tongfei; Guimaraes, Carla P; Blom, Annet E M; Ploegh, Hidde L

2013-09-01

Chimeric proteins, including bispecific antibodies, are biological tools with therapeutic applications. Genetic fusion and ligation methods allow the creation of N-to-C and C-to-N fused recombinant proteins, but not unnaturally linked N-to-N and C-to-C fusion proteins. This protocol describes a simple procedure for the production of such chimeric proteins, starting from correctly folded proteins and readily available peptides. By equipping the N terminus or C terminus of the proteins of interest with a set of click handles using sortase A, followed by a strain-promoted click reaction, unnatural N-to-N and C-to-C linked (hetero) fusion proteins are established. Examples of proteins that have been conjugated via this method include interleukin-2, interferon-α, ubiquitin, antibodies and several single-domain antibodies. If the peptides, sortase A and the proteins of interest are in hand, the unnaturally N-to-N and C-to-C fused proteins can be obtained in 3-4 d.

Cammp Team

NASA Technical Reports Server (NTRS)

Evertt, Shonn F.; Collins, Michael; Hahn, William

2008-01-01

The International Space Station (ISS) Configuration Analysis Modeling and Mass Properties (CAMMP) Team is presenting a demo of certain CAMMP capabilities at a Booz Allen Hamilton conference in San Antonio. The team will be showing pictures of low fidelity, simplified ISS models, but no dimensions or technical data. The presentation will include a brief description of the contract and task, description and picture of the Topology, description of Generic Ground Rules and Constraints (GGR&C), description of Stage Analysis with constraints applied, and wrap up with description of other tasks such as Special Studies, Cable Routing, etc. The models include conceptual Crew Exploration Vehicle (CEV) and Lunar Lander images and animations created for promotional purposes, which are based entirely on public domain conceptual images from public NASA web sites and publicly available magazine articles and are not based on any actual designs, measurements, or 3D models. Conceptual Mars rover and lander are completely conceptual and are not based on any NASA designs or data. The demonstration includes High Fidelity Computer Aided Design (CAD) models of ISS provided by the ISS 3D CAD Team which will be used in a visual display to demonstrate the capabilities of the Teamcenter Visualization software. The demonstration will include 3D views of the CAD models including random measurements that will be taken to demonstrate the measurement tool. A 3D PDF file will be demonstrated of the Blue Book fidelity assembly complete model with no vehicles attached. The 3D zoom and rotation will be displayed as well as random measurements from the measurement tool. The External Configuration Analysis and Tracking Tool (ExCATT) Microsoft Access Database will be demonstrated to show its capabilities to organize and track hardware on ISS. The data included will be part numbers, serial numbers, historical, current, and future locations, of external hardware components on station. It includes dates of all external ISS events and flights and the associated hardware changes for each event. The hardware location information does not always reveal the exact location of the hardware, only the general location. In some cases the location is a module or carrier, in other cases it is a WIF socket, handrail, or attach point. Only small portions of the data will be displayed for demonstration purposes.

A low-cost tracked C-arm (TC-arm) upgrade system for versatile quantitative intraoperative imaging.

PubMed

Amiri, Shahram; Wilson, David R; Masri, Bassam A; Anglin, Carolyn

2014-07-01

C-arm fluoroscopy is frequently used in clinical applications as a low-cost and mobile real-time qualitative assessment tool. C-arms, however, are not widely accepted for applications involving quantitative assessments, mainly due to the lack of reliable and low-cost position tracking methods, as well as adequate calibration and registration techniques. The solution suggested in this work is a tracked C-arm (TC-arm) which employs a low-cost sensor tracking module that can be retrofitted to any conventional C-arm for tracking the individual joints of the device. Registration and offline calibration methods were developed that allow accurate tracking of the gantry and determination of the exact intrinsic and extrinsic parameters of the imaging system for any acquired fluoroscopic image. The performance of the system was evaluated in comparison to an Optotrak[Formula: see text] motion tracking system and by a series of experiments on accurately built ball-bearing phantoms. Accuracies of the system were determined for 2D-3D registration, three-dimensional landmark localization, and for generating panoramic stitched views in simulated intraoperative applications. The system was able to track the center point of the gantry with an accuracy of [Formula: see text] mm or better. Accuracies of 2D-3D registrations were [Formula: see text] mm and [Formula: see text]. Three-dimensional landmark localization had an accuracy of [Formula: see text] of the length (or [Formula: see text] mm) on average, depending on whether the landmarks were located along, above, or across the table. The overall accuracies of the two-dimensional measurements conducted on stitched panoramic images of the femur and lumbar spine were 2.5 [Formula: see text] 2.0 % [Formula: see text] and [Formula: see text], respectively. The TC-arm system has the potential to achieve sophisticated quantitative fluoroscopy assessment capabilities using an existing C-arm imaging system. This technology may be useful to improve the quality of orthopedic surgery and interventional radiology.

Automatic depth grading tool to successfully adapt stereoscopic 3D content to digital cinema and home viewing environments

NASA Astrophysics Data System (ADS)

Thébault, Cédric; Doyen, Didier; Routhier, Pierre; Borel, Thierry

2013-03-01

To ensure an immersive, yet comfortable experience, significant work is required during post-production to adapt the stereoscopic 3D (S3D) content to the targeted display and its environment. On the one hand, the content needs to be reconverged using horizontal image translation (HIT) so as to harmonize the depth across the shots. On the other hand, to prevent edge violation, specific re-convergence is required and depending on the viewing conditions floating windows need to be positioned. In order to simplify this time-consuming work we propose a depth grading tool that automatically adapts S3D content to digital cinema or home viewing environments. Based on a disparity map, a stereo point of interest in each shot is automatically evaluated. This point of interest is used for depth matching, i.e. to position the objects of interest of consecutive shots in a same plane so as to reduce visual fatigue. The tool adapts the re-convergence to avoid edge-violation, hyper-convergence and hyper-divergence. Floating windows are also automatically positioned. The method has been tested on various types of S3D content, and the results have been validated by a stereographer.

What does leaf wax δD from a mixed C3/C4 vegetation region tell us?

NASA Astrophysics Data System (ADS)

Wang, Yiming V.; Larsen, Thomas; Leduc, Guillaume; Andersen, Nils; Blanz, Thomas; Schneider, Ralph R.

2013-06-01

Hydrogen isotope values (δD) of sedimentary terrestrial leaf wax such as n-alkanes or n-acids have been used to map and understand past changes in rainfall amount in the tropics because δD of precipitation is commonly assumed as the first order controlling factor of leaf wax δD. Plant functional types and their photosynthetic pathways can also affect leaf wax δD but these biological effects are rarely taken into account in paleo studies relying on this rainfall proxy. To investigate how biological effects may influence δD values we here present a 37,000-year old record of δD and stable carbon isotopes (δ13C) measured on four n-alkanes (n-C27, n-C29, n-C31, n-C33) from a marine sediment core collected off the Zambezi River mouth. Our paleo δ13C records suggest that each individual n-alkanes had different C3/C4 proportional contributions. n-C29 was mostly derived from a C3 dicots (trees, shrubs and forbs) dominant vegetation throughout the entire record. In contrast, the longer chain n-C33 and n-C31 were mostly contributed by C4 grasses during the Glacial period but shifted to a mixture of C4 grasses and C3 dicots during the Holocene. Strong correlations between δD and δ13C values of n-C33 (correlation coefficient R2 = 0.75, n = 58) and n-C31 (R2 = 0.48, n = 58) suggest that their δD values were strongly influenced by changes in the relative contributions of C3/C4 plant types in contrast to n-C29 (R2 = 0.07, n = 58). Within regions with variable C3/C4 input, we conclude that δD values of n-C29 are the most reliable and unbiased indicator for past changes in rainfall, and that δD and δ13C values of n-C31 and n-C33 are sensitive to C3/C4 vegetation changes. Our results demonstrate that a robust interpretation of palaeohydrological data using n-alkane δD requires additional knowledge of regional vegetation changes from which n-alkanes are synthesized, and that the combination of δD and δ13C values of multiple n-alkanes can help to differentiate biological effects from those related to the hydrological cycle.

0D/2D Z-Scheme Heterojunctions of Bismuth Tantalate Quantum Dots/Ultrathin g-C3N4 Nanosheets for Highly Efficient Visible Light Photocatalytic Degradation of Antibiotics.

PubMed

Wang, Kai; Zhang, Gaoke; Li, Jun; Li, Yuan; Wu, Xiaoyong

2017-12-20

Constructing 0D/2D Z-scheme photocatalysts is a great promising path to improve photocatalytic activity by  efficiently enhancing charge separation. Herein, we fabricated a visible-light-responsive Bi 3 TaO 7 quantum dots (QDs)/g-C 3 N 4 nanosheets (NSs) 0D/2D Z-scheme composite via a facile ultrasound method, and Bi 3 TaO 7 QDs could be interspersed on the surface of g-C 3 N 4 NSs uniformly. Furthermore, the strong interaction between Bi 3 TaO 7 QDs and g-C 3 N 4 NSs disturbed the CN heterocycles by forming C═O bonds between C atoms of the N-(C) 3 group and O atoms of the Ta-O bond. The optimum composite with 20 wt % g-C 3 N 4 NSs showed the superior photocatalytic activity for degradation of ciprofloxacin (CIP) over the composites prepared by mechanical mixing and solid-state methods, the photocatalytic efficiency of which were 4 and 12.2 times higher than those of bare Bi 3 TaO 7 and g-C 3 N 4 . Photoluminescence (PL), time-resolved transient PL decay spectra, and photocurrent together verify that the photogenerated hole-electron pairs in this 0D/2D Z-scheme composite have been effectively separated. The enhanced photocatalytic activity of as-synthesized photocatalysts could be attributed to the synergistic effect of efficient Z-scheme charge separation, highly dispersed 0D Bi 3 TaO 7 nanocrystals, coordinating sites of 2D g-C 3 N 4 NSs and the strong coupling between them. This study might pave the way toward designing novel visible-light-induced 0D/2D photocatalyst systems for highly efficient degradation of antibiotics.

Electrostatic Steering Accelerates C3d:CR2 Association

PubMed Central

2016-01-01

Electrostatic effects are ubiquitous in protein interactions and are found to be pervasive in the complement system as well. The interaction between complement fragment C3d and complement receptor 2 (CR2) has evolved to become a link between innate and adaptive immunity. Electrostatic interactions have been suggested to be the driving factor for the association of the C3d:CR2 complex. In this study, we investigate the effects of ionic strength and mutagenesis on the association of C3d:CR2 through Brownian dynamics simulations. We demonstrate that the formation of the C3d:CR2 complex is ionic strength-dependent, suggesting the presence of long-range electrostatic steering that accelerates the complex formation. Electrostatic steering occurs through the interaction of an acidic surface patch in C3d and the positively charged CR2 and is supported by the effects of mutations within the acidic patch of C3d that slow or diminish association. Our data are in agreement with previous experimental mutagenesis and binding studies and computational studies. Although the C3d acidic patch may be locally destabilizing because of unfavorable Coulombic interactions of like charges, it contributes to the acceleration of association. Therefore, acceleration of function through electrostatic steering takes precedence to stability. The site of interaction between C3d and CR2 has been the target for delivery of CR2-bound nanoparticle, antibody, and small molecule biomarkers, as well as potential therapeutics. A detailed knowledge of the physicochemical basis of C3d:CR2 association may be necessary to accelerate biomarker and drug discovery efforts. PMID:27092816

Optimal water networks in protein cavities with GAsol and 3D-RISM.

PubMed

Fusani, Lucia; Wall, Ian; Palmer, David; Cortes, Alvaro

2018-06-01

Water molecules in protein binding sites play essential roles in biological processes. The popular 3D-RISM prediction method can calculate the solvent density distribution within minutes, but is difficult to convert it into explicit water molecules. We present GAsol, a tool that is capable of finding the network of water molecules that best fits a particular 3D-RISM density distribution in a fast and accurate manner and that outperforms other available tools by finding the globally optimal solution thanks to its genetic algorithm. https://github.com/accsc/GAsol. BSD 3-clauses license. alvaro.x.cortes@gsk.com. Supplementary data are available at Bioinformatics online.

On the holographic 3D tracking of in vitro cells characterized by a highly-morphological change.

PubMed

Memmolo, Pasquale; Iannone, Maria; Ventre, Maurizio; Netti, Paolo Antonio; Finizio, Andrea; Paturzo, Melania; Ferraro, Pietro

2012-12-17

Digital Holography (DH) in microscopic configuration is a powerful tool for the imaging of micro-objects contained into a three dimensional (3D) volume, by a single-shot image acquisition. Many studies report on the ability of DH to track particle, microorganism and cells in 3D. However, very few investigations are performed with objects that change severely their morphology during the observation period. Here we study DH as a tool for 3D tracking an osteosarcoma cell line for which extensive changes in cell morphology are associated to cell motion. Due to the great unpredictable morphological change, retrieving cell's position in 3D can become a complicated issue. We investigate and discuss in this paper how the tridimensional position can be affected by the continuous change of the cells. Moreover we propose and test some strategies to afford the problems and compare it with others approaches. Finally, results on the 3D tracking and comments are reported and illustrated.

Increased xylose affinity of Hxt2 through gene shuffling of hexose transporters in Saccharomyces cerevisiae.

PubMed

Nijland, J G; Shin, H Y; de Waal, P P; Klaassen, P; Driessen, A J M

2018-02-01

Optimizing D-xylose transport in Saccharomyces cerevisiae is essential for efficient bioethanol production from cellulosic materials. We have used a gene shuffling approach of hexose (Hxt) transporters in order to increase the affinity for D-xylose. Various libraries were transformed to a hexose transporter deletion strain, and shuffled genes were selected via growth on low concentrations of D-xylose. This screening yielded two homologous fusion proteins (fusions 9,4 and 9,6), both consisting of the major central part of Hxt2 and various smaller parts of other Hxt proteins. Both chimeric proteins showed the same increase in D-xylose affinity (8·1 ± 3·0 mmol l -1 ) compared with Hxt2 (23·7 ± 2·1 mmol l -1 ). The increased D-xylose affinity could be related to the C terminus, more specifically to a cysteine to proline mutation at position 505 in Hxt2. The Hxt2 C505P mutation increased the affinity for D-xylose for Hxt2, thus providing a way to increase D-xylose transport flux at low D-xylose concentration. The gene shuffling protocol using the highly homologues hexose transporters family provides a powerful tool to enhance the D-xylose affinity of Hxt transporters in S. cerevisiae, thus providing a means to increase the D-xylose uptake flux at low D-xylose concentrations. © 2017 The Society for Applied Microbiology.

76 FR 70046 - Airworthiness Directives; Eurocopter France Model AS350B, B1, B2, B3, BA, C, D, and D1; and...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-10

... Airworthiness Directives; Eurocopter France Model AS350B, B1, B2, B3, BA, C, D, and D1; and AS355E, F, F1, F2, N... France (Eurocopter) Model AS350B, B1, B2, B3, BA, C, D, and D1 helicopters; and Model AS355E, F, F1, F2... (AD 2003- 22-06), for Eurocopter Model AS350B, B1, B2, B3, BA, C, D, and D1; and Model AS355E, F, F1...

Assessment of post-contamination treatments affecting different bonding stages to dentin

PubMed Central

Elkassas, Dina; Arafa, Abla

2016-01-01

Objectives: To assess the effect of cleansing treatments following saliva and blood contamination at different bonding stages to dentin. Materials and Methods: Labial surfaces of 168 permanent maxillary central incisors were ground flat exposing superficial dentin. Specimens were divided into: uncontaminated control (A), contamination after etching (B), contamination after adhesive application (C), contamination after adhesive polymerization (D). Groups were further subdivided according to cleansing treatments into: rinsing (B1, C1, D1), re-etching (B2, D3), sodium hypochlorite application (B3), ethyl alcohol application (C2), acetone application (C3), rinsing and rebonding (D2), re-etching and rebonding (D4). Composite microcylinders were bonded to treated substrates and shear loaded micro-shear bond strength (μSBS) until failure and treated surfaces were examined with scanning electron microscope. Debonded surfaces were classified as adhesive, cohesive or mixed failure. The data were analyzed using one-way ANOVA and Tukey's post hoc test. Results: The μSBS values were ranked as follow; Group B: A > B3 > B2 > B1 > B, Group C: A > C3 > C2 > C1 > C, Group D: A > D4 > D1 = D2 ≥ D3. Debonded surfaces showed adhesive failure in Group B while cohesive failure in Groups C and D. Conclusions: Cleansing treatments differ according to bonding step; re-etching then rebonding suggested if etched substrate or polymerized adhesive were contaminated while acetone application decontaminated affected unpolymerized adhesive. PMID:27403048

3D data processing with advanced computer graphics tools

NASA Astrophysics Data System (ADS)

Zhang, Song; Ekstrand, Laura; Grieve, Taylor; Eisenmann, David J.; Chumbley, L. Scott

2012-09-01

Often, the 3-D raw data coming from an optical profilometer contains spiky noises and irregular grid, which make it difficult to analyze and difficult to store because of the enormously large size. This paper is to address these two issues for an optical profilometer by substantially reducing the spiky noise of the 3-D raw data from an optical profilometer, and by rapidly re-sampling the raw data into regular grids at any pixel size and any orientation with advanced computer graphics tools. Experimental results will be presented to demonstrate the effectiveness of the proposed approach.

