Science.gov

Sample records for 3d structural features

  1. 3D Solar Wind Structure Features Characterizing the Rise of Cycle 24

    NASA Astrophysics Data System (ADS)

    Luhmann, J. G.; Ellenburg, M. A.; Riley, P.; Lee, C. O.; Arge, C. N.; Jian, L.; Russell, C. T.; Simunac, K.; Galvin, A. B.; Petrie, G. J.

    2011-12-01

    Since the launch of the STEREO mission in 2006, there has been renewed interest in the 3D structure of the solar wind, spurred in part by the unusual cycle 23 solar minimum and current solar cycle rise. Of particular significance for this subject has been the ubiquitous occurrence of low latitude coronal holes and coronal pseudo-streamers. These coupled features have been common both because of the relative strength of high order spherical harmonic content of the global coronal field, and the weakness of the field compared to the previous two well-observed cycles. We consider the effects of the low latitude coronal holes and pseudo-streamers on the near-ecliptic solar wind and interplanetary field. In particular, we illustrate how the now common passage of streams with low latitude sources and pseudo-streamer boundaries is changing our traditional perceptions of local solar wind structures.

  2. Mesh Convolutional Restricted Boltzmann Machines for Unsupervised Learning of Features With Structure Preservation on 3-D Meshes.

    PubMed

    Han, Zhizhong; Liu, Zhenbao; Han, Junwei; Vong, Chi-Man; Bu, Shuhui; Chen, Chun Long Philip

    2016-06-30

    Discriminative features of 3-D meshes are significant to many 3-D shape analysis tasks. However, handcrafted descriptors and traditional unsupervised 3-D feature learning methods suffer from several significant weaknesses: 1) the extensive human intervention is involved; 2) the local and global structure information of 3-D meshes cannot be preserved, which is in fact an important source of discriminability; 3) the irregular vertex topology and arbitrary resolution of 3-D meshes do not allow the direct application of the popular deep learning models; 4) the orientation is ambiguous on the mesh surface; and 5) the effect of rigid and nonrigid transformations on 3-D meshes cannot be eliminated. As a remedy, we propose a deep learning model with a novel irregular model structure, called mesh convolutional restricted Boltzmann machines (MCRBMs). MCRBM aims to simultaneously learn structure-preserving local and global features from a novel raw representation, local function energy distribution. In addition, multiple MCRBMs can be stacked into a deeper model, called mesh convolutional deep belief networks (MCDBNs). MCDBN employs a novel local structure preserving convolution (LSPC) strategy to convolve the geometry and the local structure learned by the lower MCRBM to the upper MCRBM. LSPC facilitates resolving the challenging issue of the orientation ambiguity on the mesh surface in MCDBN. Experiments using the proposed MCRBM and MCDBN were conducted on three common aspects: global shape retrieval, partial shape retrieval, and shape correspondence. Results show that the features learned by the proposed methods outperform the other state-of-the-art 3-D shape features.

  3. The Learner Characteristics, Features of Desktop 3D Virtual Reality Environments, and College Chemistry Instruction: A Structural Equation Modeling Analysis

    ERIC Educational Resources Information Center

    Merchant, Zahira; Goetz, Ernest T.; Keeney-Kennicutt, Wendy; Kwok, Oi-man; Cifuentes, Lauren; Davis, Trina J.

    2012-01-01

    We examined a model of the impact of a 3D desktop virtual reality environment on the learner characteristics (i.e. perceptual and psychological variables) that can enhance chemistry-related learning achievements in an introductory college chemistry class. The relationships between the 3D virtual reality features and the chemistry learning test as…

  4. A Retrieval of Tropical Latent Heating Using the 3D Structure of Precipitation Features

    SciTech Connect

    Ahmed, Fiaz; Schumacher, Courtney; Feng, Zhe; Hagos, Samson

    2016-09-01

    Traditionally, radar-based latent heating retrievals use rainfall to estimate the total column-integrated latent heating and then distribute that heating in the vertical using a model-based look-up table (LUT). In this study, we develop a new method that uses size characteristics of radar-observed precipitating echo (i.e., area and mean echo-top height) to estimate the vertical structure of latent heating. This technique (named the Convective-Stratiform Area [CSA] algorithm) builds on the fact that the shape and magnitude of latent heating profiles are dependent on the organization of convective systems and aims to avoid some of the pitfalls involved in retrieving accurate rainfall amounts and microphysical information from radars and models. The CSA LUTs are based on a high-resolution Weather Research and Forecasting model (WRF) simulation whose domain spans much of the near-equatorial Indian Ocean. When applied to S-PolKa radar observations collected during the DYNAMO/CINDY2011/AMIE field campaign, the CSA retrieval compares well to heating profiles from a sounding-based budget analysis and improves upon a simple rain-based latent heating retrieval. The CSA LUTs also highlight the fact that convective latent heating increases in magnitude and height as cluster area and echo-top heights grow, with a notable congestus signature of cooling at mid levels. Stratiform latent heating is less dependent on echo-top height, but is strongly linked to area. Unrealistic latent heating profiles in the stratiform LUT, viz., a low-level heating spike, an elevated melting layer, and net column cooling were identified and corrected for. These issues highlight the need for improvement in model parameterizations, particularly in linking microphysical phase changes to larger mesoscale processes.

  5. Automatic segmentation of solitary pulmonary nodules based on local intensity structure analysis and 3D neighborhood features in 3D chest CT images

    NASA Astrophysics Data System (ADS)

    Chen, Bin; Kitasaka, Takayuki; Honma, Hirotoshi; Takabatake, Hirotsugu; Mori, Masaki; Natori, Hiroshi; Mori, Kensaku

    2012-03-01

    This paper presents a solitary pulmonary nodule (SPN) segmentation method based on local intensity structure analysis and neighborhood feature analysis in chest CT images. Automated segmentation of SPNs is desirable for a chest computer-aided detection/diagnosis (CAS) system since a SPN may indicate early stage of lung cancer. Due to the similar intensities of SPNs and other chest structures such as blood vessels, many false positives (FPs) are generated by nodule detection methods. To reduce such FPs, we introduce two features that analyze the relation between each segmented nodule candidate and it neighborhood region. The proposed method utilizes a blob-like structure enhancement (BSE) filter based on Hessian analysis to augment the blob-like structures as initial nodule candidates. Then a fine segmentation is performed to segment much more accurate region of each nodule candidate. FP reduction is mainly addressed by investigating two neighborhood features based on volume ratio and eigenvector of Hessian that are calculates from the neighborhood region of each nodule candidate. We evaluated the proposed method by using 40 chest CT images, include 20 standard-dose CT images that we randomly chosen from a local database and 20 low-dose CT images that were randomly chosen from a public database: LIDC. The experimental results revealed that the average TP rate of proposed method was 93.6% with 12.3 FPs/case.

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

    PubMed

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

    2011-12-01

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

  7. 3D-graphite structure

    SciTech Connect

    Belenkov, E. A. Ali-Pasha, V. A.

    2011-01-15

    The structure of clusters of some new carbon 3D-graphite phases have been calculated using the molecular-mechanics methods. It is established that 3D-graphite polytypes {alpha}{sub 1,1}, {alpha}{sub 1,3}, {alpha}{sub 1,5}, {alpha}{sub 2,1}, {alpha}{sub 2,3}, {alpha}{sub 3,1}, {beta}{sub 1,2}, {beta}{sub 1,4}, {beta}{sub 1,6}, {beta}{sub 2,1}, and {beta}{sub 3,2} consist of sp{sup 2}-hybridized atoms, have hexagonal unit cells, and differ in regards to the structure of layers and order of their alternation. A possible way to experimentally synthesize new carbon phases is proposed: the polymerization and carbonization of hydrocarbon molecules.

  8. 3D structured illumination microscopy

    NASA Astrophysics Data System (ADS)

    Dougherty, William M.; Goodwin, Paul C.

    2011-03-01

    Three-dimensional structured illumination microscopy achieves double the lateral and axial resolution of wide-field microscopy, using conventional fluorescent dyes, proteins and sample preparation techniques. A three-dimensional interference-fringe pattern excites the fluorescence, filling in the "missing cone" of the wide field optical transfer function, thereby enabling axial (z) discrimination. The pattern acts as a spatial carrier frequency that mixes with the higher spatial frequency components of the image, which usually succumb to the diffraction limit. The fluorescence image encodes the high frequency content as a down-mixed, moiré-like pattern. A series of images is required, wherein the 3D pattern is shifted and rotated, providing down-mixed data for a system of linear equations. Super-resolution is obtained by solving these equations. The speed with which the image series can be obtained can be a problem for the microscopy of living cells. Challenges include pattern-switching speeds, optical efficiency, wavefront quality and fringe contrast, fringe pitch optimization, and polarization issues. We will review some recent developments in 3D-SIM hardware with the goal of super-resolved z-stacks of motile cells.

  9. Automated Recognition of 3D Features in GPIR Images

    NASA Technical Reports Server (NTRS)

    Park, Han; Stough, Timothy; Fijany, Amir

    2007-01-01

    A method of automated recognition of three-dimensional (3D) features in images generated by ground-penetrating imaging radar (GPIR) is undergoing development. GPIR 3D images can be analyzed to detect and identify such subsurface features as pipes and other utility conduits. Until now, much of the analysis of GPIR images has been performed manually by expert operators who must visually identify and track each feature. The present method is intended to satisfy a need for more efficient and accurate analysis by means of algorithms that can automatically identify and track subsurface features, with minimal supervision by human operators. In this method, data from multiple sources (for example, data on different features extracted by different algorithms) are fused together for identifying subsurface objects. The algorithms of this method can be classified in several different ways. In one classification, the algorithms fall into three classes: (1) image-processing algorithms, (2) feature- extraction algorithms, and (3) a multiaxis data-fusion/pattern-recognition algorithm that includes a combination of machine-learning, pattern-recognition, and object-linking algorithms. The image-processing class includes preprocessing algorithms for reducing noise and enhancing target features for pattern recognition. The feature-extraction algorithms operate on preprocessed data to extract such specific features in images as two-dimensional (2D) slices of a pipe. Then the multiaxis data-fusion/ pattern-recognition algorithm identifies, classifies, and reconstructs 3D objects from the extracted features. In this process, multiple 2D features extracted by use of different algorithms and representing views along different directions are used to identify and reconstruct 3D objects. In object linking, which is an essential part of this process, features identified in successive 2D slices and located within a threshold radius of identical features in adjacent slices are linked in a

  10. 3D Structured Grid Adaptation

    NASA Technical Reports Server (NTRS)

    Banks, D. W.; Hafez, M. M.

    1996-01-01

    Grid adaptation for structured meshes is the art of using information from an existing, but poorly resolved, solution to automatically redistribute the grid points in such a way as to improve the resolution in regions of high error, and thus the quality of the solution. This involves: (1) generate a grid vis some standard algorithm, (2) calculate a solution on this grid, (3) adapt the grid to this solution, (4) recalculate the solution on this adapted grid, and (5) repeat steps 3 and 4 to satisfaction. Steps 3 and 4 can be repeated until some 'optimal' grid is converged to but typically this is not worth the effort and just two or three repeat calculations are necessary. They also may be repeated every 5-10 time steps for unsteady calculations.

  11. Standard Features and Their Impact on 3D Engineering Graphics

    ERIC Educational Resources Information Center

    Waldenmeyer, K. M.; Hartman, N. W.

    2009-01-01

    The prevalence of feature-based 3D modeling in industry has necessitated the accumulation and maintenance of standard feature libraries. Currently, firms who use standard features to design parts are storing and utilizing these libraries through their existing product data management (PDM) systems. Standard features have enabled companies to…

  12. Extracting Feature Points of the Human Body Using the Model of a 3D Human Body

    NASA Astrophysics Data System (ADS)

    Shin, Jeongeun; Ozawa, Shinji

    The purpose of this research is to recognize 3D shape features of a human body automatically using a 3D laser-scanning machine. In order to recognize the 3D shape features, we selected the 23 feature points of a body and modeled its 3D features. The set of 23 feature points consists of the motion axis of a joint, the main point for the bone structure of a human body. For extracting feature points of object model, we made 2.5D templates neighbor for each feature points were extracted according to the feature points of the standard model of human body. And the feature points were extracted by the template matching. The extracted feature points can be applied as body measurement, the 3D virtual fitting system for apparel etc.

  13. Self assembled structures for 3D integration

    NASA Astrophysics Data System (ADS)

    Rao, Madhav

    Three dimensional (3D) micro-scale structures attached to a silicon substrate have various applications in microelectronics. However, formation of 3D structures using conventional micro-fabrication techniques are not efficient and require precise control of processing parameters. Self assembly is a method for creating 3D structures that takes advantage of surface area minimization phenomena. Solder based self assembly (SBSA), the subject of this dissertation, uses solder as a facilitator in the formation of 3D structures from 2D patterns. Etching a sacrificial layer underneath a portion of the 2D pattern allows the solder reflow step to pull those areas out of the substrate plane resulting in a folded 3D structure. Initial studies using the SBSA method demonstrated low yields in the formation of five different polyhedra. The failures in folding were primarily attributed to nonuniform solder deposition on the underlying metal pads. The dip soldering method was analyzed and subsequently refined. A modified dip soldering process provided improved yield among the polyhedra. Solder bridging referred as joining of solder deposited on different metal patterns in an entity influenced the folding mechanism. In general, design parameters such as small gap-spacings and thick metal pads were found to favor solder bridging for all patterns studied. Two types of soldering: face and edge soldering were analyzed. Face soldering refers to the application of solder on the entire metal face. Edge soldering indicates application of solder only on the edges of the metal face. Mechanical grinding showed that face soldered SBSA structures were void free and robust in nature. In addition, the face soldered 3D structures provide a consistent heat resistant solder standoff height that serve as attachments in the integration of dissimilar electronic technologies. Face soldered 3D structures were developed on the underlying conducting channel to determine the thermo-electric reliability of