Evaluating the Use of Cleft Lip and Palate 3D-Printed Models as a Teaching Aid.

PubMed

AlAli, Ahmad B; Griffin, Michelle F; Calonge, Wenceslao M; Butler, Peter E

Visualization tools are essential for effective medical education, to aid students understanding of complex anatomical systems. Three dimensional (3D) printed models are showing a wide-reaching potential in the field of medical education, to aid the interpretation of 2D imaging. This study investigates the use of 3D-printed models in educational seminars on cleft lip and palate, by comparing integrated "hands-on" student seminars, with 2D presentation seminar methods. Cleft lip and palate models were manufactured using 3D-printing technology at the medical school. Sixty-seven students from two medical schools participated in the study. The students were randomly allocated to 2 groups. Knowledge was compared between the groups using a multiple-choice question test before and after the teaching intervention. Group 1 was the control group with a PowerPoint presentation-based educational seminar and group 2 was the test group, with the same PowerPoint presentation, but with the addition of a physical demonstration using 3D-printed models of unilateral and bilateral cleft lips and palate. The level of knowledge gained was established using a preseminar and postseminar assessment, in 2 different institutions, where the addition of the 3D-printed model resulted in a significant improvement in the mean percentage of knowledge gained (44.65% test group; 32.16%; control group; p = 0.038). Student experience was assessed using a postseminar survey, where students felt the 3D-printed model significantly improved the learning experience (p = 0.005) and their visualization (p = 0.001). This study highlights the benefits of the use of 3D-printed models as visualization tools in medical education and the potential of 3D-printing technology to become a standard and effective tool in the interpretation of 2D imaging. Copyright © 2018 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

In situ evidence of mineral physical protection and carbon stabilization revealed by nanoscale 3-D tomography

NASA Astrophysics Data System (ADS)

Weng, Yi-Tse; Wang, Chun-Chieh; Chiang, Cheng-Cheng; Tsai, Heng; Song, Yen-Fang; Huang, Shiuh-Tsuen; Liang, Biqing

2018-05-01

An approach for nanoscale 3-D tomography of organic carbon (OC) and associated mineral nanoparticles was developed to illustrate their spatial distribution and boundary interplay, using synchrotron-based transmission X-ray microscopy (TXM). The proposed 3-D tomography technique was first applied to in situ observation of a laboratory-made consortium of black carbon (BC) and nanomineral (TiO2, 15 nm), and its performance was evaluated using dual-scan (absorption contrast and phase contrast) modes. This novel tool was then successfully applied to a natural OC-mineral consortium from mountain soil at a spatial resolution of 60 nm, showing the fine structure and boundary of OC, the distribution of abundant nano-sized minerals, and the 3-D organo-mineral association in situ. The stabilization of 3500-year-old natural OC was mainly attributed to the physical protection of nano-sized iron (Fe)-containing minerals (Fe oxyhydroxides including ferrihydrite, goethite, and lepidocrocite), and the strong organo-mineral complexation. In situ evidence revealed an abundance of mineral nanoparticles, in dense thin layers or nano-aggregates/clusters, instead of crystalline clay-sized minerals on or near OC surfaces. The key working minerals for C stabilization were reactive short-range-order (SRO) mineral nanoparticles and poorly crystalline submicron-sized clay minerals. Spectroscopic analyses demonstrated that the studied OC was not merely in crisscross co-localization with reactive SRO minerals; there could be a significant degree of binding between OC and the minerals. The ubiquity and abundance of mineral nanoparticles on the OC surface, and their heterogeneity in the natural environment may have been severely underestimated by traditional research approaches. Our in situ description of organo-mineral interplay at the nanoscale provides direct evidence to substantiate the importance of mineral physical protection for the long-term stabilization of OC. This high-resolution 3-D tomography approach is a promising tool for generating new insight into the interior 3-D structure of micro-aggregates, the in situ interplay between OC and minerals, and the fate of mineral nanoparticles (including heavy metals) in natural environments.

Bioengineering Anabolic Vitamin D-25-Hydroxylase Activity into the Human Vitamin D Catabolic Enzyme, Cytochrome P450 CYP24A1, by a V391L Mutation*

PubMed Central

Kaufmann, Martin; Prosser, David E.; Jones, Glenville

2011-01-01

CYP24A1 is a mitochondrial cytochrome P450 (CYP) that catabolizes 1α,25-dihydroxyvitamin D3 (1α,25-(OH)2D3) to different products: calcitroic acid or 1α,25-(OH)2D3-26,23-lactone via multistep pathways commencing with C24 and C23 hydroxylation, respectively. Despite the ability of CYP24A1 to catabolize a wide range of 25-hydroxylated analogs including 25-hydroxyvitamin D3, the enzyme is unable to metabolize the synthetic prodrug, 1α-hydroxyvitamin D3 (1α-OH-D3), presumably because it lacks a C25-hydroxyl. In the current study we show that a single V391L amino acid substitution in the β3a-strand of human CYP24A1 converts this enzyme from a catabolic 1α,25-(OH)2D3-24-hydroxylase into an anabolic 1α-OH-D3-25-hydroxylase, thereby forming the hormone, 1α,25-(OH)2D3. Furthermore, because the mutant enzyme retains its basal ability to catabolize 1α,25-(OH)2D3 via C24 hydroxylation, it can also make calcitroic acid. Previous work has shown that an A326G mutation is responsible for the regioselectivity differences observed between human (primarily C24-hydroxylating) and opossum (C23-hydroxylating) CYP24A1. When the V391L and A326G mutations were combined (V391L/A326G), the mutant enzyme continued to form 1α,25-(OH)2D3 from 1α-OH-D3, but this initial product was diverted via the C23 hydroxylation pathway into the 26,23-lactone. The relative position of Val-391 in the β3a-strand of a homology model and the crystal structure of rat CYP24A1 is consistent with hydrophobic contact of Val-391 and the substrate side chain near C21. We interpret that the substrate specificity of V391L-modified human CYP24A1 toward 1α-OH-D3 is enabled by an altered contact with the substrate side chain that optimally positions C25 of the 1α-OH-D3 above the heme for hydroxylation. PMID:21697097

Validity of a quantitative clinical measurement tool of trunk posture in idiopathic scoliosis.

PubMed

Fortin, Carole; Feldman, Debbie E; Cheriet, Farida; Labelle, Hubert

2010-09-01

Concurrent validity between postural indices obtained from digital photographs (two-dimensional [2D]), surface topography imaging (three-dimensional [3D]), and radiographs. To assess the validity of a quantitative clinical postural assessment tool of the trunk based on photographs (2D) as compared to a surface topography system (3D) as well as indices calculated from radiographs. To monitor progression of scoliosis or change in posture over time in young persons with idiopathic scoliosis (IS), noninvasive and nonionizing methods are recommended. In a clinical setting, posture can be quite easily assessed by calculating key postural indices from photographs. Quantitative postural indices of 70 subjects aged 10 to 20 years old with IS (Cobb angle, 15 degrees -60 degrees) were measured from photographs and from 3D trunk surface images taken in the standing position. Shoulder, scapula, trunk list, pelvis, scoliosis, and waist angles indices were calculated with specially designed software. Frontal and sagittal Cobb angles and trunk list were also calculated on radiographs. The Pearson correlation coefficients (r) was used to estimate concurrent validity of the 2D clinical postural tool of the trunk with indices extracted from the 3D system and with those obtained from radiographs. The correlation between 2D and 3D indices was good to excellent for shoulder, pelvis, trunk list, and thoracic scoliosis (0.81>r<0.97; P<0.01) but fair to moderate for thoracic kyphosis, lumbar lordosis, and thoracolumbar or lumbar scoliosis (0.30>r<0.56; P<0.05). The correlation between 2D and radiograph spinal indices was fair to good (-0.33 to -0.80 with Cobb angles and 0.76 for trunk list; P<0.05). This tool will facilitate clinical practice by monitoring trunk posture among persons with IS. Further, it may contribute to a reduction in the use of radiographs to monitor scoliosis progression.

Hydrological Scenario Using Tools and Applications Available in enviroGRIDS Portal

NASA Astrophysics Data System (ADS)

Bacu, V.; Mihon, D.; Stefanut, T.; Rodila, D.; Cau, P.; Manca, S.; Soru, C.; Gorgan, D.

2012-04-01

Nowadays the decision makers but also citizens are concerning with the sustainability and vulnerability of land management practices on various aspects and in particular on water quality and quantity in complex watersheds. The Black Sea Catchment is an important watershed in the Central and East Europe. In the FP7 project enviroGRIDS [1] was developed a Web Portal that incorporates different tools and applications focused on geospatial data management, hydrologic model calibration, execution and visualization and training activities. This presentation highlights, from the end-user point of view, the scenario related with hydrological models using the tools and applications available in the enviroGRIDS Web Portal [2]. The development of SWAT (Soil Water Assessment Tool) hydrological models is a well known procedure for the hydrological specialists [3]. Starting from the primary data (information related to weather, soil properties, topography, vegetation, and land management practices of the particular watershed) that are used to develop SWAT hydrological models, to specific reports, about the water quality in the studied watershed, the hydrological specialist will use different applications available in the enviroGRIDS portal. The tools and applications available through the enviroGRIDS portal are not dealing with the building up of the SWAT hydrological models. They are mainly focused on: calibration procedure (gSWAT [4]) - uses the GRID computational infrastructure to speed-up the calibration process; development of specific scenarios (BASHYT [5]) - starts from an already calibrated SWAT hydrological model and defines new scenarios; execution of scenarios (gSWATSim [6]) - executes the scenarios exported from BASHYT; visualization (BASHYT) - displays charts, tables and maps. Each application is built-up as a stack of functional layers. We combine different layers of applications by vertical interoperability in order to build the desired complex functionality. On the other hand, the applications can collaborate at the same architectural levels, which represent the horizontal interoperability. Both the horizontal and vertical interoperability is accomplished by services and by exchanging data. The calibration procedure requires huge computational resources, which are provided by the Grid infrastructure. On the other hand the scenario development through BASHYT requires a flexible way of interaction with the SWAT model in order to easily change the input model. The large user community of SWAT from the enviroGRIDS consortium or outside may greatly benefit from tools and applications related with the calibration process, scenario development and execution from the enviroGRIDS portal. [1]. enviroGRIDS project, http://envirogrids.net/ [2]. Gorgan D., Abbaspour K., Cau P., Bacu V., Mihon D., Giuliani G., Ray N., Lehmann A., Grid Based Data Processing Tools and Applications for Black Sea Catchment Basin. IDAACS 2011 - The 6th IEEE International Conference on Intelligent Data Acquisition and Advanced Computing Systems: Technology and Applications 15-17 September 2011, Prague. IEEE Computer Press, pp. 223 - 228 (2011). [3]. Soil and Water Assessment Tool, http://www.brc.tamus.edu/swat/index.html [4]. Bacu V., Mihon D., Rodila D., Stefanut T., Gorgan D., Grid Based Architectural Components for SWAT Model Calibration. HPCS 2011 - International Conference on High Performance Computing and Simulation, 4-8 July, Istanbul, Turkey, ISBN 978-1-61284-381-0, doi: 10.1109/HPCSim.2011.5999824, pp. 193-198 (2011). [5]. Manca S., Soru C., Cau P., Meloni G., Fiori M., A multi model and multiscale, GIS oriented Web framework based on the SWAT model to face issues of water and soil resource vulnerability. Presentation at the 5th International SWAT Conference, August 3-7, 2009, http://www.brc.tamus.edu/swat/4thswatconf/docs/rooma/session5/Cau-Bashyt.pdf [6]. Bacu V., Mihon D., Stefanut T., Rodila D., Gorgan D., Cau P., Manca S., Grid Based Services and Tools for Hydrological Model Processing and Visualization. SYNASC 2011 - 13 International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (in press).

δ 13C and δD identification of sources of lipid biomarkers in sediments of Lake Haruna (Japan)

NASA Astrophysics Data System (ADS)

Chikaraishi, Yoshito; Naraoka, Hiroshi

2005-07-01

Organic materials in lacustrine sediments are from multiple terrestrial and aquatic sources. In this study, carbon (δ 13C) and hydrogen isotopic compositions (δD) of phytol, various sterols, and major n-fatty acids in sediments at Lake Haruna, Japan, were determined in their solvent-extractable (free) and saponification-released forms (bound). The δ 13C-δD distributions of these lipid molecules in sediments are compared with those of terrestrial C3 and C4 plants, aquatic C3 plants, and plankton to evaluate their relative contributions. δ 13C-δD of free phytol in sediments is very close to that of phytol in plankton samples, whereas δ 13C-δD of bound phytol in sediments is on a mixing line between terrestrial C3 plant and plankton material. Unlike phytol, no significant δ 13C-δD difference between free and bound forms was found in sterols and n-fatty acids. δ 13C-δD values of algal sterols such as 24-methylcholesta-5,22-dien-3β-ol in sediments are close to those of plankton, whereas δ 13C-δD of multiple-source sterols such as 24-ethylcholest-5-en-3β-ol and of major n-fatty acids such as n-hexadecanoic acid in sediments are between those of terrestrial C3 plants and plankton samples. Thus, δ 13C-δD distributions clearly indicate the specific source contributions of biomarkers preserved in a lacustrine environment. Free phytol and algal sterols can be attributed to phytoplankton, and bound phytol, multiple source sterols, and major n-fatty acids are contributed by both terrestrial C3 plants and phytoplankton.

Creating and facilitating change for Person-Centred Coordinated Care (P3C): The development of the Organisational Change Tool (P3C-OCT).

PubMed

Horrell, Jane; Lloyd, Helen; Sugavanam, Thavapriya; Close, James; Byng, Richard

2018-04-01

Person Centred Coordinated Care (P3C) is a UK priority for patients, carers, professionals, commissioners and policy makers. Services are developing a range of approaches to deliver this care with a lack of tools to guide implementation. A scoping review and critical examination of current policy, key literature and NHS guidelines, together with stakeholder involvement led to the identification of domains, subdomains and component activities (processes and behaviours) required to deliver P3C. These were validated through codesign with stakeholders via a series of workshops and cognitive interviews. Six core domains of P3C were identified as follows: (i) my goals, (ii) care planning, (iii) transitions, (iv) decision making (v), information and communication and (vi) organizational support activities. These were populated by 29 core subdomains (question items). A number of response codes (components) to each question provide examples of the processes and activities that can be actioned to achieve each core subdomain of P3C. The P3C-OCT provides a coherent approach to monitoring progress and supporting practice development towards P3C. It can be used to generate a shared understanding of the core domains of P3C at a service delivery level, and support reorganization of care for those with complex needs. The tool can reliably detect change over time, as demonstrated in a sample of 40 UK general practices. It is currently being used in four UK evaluations of new models of care and being further developed as a training tool for the delivery of P3C. © 2017 The Authors Health Expectations Published by John Wiley & Sons Ltd.

The use of 3D planning in facial surgery: preliminary observations.

PubMed

Hoarau, R; Zweifel, D; Simon, C; Broome, M

2014-12-01

Three-dimensional (3D) planning is becoming a more commonly used tool in maxillofacial surgery. At first used only virtually, 3D planning now also enables the creation of useful intraoperative aids such as cutting guides, which decrease the operative difficulty. In our center, we have used 3D planning in various domains of facial surgery and have investigated the advantages of this technique. We have also addressed the difficulties associated with its use. 3D planning increases the accuracy of reconstructive surgery, decreases operating time, whilst maintaining excellent esthetic results. However, its use is restricted to osseous reconstruction at this stage and once planning has been undertaken, it cannot be reversed or altered intraoperatively. Despite the attractive nature of this new tool, its uses and practicalities must be further evaluated. In particular, cost-effectiveness, hospital stay, and patient perceived benefits must be assessed. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

[Exploratory study of 3D printing technique in the treatment of basilar invagination and atlantoaxial dislocation].