  14. 3-D electrical resistivity structure based on geomagnetic transfer functions exploring the features of arc magmatism beneath Kyushu, Southwest Japan Arc

    NASA Astrophysics Data System (ADS)

    Hata, Maki; Uyeshima, Makoto; Handa, Shun; Shimoizumi, Masashi; Tanaka, Yoshikazu; Hashimoto, Takeshi; Kagiyama, Tsuneomi; Utada, Hisashi; Munekane, Hiroshi; Ichiki, Masahiro; Fuji-ta, Kiyoshi

    2017-01-01

    Our 3-D electrical resistivity model clearly detects particular subsurface features for magmatism associated with subduction of the Philippine Sea Plate (PSP) in three regions: a southern and a northern volcanic region, and a nonvolcanic region on the island of Kyushu. We apply 3-D inversion analyses for geomagnetic transfer function data of a short-period band, in combination with results of a previous 3-D model that was determined by using Network-Magnetotelluric response function data of a longer-period band as an initial model in the present inversion to improve resolution at shallow depths; specifically, a two-stage inversion is used instead of a joint inversion. In contrast to the previous model, the presented model clearly reveals a conductive block on the back-arc side of Kirishima volcano at shallow depths of 50 km; the block is associated with hydrothermal fluids and hydrothermal alteration zones related to the formation of epithermal gold deposits. A second feature revealed by the model is another conductive block regarded as upwelling fluids, extending from the upper surface of the PSP in the mantle under Kirishima volcano in the southern volcanic region. Third, a resistive crustal layer, which confines the conductive block in the mantle, is distributed beneath the nonvolcanic region. Fourth, our model reveals a significant resistive block, which extends below the continental Moho at the fore-arc side of the volcanic front and extends into the nonvolcanic region in central Kyushu.

  15. MSV3d: database of human MisSense Variants mapped to 3D protein structure.

    PubMed

    Luu, Tien-Dao; Rusu, Alin-Mihai; Walter, Vincent; Ripp, Raymond; Moulinier, Luc; Muller, Jean; Toursel, Thierry; Thompson, Julie D; Poch, Olivier; Nguyen, Hoan

    2012-01-01

    The elucidation of the complex relationships linking genotypic and phenotypic variations to protein structure is a major challenge in the post-genomic era. We present MSV3d (Database of human MisSense Variants mapped to 3D protein structure), a new database that contains detailed annotation of missense variants of all human proteins (20 199 proteins). The multi-level characterization includes details of the physico-chemical changes induced by amino acid modification, as well as information related to the conservation of the mutated residue and its position relative to functional features in the available or predicted 3D model. Major releases of the database are automatically generated and updated regularly in line with the dbSNP (database of Single Nucleotide Polymorphism) and SwissVar releases, by exploiting the extensive Décrypthon computational grid resources. The database (http://decrypthon.igbmc.fr/msv3d) is easily accessible through a simple web interface coupled to a powerful query engine and a standard web service. The content is completely or partially downloadable in XML or flat file formats. Database URL: http://decrypthon.igbmc.fr/msv3d.

  16. Digital holography and 3D imaging: introduction to feature issue.

    PubMed

    Kim, Myung K; Hayasaki, Yoshio; Picart, Pascal; Rosen, Joseph

    2013-01-01

    This feature issue of Applied Optics on Digital Holography and 3D Imaging is the sixth of an approximately annual series. Forty-seven papers are presented, covering a wide range of topics in phase-shifting methods, low coherence methods, particle analysis, biomedical imaging, computer-generated holograms, integral imaging, and many others.

  17. Extraction of features from 3D laser scanner cloud data

    NASA Astrophysics Data System (ADS)

    Chan, Vincent H.; Bradley, Colin H.; Vickers, Geoffrey W.

    1997-12-01

    One of the road blocks on the path of automated reverse engineering has been the extraction of useful data from the copious range data generated from 3-D laser scanning systems. A method to extract the relevant features of a scanned object is presented. A 3-D laser scanner is automatically directed to obtain discrete laser cloud data on each separate patch that constitutes the object's surface. With each set of cloud data treated as a separate entity, primitives are fitted to the data resulting in a geometric and topologic database. Using a feed-forewarn neural network, the data is analyzed for geometric combinations that make up machine features such as through holes and slots. These features are required for the reconstruction of the solid model by a machinist or feature based CAM algorithms, thus completing the reverse engineering cycle.

  18. Automatic scan registration using 3D linear and planar features

    NASA Astrophysics Data System (ADS)

    Yao, Jian; Ruggeri, Mauro R.; Taddei, Pierluigi; Sequeira, Vítor

    2010-09-01

    We present a common framework for accurate and automatic registration of two geometrically complex 3D range scans by using linear or planar features. The linear features of a range scan are extracted with an efficient split-and-merge line-fitting algorithm, which refines 2D edges extracted from the associated reflectance image considering the corresponding 3D depth information. The planar features are extracted employing a robust planar segmentation method, which partitions a range image into a set of planar patches. We propose an efficient probability-based RANSAC algorithm to automatically register two overlapping range scans. Our algorithm searches for matching pairs of linear (planar) features in the two range scans leading to good alignments. Line orientation (plane normal) angles and line (plane) distances formed by pairs of linear (planar) features are invariant with respect to the rigid transformation and are utilized to find candidate matches. To efficiently seek for candidate pairs and groups of matched features we build a fast search codebook. Given two sets of matched features, the rigid transformation between two scans is computed by using iterative linear optimization algorithms. The efficiency and accuracy of our registration algorithm were evaluated on several challenging range data sets.

  19. Prostate Mechanical Imaging: 3-D Image Composition and Feature Calculations

    PubMed Central

    Egorov, Vladimir; Ayrapetyan, Suren; Sarvazyan, Armen P.

    2008-01-01

    We have developed a method and a device entitled prostate mechanical imager (PMI) for the real-time imaging of prostate using a transrectal probe equipped with a pressure sensor array and position tracking sensor. PMI operation is based on measurement of the stress pattern on the rectal wall when the probe is pressed against the prostate. Temporal and spatial changes in the stress pattern provide information on the elastic structure of the gland and allow two-dimensional (2-D) and three-dimensional (3-D) reconstruction of prostate anatomy and assessment of prostate mechanical properties. The data acquired allow the calculation of prostate features such as size, shape, nodularity, consistency/hardness, and mobility. The PMI prototype has been validated in laboratory experiments on prostate phantoms and in a clinical study. The results obtained on model systems and in vivo images from patients prove that PMI has potential to become a diagnostic tool that could largely supplant DRE through its higher sensitivity, quantitative record storage, ease-of-use and inherent low cost. PMID:17024836

  20. 3D Structures of Responsive Nanocompartmentalized Microgels.

    PubMed

    Gelissen, Arjan P H; Oppermann, Alex; Caumanns, Tobias; Hebbeker, Pascal; Turnhoff, Sarah K; Tiwari, Rahul; Eisold, Sabine; Simon, Ulrich; Lu, Yan; Mayer, Joachim; Richtering, Walter; Walther, Andreas; Wöll, Dominik

    2016-11-09

    Compartmentalization in soft matter is important for segregating and coordinating chemical reactions, sequestering (re)active components, and integrating multifunctionality. Advances depend crucially on quantitative 3D visualization in situ with high spatiotemporal resolution. Here, we show the direct visualization of different compartments within adaptive microgels using a combination of in situ electron and super-resolved fluorescence microscopy. We unravel new levels of structural details and address the challenge of reconstructing 3D information from 2D projections for nonuniform soft matter as opposed to monodisperse proteins. Moreover, we visualize the thermally induced shrinkage of responsive core-shell microgels live in water. This strategy opens doors for systematic in situ studies of soft matter systems and their application as smart materials.

  1. Identification of the Structural Features of Guanine Derivatives as MGMT Inhibitors Using 3D-QSAR Modeling Combined with Molecular Docking.

    PubMed

    Sun, Guohui; Fan, Tengjiao; Zhang, Na; Ren, Ting; Zhao, Lijiao; Zhong, Rugang

    2016-06-23

    DNA repair enzyme O⁶-methylguanine-DNA methyltransferase (MGMT), which plays an important role in inducing drug resistance against alkylating agents that modify the O⁶ position of guanine in DNA, is an attractive target for anti-tumor chemotherapy. A series of MGMT inhibitors have been synthesized over the past decades to improve the chemotherapeutic effects of O⁶-alkylating agents. In the present study, we performed a three-dimensional quantitative structure activity relationship (3D-QSAR) study on 97 guanine derivatives as MGMT inhibitors using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods. Three different alignment methods (ligand-based, DFT optimization-based and docking-based alignment) were employed to develop reliable 3D-QSAR models. Statistical parameters derived from the models using the above three alignment methods showed that the ligand-based CoMFA (Qcv² = 0.672 and Rncv² = 0.997) and CoMSIA (Qcv² = 0.703 and Rncv² = 0.946) models were better than the other two alignment methods-based CoMFA and CoMSIA models. The two ligand-based models were further confirmed by an external test-set validation and a Y-randomization examination. The ligand-based CoMFA model (Qext² = 0.691, Rpred² = 0.738 and slope k = 0.91) was observed with acceptable external test-set validation values rather than the CoMSIA model (Qext² = 0.307, Rpred² = 0.4 and slope k = 0.719). Docking studies were carried out to predict the binding modes of the inhibitors with MGMT. The results indicated that the obtained binding interactions were consistent with the 3D contour maps. Overall, the combined results of the 3D-QSAR and the docking obtained in this study provide an insight into the understanding of the interactions between guanine derivatives and MGMT protein, which will assist in designing novel MGMT inhibitors with desired activity.

  2. Inferential modeling of 3D chromatin structure.

    PubMed

    Wang, Siyu; Xu, Jinbo; Zeng, Jianyang

    2015-04-30

    For eukaryotic cells, the biological processes involving regulatory DNA elements play an important role in cell cycle. Understanding 3D spatial arrangements of chromosomes and revealing long-range chromatin interactions are critical to decipher these biological processes. In recent years, chromosome conformation capture (3C) related techniques have been developed to measure the interaction frequencies between long-range genome loci, which have provided a great opportunity to decode the 3D organization of the genome. In this paper, we develop a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data. By modeling each chromosome as a polymer chain, we define the conformational energy based on our current knowledge on polymer physics and use it as prior information in the Bayesian framework. We also propose an expectation-maximization (EM) based algorithm to estimate the unknown parameters of the Bayesian model and infer an ensemble of chromatin structures based on interaction frequency data. We have validated our Bayesian inference approach through cross-validation and verified the computed chromatin conformations using the geometric constraints derived from fluorescence in situ hybridization (FISH) experiments. We have further confirmed the inferred chromatin structures using the known genetic interactions derived from other studies in the literature. Our test results have indicated that our Bayesian framework can compute an accurate ensemble of 3D chromatin conformations that best interpret the distance constraints derived from 3C-based data and also agree with other sources of geometric constraints derived from experimental evidence in the previous studies. The source code of our approach can be found in https://github.com/wangsy11/InfMod3DGen.

  3. Feature detection on 3D images of dental imprints

    NASA Astrophysics Data System (ADS)

    Mokhtari, Marielle; Laurendeau, Denis

    1994-09-01

    A computer vision approach for the extraction of feature points on 3D images of dental imprints is presented. The position of feature points are needed for the measurement of a set of parameters for automatic diagnosis of malocclusion problems in orthodontics. The system for the acquisition of the 3D profile of the imprint, the procedure for the detection of the interstices between teeth, and the approach for the identification of the type of tooth are described, as well as the algorithm for the reconstruction of the surface of each type of tooth. A new approach for the detection of feature points, called the watershed algorithm, is described in detail. The algorithm is a two-stage procedure which tracks the position of local minima at four different scales and produces a final map of the position of the minima. Experimental results of the application of the watershed algorithm on actual 3D images of dental imprints are presented for molars, premolars and canines. The segmentation approach for the analysis of the shape of incisors is also described in detail.

  4. Self-assembled 3D heterometallic Cu(II)/Fe(II) coordination polymers with octahedral net skeletons: structural features, molecular magnetism, thermal and oxidation catalytic properties.