PubMed

Yin, Yiheng; Yu, Xinguang; Tong, Huaiyu; Xu, Tao; Wang, Peng; Qiao, Guangyu

2015-10-06

To investigate the clinical application value of the 3D printing technique in the treatment of basilar invagination and atlantoaxial dislocation. From January 2013 to September 2013, 10 patients with basilar invagination and atlantoaxial dislocation needing posterior fixation undertook 3D printing modes at the Department of Neurosurgery in PLA General Hospital. The 1:1 size models were established from skull base to C4 level with different colors between bone structures and vertebral arteries. The simulation of screw insertion was made to investigate the fixation plan and ideal entry point to avoid vertebral artery injury. After obtaining the individual screw insertion data in 3D printing modes, the according surgical operations were performed. The actual clinical results and virtual screw data in 3D printing mode were compared with each other. The 3D printing modes revealed that all the 10 patients had the dysplasia or occipitalized C1 posterior arch indicating C1 posterior arch screw implantation was not suitable. C1 lateral masses were chosen as the screws entry points. C2 screws were designed individually based on the 3D printing modes as follows: 3 patients with aberrant vertebral artery or narrow C2 pedicle less than 3.5 mm were not suitable for pedicle screw implantation. Among the 3 patients, 1 was fixed with C2 laminar screw, and 1 with C2-3 transarticular screw and 1 with C3 pedicle screw (also combined with congenital C2-3 vertebral fusion). Two patients with narrow C2 pedicle between 3.5 and 4mm were designed to choose pedicle screw fixation after 3D printing mode evaluation. One patient with C1 lateral mass vertically dislocated axis was planned with C1-2 transarticular screw fixation. All the other patients were planned with C2 pedicle screws. All the 10 patients had operation designed as the 3D printing modes schemes. The follow-up ranged from 12 to 18 months and all the patients recovered from the clinical symptoms and the bony fusion attained to 100%. 3D printing mode could provide thorough information of the bony structure abnormalities and route of vertebral artery. It is helpful for setting operation strategy and designing screw entry point and trajectory and avoiding vertebral artery and spinal cord injury and thus deserves generalization.

Three-dimensional (3D) structure prediction of the American and African oil-palms β-ketoacyl-[ACP] synthase-II protein by comparative modelling

PubMed Central

Wang, Edina; Chinni, Suresh; Bhore, Subhash Janardhan

2014-01-01

Background: The fatty-acid profile of the vegetable oils determines its properties and nutritional value. Palm-oil obtained from the African oil-palm [Elaeis guineensis Jacq. (Tenera)] contains 44% palmitic acid (C16:0), but, palm-oil obtained from the American oilpalm [Elaeis oleifera] contains only 25% C16:0. In part, the b-ketoacyl-[ACP] synthase II (KASII) [EC: 2.3.1.179] protein is responsible for the high level of C16:0 in palm-oil derived from the African oil-palm. To understand more about E. guineensis KASII (EgKASII) and E. oleifera KASII (EoKASII) proteins, it is essential to know its structures. Hence, this study was undertaken. Objective: The objective of this study was to predict three-dimensional (3D) structure of EgKASII and EoKASII proteins using molecular modelling tools. Materials and Methods: The amino-acid sequences for KASII proteins were retrieved from the protein database of National Center for Biotechnology Information (NCBI), USA. The 3D structures were predicted for both proteins using homology modelling and ab-initio technique approach of protein structure prediction. The molecular dynamics (MD) simulation was performed to refine the predicted structures. The predicted structure models were evaluated and root mean square deviation (RMSD) and root mean square fluctuation (RMSF) values were calculated. Results: The homology modelling showed that EgKASII and EoKASII proteins are 78% and 74% similar with Streptococcus pneumonia KASII and Brucella melitensis KASII, respectively. The EgKASII and EoKASII structures predicted by using ab-initio technique approach shows 6% and 9% deviation to its structures predicted by homology modelling, respectively. The structure refinement and validation confirmed that the predicted structures are accurate. Conclusion: The 3D structures for EgKASII and EoKASII proteins were predicted. However, further research is essential to understand the interaction of EgKASII and EoKASII proteins with its substrates. PMID:24748752

Three-dimensional (3D) structure prediction of the American and African oil-palms β-ketoacyl-[ACP] synthase-II protein by comparative modelling.

PubMed

Wang, Edina; Chinni, Suresh; Bhore, Subhash Janardhan

2014-01-01

The fatty-acid profile of the vegetable oils determines its properties and nutritional value. Palm-oil obtained from the African oil-palm [Elaeis guineensis Jacq. (Tenera)] contains 44% palmitic acid (C16:0), but, palm-oil obtained from the American oilpalm [Elaeis oleifera] contains only 25% C16:0. In part, the b-ketoacyl-[ACP] synthase II (KASII) [EC: 2.3.1.179] protein is responsible for the high level of C16:0 in palm-oil derived from the African oil-palm. To understand more about E. guineensis KASII (EgKASII) and E. oleifera KASII (EoKASII) proteins, it is essential to know its structures. Hence, this study was undertaken. The objective of this study was to predict three-dimensional (3D) structure of EgKASII and EoKASII proteins using molecular modelling tools. The amino-acid sequences for KASII proteins were retrieved from the protein database of National Center for Biotechnology Information (NCBI), USA. The 3D structures were predicted for both proteins using homology modelling and ab-initio technique approach of protein structure prediction. The molecular dynamics (MD) simulation was performed to refine the predicted structures. The predicted structure models were evaluated and root mean square deviation (RMSD) and root mean square fluctuation (RMSF) values were calculated. The homology modelling showed that EgKASII and EoKASII proteins are 78% and 74% similar with Streptococcus pneumonia KASII and Brucella melitensis KASII, respectively. The EgKASII and EoKASII structures predicted by using ab-initio technique approach shows 6% and 9% deviation to its structures predicted by homology modelling, respectively. The structure refinement and validation confirmed that the predicted structures are accurate. The 3D structures for EgKASII and EoKASII proteins were predicted. However, further research is essential to understand the interaction of EgKASII and EoKASII proteins with its substrates.

3D Printing in Instructional Settings: Identifying a Curricular Hierarchy of Activities

ERIC Educational Resources Information Center

Brown, Abbie

2015-01-01

A report of a year-long study in which the author engaged in 3D printing activity in order to determine how to facilitate and support skill building, concept attainment, and increased confidence with its use among teachers. Use of 3D printing tools and their applications in instructional settings are discussed. A hierarchy of 3D printing…

Cell illustrator 4.0: a computational platform for systems biology.

PubMed

Nagasaki, Masao; Saito, Ayumu; Jeong, Euna; Li, Chen; Kojima, Kaname; Ikeda, Emi; Miyano, Satoru

2011-01-01

Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.

Cell Illustrator 4.0: a computational platform for systems biology.

PubMed

Nagasaki, Masao; Saito, Ayumu; Jeong, Euna; Li, Chen; Kojima, Kaname; Ikeda, Emi; Miyano, Satoru

2010-01-01

Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.

Neighboring block based disparity vector derivation for multiview compatible 3D-AVC

NASA Astrophysics Data System (ADS)

Kang, Jewon; Chen, Ying; Zhang, Li; Zhao, Xin; Karczewicz, Marta

2013-09-01

3D-AVC being developed under Joint Collaborative Team on 3D Video Coding (JCT-3V) significantly outperforms the Multiview Video Coding plus Depth (MVC+D) which simultaneously encodes texture views and depth views with the multiview extension of H.264/AVC (MVC). However, when the 3D-AVC is configured to support multiview compatibility in which texture views are decoded without depth information, the coding performance becomes significantly degraded. The reason is that advanced coding tools incorporated into the 3D-AVC do not perform well due to the lack of a disparity vector converted from the depth information. In this paper, we propose a disparity vector derivation method utilizing only the information of texture views. Motion information of neighboring blocks is used to determine a disparity vector for a macroblock, so that the derived disparity vector is efficiently used for the coding tools in 3D-AVC. The proposed method significantly improves a coding gain of the 3D-AVC in the multiview compatible mode about 20% BD-rate saving in the coded views and 26% BD-rate saving in the synthesized views on average.

Validation of TGLF in C-Mod and DIII-D using machine learning and integrated modeling tools

NASA Astrophysics Data System (ADS)

Rodriguez-Fernandez, P.; White, Ae; Cao, Nm; Creely, Aj; Greenwald, Mj; Grierson, Ba; Howard, Nt; Meneghini, O.; Petty, Cc; Rice, Je; Sciortino, F.; Yuan, X.

2017-10-01

Predictive models for steady-state and perturbative transport are necessary to support burning plasma operations. A combination of machine learning algorithms and integrated modeling tools is used to validate TGLF in C-Mod and DIII-D. First, a new code suite, VITALS, is used to compare SAT1 and SAT0 models in C-Mod. VITALS exploits machine learning and optimization algorithms for the validation of transport codes. Unlike SAT0, the SAT1 saturation rule contains a model to capture cross-scale turbulence coupling. Results show that SAT1 agrees better with experiments, further confirming that multi-scale effects are needed to model heat transport in C-Mod L-modes. VITALS will next be used to analyze past data from DIII-D: L-mode ``Shortfall'' plasma and ECH swing experiments. A second code suite, PRIMA, allows for integrated modeling of the plasma response to Laser Blow-Off cold pulses. Preliminary results show that SAT1 qualitatively reproduces the propagation of cold pulses after LBO injections and SAT0 does not, indicating that cross-scale coupling effects play a role in the plasma response. PRIMA will be used to ``predict-first'' cold pulse experiments using the new LBO system at DIII-D, and analyze existing ECH heat pulse data. Work supported by DE-FC02-99ER54512, DE-FC02-04ER54698.

Summary of NDE of Additive Manufacturing Efforts in NASA

NASA Technical Reports Server (NTRS)

Waller, Jess; Saulsberry, Regor; Parker, Bradford; Hodges, Kenneth; Burke, Eric; Taminger, Karen

2014-01-01

(1) General Rationale for Additive Manufacturing (AM): (a) Operate under a 'design-to-constraint' paradigm, make parts too complicated to fabricate otherwise, (b) Reduce weight by 20 percent with monolithic parts, (c) Reduce waste (green manufacturing), (e) Eliminate reliance on Original Equipment Manufacturers for critical spares, and (f) Extend life of in-service parts by innovative repair methods; (2) NASA OSMA NDE of AM State-of-the-Discipline Report; (3) Overview of NASA AM Efforts at Various Centers: (a) Analytical Tools, (b) Ground-Based Fabrication (c) Space-Based Fabrication; and (d) Center Activity Summaries; (4) Overview of NASA NDE data to date on AM parts; and (5) Gap Analysis/Recommendations for NDE of AM.

Video-Game-Like Engine for Depicting Spacecraft Trajectories

NASA Technical Reports Server (NTRS)

Upchurch, Paul R.

2009-01-01

GoView is a video-game-like software engine, written in the C and C++ computing languages, that enables real-time, three-dimensional (3D)-appearing visual representation of spacecraft and trajectories (1) from any perspective; (2) at any spatial scale from spacecraft to Solar-system dimensions; (3) in user-selectable time scales; (4) in the past, present, and/or future; (5) with varying speeds; and (6) forward or backward in time. GoView constructs an interactive 3D world by use of spacecraft-mission data from pre-existing engineering software tools. GoView can also be used to produce distributable application programs for depicting NASA orbital missions on personal computers running the Windows XP, Mac OsX, and Linux operating systems. GoView enables seamless rendering of Cartesian coordinate spaces with programmable graphics hardware, whereas prior programs for depicting spacecraft trajectories variously require non-Cartesian coordinates and/or are not compatible with programmable hardware. GoView incorporates an algorithm for nonlinear interpolation between arbitrary reference frames, whereas the prior programs are restricted to special classes of inertial and non-inertial reference frames. Finally, whereas the prior programs present complex user interfaces requiring hours of training, the GoView interface provides guidance, enabling use without any training.

Time-resolved 3D MR velocity mapping at 3T: improved navigator-gated assessment of vascular anatomy and blood flow.

PubMed

Markl, Michael; Harloff, Andreas; Bley, Thorsten A; Zaitsev, Maxim; Jung, Bernd; Weigang, Ernst; Langer, Mathias; Hennig, Jürgen; Frydrychowicz, Alex

2007-04-01

To evaluate an improved image acquisition and data-processing strategy for assessing aortic vascular geometry and 3D blood flow at 3T. In a study with five normal volunteers and seven patients with known aortic pathology, prospectively ECG-gated cine three-dimensional (3D) MR velocity mapping with improved navigator gating, real-time adaptive k-space ordering and dynamic adjustment of the navigator acceptance criteria was performed. In addition to morphological information and three-directional blood flow velocities, phase-contrast (PC)-MRA images were derived from the same data set, which permitted 3D isosurface rendering of vascular boundaries in combination with visualization of blood-flow patterns. Analysis of navigator performance and image quality revealed improved scan efficiencies of 63.6%+/-10.5% and temporal resolution (<50 msec) compared to previous implementations. Semiquantitative evaluation of image quality by three independent observers demonstrated excellent general image appearance with moderate blurring and minor ghosting artifacts. Results from volunteer and patient examinations illustrate the potential of the improved image acquisition and data-processing strategy for identifying normal and pathological blood-flow characteristics. Navigator-gated time-resolved 3D MR velocity mapping at 3T in combination with advanced data processing is a powerful tool for performing detailed assessments of global and local blood-flow characteristics in the aorta to describe or exclude vascular alterations. Copyright (c) 2007 Wiley-Liss, Inc.

Predictive Engineering Tools for Injection-Molded Long-Carbon-Fiber Thermoplastic Composites - FY 2014 Fourth Quarterly Report

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

Nguyen, Ba Nghiep; Fifield, Leonard S.; Mathur, Raj N.

2014-09-30

During the last quarter of FY 2014, the following technical progress has been made toward project milestones: 1) Autodesk, Inc. (Autodesk) has implemented a new fiber length distribution (FLD) model based on an unbreakable length assumption with Reduced Order Modeling (ROM) by the Proper Orthogonal Decomposition (POD) approach in the mid-plane, dual-domain and 3D solvers. 2) Autodesk improved the ASMI 3D solver for fiber orientation prediction using the anisotropic rotary diffusion (ARD) – reduced strain closure (RSC) model. 3) Autodesk received consultant services from Prof. C.L. Tucker at the University of Illinois on numerical simulation of fiber orientation and fibermore » length. 4) PlastiComp, Inc. (PlastiComp) suggested to Purdue University a procedure for fiber separation using an inert-gas atmosphere in the burn-off furnace. 5) Purdue University (Purdue) hosted a face-to-face project review meeting at Purdue University on August 6-7, 2014. 6) Purdue conducted fiber orientation measurements for 3 PlastiComp plaques: fast-fill 30wt% LCF/PP edged-gated, slow-fill 50wt% LCF/PP edge-gated, and slow-fill 50wt% LCF/PP center-gated plaques, and delivered the orientation data for these plaques at the selected locations (named A, B, and C) to PNNL. 7) PNNL conducted ASMI mid-plane analyses for the above PlastiComp plaques and compared the predicted fiber orientations with the measured data provided by Purdue at Locations A, B, and C on these plaques. 8) PNNL planned the project review meeting (August 6-7, 2014) with Purdue. 9) PNNL performed ASMI analyses for the Toyota complex parts with and without ribs, having different wall thicknesses, and using the PlastiComp 50wt% LCF/PP, 50wt% LCF/PA66, 30wt% LCF/PP, and 30wt% LCF/PA66 materials to provide guidance for tool design and modifications needed for molding these parts. 10) Magna Exteriors and Interiors Corp. (Magna) molded plaques from the 50% LCF/PP and 50% LCF/PA66 materials received from Plasticomp in order to extract machine purgings (purge materials) from Magna’s 200-Ton Injection Molding machine targeted to mold the complex part. 11) Toyota and Magna discussed with PNNL tool modification for molding the complex part.« less

Femtosecond fiber laser additive manufacturing and welding for 3D manufacturing

NASA Astrophysics Data System (ADS)

Huang, Huan; Nie, Bai; Wan, Peng; Yang, Lih-Mei; Bai, Shuang; Liu, Jian

2015-03-01

Due to the unique ultra-short pulse duration and high peak power, femtosecond (fs) laser has emerged as a powerful tool for many applications but has rarely been studied for 3D printing. In this paper, welding of both bulk and powder materials is demonstrated for the first time by using high energy and high repetition rate fs fiber lasers. It opens up new scenarios and opportunities for 3D printing with the following advantages - greater range of materials especially with high melting temperature, greater-than-ever level of precision (sub-micron) and less heat-affected-zone (HAZ). Mechanical properties (strength and hardness) and micro-structures (grain size) of the fabricated parts are investigated. For dissimilar materials bulk welding, good welding quality with over 210 MPa tensile strength is obtained. Also full melting of the micron-sized refractory powders with high melting temperature (above 3000 degree C) is achieved for the first time. 3D parts with shapes like ring and cube are fabricated. Not only does this study explore the feasibility of melting dissimilar and high melting temperature materials using fs lasers, but it also lays out a solid foundation for 3D printing of complex structure with designed compositions, microstructures and properties. This can greatly benefit the applications in automobile, aerospace and biomedical industries, by producing parts like nozzles, engines and miniaturized biomedical devices.

Data Visualization Using Immersive Virtual Reality Tools

NASA Astrophysics Data System (ADS)

Cioc, Alexandru; Djorgovski, S. G.; Donalek, C.; Lawler, E.; Sauer, F.; Longo, G.

2013-01-01

The growing complexity of scientific data poses serious challenges for an effective visualization. Data sets, e.g., catalogs of objects detected in sky surveys, can have a very high dimensionality, ~ 100 - 1000. Visualizing such hyper-dimensional data parameter spaces is essentially impossible, but there are ways of visualizing up to ~ 10 dimensions in a pseudo-3D display. We have been experimenting with the emerging technologies of immersive virtual reality (VR) as a platform for a scientific, interactive, collaborative data visualization. Our initial experiments used the virtual world of Second Life, and more recently VR worlds based on its open source code, OpenSimulator. There we can visualize up to ~ 100,000 data points in ~ 7 - 8 dimensions (3 spatial and others encoded as shapes, colors, sizes, etc.), in an immersive virtual space where scientists can interact with their data and with each other. We are now developing a more scalable visualization environment using the popular (practically an emerging standard) Unity 3D Game Engine, coded using C#, JavaScript, and the Unity Scripting Language. This visualization tool can be used through a standard web browser, or a standalone browser of its own. Rather than merely plotting data points, the application creates interactive three-dimensional objects of various shapes, colors, and sizes, and of course the XYZ positions, encoding various dimensions of the parameter space, that can be associated interactively. Multiple users can navigate through this data space simultaneously, either with their own, independent vantage points, or with a shared view. At this stage ~ 100,000 data points can be easily visualized within seconds on a simple laptop. The displayed data points can contain linked information; e.g., upon a clicking on a data point, a webpage with additional information can be rendered within the 3D world. A range of functionalities has been already deployed, and more are being added. We expect to make this visualization tool freely available to the academic community within a few months, on an experimental (beta testing) basis.

Evaluation of the User Strategy on 2d and 3d City Maps Based on Novel Scanpath Comparison Method and Graph Visualization

NASA Astrophysics Data System (ADS)

Dolezalova, J.; Popelka, S.

2016-06-01

The paper is dealing with scanpath comparison of eye-tracking data recorded during case study focused on the evaluation of 2D and 3D city maps. The experiment contained screenshots from three map portals. Two types of maps were used - standard map and 3D visualization. Respondents' task was to find particular point symbol on the map as fast as possible. Scanpath comparison is one group of the eye-tracking data analyses methods used for revealing the strategy of the respondents. In cartographic studies, the most commonly used application for scanpath comparison is eyePatterns that output is hierarchical clustering and a tree graph representing the relationships between analysed sequences. During an analysis of the algorithm generating a tree graph, it was found that the outputs do not correspond to the reality. We proceeded to the creation of a new tool called ScanGraph. This tool uses visualization of cliques in simple graphs and is freely available at www.eyetracking.upol.cz/scangraph. Results of the study proved the functionality of the tool and its suitability for analyses of different strategies of map readers. Based on the results of the tool, similar scanpaths were selected, and groups of respondents with similar strategies were identified. With this knowledge, it is possible to analyse the relationship between belonging to the group with similar strategy and data gathered from the questionnaire (age, sex, cartographic knowledge, etc.) or type of stimuli (2D, 3D map).

In Vivo Imaging of Cerebral Dopamine D3 Receptors in Alcoholism

PubMed Central

Erritzoe, David; Tziortzi, Andri; Bargiela, David; Colasanti, Alessandro; Searle, Graham E; Gunn, Roger N; Beaver, John D; Waldman, Adam; Nutt, David J; Bani, Massimo; Merlo-Pich, Emilio; Rabiner, Eugenii A; Lingford-Hughes, Anne

2014-01-01

Animal studies support the role of the dopamine D3 receptor (DRD3) in alcohol reinforcement or liking. Sustained voluntary alcohol drinking in rats has been associated with an upregulation of striatal DRD3 gene expression and selective blockade of DRD3 reduces ethanol preference, consumption, and cue-induced reinstatement. In vivo measurement of DRD3 in the living human brain has not been possible until recently owing to a lack of suitable tools. In this study, DRD3 status was assessed for the first time in human alcohol addiction. Brain DRD3 availability was compared between 16 male abstinent alcohol-dependent patients and 13 healthy non-dependent age-matched males using the DRD3-preferring agonist positron emission tomography (PET) radioligand [11C]PHNO with and without blockade with a selective DRD3 antagonist (GSK598809 60 mg p.o.). In striatal regions of interest, where the [11C]PHNO PET signal represents primarily DRD2 binding, no differences were seen in [11C]PHNO binding between the groups at baseline. However, baseline [11C]PHNO binding was higher in alcohol-dependent patients in hypothalamus (VT: 16.5±4 vs 13.7±2.9, p=0.040), a region in which the [11C]PHNO signal almost entirely reflects DRD3 availability. The reductions in regional receptor binding (VT) following a single oral dose of GSK598809 (60 mg) were consistent with those observed in previous studies across all regions. There were no differences in regional changes in VT following DRD3 blockade between the two groups, indicating that the regional fractions of DRD3 are similar in the two groups, and the increased [11C]PHNO binding in the hypothalamus in alcohol-dependent patients is explained by elevated DRD3 in this group. Although we found no difference between alcohol-dependent patients and controls in striatal DRD3 levels, increased DRD3 binding in the hypothalamus of alcohol-dependent patients was observed. This may be relevant to the development of future therapeutic strategies to treat alcohol abuse. PMID:24469594

VOFTools - A software package of calculation tools for volume of fluid methods using general convex grids

NASA Astrophysics Data System (ADS)

López, J.; Hernández, J.; Gómez, P.; Faura, F.

2018-02-01

The VOFTools library includes efficient analytical and geometrical routines for (1) area/volume computation, (2) truncation operations that typically arise in VOF (volume of fluid) methods, (3) area/volume conservation enforcement (VCE) in PLIC (piecewise linear interface calculation) reconstruction and(4) computation of the distance from a given point to the reconstructed interface. The computation of a polyhedron volume uses an efficient formula based on a quadrilateral decomposition and a 2D projection of each polyhedron face. The analytical VCE method is based on coupling an interpolation procedure to bracket the solution with an improved final calculation step based on the above volume computation formula. Although the library was originally created to help develop highly accurate advection and reconstruction schemes in the context of VOF methods, it may have more general applications. To assess the performance of the supplied routines, different tests, which are provided in FORTRAN and C, were implemented for several 2D and 3D geometries.

Effect of 3,5,3'-Triiodothyronine (T3) administration on dio1 gene expression and T3 metabolism in normal and type 1 deiodinase-deficient mice.

PubMed

Maia, A L; Kieffer, J D; Harney, J W; Larsen, P R

1995-11-01

The type 1 deiodinase (D1) catalyzes the monodeiodination of T4 to produce T3, the active thyroid hormone. In the C3H mouse, hepatic D1 and the dio1 messenger RNA (mRNA) are only 10% that in the C57 strain, the common phenotype. Low activity cosegregated with a series of five GCT repeats located in the 5'-flanking region of the C3H dio1 gene that impaired C3H promoter potency and provided a partial explanation for the lower D1. The present studies were performed to search for additional explanations for low D1 activity in C3H mice. Previous studies have shown that T3 up-regulates the dio1 gene. Therefore, loss of the capacity to respond to endogenous T3 is a possible additional cause of the lower D1 levels in the C3H mice. The hepatic C3H dio1 mRNA increases 10- to 20 fold after T3 administration. The t3 effect occurs at a transplantation level and T3 does not alter the dio1 mRNA half-life. Despite the transcriptional response to T3, no functional thyroid response elements were identified in the 1.5-kilobase 5'-flanking region of either the C57 or C3H dio1 gene. After the same dose of exogenous T3, both dio1 mRNA and D1 of the C3H mouse respond to a greater extent than those of the C57 strain. This can be explained in part by the reduction in T3 clearance due to the lower D1 levels in C3H mice in which higher concentrations of circulating T3 are maintained. The decrease in serum T3 levels and T3 production observed in fasting and systemic illness in both human and experimental animals has been attributed in part to a decrease in hepatic D1. In contrast, despite markedly lower hepatic and renal D1 levels, serum T3 concentrations remain normal in C3H mice. The present studies suggest that the absence of stress-induced hypothalamic-pituitary suppression that allows T4 production to be maintained together with the reduced clearance of T3 and T4 via inner ring deiodination compensate for the D1 deficiency.

A Bridging Water Anchors the Tethered 5-(3-Aminopropyl)-2′-deoxyuridine Amine in the DNA Major Groove Proximate to the N+2 C·G Base Pair: Implications for Formation of Interstrand 5′-GNC-3′ Cross-Links by Nitrogen Mustards‡

PubMed Central

Wang, Feng; Li, Feng; Ganguly, Manjori; Marky, Luis A.; Gold, Barry; Egli, Martin; Stone, Michael P.

2009-01-01

Site-specific insertion of 5-(3-aminopropyl)-2′-deoxyuridine (Z3dU) and 7-deaza-dG into the Dickerson-Drew dodecamers 5′-d(C1G2C3G4A5A6T7T8C9Z10C11G12)-3′ · 5′-d(C13G14C15G16A17A18T19T20-C21Z22C23G24)-3′ (named DDDZ10) and 5′-d(C1G2C3G4A5A6T7X8C9Z10C11G12)-3′ · 5′-d(C13G14C15G16A17A18-T19X20C21Z22C23G24)-3′ (named DDD2+Z10)(X = Z3dU; Z = 7-deaza-dG) suggests a mechanism underlying the formation of interstrand N+2 DNA cross-links by nitrogen mustards, e.g., melphalan and mechlorethamine. Analysis of the DDD2+Z10 duplex reveals that the tethered cations at base pairs A5 · X20 and X8 · A17 extend within the major groove in the 3′-direction, toward conserved Mg2+ binding sites located adjacent to N+2 base pairs C3 · Z22 and Z10 · C15. Bridging waters located between the tethered amines and either Z10 or Z22 O6 stabilize the tethered cations and allow interactions with the N + 2 base pairs without DNA bending. Incorporation of 7-deaza-dG into the DDD2+Z10 duplex weakens but does not eliminate electrostatic interactions between tethered amines and Z10 O6 and Z22 O6. The results suggest a mechanism by which tethered N7-dG aziridinium ions, the active species involved in formation of interstrand 5′-GNC-3′ cross-links by nitrogen mustards, modify the electrostatics of the major groove and position the aziridinium ions proximate to the major groove edge of the N+2 C · G base pair, facilitating interstrand cross-linking. PMID:18549246

Concurrent Infections of Giardia duodenalis, Enterocytozoon bieneusi, and Clostridium difficile in Children during a Cryptosporidiosis Outbreak in a Pediatric Hospital in China

PubMed Central

Wang, Lin; Xiao, Lihua; Duan, Liping; Ye, Jianbin; Guo, Yaqiong; Guo, Meijin; Liu, Lili; Feng, Yaoyu

2013-01-01

Background Over 200 cryptosporidiosis outbreaks have been reported, but little is known if other enteric pathogens were also involved in some of these outbreaks. Recently, an outbreak of cryptosporidiosis linked to poor hygiene by two Cryptosporidium hominis subtypes occurred in a pediatric hospital ward (Ward A) in China, lasting for more than 14 months. In this study, the concurrence during the outbreak of three other enteric pathogens with a similar transmission route, Giardia duodenalis, Enterocytozoon bieneusi, and Clostridium difficile, was assessed. Methods/Principal Findings The occurrence of G. duodenalis, E. bieneusi, and C. difficile in 78 inpatients from Ward A and 283 and 216 inpatients from two control wards (Wards C and D) in the same hospital was examined using molecular diagnostic tools. Significantly higher infection rates were found in children in Ward A for all study pathogens than in Wards C and D (P<0.01): 9.5% versus 1.4% and 0% for G. duodenalis, 10.8% versus 2.8% and 3.7% for E. bieneusi, and 60.8% versus 37.8% and 27.8% for C. difficile, respectively. These differences were mostly seen in children ≤12 months. Enteric pathogen-positive children in Ward A (31/58 or 53.4%) were more likely to have mixed infections than those in Ward C (4/119 or 3.4%) or D (5/68, 7.4%; P<0.01). Having cryptosporidiosis was a risk factor for G. duodenalis (OR = 4.3; P = 0.08), E. bieneusi (OR = 3.1; P = 0.04), and C. difficile (OR = 4.7; P<0.01) infection. In addition, a lower diversity of G. duodenalis, E. bieneusi, and C. difficile genotypes/subtypes was observed in Ward A. Conclusions/Significance Data from this study suggest that multiple pathogens were concurrently present during the previous cryptosporidiosis outbreak. Examination of multiple enteric pathogens should be conducted when poor hygiene is the likely cause of outbreaks of diarrhea. PMID:24069491

Site-Specific Hydrogen Isotope Composition of Propane: Mass spectrometric methods, equilibrium temperature dependence, and kinetics of exchange

NASA Astrophysics Data System (ADS)

Xie, H.; Ponton, C.; Kitchen, N.; Lloyd, M. K.; Lawson, M.; Formolo, M. J.; Eiler, J. M.

2016-12-01

Intramolecular isotope ordering can constrain temperatures of synthesis, mechanisms of formation, and/or source substrates of organic compounds. Here we explore site-specific hydrogen isotope variations of propane. Statistical thermodynamic models predict that at equilibrium methylene hydrogen (-CH2-) in propane will be 10's of per mil higher in D/H ratio than methyl hydrogen (-CH3) at geologically relevant temperatures, and that this difference is highly temperature dependent ( 0.5-1 ‰/°C). Chemical-kinetic controls on site-specific D/H in propane could constrain the mechanisms, conditions and extents of propane synthesis or destruction. We have developed a method for measuring the difference in D/H ratio between methylene and methyl hydrogen in propane by gas source mass spectrometry. The data were measured using the Thermo Fisher Double Focusing Sector high resolution mass spectrometer (DFS), and involve comparison of the D/H ratios of molecular ion (C3H8+) and the ethyl fragmental ion (C2H5+). We demonstrate the accuracy and precision of this method through analysis of D-labeled and independently analyzed propanes. In the exchange experiments, propane was heated (100-200 oC) either alone or in the presence of D-enriched water (δD=1,1419 ‰ SMOW), with or without one of several potentially catalytic substrates for hours to weeks. Propane was found to exchange hydrogen with water vigorously at 200 °C in the presence of metal catalysts. In the presence of Ni catalyst, methylene hydrogen exchanges 2.5 times faster than methyl hydrogen. Hydrogen exchange in the presence of Pd catalyst is more effective and can equilibrate hydrogen isotope distribution on propane on the order of 7 days. Isotopic exchange in the presence of natural materials have also been tested, but is only measurable in the methylene group at 200 °C. High catalytic activity of Pd permits attainment of a bracketed, time-invariant equilibrium state that we use to calibrate the site-specific thermometer; these experiments also provide a reference frame for reporting mass spectrometric data. Differential H-exchange rates of the two molecular sites in propane could be a new tool to constrain thermal history of sub-surface propane. Our experimental and mass spectrometric approaches should be generalizable to other hydrocarbon compounds.

Detecting evidence of luteal activity by least-squares quantitative basal temperature analysis against urinary progesterone metabolites and the effect of wake-time variability.

PubMed

Bedford, Jennifer L; Prior, Jerilynn C; Hitchcock, Christine L; Barr, Susan I

2009-09-01

To assess computerised least-squares analysis of quantitative basal temperature (LS-BT) against urinary pregnanediol glucuronide (PdG) as an indirect measure of ovulation, and to evaluate the stability of LS-QBT to wake-time variation. Cross-sectional study of 40 healthy, normal-weight, regularly menstruating women aged 19-34. Participants recorded basal temperature and collected first void urine daily for one complete menstrual cycle. Evidence of luteal activity (ELA), an indirect ovulation indicator, was assessed using Kassam's PdG algorithm, which identifies a sustained 3-day PdG rise, and the LS-QBT algorithm, by determining whether the temperature curve is significantly biphasic. Cycles were classified as ELA(+) or ELA(-). We explored the need to pre-screen for wake-time variations by repeating the analysis using: (A) all recorded temperatures, (B) wake-time adjusted temperatures, (C) temperatures within 2h of average wake-time, and (D) expert reviewed temperatures. Relative to PdG, classification of cycles as ELA(+) was 35 of 36 for LS-QBT methods A and B, 33 of 34 (method C) and 30 of 31 (method D). Classification of cycles as ELA(-) was 1 of 4 (methods A and B) and 0 of 3 (methods C and D). Positive predictive value was 92% for methods A-C and 91% for method D. Negative predictive value was 50% for methods A and B and 0% for methods C and D. Overall accuracy was 90% for methods A and B, 89% for method C and 88% for method D. The day of a significant temperature increase by LS-QBT and the first day of a sustained PdG rise were correlated (r=0.803, 0.741, 0.651, 0.747 for methods A-D, respectively, all p<0.001). LS-QBT showed excellent detection of ELA(+) cycles (sensitivity, positive predictive value) but poor detection of ELA(-) cycles (specificity, negative predictive value) relative to urinary PdG. Correlations between the methods and overall accuracy were good and similar for all analyses. Findings suggest that LS-QBT is robust to wake-time variability and that expert interpretation is unnecessary. This method shows promise for use as an epidemiological tool to document cyclic progesterone increase. Further validation relative to daily transvaginal ultrasound is required.