    PubMed

    Karabach, Yauhen Y; Guedes da Silva, M Fátima C; Kopylovich, Maximilian N; Gil-Hernández, Beatriz; Sanchiz, Joaquin; Kirillov, Alexander M; Pombeiro, Armando J L

    2010-12-06

    The new three-dimensional (3D) heterometallic Cu(II)/Fe(II) coordination polymers [Cu(6)(H(2)tea)(6)Fe(CN)(6)](n)(NO(3))(2n)·6nH(2)O (1) and [Cu(6)(Hmdea)(6)Fe(CN)(6)](n)(NO(3))(2n)·7nH(2)O (2) have been easily generated by aqueous-medium self-assembly reactions of copper(II) nitrate with triethanolamine or N-methyldiethanolamine (H(3)tea or H(2)mdea, respectively), in the presence of potassium ferricyanide and sodium hydroxide. They have been isolated as air-stable crystalline solids and fully characterized including by single-crystal X-ray diffraction analyses. The latter reveal the formation of 3D metal-organic frameworks that are constructed from the [Cu(2)(μ-H(2)tea)(2)](2+) or [Cu(2)(μ-Hmdea)(2)](2+) nodes and the octahedral [Fe(CN)(6)](4-) linkers, featuring regular (1) or distorted (2) octahedral net skeletons. Upon dehydration, both compounds show reversible escape and binding processes toward water or methanol molecules. Magnetic susceptibility measurements of 1 and 2 reveal strong antiferromagnetic [J = -199(1) cm(-1)] or strong ferromagnetic [J = +153(1) cm(-1)] couplings between the copper(II) ions through the μ-O-alkoxo atoms in 1 or 2, respectively. The differences in magnetic behavior are explained in terms of the dependence of the magnetic coupling constant on the Cu-O-Cu bridging angle. Compounds 1 and 2 also act as efficient catalyst precursors for the mild oxidation of cyclohexane by aqueous hydrogen peroxide to cyclohexanol and cyclohexanone (homogeneous catalytic system), leading to maximum total yields (based on cyclohexane) and turnover numbers (TONs) up to about 22% and 470, respectively.

  5. R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures

    PubMed Central

    Rahrig, Ryan R.; Petrov, Anton I.; Leontis, Neocles B.; Zirbel, Craig L.

    2013-01-01

    The R3D Align web server provides online access to ‘RNA 3D Align’ (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/. PMID:23716643

  6. Proposed traceable structural resolution protocols for 3D imaging systems

    NASA Astrophysics Data System (ADS)

    MacKinnon, David; Beraldin, J.-Angelo; Cournoyer, Luc; Carrier, Benjamin; Blais, François

    2009-08-01

    A protocol for determining structural resolution using a potentially-traceable reference material is proposed. Where possible, terminology was selected to conform to those published in ISO JCGM 200:2008 (VIM) and ASTM E 2544-08 documents. The concepts of resolvability and edge width are introduced to more completely describe the ability of an optical non-contact 3D imaging system to resolve small features. A distinction is made between 3D range cameras, that obtain spatial data from the total field of view at once, and 3D range scanners, that accumulate spatial data for the total field of view over time. The protocol is presented through the evaluation of a 3D laser line range scanner.

  7. Robust feature detection for 3D object recognition and matching

    NASA Astrophysics Data System (ADS)

    Pankanti, Sharath; Dorai, Chitra; Jain, Anil K.

    1993-06-01

    Salient surface features play a central role in tasks related to 3-D object recognition and matching. There is a large body of psychophysical evidence demonstrating the perceptual significance of surface features such as local minima of principal curvatures in the decomposition of objects into a hierarchy of parts. Many recognition strategies employed in machine vision also directly use features derived from surface properties for matching. Hence, it is important to develop techniques that detect surface features reliably. Our proposed scheme consists of (1) a preprocessing stage, (2) a feature detection stage, and (3) a feature integration stage. The preprocessing step selectively smoothes out noise in the depth data without degrading salient surface details and permits reliable local estimation of the surface features. The feature detection stage detects both edge-based and region-based features, of which many are derived from curvature estimates. The third stage is responsible for integrating the information provided by the individual feature detectors. This stage also completes the partial boundaries provided by the individual feature detectors, using proximity and continuity principles of Gestalt. All our algorithms use local support and, therefore, are inherently parallelizable. We demonstrate the efficacy and robustness of our approach by applying it to two diverse domains of applications: (1) segmentation of objects into volumetric primitives and (2) detection of salient contours on free-form surfaces. We have tested our algorithms on a number of real range images with varying degrees of noise and missing data due to self-occlusion. The preliminary results are very encouraging.

  8. Automated modeling of RNA 3D structure.

    PubMed

    Rother, Kristian; Rother, Magdalena; Skiba, Pawel; Bujnicki, Janusz M

    2014-01-01

    This chapter gives an overview over the current methods for automated modeling of RNA structures, with emphasis on template-based methods. The currently used approaches to RNA modeling are presented with a side view on the protein world, where many similar ideas have been used. Two main programs for automated template-based modeling are presented: ModeRNA assembling structures from fragments and MacroMoleculeBuilder performing a simulation to satisfy spatial restraints. Both approaches have in common that they require an alignment of the target sequence to a known RNA structure that is used as a modeling template. As a way to find promising template structures and to align the target and template sequences, we propose a pipeline combining the ParAlign and Infernal programs on RNA family data from Rfam. We also briefly summarize template-free methods for RNA 3D structure prediction. Typically, RNA structures generated by automated modeling methods require local or global optimization. Thus, we also discuss methods that can be used for local or global refinement of RNA structures.

  9. A novel 3D wavelet based filter for visualizing features in noisy biological data

    SciTech Connect

    Moss, W C; Haase, S; Lyle, J M; Agard, D A; Sedat, J W

    2005-01-05

    We have developed a 3D wavelet-based filter for visualizing structural features in volumetric data. The only variable parameter is a characteristic linear size of the feature of interest. The filtered output contains only those regions that are correlated with the characteristic size, thus denoising the image. We demonstrate the use of the filter by applying it to 3D data from a variety of electron microscopy samples including low contrast vitreous ice cryogenic preparations, as well as 3D optical microscopy specimens.

  10. Discovering Structural Regularity in 3D Geometry

    PubMed Central

    Pauly, Mark; Mitra, Niloy J.; Wallner, Johannes; Pottmann, Helmut; Guibas, Leonidas J.

    2010-01-01

    We introduce a computational framework for discovering regular or repeated geometric structures in 3D shapes. We describe and classify possible regular structures and present an effective algorithm for detecting such repeated geometric patterns in point- or mesh-based models. Our method assumes no prior knowledge of the geometry or spatial location of the individual elements that define the pattern. Structure discovery is made possible by a careful analysis of pairwise similarity transformations that reveals prominent lattice structures in a suitable model of transformation space. We introduce an optimization method for detecting such uniform grids specifically designed to deal with outliers and missing elements. This yields a robust algorithm that successfully discovers complex regular structures amidst clutter, noise, and missing geometry. The accuracy of the extracted generating transformations is further improved using a novel simultaneous registration method in the spatial domain. We demonstrate the effectiveness of our algorithm on a variety of examples and show applications to compression, model repair, and geometry synthesis. PMID:21170292

  11. Structured Light-Based 3D Reconstruction System for Plants.

    PubMed

    Nguyen, Thuy Tuong; Slaughter, David C; Max, Nelson; Maloof, Julin N; Sinha, Neelima

    2015-07-29

    Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants. This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance.

  12. Structured Light-Based 3D Reconstruction System for Plants

    PubMed Central

    Nguyen, Thuy Tuong; Slaughter, David C.; Max, Nelson; Maloof, Julin N.; Sinha, Neelima

    2015-01-01

    Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants.This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance. PMID:26230701

  13. 3D Printing: 3D Printing of Highly Stretchable and Tough Hydrogels into Complex, Cellularized Structures.