Kinetic analysis of human CYP24A1 metabolism of vitamin D via the C24-oxidation pathway.

PubMed

Tieu, Elaine W; Tang, Edith K Y; Tuckey, Robert C

2014-07-01

CYP24A1 is the multicatalytic cytochrome P450 responsible for the catabolism of vitamin D via the C23- and C24-oxidation pathways. We successfully expressed the labile human enzyme in Escherichia coli and partially purified it in an active state that permitted detailed characterization of its metabolism of 1,25-dihydroxyvitamin D3 [1,25(OH)2 D3] and the intermediates of the C24-oxidation pathway in a phospholipid-vesicle reconstituted system. The C24-oxidation pathway intermediates, 1,24,25-trihydroxyvitamin D3, 24-oxo-1,25-dihydroxyvitamin D3, 24-oxo-1,23,25-trihydroxyvitamin D3 and tetranor-1,23-dihydroxyvitamin D3, were enzymatically produced from 1,25(OH)2 D3 using rat CYP24A1. Both 1,25(OH)2 D3 and 1,23-dihydroxy-24,25,26,27-tetranorvitamin D3 were found to partition strongly into the phospholipid bilayer when in aqueous medium. Changes to the phospholipid concentration did not affect the kinetic parameters for the metabolism of 1,25(OH)2 D3 by CYP24A1, indicating that it is the concentration of substrates in the membrane phase (mol substrate·mol phospholipid(-1) ) that determines their rate of metabolism. CYP24A1 exhibited Km values for the different C24-intermediates ranging from 0.34 to 15 mmol·mol phospholipid(-1) , with 24-oxo-1,23,25-trihydroxyvitamin D3 [24-oxo-1,23,25(OH)3 D3] displaying the lowest and 1,24,25-trihydroxyvitamin D3 [1,24,25(OH)3 D3] displaying the highest. The kcat values varied by up to 3.8-fold, with 1,24,25(OH)3 D3 displaying the highest kcat (34 min(-1) ) and 24-oxo-1,23,25(OH)3 D3 the lowest. The data show that the cleavage of the side chain of 24-oxo-1,23,25(OH)3 D3 occurs with the highest catalytic efficiency (kcat /Km ) and produces 1-hydroxy-23-oxo-24,25,26,27-tetranorvitamin D3 and not 1,23-dihydroxy-24,25,26,27-tetranorvitamin D3, as the primary product. These kinetic analyses also show that intermediates of the C24-oxidation pathway effectively compete with precursor substrates for binding to the active site of the enzyme, which manifests as an accumulation of intermediates, indicating that they dissociate after each catalytic step. © 2014 FEBS.

Expanded Capabilities for the Hydrogen Financial Analysis Scenario Tool (H2FAST)

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

Bush, Brian; Melaina, Marc; Penev, Michael

This presentation describes how NREL expanded the capabilities for the Hydrogen Financial Analysis Scenario Tool (H2FAST) in FY16. It was presented at the U.S. Department of Energy Hydrogen and Fuel Cells Program 2016 Annual Merit Review and Peer Evaluation Meeting on June 8, 2016, in Washington, D.C.

Spherical subjective refraction with a novel 3D virtual reality based system.

PubMed

Pujol, Jaume; Ondategui-Parra, Juan Carlos; Badiella, Llorenç; Otero, Carles; Vilaseca, Meritxell; Aldaba, Mikel

To conduct a clinical validation of a virtual reality-based experimental system that is able to assess the spherical subjective refraction simplifying the methodology of ocular refraction. For the agreement assessment, spherical refraction measurements were obtained from 104 eyes of 52 subjects using three different methods: subjectively with the experimental prototype (Subj.E) and the classical subjective refraction (Subj.C); and objectively with the WAM-5500 autorefractor (WAM). To evaluate precision (intra- and inter-observer variability) of each refractive tool independently, 26 eyes were measured in four occasions. With regard to agreement, the mean difference (±SD) for the spherical equivalent (M) between the new experimental subjective method (Subj.E) and the classical subjective refraction (Subj.C) was -0.034D (±0.454D). The corresponding 95% Limits of Agreement (LoA) were (-0.856D, 0.924D). In relation to precision, intra-observer mean difference for the M component was 0.034±0.195D for the Subj.C, 0.015±0.177D for the WAM and 0.072±0.197D for the Subj.E. Inter-observer variability showed worse precision values, although still clinically valid (below 0.25D) in all instruments. The spherical equivalent obtained with the new experimental system was precise and in good agreement with the classical subjective routine. The algorithm implemented in this new system and its optical configuration has been shown to be a first valid step for spherical error correction in a semiautomated way. Copyright © 2016 Spanish General Council of Optometry. Published by Elsevier España, S.L.U. All rights reserved.

Evaluation of 3D metrology potential using a multiple detector CDSEM

NASA Astrophysics Data System (ADS)

Hakii, Hidemitsu; Yonekura, Isao; Nishiyama, Yasushi; Tanaka, Keishi; Komoto, Kenji; Murakawa, Tsutomu; Hiroyama, Mitsuo; Shida, Soichi; Kuribara, Masayuki; Iwai, Toshimichi; Matsumoto, Jun; Nakamura, Takayuki

2012-06-01

As feature sizes of semiconductor device structures have continuously decreased, needs for metrology tools with high precision and excellent linearity over actual pattern sizes have been growing. And it has become important to measure not only two-dimensional (2D) but also three-dimensional (3D) shapes of patterns at 22 nm node and beyond. To meet requirements for 3D metrology capabilities, various pattern metrology tools have been developed. Among those, we assume that CDSEM metrology is the most qualified candidate in the light of its non-destructive, high throughput measurement capabilities that are expected to be extended to the much-awaited 3D metrology technology. On the basis of this supposition, we have developed the 3D metrology system, in which side wall angles and heights of photomask patterns can be measured with high accuracy through analyzing CDSEM images generated by multi-channel detectors. In this paper, we will discuss our attempts to measure 3D shapes of defect patterns on a photomask by using Advantest's "Multi Vision Metrology SEM" E3630 (MVM-SEM' E3630).

Applications of Automation Methods for Nonlinear Fracture Test Analysis

NASA Technical Reports Server (NTRS)

Allen, Phillip A.; Wells, Douglas N.

2013-01-01

Using automated and standardized computer tools to calculate the pertinent test result values has several advantages such as: 1. allowing high-fidelity solutions to complex nonlinear phenomena that would be impractical to express in written equation form, 2. eliminating errors associated with the interpretation and programing of analysis procedures from the text of test standards, 3. lessening the need for expertise in the areas of solid mechanics, fracture mechanics, numerical methods, and/or finite element modeling, to achieve sound results, 4. and providing one computer tool and/or one set of solutions for all users for a more "standardized" answer. In summary, this approach allows a non-expert with rudimentary training to get the best practical solution based on the latest understanding with minimum difficulty.Other existing ASTM standards that cover complicated phenomena use standard computer programs: 1. ASTM C1340/C1340M-10- Standard Practice for Estimation of Heat Gain or Loss Through Ceilings Under Attics Containing Radiant Barriers by Use of a Computer Program 2. ASTM F 2815 - Standard Practice for Chemical Permeation through Protective Clothing Materials: Testing Data Analysis by Use of a Computer Program 3. ASTM E2807 - Standard Specification for 3D Imaging Data Exchange, Version 1.0 The verification, validation, and round-robin processes required of a computer tool closely parallel the methods that are used to ensure the solution validity for equations included in test standard. The use of automated analysis tools allows the creation and practical implementation of advanced fracture mechanics test standards that capture the physics of a nonlinear fracture mechanics problem without adding undue burden or expense to the user. The presented approach forms a bridge between the equation-based fracture testing standards of today and the next generation of standards solving complex problems through analysis automation.

Risk Factors for Chorioamnion Infection and Adverse Pregnancy Outcome Among Active-Duty Military women and Dependent Women

DTIC Science & Technology

1998-10-01

0 00 012 IIOTI -- 00 0 Z 0 0 REFERENCES 1. McGann, E. F., Winchester, M. I., Carter, D . P ., Martin, J. N., Jr., Bass, D ., Morrison, J. C. Factors...Women: 1982-1992. 0a014 14. Magann, E. F., Winchester, M. I., Carter, D . P ., Martin, J. N., Jr., Bass, D ., and Morrison, J. C. Factors adversely...D ZHI CE) 10T CD ZC I eC-) 3Z co 00 000 CD CD) z_ < zll CD 1a 1 1 S C) I 1 icD=---I i !! Iz .i 3, z6 z,- !0 D Iz~=3 S--I_ 11001D The current C

Paviosides A-H, eight new oleane type saponins from Aesculus pavia with cytotoxic activity.

PubMed

Lanzotti, Virginia; Termolino, Pasquale; Dolci, Marcello; Curir, Paolo

2012-05-15

A phytochemical analysis of Aesculus pavia has led to the isolation of eight novel triterpenoid saponins, based on oleane type skeleton and named paviosides A-H (1a, 1b-4a, 4b). On the basis of chemical, and 2D NMR and mass spectrometry data, the structures of the new compounds were elucidated as 3-O-[β-D-xylopyranosyl (1 → 2)] [-β-d-glucopyranosyl (1 → 4)]-β-D-glucopyranosiduronic acid 21-tigloyl-22-acetyl barringtogenol C (1a), 3-O-[β-D-xylopyranosyl (1 → 2)] [-β-D-glucopyranosyl (1 → 4)]-β-D-glucopyranosiduronic acid 21-angeloyl-22-acetyl barringtogenol C (1b), 3-O-[β-D-xylopyranosyl (1 → 2)] [-β-D-galactopyranosyl (1 → 4)]-β-D-glucopyranosiduronic acid 21-tigloyl-22-acetyl barringtogenol C (2a), 3-O-[β-D-xylopyranosyl (1 → 2)] [-β-D-galactopyranosyl (1 → 4)]-β-D-glucopyranosiduronic acid 21-angeloyl-22-acetyl barringtogenol C (2b), 3-O-[β-D-xylopyranosyl (1 → 2)] [-β-D-xylopyranosyl (1 → 4)]-β-D-glucopyranosiduronic acid 21-tigloyl-22-acetyl barringtogenol C (3a), 3-O-[β-D-xylopyranosyl (1 → 2)] [-β-D-xylopyranosyl (1 → 4)]-β-d-glucopyranosiduronic acid 21-angeloyl-22-acetyl barringtogenol C (3b), 3-O-[β-D-xylopyranosyl (1 → 2)] [-β-D-xylopyranosyl (1 → 4)]-β-D-glucopyranosiduronic acid 21-tigloyl-22-acetyl protoaescigenin (4a), and 3-O-[β-D-xylopyranosyl (1 → 2)] [-β-D-xylopyranosyl (1 → 4)]-β-D-glucopyranosiduronic acid 21-angeloyl-22-acetyl protoaescigenin (4b). The compounds showed cytotoxic activity on J-774, murine monocyte/macrophage, and WEHI-164, murine fibrosarcoma, cell lines. Among them, paviosides E-H (3a, 3b and 4a, 4b) showed higher activity with values ranging from 2.1 to 3.6 μg/mL. Structure-activity relationship studies indicated the positive effect on the activity of xylose unit in the place of glucose, while a little detrimental effect is observed when glucose is substituted by galactose. The aglycone structure and the presence of a tigloyl or an angeloyl group at C-21 do not affect significantly the inhibitory activity on both tested cell lines. Copyright © 2012 Elsevier Ltd. All rights reserved.

AxiSEM3D: broadband seismic wavefields in 3-D aspherical Earth models

NASA Astrophysics Data System (ADS)

Leng, K.; Nissen-Meyer, T.; Zad, K. H.; van Driel, M.; Al-Attar, D.

2017-12-01

Seismology is the primary tool for data-informed inference of Earth structure and dynamics. Simulating seismic wave propagation at a global scale is fundamental to seismology, but remains as one of most challenging problems in scientific computing, because of both the multiscale nature of Earth's interior and the observable frequency band of seismic data. We present a novel numerical method to simulate global seismic wave propagation in realistic 3-D Earth models. Our method, named AxiSEM3D, is a hybrid of spectral element method and pseudospectral method. It reduces the azimuthal dimension of wavefields by means of a global Fourier series parameterization, of which the number of terms can be locally adapted to the inherent azimuthal smoothness of the wavefields. AxiSEM3D allows not only for material heterogeneities, such as velocity, density, anisotropy and attenuation, but also for finite undulations on radial discontinuities, both solid-solid and solid-fluid, and thereby a variety of aspherical Earth features such as ellipticity, topography, variable crustal thickness, and core-mantle boundary topography. Such interface undulations are equivalently interpreted as material perturbations of the contiguous media, based on the "particle relabelling transformation". Efficiency comparisons show that AxiSEM3D can be 1 to 3 orders of magnitude faster than conventional 3-D methods, with the speedup increasing with simulation frequency and decreasing with model complexity, but for all realistic structures the speedup remains at least one order of magnitude. The observable frequency range of global seismic data (up to 1 Hz) has been covered for wavefield modelling upon a 3-D Earth model with reasonable computing resources. We show an application of surface wave modelling within a state-of-the-art global crustal model (Crust1.0), with the synthetics compared to real data. The high-performance C++ code is released at github.com/AxiSEM3D/AxiSEM3D.

Visualizing UAS-collected imagery using augmented reality

NASA Astrophysics Data System (ADS)

Conover, Damon M.; Beidleman, Brittany; McAlinden, Ryan; Borel-Donohue, Christoph C.

2017-05-01

One of the areas where augmented reality will have an impact is in the visualization of 3-D data. 3-D data has traditionally been viewed on a 2-D screen, which has limited its utility. Augmented reality head-mounted displays, such as the Microsoft HoloLens, make it possible to view 3-D data overlaid on the real world. This allows a user to view and interact with the data in ways similar to how they would interact with a physical 3-D object, such as moving, rotating, or walking around it. A type of 3-D data that is particularly useful for military applications is geo-specific 3-D terrain data, and the visualization of this data is critical for training, mission planning, intelligence, and improved situational awareness. Advances in Unmanned Aerial Systems (UAS), photogrammetry software, and rendering hardware have drastically reduced the technological and financial obstacles in collecting aerial imagery and in generating 3-D terrain maps from that imagery. Because of this, there is an increased need to develop new tools for the exploitation of 3-D data. We will demonstrate how the HoloLens can be used as a tool for visualizing 3-D terrain data. We will describe: 1) how UAScollected imagery is used to create 3-D terrain maps, 2) how those maps are deployed to the HoloLens, 3) how a user can view and manipulate the maps, and 4) how multiple users can view the same virtual 3-D object at the same time.

Comparative NMR studies of diffusional water permeability of red blood cells from different species: XV. Agile wallaby (Macropus agilis), red-necked wallaby (Macropus rufogriseus) and Goodfellow's tree kangaroo (Dendrolagus goodfellowi).

PubMed

Benga, Gheorghe; Chapman, Bogdan E; Kuchel, Philip W

2009-09-01

The water diffusional permeability (P(d)) of red blood cells (RBC) from agile wallaby (Macropus agilis), red-necked wallaby (Macropus rufogriseus) and Goodfellow's tree kangaroo (Dendrolagus goodfellowi) was monitored using an Mn(2+)-doping (1)H nuclear magnetic resonance (NMR) technique at 400 MHz. The P(d) (cm s(-1)) values of agile wallaby RBCs were 7.5 x 10(-3) at 25 degrees C, 9 x 10(-3) at 30 degrees C, 11 x 10(-3) at 37 degrees C, and 13 x 10(-3) at 42 degrees C. The inhibitory effect of a mercury-containing sulfhydryl (SH)-modifying reagent p-chloromercuribenzoate (PCMB) on agile wallaby RBCs was investigated. The maximal inhibition was reached in 90 min at 37 degrees C with 2 mmol L(-1) PCMB. The value of maximal inhibition was approximately 63% when measured at 25 degrees C, approximately 52% at 37 degrees C and approximately 45% at 42 degrees C. The lowest value of P(d) (corresponding to the basal permeability to water) was approximately 3 x 10(-3) cm s(-1) at 25 degrees C. For the RBCs from red-necked wallaby (M. rufogriseus) the values of P(d) (cm s(-1)) were 7 x 10(-3) at 25 degrees C, 8 x 10(-3) at 30 degrees C, 10 x 10(-3) at 37 degrees C, and 12 x 10(-3) at 42 degrees C. Higher values of P(d) (cm s(-1)) were found for the RBCs from Goodfellow's tree kangaroo (D. goodfellowi): 8.5 x 10(-3) at 25 degrees C, 10 x 10(-3) at 30 degrees C, 13 x 10(-3) at 37 degrees C, and 15 x 10(-3) at 42 degrees C. The mean values of the activation energy of water diffusion (E(a,d)) were approximately 25 kJ mol(-1) for RBCs from the agile wallaby and tree kangaroo, respectively, and approximately 23 kJ mol(-1) for RBCs from red-necked wallaby. The values of E(a,d) increased after exposure of agile wallaby RBCs to PCMB, reaching a value of approximately 43-46 kJ mol(-1) when the maximal inhibition of P(d) was achieved.

Real-time 3D radiation risk assessment supporting simulation of work in nuclear environments.

PubMed

Szőke, I; Louka, M N; Bryntesen, T R; Bratteli, J; Edvardsen, S T; RøEitrheim, K K; Bodor, K

2014-06-01

This paper describes the latest developments at the Institute for Energy Technology (IFE) in Norway, in the field of real-time 3D (three-dimensional) radiation risk assessment for the support of work simulation in nuclear environments. 3D computer simulation can greatly facilitate efficient work planning, briefing, and training of workers. It can also support communication within and between work teams, and with advisors, regulators, the media and public, at all the stages of a nuclear installation's lifecycle. Furthermore, it is also a beneficial tool for reviewing current work practices in order to identify possible gaps in procedures, as well as to support the updating of international recommendations, dissemination of experience, and education of the current and future generation of workers.IFE has been involved in research and development into the application of 3D computer simulation and virtual reality (VR) technology to support work in radiological environments in the nuclear sector since the mid 1990s. During this process, two significant software tools have been developed, the VRdose system and the Halden Planner, and a number of publications have been produced to contribute to improving the safety culture in the nuclear industry.This paper describes the radiation risk assessment techniques applied in earlier versions of the VRdose system and the Halden Planner, for visualising radiation fields and calculating dose, and presents new developments towards implementing a flexible and up-to-date dosimetric package in these 3D software tools, based on new developments in the field of radiation protection. The latest versions of these 3D tools are capable of more accurate risk estimation, permit more flexibility via a range of user choices, and are applicable to a wider range of irradiation situations than their predecessors.

[Detection of tibial condylar fractures using 3D imaging with a mobile image amplifier (Siemens ISO-C-3D): Comparison with plain films and spiral CT].

PubMed

Kotsianos, D; Rock, C; Wirth, S; Linsenmaier, U; Brandl, R; Fischer, T; Euler, E; Mutschler, W; Pfeifer, K J; Reiser, M

2002-01-01

To analyze a prototype mobile C-arm 3D image amplifier in the detection and classification of experimental tibial condylar fractures with multiplanar reconstructions (MPR). Human knee specimens (n = 22) with tibial condylar fractures were examined with a prototype C-arm (ISO-C-3D, Siemens AG), plain films (CR) and spiral CT (CT). The motorized C-arm provides fluoroscopic images during a 190 degrees orbital rotation computing a 119 mm data cube. From these 3D data sets MP reconstructions were obtained. All images were evaluated by four independent readers for the detection and assessment of fracture lines. All fractures were classified according to the Müller AO classification. To confirm the results, the specimens were finally surgically dissected. 97 % of the tibial condylar fractures were easily seen and correctly classified according to the Müller AO classification on MP reconstruction of the ISO-C-3D. There is no significant difference between ISO-C and CT in detection and correct classification of fractures, but ISO-CD-3D is significant by better than CR. The evaluation of fractures with the ISO-C is better than with plain films alone and comparable to CT scans. The three-dimensional reconstruction of the ISO-C can provide important information which cannot be obtained from plain films. The ISO-C-3D may be useful in planning operative reconstructions and evaluating surgical results in orthopaedic surgery of the limbs.

Acquisition of a Thermophoresis Instrument for Molecular Association Thermodynamic Studies

DTIC Science & Technology

2015-05-20

using NAMD.27 Crystallographic structures of C3d ( PDB code 1C3D) and C3d-CR2 ( PDB code 3OED) were obtained from the protein data bank ( PDB ).28 Missing...This project is funded by DTRA (Defense Threat Reduction Agency) and aims to develop new multienzyme structures for the controlled destruction of...enable detection. Pharmacophore models were developed based on known C3d-ligand interactions and information from computational analysis of structural

ShapeRotator: An R tool for standardized rigid rotations of articulated three-dimensional structures with application for geometric morphometrics.

PubMed

Vidal-García, Marta; Bandara, Lashi; Keogh, J Scott

2018-05-01

The quantification of complex morphological patterns typically involves comprehensive shape and size analyses, usually obtained by gathering morphological data from all the structures that capture the phenotypic diversity of an organism or object. Articulated structures are a critical component of overall phenotypic diversity, but data gathered from these structures are difficult to incorporate into modern analyses because of the complexities associated with jointly quantifying 3D shape in multiple structures. While there are existing methods for analyzing shape variation in articulated structures in two-dimensional (2D) space, these methods do not work in 3D, a rapidly growing area of capability and research. Here, we describe a simple geometric rigid rotation approach that removes the effect of random translation and rotation, enabling the morphological analysis of 3D articulated structures. Our method is based on Cartesian coordinates in 3D space, so it can be applied to any morphometric problem that also uses 3D coordinates (e.g., spherical harmonics). We demonstrate the method by applying it to a landmark-based dataset for analyzing shape variation using geometric morphometrics. We have developed an R tool (ShapeRotator) so that the method can be easily implemented in the commonly used R package geomorph and MorphoJ software. This method will be a valuable tool for 3D morphological analyses in articulated structures by allowing an exhaustive examination of shape and size diversity.

Design and implementation of a new autonomous sensor fish to support advanced hydropower development.

PubMed

Deng, Z D; Lu, J; Myjak, M J; Martinez, J J; Tian, C; Morris, S J; Carlson, T J; Zhou, D; Hou, H

2014-11-01

Acceleration in development of additional conventional hydropower requires tools and methods to perform laboratory and in-field validation of turbine performance and fish passage claims. The new-generation Sensor Fish has been developed with more capabilities to accommodate a wider range of users over a broader range of turbine designs and operating environments. It provides in situ measurements of three-dimensional (3D) linear accelerations, 3D rotational velocities, 3D orientation, pressure, and temperature at a sampling frequency of 2048 Hz. It also has an automatic floatation system and built-in radio-frequency transmitter for recovery. The relative errors of the pressure, acceleration, and rotational velocity were within ±2%, ±5%, and ±5%, respectively. The accuracy of orientation was within ±4° and accuracy of temperature was ±2 °C. The new-generation Sensor Fish is becoming a major technology and being deployed for evaluating the conditions for fish passage of turbines or other hydraulic structures in both the United States and several other countries.

Three-Dimensional Geometric Modeling of Membrane-bound Organelles in Ventricular Myocytes: Bridging the Gap between Microscopic Imaging and Mathematical Simulation

PubMed Central

Yu, Zeyun; Holst, Michael J.; Hayashi, Takeharu; Bajaj, Chandrajit L.; Ellisman, Mark H.; McCammon, J. Andrew; Hoshijima, Masahiko

2009-01-01

A general framework of image-based geometric processing is presented to bridge the gap between three-dimensional (3D) imaging that provides structural details of a biological system and mathematical simulation where high-quality surface or volumetric meshes are required. A 3D density map is processed in the order of image pre-processing (contrast enhancement and anisotropic filtering), feature extraction (boundary segmentation and skeletonization), and high-quality and realistic surface (triangular) and volumetric (tetrahedral) mesh generation. While the tool-chain described is applicable to general types of 3D imaging data, the performance is demonstrated specifically on membrane-bound organelles in ventricular myocytes that are imaged and reconstructed with electron microscopic (EM) tomography and two-photon microscopy (T-PM). Of particular interest in this study are two types of membrane-bound Ca2+-handling organelles, namely, transverse tubules (T-tubules) and junctional sarcoplasmic reticulum (jSR), both of which play an important role in regulating the excitation-contraction (E-C) coupling through dynamic Ca2+ mobilization in cardiomyocytes. PMID:18835449

Three-dimensional geometric modeling of membrane-bound organelles in ventricular myocytes: bridging the gap between microscopic imaging and mathematical simulation.

PubMed

Yu, Zeyun; Holst, Michael J; Hayashi, Takeharu; Bajaj, Chandrajit L; Ellisman, Mark H; McCammon, J Andrew; Hoshijima, Masahiko

2008-12-01

A general framework of image-based geometric processing is presented to bridge the gap between three-dimensional (3D) imaging that provides structural details of a biological system and mathematical simulation where high-quality surface or volumetric meshes are required. A 3D density map is processed in the order of image pre-processing (contrast enhancement and anisotropic filtering), feature extraction (boundary segmentation and skeletonization), and high-quality and realistic surface (triangular) and volumetric (tetrahedral) mesh generation. While the tool-chain described is applicable to general types of 3D imaging data, the performance is demonstrated specifically on membrane-bound organelles in ventricular myocytes that are imaged and reconstructed with electron microscopic (EM) tomography and two-photon microscopy (T-PM). Of particular interest in this study are two types of membrane-bound Ca(2+)-handling organelles, namely, transverse tubules (T-tubules) and junctional sarcoplasmic reticulum (jSR), both of which play an important role in regulating the excitation-contraction (E-C) coupling through dynamic Ca(2+) mobilization in cardiomyocytes.

Comparative Analysis of 2-D Versus 3-D Ultrasound Estimation of the Fetal Adrenal Gland Volume and Prediction of Preterm Birth

PubMed Central

Turan, Ozhan M.; Turan, Sifa; Buhimschi, Irina A.; Funai, Edmund F.; Campbell, Katherine H.; Bahtiyar, Ozan M.; Harman, Chris R.; Copel, Joshua A.; Baschat, Ahmet A; Buhimschi, Catalin S.

2013-01-01

Objective We aim to test the hypothesis that 2D fetal AGV measurements offer similar volume estimates as volume calculations based on 3D technique Methods Fetal AGV was estimated by 3D ultrasound (VOCAL) in 93 women with signs/symptoms of preterm labor and 73 controls. Fetal AGV was calculated using an ellipsoid formula derived from 2D measurements of the same blocks (0.523× length × width × depth). Comparisons were performed by intra-class correlation coefficient (ICC), coefficient of repeatability, and Bland-Altman method. The cAGV (AGV/fetal weight) was calculated for both methods and compared for prediction of PTB within 7 days. Results Among 168 volumes, there was a significant correlation between 3D and 2D methods (ICC=0.979[95%CI: 0.971-0.984]). The coefficient of repeatability for the 3D was superior to the 2D method (Intra-observer 3D: 30.8, 2D:57.6; inter-observer 3D: 12.2, 2D: 15.6). Based on 2D calculations, a cAGV≥433mm3/kg, was best for prediction of PTB (sensitivity: 75%(95%CI=59-87); specificity: 89%(95%CI=82-94). Sensitivity and specificity for the 3D cAGV (cut-off ≥420mm3/kg) was 85%(95%CI=70-94) and 95%(95%CI=90-98), respectively. In receiver-operating-curve curve analysis, 3D cAGV was superior to 2D cAGV for prediction of PTB (z=1.99, p=0.047). Conclusion 2D volume estimation of fetal adrenal gland using ellipsoid formula cannot replace 3D AGV calculations for prediction of PTB. PMID:22644825

Complexes of plexin-A4 and plexin-D1 convey semaphorin-3C signals to induce cytoskeletal collapse in the absence of neuropilins.

PubMed

Smolkin, Tatyana; Nir-Zvi, Inbal; Duvshani, Nerri; Mumblat, Yelena; Kessler, Ofra; Neufeld, Gera

2018-05-04

Class-3 semaphorin guidance factors bind to receptor complexes containing neuropilin and plexin receptors. A semaphorin may bind to several receptor complexes containing somewhat different constituents, resulting in diverse effects on cell migration. U87MG glioblastoma cells express both neuropilins and the four class-A plexins. Here, we show that these cells respond to Sema3A or Sema3B by cytoskeletal collapse and cell contraction but fail to contract in response to Sema3C, Sema3D, Sema3G or Sema3E, even when class-A plexins are overexpressed in the cells. In contrast, expression of recombinant plexin-D1 enabled contraction in response to these semaphorins. Surprisingly, unlike Sema3D and Sema3G, Sema3C also induced the contraction and repulsion of plexin-D1-expressing U87MG cells in which both neuropilins were knocked out using CRISPR/Cas9. In the absence of neuropilins, the EC50 of Sema3C was 5.5 times higher, indicating that the neuropilins function as enhancers of plexin-D1-mediated Sema3C signaling but are not absolutely required for Sema3C signal transduction. Interestingly, in the absence of neuropilins, plexin-A4 formed complexes with plexin-D1, and was required in addition to plexin-D1 to enable Sema3C-induced signal transduction. © 2018. Published by The Company of Biologists Ltd.

First responder tracking and visualization for command and control toolkit

NASA Astrophysics Data System (ADS)

Woodley, Robert; Petrov, Plamen; Meisinger, Roger

2010-04-01

In order for First Responder Command and Control personnel to visualize incidents at urban building locations, DHS sponsored a small business research program to develop a tool to visualize 3D building interiors and movement of First Responders on site. 21st Century Systems, Inc. (21CSI), has developed a toolkit called Hierarchical Grid Referenced Normalized Display (HiGRND). HiGRND utilizes three components to provide a full spectrum of visualization tools to the First Responder. First, HiGRND visualizes the structure in 3D. Utilities in the 3D environment allow the user to switch between views (2D floor plans, 3D spatial, evacuation routes, etc.) and manually edit fast changing environments. HiGRND accepts CAD drawings and 3D digital objects and renders these in the 3D space. Second, HiGRND has a First Responder tracker that uses the transponder signals from First Responders to locate them in the virtual space. We use the movements of the First Responder to map the interior of structures. Finally, HiGRND can turn 2D blueprints into 3D objects. The 3D extruder extracts walls, symbols, and text from scanned blueprints to create the 3D mesh of the building. HiGRND increases the situational awareness of First Responders and allows them to make better, faster decisions in critical urban situations.

Phosphoglucoisomerase-catalyzed interconversion of hexose phosphates: isotopic discrimination between hydrogen and deuterium.

PubMed

Malaisse, W J; Malaisse-Lagae, F; Liemans, V; Ottinger, R; Willem, R

1990-03-27

The discrimination between the isotopes of hydrogen in the reaction catalyzed by yeast phosphoglucoisomerase is examined by NMR, as well as by spectrofluorometric or radioisotopic methods. The monodirectional conversion of D-glucose 6-phosphate to D-fructose 6-phosphate displays a lower maximal velocity with D-[2-2H]glucose 6-phosphate than unlabelled D-glucose 6-phosphate, with little difference in the affinity of the enzyme for these two substrates. About 72% of the deuterium located on the C2 of D-[1-13C,2-2H]glucose 6-phosphate is transferred intramolecularly to the C1 of D-[1-13C,1-2H]fructose 6-phosphate. The velocity of the monodirectional conversion of D-[U-14C]glucose 6-phosphate (or D-[2-3H]glucose 6-phosphate) to D-fructose 6-phosphate is virtually identical in H2O and D2O, respectively, but is four times lower with the tritiated than 14C-labelled ester. In the monodirectional reaction, the intramolecular transfer from the C2 of D-[2-3H]glucose 6-phosphate is higher in the presence of D2O than H2O. Whereas prolonged exposure of D-[1-13C]glucose 6-phosphate to D2O, in the presence of phosphoglucoisomerase, leads to the formation of both D-[1-13C,2-2H]glucose 6-phosphate and D-[1-13C,1-2H]fructose 6-phosphate, no sizeable incorporation of dueterium from D2O on the C1 of D-[1-13C]fructose 1,6-bisphosphate is observed when the monodirectional conversion of D-[1-13C]glucose 6-phosphate occurs in the concomitant presence of phosphoglucoisomerase and phosphofructokinase. The latter finding contrasts with the incorporation of hydrogen from 1H2O or tritium from 3H2O in the monodirectional conversion of D-[2-3H]glucose 6-phosphate and unlabelled D-glucose 6-phosphate, respectively, to their corresponding ketohexose esters.

Visuospatial Attention in Children with Autism Spectrum Disorder: A Comparison between 2-D and 3-D Environments

ERIC Educational Resources Information Center

Ip, Horace H. S.; Lai, Candy Hoi-Yan; Wong, Simpson W. L.; Tsui, Jenny K. Y.; Li, Richard Chen; Lau, Kate Shuk-Ying; Chan, Dorothy F. Y.