    PubMed

    Hong, Sungmin; Sycks, Dalton; Chan, Hon Fai; Lin, Shaoting; Lopez, Gabriel P; Guilak, Farshid; Leong, Kam W; Zhao, Xuanhe

    2015-07-15

    X. Zhao and co-workers develop on page 4035 a new biocompatible hydrogel system that is extremely tough and stretchable and can be 3D printed into complex structures, such as the multilayer mesh shown. Cells encapsulated in the tough and printable hydrogel maintain high viability. 3D-printed structures of the tough hydrogel can sustain high mechanical loads and deformations.

  14. 3D Structure of Tillage Soils

    NASA Astrophysics Data System (ADS)

    González-Torre, Iván; Losada, Juan Carlos; Falconer, Ruth; Hapca, Simona; Tarquis, Ana M.

    2015-04-01

    Soil structure may be defined as the spatial arrangement of soil particles, aggregates and pores. The geometry of each one of these elements, as well as their spatial arrangement, has a great influence on the transport of fluids and solutes through the soil. Fractal/Multifractal methods have been increasingly applied to quantify soil structure thanks to the advances in computer technology (Tarquis et al., 2003). There is no doubt that computed tomography (CT) has provided an alternative for observing intact soil structure. These CT techniques reduce the physical impact to sampling, providing three-dimensional (3D) information and allowing rapid scanning to study sample dynamics in near real-time (Houston et al., 2013a). However, several authors have dedicated attention to the appropriate pore-solid CT threshold (Elliot and Heck, 2007; Houston et al., 2013b) and the better method to estimate the multifractal parameters (Grau et al., 2006; Tarquis et al., 2009). The aim of the present study is to evaluate the effect of the algorithm applied in the multifractal method (box counting and box gliding) and the cube size on the calculation of generalized fractal dimensions (Dq) in grey images without applying any threshold. To this end, soil samples were extracted from different areas plowed with three tools (moldboard, chissel and plow). Soil samples for each of the tillage treatment were packed into polypropylene cylinders of 8 cm diameter and 10 cm high. These were imaged using an mSIMCT at 155keV and 25 mA. An aluminium filter (0.25 mm) was applied to reduce beam hardening and later several corrections where applied during reconstruction. References Elliot, T.R. and Heck, R.J. 2007. A comparison of 2D and 3D thresholding of CT imagery. Can. J. Soil Sci., 87(4), 405-412. Grau, J, Médez, V.; Tarquis, A.M., Saa, A. and Díaz, M.C.. 2006. Comparison of gliding box and box-counting methods in soil image analysis. Geoderma, 134, 349-359. González-Torres, Iván. Theory and

  15. 3D printing of nano- and micro-structures

    NASA Astrophysics Data System (ADS)

    Ramasamy, Mouli; Varadan, Vijay K.

    2016-04-01

    Additive manufacturing or 3D printing techniques are being vigorously investigated as a replacement to the traditional and conventional methods in fabrication to bring forth cost and time effective approaches. Introduction of 3D printing has led to printing micro and nanoscale structures including tissues and organelles, bioelectric sensors and devices, artificial bones and transplants, microfluidic devices, batteries and various other biomaterials. Various microfabrication processes have been developed to fabricate micro components and assemblies at lab scale. 3D Fabrication processes that can accommodate the functional and geometrical requirements to realize complicated structures are becoming feasible through advances in additive manufacturing. This advancement could lead to simpler development mechanisms of novel components and devices exhibiting complex features. For instance, development of microstructure electrodes that can penetrate the epidermis of the skin to collect the bio potential signal may prove very effective than the electrodes that measure signal from the skin's surface. The micro and nanostructures will have to possess extraordinary material and mechanical properties for its dexterity in the applications. A substantial amount of research being pursued on stretchable and flexible devices based on PDMA, textiles, and organic electronics. Despite the numerous advantages these substrates and techniques could solely offer, 3D printing enables a multi-dimensional approach towards finer and complex applications. This review emphasizes the use of 3D printing to fabricate micro and nanostructures for that can be applied for human healthcare.

  16. Fuzzy zoning for feature matching technique in 3D reconstruction of nasal endoscopic images.

    PubMed

    Rattanalappaiboon, Surapong; Bhongmakapat, Thongchai; Ritthipravat, Panrasee

    2015-12-01

    3D reconstruction from nasal endoscopic images greatly supports an otolaryngologist in examining nasal passages, mucosa, polyps, sinuses, and nasopharyx. In general, structure from motion is a popular technique. It consists of four main steps; (1) camera calibration, (2) feature extraction, (3) feature matching, and (4) 3D reconstruction. Scale Invariant Feature Transform (SIFT) algorithm is normally used for both feature extraction and feature matching. However, SIFT algorithm relatively consumes computational time particularly in the feature matching process because each feature in an image of interest is compared with all features in the subsequent image in order to find the best matched pair. A fuzzy zoning approach is developed for confining feature matching area. Matching between two corresponding features from different images can be efficiently performed. With this approach, it can greatly reduce the matching time. The proposed technique is tested with endoscopic images created from phantoms and compared with the original SIFT technique in terms of the matching time and average errors of the reconstructed models. Finally, original SIFT and the proposed fuzzy-based technique are applied to 3D model reconstruction of real nasal cavity based on images taken from a rigid nasal endoscope. The results showed that the fuzzy-based approach was significantly faster than traditional SIFT technique and provided similar quality of the 3D models. It could be used for creating a nasal cavity taken by a rigid nasal endoscope.

  17. Microfabricating 3D Structures by Laser Origami

    DTIC Science & Technology

    2011-11-09

    technique generates 3D microstructures by controlled out-of- plane folding of 2D patterns through a variety of laser-based digital fabrication...processes. Digital microfabrication techniques such as laser direct-write (LDW) offer a viable alternative for generating 3D self-folding designs. These...folding at the microscale where manual or mechanized actuation of the smaller struc- tures is not practical. LDW techniques allow micromachining and

  18. 3-D Attenuation Structure around the SAFOD site, Parkfield, California

    NASA Astrophysics Data System (ADS)

    Harrington, N. L.; Thurber, C. H.; Zhang, H.; Roecker, S.