2017-01-01

Previous research has illustrated the unique benefits of three-dimensional (3-D) Virtual Reality (VR) technology in Autism Spectrum Disorder (ASD) children. This study examined the use of 3-D VR technology as an assessment tool in ASD children, and further compared its use to two-dimensional (2-D) tasks. Additionally, we aimed to examine…

Prime Contract Awards Alphabetically by Contractor, by State or Country, and Place, Fiscal Year 1985. Part 6 (Delaco Supreme Tool & Gear Inc - Electronic Measurements Inc).

DTIC Science & Technology

1985-01-01

itt0D()cu o L CJ L 4P -mo rM1 00 tD )0) 44D um acWnr * t L nŘrm- 40) Ia 4 "NNNN.O Z-4 to 0 WA4 q 4 -4 )) m q 4 Ln M )A(ONc to0 -04 0 0000-4 20 Nl...00000004441 -Q 00 0 0 C9 1 -00000 i wmV-w-w 110qf 0i 04 04C, : 0 wM WO OI * I 00001 - Xi in - X:00 1 .4zI-4o 0 ~ ~ ~ C -4 Q00 Il .I-1 r’.-C 0)) 0kI -- V~I~ El

A new heat transfer analysis in machining based on two steps of 3D finite element modelling and experimental validation

NASA Astrophysics Data System (ADS)

Haddag, B.; Kagnaya, T.; Nouari, M.; Cutard, T.

2013-01-01

Modelling machining operations allows estimating cutting parameters which are difficult to obtain experimentally and in particular, include quantities characterizing the tool-workpiece interface. Temperature is one of these quantities which has an impact on the tool wear, thus its estimation is important. This study deals with a new modelling strategy, based on two steps of calculation, for analysis of the heat transfer into the cutting tool. Unlike the classical methods, considering only the cutting tool with application of an approximate heat flux at the cutting face, estimated from experimental data (e.g. measured cutting force, cutting power), the proposed approach consists of two successive 3D Finite Element calculations and fully independent on the experimental measurements; only the definition of the behaviour of the tool-workpiece couple is necessary. The first one is a 3D thermomechanical modelling of the chip formation process, which allows estimating cutting forces, chip morphology and its flow direction. The second calculation is a 3D thermal modelling of the heat diffusion into the cutting tool, by using an adequate thermal loading (applied uniform or non-uniform heat flux). This loading is estimated using some quantities obtained from the first step calculation, such as contact pressure, sliding velocity distributions and contact area. Comparisons in one hand between experimental data and the first calculation and at the other hand between measured temperatures with embedded thermocouples and the second calculation show a good agreement in terms of cutting forces, chip morphology and cutting temperature.

3D equilibrium reconstruction with islands

NASA Astrophysics Data System (ADS)

Cianciosa, M.; Hirshman, S. P.; Seal, S. K.; Shafer, M. W.

2018-04-01

This paper presents the development of a 3D equilibrium reconstruction tool and the results of the first-ever reconstruction of an island equilibrium. The SIESTA non-nested equilibrium solver has been coupled to the V3FIT 3D equilibrium reconstruction code. Computed from a coupled VMEC and SIESTA model, synthetic signals are matched to measured signals by finding an optimal set of equilibrium parameters. By using the normalized pressure in place of normalized flux, non-equilibrium quantities needed by diagnostic signals can be efficiently mapped to the equilibrium. The effectiveness of this tool is demonstrated by reconstructing an island equilibrium of a DIII-D inner wall limited L-mode case with an n = 1 error field applied. Flat spots in Thomson and ECE temperature diagnostics show the reconstructed islands have the correct size and phase. ).

Role of the Box C/D Motif in Localization of Small Nucleolar RNAs to Coiled Bodies and Nucleoli

PubMed Central

Narayanan, Aarthi; Speckmann, Wayne; Terns, Rebecca; Terns, Michael P.

1999-01-01

Small nucleolar RNAs (snoRNAs) are a large family of eukaryotic RNAs that function within the nucleolus in the biogenesis of ribosomes. One major class of snoRNAs is the box C/D snoRNAs named for their conserved box C and box D sequence elements. We have investigated the involvement of cis-acting sequences and intranuclear structures in the localization of box C/D snoRNAs to the nucleolus by assaying the intranuclear distribution of fluorescently labeled U3, U8, and U14 snoRNAs injected into Xenopus oocyte nuclei. Analysis of an extensive panel of U3 RNA variants showed that the box C/D motif, comprised of box C′, box D, and the 3′ terminal stem of U3, is necessary and sufficient for the nucleolar localization of U3 snoRNA. Disruption of the elements of the box C/D motif of U8 and U14 snoRNAs also prevented nucleolar localization, indicating that all box C/D snoRNAs use a common nucleolar-targeting mechanism. Finally, we found that wild-type box C/D snoRNAs transiently associate with coiled bodies before they localize to nucleoli and that variant RNAs that lack an intact box C/D motif are detained within coiled bodies. These results suggest that coiled bodies play a role in the biogenesis and/or intranuclear transport of box C/D snoRNAs. PMID:10397754

WE-AB-BRA-07: Quantitative Evaluation of 2D-2D and 2D-3D Image Guided Radiation Therapy for Clinical Trial Credentialing, NRG Oncology/RTOG

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

Giaddui, T; Yu, J; Xiao, Y

Purpose: 2D-2D kV image guided radiation therapy (IGRT) credentialing evaluation for clinical trial qualification was historically qualitative through submitting screen captures of the fusion process. However, as quantitative DICOM 2D-2D and 2D-3D image registration tools are implemented in clinical practice for better precision, especially in centers that treat patients with protons, better IGRT credentialing techniques are needed. The aim of this work is to establish methodologies for quantitatively reviewing IGRT submissions based on DICOM 2D-2D and 2D-3D image registration and to test the methodologies in reviewing 2D-2D and 2D-3D IGRT submissions for RTOG/NRG Oncology clinical trials qualifications. Methods: DICOM 2D-2Dmore » and 2D-3D automated and manual image registration have been tested using the Harmony tool in MIM software. 2D kV orthogonal portal images are fused with the reference digital reconstructed radiographs (DRR) in the 2D-2D registration while the 2D portal images are fused with DICOM planning CT image in the 2D-3D registration. The Harmony tool allows alignment of the two images used in the registration process and also calculates the required shifts. Shifts calculated using MIM are compared with those submitted by institutions for IGRT credentialing. Reported shifts are considered to be acceptable if differences are less than 3mm. Results: Several tests have been performed on the 2D-2D and 2D-3D registration. The results indicated good agreement between submitted and calculated shifts. A workflow for reviewing these IGRT submissions has been developed and will eventually be used to review IGRT submissions. Conclusion: The IROC Philadelphia RTQA center has developed and tested a new workflow for reviewing DICOM 2D-2D and 2D-3D IGRT credentialing submissions made by different cancer clinical centers, especially proton centers. NRG Center for Innovation in Radiation Oncology (CIRO) and IROC RTQA center continue their collaborative efforts to enhance quality assurance services and to be consistently adaptive to the new advances in radiation therapy. This project was supported by NCI grants U10CA180868, U10CA180822, U24CA180803, U24CA12014 and PA CURE Grant.« less

Indian Ocean Validation,

DTIC Science & Technology

1987-09-01

S9 fd 30 2 D0i 0m10 20 802 AR. Oy ad n A o io in 3 0 3 7 ..n . . . w o w., , ... .. . . . . d ata m gaterng eie ws amdfe Lito sT-1 Omeg nav~igtion AE...signals propagated from each of N stations over paths of 2-10 length dl, d2, ... as shown in Figure 2.1. Station 2 Station N Station 1 D dl SUBJECT Figure...t2* = (d1* - d2*)/c + ( El - 62) t2* - t3* = (d2* - d3*)/c + ( E2 - E3) t*N 1 - t*N - ( d *N 1 - dN*)/c + ( N-1 EN) (6) 47he results obtained in

Basics of Compounding: 3D Printing--Pharmacy Applications, Part 2.

PubMed

Allen, Loyd V

2017-01-01

3D printing is a standard tool in the automotive, aerospace, and consumer goods in industry and is gaining traction in pharmaceutical manufacturing, which has introduced a new element into dosage-form development. This article, which represents part 2 of a 3-part article on the topic of 3D printing, discusses the different technologies available for 3D printing. Copyright© by International Journal of Pharmaceutical Compounding, Inc.

Reduction in erythrocyte-bound complement activation products and titres of anti-C1q antibodies associate with clinical improvement in systemic lupus erythematosus.

PubMed

Buyon, Jill; Furie, Richard; Putterman, Chaim; Ramsey-Goldman, Rosalind; Kalunian, Kenneth; Barken, Derren; Conklin, John; Dervieux, Thierry

2016-01-01

The relationship between cell-bound complement activation products (CB-CAPs: EC4d, EC3d), anti-C1q, soluble complement C3/C4 and disease activity in systemic lupus erythematosus (SLE) was evaluated. Per protocol, at baseline all SLE subjects enrolled in this longitudinal study presented with active disease and elevated CB-CAPs. At each monthly visit, the non-serological (ns) Safety of Estrogens in Lupus Erythematosus: National Assessment (SELENA-SLEDAI) and the British Isles Lupus Assessment Group (BILAG)-2004 index scores were determined as was a random urinary protein to creatinine ratio (uPCR). Short-form 36 (SF-36) questionnaires were also collected. All soluble markers were determined using immunoassays, while EC4d and EC3d were determined using flow cytometry. Statistical analysis consisted of linear mixed models with random intercept and fixed slopes. A total of 36 SLE subjects (mean age 34 years; 94% female) were enrolled and evaluated monthly for an average 11 visits per subject. Clinical improvements were observed during the study, with significant decreases in ns-SELENA-SLEDAI scores, BILAG-2004 index scores and uPCR, and increases in all domains of SF-36 (p<0.01). The longitudinal decrease in ns-SELENA-SLEDAI and BILAG-2004 index scores was significantly associated with reduced EC4d and EC3d levels, reduced anti-C1q titres and increased serum complement C3/C4 (p<0.05). The changes in uPCR significantly correlated with C3, C4, anti-C1q and EC4d, with EC4d outperforming C3/C4 by a multivariate analysis. The reduced EC4d or EC3d was associated with improvements in at least six out of the eight domains of SF-36 and outperformed C3/C4. Anti-dsDNA titres did not correlate with changes in disease activity. These data indicate that CB-CAPs and anti-C1q are helpful in monitoring patients with SLE.

Virtual and Printed 3D Models for Teaching Crystal Symmetry and Point Groups

ERIC Educational Resources Information Center

Casas, Lluís; Estop, Euge`nia

2015-01-01

Both, virtual and printed 3D crystal models can help students and teachers deal with chemical education topics such as symmetry and point groups. In the present paper, two freely downloadable tools (interactive PDF files and a mobile app) are presented as examples of the application of 3D design to study point-symmetry. The use of 3D printing to…

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

Pang, Xiaoying; Rybarcyk, Larry

HPSim is a GPU-accelerated online multi-particle beam dynamics simulation tool for ion linacs. It was originally developed for use on the Los Alamos 800-MeV proton linac. It is a “z-code” that contains typical linac beam transport elements. The linac RF-gap transformation utilizes transit-time-factors to calculate the beam acceleration therein. The space-charge effects are computed using the 2D SCHEFF (Space CHarge EFFect) algorithm, which calculates the radial and longitudinal space charge forces for cylindrically symmetric beam distributions. Other space- charge routines to be incorporated include the 3D PICNIC and a 3D Poisson solver. HPSim can simulate beam dynamics in drift tubemore » linacs (DTLs) and coupled cavity linacs (CCLs). Elliptical superconducting cavity (SC) structures will also be incorporated into the code. The computational core of the code is written in C++ and accelerated using the NVIDIA CUDA technology. Users access the core code, which is wrapped in Python/C APIs, via Pythons scripts that enable ease-of-use and automation of the simulations. The overall linac description including the EPICS PV machine control parameters is kept in an SQLite database that also contains calibration and conversion factors required to transform the machine set points into model values used in the simulation.« less

3D photography is a reliable burn wound area assessment tool compared to digital planimetry in very young children.

PubMed

Gee Kee, E L; Kimble, R M; Stockton, K A

2015-09-01

Reliability and validity of 3D photography (3D LifeViz™ System) compared to digital planimetry (Visitrak™) has been established in a compliant cohort of children with acute burns. Further research is required to investigate these assessment tools in children representative of the general pediatric burns population, specifically children under the age of three years. To determine if 3D photography is a reliable wound assessment tool compared to Visitrak™ in children of all ages with acute burns ≤10% TBSA. Ninety-six children (median age 1 year 9 months) who presented to the Royal Children's Hospital Brisbane with an acute burn ≤10% TBSA were recruited into the study. Wounds were measured at the first dressing change using the Visitrak™ system and 3D photography. All measurements were completed by one investigator and level of agreement between wound surface area measurements was calculated. Wound surface area measurements were complete (i.e. participants had measurements from both techniques) for 75 participants. Level of agreement between wound surface area measurements calculated using an intra-class correlation coefficient (ICC) was excellent (ICC 0.96, 95% CI 0.93, 0.97). Visitrak™ tracings could not be completed in 19 participants with 16 aged less than two years. 3D photography could not be completed for one participant. Barriers to completing tracings were: excessive movement, pain, young age or wound location (e.g. face or perineum). This study has confirmed 3D photography as a reliable alternative to digital planimetry in children of all ages with acute burns ≤10% TBSA. In addition, 3D photography is more suitable for very young children given its non-invasive nature. Copyright © 2015 Elsevier Ltd and ISBI. All rights reserved.

Technical note: 3D from standard digital photography of human crania-a preliminary assessment.

PubMed

Katz, David; Friess, Martin

2014-05-01

This study assessed three-dimensional (3D) photogrammetry as a tool for capturing and quantifying human skull morphology. While virtual reconstruction with 3D surface scanning technology has become an accepted part of the paleoanthropologist's tool kit, recent advances in 3D photogrammetry make it a potential alternative to dedicated surface scanners. The principal advantages of photogrammetry are more rapid raw data collection, simplicity and portability of setup, and reduced equipment costs. We tested the precision and repeatability of 3D photogrammetry by comparing digital models of human crania reconstructed from conventional, 2D digital photographs to those generated using a 3D surface scanner. Overall, the photogrammetry and scanner meshes showed low degrees of deviation from one another. Surface area estimates derived from photogrammetry models tended to be slightly larger. Landmark configurations generally did not cluster together based upon whether the reconstruction was created with photogrammetry or surface scanning technology. Average deviations of landmark coordinates recorded on photogrammetry models were within the generally allowable range of error in osteometry. Thus, while dependent upon the needs of the particular research project, 3D photogrammetry appears to be a suitable, lower-cost alternative to 3D imaging and scanning options. Copyright © 2014 Wiley Periodicals, Inc.

A Supramolecular Approach toward Bioinspired PAMAM-Dendronized Fusion Toxins.