    2006-12-01

    We are developing models of the 3-D attenuation structure, both Qp and Qs, for a region about 15 km square centered on SAFOD. We are analyzing local earthquake data collected in 2001 and 2002 from the UW/RPI PASO array, the UC-Berkeley HRSN, and USGS seismic network stations around Parkfield. We determine the P- or S-wave t* values for an individual local earthquake for each of the observing stations by fitting observed spectra using a joint inversion for a common corner frequency, low-frequency amplitude, and t*. Within our initial data set, we examine 575 events recorded at up to 111 stations and obtain over 19000 P- wave t* values. We use these t* values in simul2000 and tomoDD to perform the inversion to obtain a 3-D, frequency-independent Qp model of the attenuation structure, using an existing 3-D Vp model and associated event locations. We will use this same procedure to obtain the Qs structure. In our preliminary Qp structure results, we observe a high Qp feature (about 250) at 0-8 km depth on the southwest side of the fault. We associate this feature with the high density, high velocity Salinian basement rocks. We also see a moderate Qp feature (about 150) in the fault zone that encompasses the hypocenters of our events. On the northeast side of the fault, we observe Qp values generally increasing with depth, from 125 at the surface to 200 at 8 km. We will present our final Qp and Qs models, identify major features within the two, and discuss how these features relate to the findings of other geophysical studies in the area (seismic velocity, electrical resistivity, anisotropy). We will discuss how these features relate to the nature of the crust in that area, including the local geology, presence of fluids, fracturing, etc.

  19. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server

    PubMed Central

    Cannone, Jamie J.; Sweeney, Blake A.; Petrov, Anton I.; Gutell, Robin R.; Zirbel, Craig L.; Leontis, Neocles

    2015-01-01

    The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. PMID:26048960

  20. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.

    PubMed

    Cannone, Jamie J; Sweeney, Blake A; Petrov, Anton I; Gutell, Robin R; Zirbel, Craig L; Leontis, Neocles

    2015-07-01

    The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa.

  1. 3D-GNOME: an integrated web service for structural modeling of the 3D genome.

    PubMed

    Szalaj, Przemyslaw; Michalski, Paul J; Wróblewski, Przemysław; Tang, Zhonghui; Kadlof, Michal; Mazzocco, Giovanni; Ruan, Yijun; Plewczynski, Dariusz

    2016-07-08

    Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/.

  2. 3D-GNOME: an integrated web service for structural modeling of the 3D genome

    PubMed Central

    Szalaj, Przemyslaw; Michalski, Paul J.; Wróblewski, Przemysław; Tang, Zhonghui; Kadlof, Michal; Mazzocco, Giovanni; Ruan, Yijun; Plewczynski, Dariusz

    2016-01-01

    Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/. PMID:27185892

  3. Three-dimensional (3D) printing of mouse primary hepatocytes to generate 3D hepatic structure

    PubMed Central

    Kim, Yohan; Kang, Kyojin; Jeong, Jaemin; Paik, Seung Sam; Kim, Ji Sook; Park, Su A; Kim, Wan Doo; Park, Jisun

    2017-01-01

    Purpose The major problem in producing artificial livers is that primary hepatocytes cannot be cultured for many days. Recently, 3-dimensional (3D) printing technology draws attention and this technology regarded as a useful tool for current cell biology. By using the 3D bio-printing, these problems can be resolved. Methods To generate 3D bio-printed structures (25 mm × 25 mm), cells-alginate constructs were fabricated by 3D bio-printing system. Mouse primary hepatocytes were isolated from the livers of 6–8 weeks old mice by a 2-step collagenase method. Samples of 4 × 107 hepatocytes with 80%–90% viability were printed with 3% alginate solution, and cultured with well-defined culture medium for primary hepatocytes. To confirm functional ability of hepatocytes cultured on 3D alginate scaffold, we conducted quantitative real-time polymerase chain reaction and immunofluorescence with hepatic marker genes. Results Isolated primary hepatocytes were printed with alginate. The 3D printed hepatocytes remained alive for 14 days. Gene expression levels of Albumin, HNF-4α and Foxa3 were gradually increased in the 3D structures. Immunofluorescence analysis showed that the primary hepatocytes produced hepatic-specific proteins over the same period of time. Conclusion Our research indicates that 3D bio-printing technique can be used for long-term culture of primary hepatocytes. It can therefore be used for drug screening and as a potential method of producing artificial livers. PMID:28203553

  4. RNA Structure: Advances and Assessment of 3D Structure Prediction.

    PubMed

    Miao, Zhichao; Westhof, Eric

    2017-03-30

    Biological functions of RNA molecules are dependent upon sustained specific three-dimensional (3D) structures of RNA, with or without the help of proteins. Understanding of RNA structure is frequently based on 2D structures, which describe only the Watson-Crick (WC) base pairs. Here, we hierarchically review the structural elements of RNA and how they contribute to RNA 3D structure. We focus our analysis on the non-WC base pairs and on RNA modules. Several computer programs have now been designed to predict RNA modules. We describe the RNA-Puzzles initiative, which is a community-wide, blind assessment of RNA 3D structure prediction programs to determine the capabilities and bottlenecks of current predictions. The assessment metrics used in RNA-Puzzles are briefly described. The detection of RNA 3D modules from sequence data and their automatic implementation belong to the current challenges in RNA 3D structure prediction. Expected final online publication date for the Annual Review of Biophysics Volume 46 is May 20, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  5. Changes in quantitative 3D shape features of the optic nerve head associated with age

    NASA Astrophysics Data System (ADS)

    Christopher, Mark; Tang, Li; Fingert, John H.; Scheetz, Todd E.; Abramoff, Michael D.

    2013-02-01

    Optic nerve head (ONH) structure is an important biological feature of the eye used by clinicians to diagnose and monitor progression of diseases such as glaucoma. ONH structure is commonly examined using stereo fundus imaging or optical coherence tomography. Stereo fundus imaging provides stereo views of the ONH that retain 3D information useful for characterizing structure. In order to quantify 3D ONH structure, we applied a stereo correspondence algorithm to a set of stereo fundus images. Using these quantitative 3D ONH structure measurements, eigen structures were derived using principal component analysis from stereo images of 565 subjects from the Ocular Hypertension Treatment Study (OHTS). To evaluate the usefulness of the eigen structures, we explored associations with the demographic variables age, gender, and race. Using regression analysis, the eigen structures were found to have significant (p < 0.05) associations with both age and race after Bonferroni correction. In addition, classifiers were constructed to predict the demographic variables based solely on the eigen structures. These classifiers achieved an area under receiver operating characteristic curve of 0.62 in predicting a binary age variable, 0.52 in predicting gender, and 0.67 in predicting race. The use of objective, quantitative features or eigen structures can reveal hidden relationships between ONH structure and demographics. The use of these features could similarly allow specific aspects of ONH structure to be isolated and associated with the diagnosis of glaucoma, disease progression and outcomes, and genetic factors.

  6. The 3D lightweight structural characteristics of the beetle forewing.

    PubMed

    Chen, Jinxiang; Tuo, Wanyong; Guo, Zhensheng; Yan, Lili

    2017-02-01

    The present paper renewedly expounds upon the characteristics of the 3D lightweight structure of beetle forewings and notes that two biomimetic structures (models) that have appeared in recent years do not comply with these characteristics based on a comparison of the structures of the biological prototypes. The first model features transverse tubules based on observations of circular holes in cross-sectional figures of the Cybister forewing. The second is a biomimetic spherical cavity model with hollow trabeculae that reportedly exhibits superior mechanical properties because its structures are most similar to the biological prototype. Finally, a false biomimetic proposition that the mechanical properties of biomimetic structures with "fiber winding" patterns are superior to those of structures constructed of pure "epoxy" is also noted. Hopefully, the present study can serve to improve the state of research on biomimetic applications of beetle forewing structures.