PubMed

Kuan, Seah Ling; Förtsch, Christina; Ng, David Yuen Wah; Fischer, Stephan; Tokura, Yu; Liu, Weina; Wu, Yuzhou; Koynov, Kaloian; Barth, Holger; Weil, Tanja

2016-06-01

Nature has provided a highly optimized toolbox in bacterial endotoxins with precise functions dictated by their clear structural division. Inspired by this streamlined design, a supramolecular approach capitalizing on the strong biomolecular (streptavidin (SA))-biotin interactions is reported herein to prepare two multipartite fusion constructs, which involves the generation 2.0 (D2) or generation 3.0 (D3) polyamidoamine-dendronized transporter proteins (dendronized streptavidin (D3SA) and dendronized human serum albumin (D2HSA)) non-covalently fused to the C3bot1 enzyme from Clostridium botulinum, a potent and specific Rho-inhibitor. The fusion constructs, D3SA-C3 and D2HSA-C3, represent the first examples of dendronized protein transporters that are fused to the C3 enzyme, and it is successfully demonstrated that the C3 Rho-inhibitor is delivered into the cytosol of mammalian cells as determined from the characteristic C3-mediated changes in cell morphology and confocal microscopy. The design circumvents the low uptake of the C3 enzyme by eukaryotic cells and holds great promise for reprogramming the properties of toxin enzymes using a supramolecular approach to broaden their therapeutic applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dynamic heterogeneity of DNA methylation and hydroxymethylation in embryonic stem cell populations captured by single-cell 3D high-content analysis

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

Tajbakhsh, Jian, E-mail: tajbakhshj@cshs.org; Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048

2015-03-15

Cell-surface markers and transcription factors are being used in the assessment of stem cell fate and therapeutic safety, but display significant variability in stem cell cultures. We assessed nuclear patterns of 5-hydroxymethylcytosine (5hmC, associated with pluripotency), a second important epigenetic mark, and its combination with 5-methylcytosine (5mC, associated with differentiation), also in comparison to more established markers of pluripotency (Oct-4) and endodermal differentiation (FoxA2, Sox17) in mouse embryonic stem cells (mESC) over a 10-day differentiation course in vitro: by means of confocal and super-resolution imaging together with 3D high-content analysis, an essential tool in single-cell screening. In summary: 1) Wemore » did not measure any significant correlation of putative markers with global 5mC or 5hmC. 2) While average Oct-4 levels stagnated on a cell-population base (0.015 lnIU/day), Sox17 and FoxA2 increased 22-fold and 3-fold faster, respectively (Sox17: 0.343 lnIU/day; FoxA2: 0.046 lnIU/day). In comparison, global DNA methylation levels increased 4-fold faster (0.068 lnIU/day), and global hydroxymethylation declined at 0.046 lnIU/day, both with a better explanation of the temporal profile. 3) This progression was concomitant with the occurrence of distinct nuclear codistribution patterns that represented a heterogeneous spectrum of states in differentiation; converging to three major coexisting 5mC/5hmC phenotypes by day 10: 5hmC{sup +}/5mC{sup −}, 5hmC{sup +}/5mC{sup +}, and 5hmC{sup −}/5mC{sup +} cells. 4) Using optical nanoscopy we could delineate the respective topologies of 5mC/5hmC colocalization in subregions of nuclear DNA: in the majority of 5hmC{sup +}/5mC{sup +} cells 5hmC and 5mC predominantly occupied mutually exclusive territories resembling euchromatic and heterochromatic regions, respectively. Simultaneously, in a smaller subset of cells we observed a tighter colocalization of the two cytosine variants, presumably delineating chromatin domains in remodeling. We conclude that 1) 5mC emerges as the most differential marker in our model system. 2) However, the combined enrollment of the two DNA modifications provided higher-definition screening and lead to the identification of cell subpopulations based on differential 5hmC/5mC phenotypes corresponding to different 5hmC/5mC ratios. The results encourage: a) assessing the regenerative potential of early-endodermal cells enriched for the three DNA methylation/hydroxymethylation categories, and b) exploring the universality of this type of epigenetic phenotyping across other lineage-specific differentiations. - Highlights: • First reported single-molecule super-resolution 3D-visualization of 5mC/5hmC sites in cells. • Identification of cells with differential 5mC/5hmC nuclear codistribution phenotypes. • Application of principle component and robust regression analyses for evaluation of 3D high-content-screening data. • Global 5mC constitutes a highly differential spatiotemporal in situ marker in early endodermal cell differentiation.« less

D Photographs in Cultural Heritage

NASA Astrophysics Data System (ADS)

Schuhr, W.; Lee, J. D.; Kiel, St.

2013-07-01

This paper on providing "oo-information" (= objective object-information) on cultural monuments and sites, based on 3D photographs is also a contribution of CIPA task group 3 to the 2013 CIPA Symposium in Strasbourg. To stimulate the interest in 3D photography for scientists as well as for amateurs, 3D-Masterpieces are presented. Exemplary it is shown, due to their high documentary value ("near reality"), 3D photography support, e.g. the recording, the visualization, the interpretation, the preservation and the restoration of architectural and archaeological objects. This also includes samples for excavation documentation, 3D coordinate calculation, 3D photographs applied for virtual museum purposes and as educational tools. In addition 3D photography is used for virtual museum purposes, as well as an educational tool and for spatial structure enhancement, which in particular holds for inscriptions and in rock arts. This paper is also an invitation to participate in a systematic survey on existing international archives of 3D photographs. In this respect it is also reported on first results, to define an optimum digitization rate for analog stereo views. It is more than overdue, in addition to the access to international archives for 3D photography, the available 3D photography data should appear in a global GIS(cloud)-system, like on, e.g., google earth. This contribution also deals with exposing new 3D photographs to document monuments of importance for Cultural Heritage, including the use of 3D and single lense cameras from a 10m telescope staff, to be used for extremely low earth based airborne 3D photography, as well as for "underwater staff photography". In addition it is reported on the use of captive balloon and drone platforms for 3D photography in Cultural Heritage. It is liked to emphasize, the still underestimated 3D effect on real objects even allows, e.g., the spatial perception of extremely small scratches as well as of nuances in color differences. Though 3D photographs are a well established basic photographic and photogrammetric tool, they are still a matter of research and practical improvement: - For example, multistage concepts for 3D heritage photographs, e.g., combining before and aft images and images showing different focus, daytime etc., as well as combining 3D imagery of different sensors and comparing 3D imagery with drawings etc. and even standards for exposing and processing 3D heritage photographs are only some topics for recent research. - To advise on state-of-the-art 3D visualisation methodology for Cultural heritage purposes an updated synoptically overview, even claiming completeness, also will be dealt with. - 3D photographs increasingly should replace old fashioned subjective interpreted manual 2D drawings (in 2D only) of heritage monuments. - Currently we are witnesses of early developments, showing Cultural Heritage objects in 3D crystal as well as in 3D printings.

Design of a Persistence Server for the Relational Hypergraph Model

DTIC Science & Technology

1999-12-01

HH C O o _CD 󈧷 u _D- CO CD...X c 2 II E 2 § o c >» C .3 .2 Q — "a O u >» 00 HH 1) Ü CJ > 00 O CO > PH S .2 .22 J 5 c -a zz O (50 to C "x ’S...X CS 3 X & O « 1 H < X X es es d d e e cj cj 3 3 o o E a 3 HH c CS e e o o 3 3 aa oa o o o <-. a o 3 — pa ^ tad

Benchmarking Naval Shipbuilding With 3D Laser Scanning, Additive Manufacturing, and Collaborative Product Lifecycle Management

DTIC Science & Technology

2016-04-30

manufacturing is also commonly referred to as 3D printing . AM differs radically from the currently dominant manufacturing methodologies. Most current...referred to as 3D printing . In the automotive industry, Ford Motor Co. uses 3D printing in several areas, including the tooling used to create production...four months and cost $500,000 to build, while a 3D - printed manifold prototype costs $3,000 to build over four days. Additive Manufacturing in the

Web-based interactive 3D visualization as a tool for improved anatomy learning.

PubMed

Petersson, Helge; Sinkvist, David; Wang, Chunliang; Smedby, Orjan

2009-01-01

Despite a long tradition, conventional anatomy education based on dissection is declining. This study tested a new virtual reality (VR) technique for anatomy learning based on virtual contrast injection. The aim was to assess whether students value this new three-dimensional (3D) visualization method as a learning tool and what value they gain from its use in reaching their anatomical learning objectives. Several 3D vascular VR models were created using an interactive segmentation tool based on the "virtual contrast injection" method. This method allows users, with relative ease, to convert computer tomography or magnetic resonance images into vivid 3D VR movies using the OsiriX software equipped with the CMIV CTA plug-in. Once created using the segmentation tool, the image series were exported in Quick Time Virtual Reality (QTVR) format and integrated within a web framework of the Educational Virtual Anatomy (EVA) program. A total of nine QTVR movies were produced encompassing most of the major arteries of the body. These movies were supplemented with associated information, color keys, and notes. The results indicate that, in general, students' attitudes towards the EVA-program were positive when compared with anatomy textbooks, but results were not the same with dissections. Additionally, knowledge tests suggest a potentially beneficial effect on learning.

Using three-dimensional-computerized tomography as a diagnostic tool for temporo-mandibular joint ankylosis: a case report.

PubMed

Kao, S Y; Chou, J; Lo, J; Yang, J; Chou, A P; Joe, C J; Chang, R C

1999-04-01

Roentgenographic examination has long been a useful diagnostic tool for temporo-mandibular joint (TMJ) disease. The methods include TMJ tomography, panoramic radiography and computerized tomography (CT) scan with or without injection of contrast media. Recently, three-dimensional CT (3D-CT), reconstructed from the two-dimensional image of a CT scan to simulate the soft tissue or bony structure of the real target, was proposed. In this report, a case of TMJ ankylosis due to traumatic injury is presented. 3D-CT was employed as one of the presurgical roentgenographic diagnostic tools. The conventional radiographic examination including panoramic radiography and tomography showed lesions in both sides of the mandible. CT scanning further suggested that the right-sided lesion was more severe than that on the left. With 3D-CT image reconstruction the size and extent of the lesions were clearly observable. The decision was made to proceed with an initial surgical approach on the right side. With condylectomy and condylar replacement using an autogenous costochondral graft on the right side, the range of mouth opening improved significantly. In this case report, 3D-CT demonstrates its advantages as a tool for the correct and precise diagnosis of TMJ ankylosis.

Architecture of a high-performance surgical guidance system based on C-arm cone-beam CT: software platform for technical integration and clinical translation

NASA Astrophysics Data System (ADS)

Uneri, Ali; Schafer, Sebastian; Mirota, Daniel; Nithiananthan, Sajendra; Otake, Yoshito; Reaungamornrat, Sureerat; Yoo, Jongheun; Stayman, J. Webster; Reh, Douglas; Gallia, Gary L.; Khanna, A. Jay; Hager, Gregory; Taylor, Russell H.; Kleinszig, Gerhard; Siewerdsen, Jeffrey H.

2011-03-01

Intraoperative imaging modalities are becoming more prevalent in recent years, and the need for integration of these modalities with surgical guidance is rising, creating new possibilities as well as challenges. In the context of such emerging technologies and new clinical applications, a software architecture for cone-beam CT (CBCT) guided surgery has been developed with emphasis on binding open-source surgical navigation libraries and integrating intraoperative CBCT with novel, application-specific registration and guidance technologies. The architecture design is focused on accelerating translation of task-specific technical development in a wide range of applications, including orthopaedic, head-and-neck, and thoracic surgeries. The surgical guidance system is interfaced with a prototype mobile C-arm for high-quality CBCT and through a modular software architecture, integration of different tools and devices consistent with surgical workflow in each of these applications is realized. Specific modules are developed according to the surgical task, such as: 3D-3D rigid or deformable registration of preoperative images, surgical planning data, and up-to-date CBCT images; 3D-2D registration of planning and image data in real-time fluoroscopy and/or digitally reconstructed radiographs (DRRs); compatibility with infrared, electromagnetic, and video-based trackers used individually or in hybrid arrangements; augmented overlay of image and planning data in endoscopic or in-room video; real-time "virtual fluoroscopy" computed from GPU-accelerated DRRs; and multi-modality image display. The platform aims to minimize offline data processing by exposing quantitative tools that analyze and communicate factors of geometric precision. The system was translated to preclinical phantom and cadaver studies for assessment of fiducial (FRE) and target registration error (TRE) showing sub-mm accuracy in targeting and video overlay within intraoperative CBCT. The work culminates in the development of a CBCT guidance system (reported here for the first time) that leverages the technical developments in Carm CBCT and associated technologies for realizing a high-performance system for translation to clinical studies.

Dynamic movement of cytochrome c from mitochondria into cytosol and peripheral circulation in massive hepatic cell injury.

PubMed

Kobayashi, Yoshinori; Mori, Masaaki; Naruto, Takuya; Kobayashi, Naoki; Sugai, Toshiyuki; Imagawa, Tomoyuki; Yokota, Shumpei

2004-12-01

In the process of apoptosis, it is known that the transition of cytochrome c from mitochondria into the cytosol occurs, and tumor necrosis factor (TNF)-alpha is one of the molecules responsible for this event. But in the state of hypercytokine induced by D-galactosamine (D-GaIN)/Lipopolysaccharide (LPS), the localization of cytochrome c is little known. Rats were administrated with D-GaIN(700 mg/kg)/LPS(200 microg/kg). Blood and tissue samples were collected and examined for levels of pro-inflammatory cytokines, the apoptosis of liver cells, and the localization of cytochrome c. Before administration of D-GaIN/LPS, cytochrome c was definitely localized in the mitochondria. At 2 h after simultaneous administration of D-GaIN/LPS, cytochrome c had accumulated in the cytosol following abrupt increases of plasma TNF-alpha. Massive cell destruction due to apoptosis proved by Terminal deoxynucleo-tidyl transferase-mediated dUTP nick end labeling staining was observed in liver tissue 4 h later and markedly increased levels of cytochrome c were detected in the plasma 12 h after D-GaIN/LPS administration. Liver injury induced by simultaneous administration of D-GaIN/LPS was closely associated with the production of TNF-alpha, and also with the dynamic movement of cytochrome c from the mitochondria into the cytosol, and then into the systemic circulation. The detection of plasma cytochrome c levels may be a useful clinical tool for the detection of apoptosis in vivo.

Induction of protective and therapeutic antitumor immunity by a DNA vaccine with C3d as a molecular adjuvant.

PubMed

Xu, Gui-lian; Zhang, Ke-qin; Guo, Bo; Zhao, Ting-ting; Yang, Fei; Jiang, Man; Wang, Qing-hong; Shang, Yu-hang; Wu, Yu-zhang

2010-10-18

Although the critical role of complement component C3d as a molecular adjuvant in preventing virus infection is well established, its role in cancer therapies is unclear. In this study, we have engineered a DNA vaccine that expresses extracellular region of murine VEGFR-2 (FLK1(265-2493)) and 3 copies of C3d (C3d3), a component of complement as a molecular adjuvant, designed to increase antitumor immunity. VEGFR-2 has a more restricted expression on endothelial cells and is upregulated once these cells proliferate during angiogenesis in the tumor vasculature. Immunization of mice with vector encoding FLK1(265-2493) alone generated only background levels of anti-VEGFR-2 antibodies and slight inhibitory effect on tumor growth. However, the addition of C3d3 to the vaccine construct significantly augmented the anti-VEGFR-2 humoral immune response and inhibited the tumor growth. The antitumor activity induced by vaccination with vector encoding FLK1(265-2493)-C3d3 fusion protein was also demonstrated via growth inhibition of established tumors following passive transfer of immune serum from vaccinated mice. Our results suggest that vaccination with vector encoding FLK1(265-2493) with C3d3 as a molecular adjuvant induces adaptive humoral activity, which is directed against the murine VEGFR-2 and can significantly inhibit tumor growth, and that administration of C3d as a molecular adjuvant to increase antibodies levels to VEGFR-2 may provide an alternative treatment modality for cancer therapies. Copyright © 2010 Elsevier Ltd. All rights reserved.

75 FR 22508 - Airworthiness Directives; Eurocopter France Model AS350B, BA, B1, B2, B3, C, D, and D1; AS 355E...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-29

... Airworthiness Directives; Eurocopter France Model AS350B, BA, B1, B2, B3, C, D, and D1; AS 355E, F, F1, F2, N... (b) None. Applicability (c) This AD applies to Model AS350B, BA, B1, B2, B3, C, D and D1; and AS 355E..., both dated November 16, 2005, is approved by the Director of the Federal Register as of May 14, 2010...

Synthetic Lectins: New Tools for Detection and Management of Prostate Cancer

DTIC Science & Technology

2013-08-01

providing a new paradigm for the development of a prostate cancer diagnostic. AIM 1 describes a library based approach for the discovery of SLs...This work was supported by funds provided from NIH COBRE grant P20RR17698.Notes and references 1 D. H. Dube and C. R. Bertozzi, Nat. Rev. Drug... Discovery , 2005, 4, 477–488. 2 V. Harmat and G. Naray-Szabo, Croat. Chim. Acta, 2009, 82, 277– 282. 3 J. J. Lavigne and E. V. Anslyn, Angew. Chem., Int. Ed

Magic User’s Manual 2006

DTIC Science & Technology

2006-12-01

K (M) M issioin Research MRC/WDC-R-556 MAGIC USER’S MANUAL 2006 Author(s): Larry Ludeking ATK Mission Research Contract No.: F49620-03-C-0030 L¾[iJiD... Magic Tool Suite for Windows. It uses the standard Windows Help so it is pretty self-explanatory. You can use the panel to the left to scan through... MAGIC Go to Part 2. MCL Commands Go to Part 3. Tirnc and Space Go to Part 4. Spatial Extensions Go to Part 5. Properties Go to Part 6. Algorithms Go

Development of Cognitive Bias Modification (CBM) Tools to Promote Adjustment during Reintegration following Deployment

DTIC Science & Technology

2017-06-01

Abnormal Psychology , 95, 15– 20. doi:10.1037//0021-843x.95.1.15 MacLeod, C., Rutherford, E., Campbell, L., Ebsworthy, G., & Holker, L. (2002). Selective...of Abnormal Psychology , 111, 107–123. doi:10.1037//0021-843x. 111.1.107 Mammen, O. K., Pilkonis, P. A., & Kolko, D. J. (2000). Anger and parent-to...cognitive basis of trait anger and reactive aggression: An integrative analysis. Personality and Social Psychology Review, 12(1), 3–21. doi:10. 1177