  7. CH5M3D: an HTML5 program for creating 3D molecular structures

    PubMed Central

    2013-01-01

    Background While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Results Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user’s computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. Conclusions A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/. PMID:24246004

  8. 2D Feature Recognition And 3d Reconstruction In Solar Euv Images

    NASA Astrophysics Data System (ADS)

    Aschwanden, Markus J.

    2005-05-01

    EUV images show the solar corona in a typical temperature range of T >rsim 1 MK, which encompasses the most common coronal structures: loops, filaments, and other magnetic structures in active regions, the quiet Sun, and coronal holes. Quantitative analysis increasingly demands automated 2D feature recognition and 3D reconstruction, in order to localize, track, and monitor the evolution of such coronal structures. We discuss numerical tools that “fingerprint” curvi-linear 1D features (e.g., loops and filaments). We discuss existing finger-printing algorithms, such as the brightness-gradient method, the oriented-connectivity method, stereoscopic methods, time-differencing, and space time feature recognition. We discuss improved 2D feature recognition and 3D reconstruction techniques that make use of additional a priori constraints, using guidance from magnetic field extrapolations, curvature radii constraints, and acceleration and velocity constraints in time-dependent image sequences. Applications of these algorithms aid the analysis of SOHO/EIT, TRACE, and STEREO/SECCHI data, such as disentangling, 3D reconstruction, and hydrodynamic modeling of coronal loops, postflare loops, filaments, prominences, and 3D reconstruction of the coronal magnetic field in general.

  9. Quantitative 3D structured illumination microscopy of nuclear structures.

    PubMed

    Kraus, Felix; Miron, Ezequiel; Demmerle, Justin; Chitiashvili, Tsotne; Budco, Alexei; Alle, Quentin; Matsuda, Atsushi; Leonhardt, Heinrich; Schermelleh, Lothar; Markaki, Yolanda

    2017-05-01

    3D structured illumination microscopy (3D-SIM) is the super-resolution technique of choice for multicolor volumetric imaging. Here we provide a validated sample preparation protocol for labeling nuclei of cultured mammalian cells, image acquisition and registration practices, and downstream image analysis of nuclear structures and epigenetic marks. Using immunostaining and replication labeling combined with image segmentation, centroid mapping and nearest-neighbor analyses in open-source environments, 3D maps of nuclear structures are analyzed in individual cells and normalized to fluorescence standards on the nanometer scale. This protocol fills an unmet need for the application of 3D-SIM to the technically challenging nuclear environment, and subsequent quantitative analysis of 3D nuclear structures and epigenetic modifications. In addition, it establishes practical guidelines and open-source solutions using ImageJ/Fiji and the TANGO plugin for high-quality and routinely comparable data generation in immunostaining experiments that apply across model systems. From sample preparation through image analysis, the protocol can be executed within one week.

  10. Computational modeling of RNA 3D structures and interactions.

    PubMed

    Dawson, Wayne K; Bujnicki, Janusz M

    2016-04-01

    RNA molecules have key functions in cellular processes beyond being carriers of protein-coding information. These functions are often dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is difficult, which has prompted the development of computational methods for structure prediction from sequence. Recent progress in 3D structure modeling of RNA and emerging approaches for predicting RNA interactions with ions, ligands and proteins have been stimulated by successes in protein 3D structure modeling.

  11. Antenatal 3-D sonographic features of uterine synechia.

    PubMed

    Sato, Miki; Kanenishi, Kenji; Ito, Megumi; Tanaka, Hirokazu; Takemoto, Mikihiko; Hata, Toshiyuki

    2013-01-01

    We present a case of uterine synechia diagnosed by conventional 2-D color Doppler, 3-D sonography, and magnetic resonance imaging at 26 weeks' gestation. 3-D sonography clearly revealed umbilical cord prolapse through an oblique transverse uterine synechia. Loops of the umbilical cord were below and the fetus was superior to the uterine synechia. The edge of the umbilical cord loops was attached to the amniotic membrane, and a small echo-free space was noted beneath the attachment. 2-D color Doppler showed arterial blood flow consistent with the maternal heart rate. Magnetic resonance imaging confirmed the oblique horizontal membrane dividing the uterus with umbilical cord prolapse, its attachment to the amniotic membrane, and a small echo-free space in the low, liquor-filled amniotic cavity. We demonstrate how 3-D sonography provided a novel visual depiction of uterine synechia, which greatly helped in prenatal diagnosis and counseling.

  12. Unit cell geometry of 3-D braided structures

    NASA Technical Reports Server (NTRS)

    Du, Guang-Wu; Ko, Frank K.

    1993-01-01

    The traditional approach used in modeling of composites reinforced by three-dimensional (3-D) braids is to assume a simple unit cell geometry of a 3-D braided structure with known fiber volume fraction and orientation. In this article, we first examine 3-D braiding methods in the light of braid structures, followed by the development of geometric models for 3-D braids using a unit cell approach. The unit cell geometry of 3-D braids is identified and the relationship of structural parameters such as yarn orientation angle and fiber volume fraction with the key processing parameters established. The limiting geometry has been computed by establishing the point at which yarns jam against each other. Using this factor makes it possible to identify the complete range of allowable geometric arrangements for 3-D braided preforms. This identified unit cell geometry can be translated to mechanical models which relate the geometrical properties of fabric preforms to the mechanical responses of composite systems.

  13. Structural analysis of tropical cyclone using INSAT-3D observations

    NASA Astrophysics Data System (ADS)

    Jaiswal, Neeru; Kishtawal, C. M.

    2016-05-01

    The continuous observations from visible and thermal infrared (TIR) channels of geostationary satellites are highly useful for obtaining the features associated with the shape and dynamics of cloud structures within the tropical cyclones (TCs). As TC develops from an unstructured cloud cluster and intensifies, the cloud structures become more axisymmetric around the centre of the TC. To better understand the structure of TC during different stages of its evolution i.e. from its cyclogenesis to maturity and dissipation, the continuous satellite observations plays a key role. The high spatial and temporal resolution observations from geostationary satellites are very useful in order to analyze the cloud organization during the cyclogenesis. The gradient of the brightness temperatures measures the level of symmetry of each structure, which characterizes the degree of cloud organization of the TC. In the present work, the structural analysis of TC during its life period using the observations from Indian geostationary satellite INSAT-3D has been discussed. The visible and TIR observations from INSAT-3D satellite were used to fix the center position of the cyclone which is an input for the cyclone track and intensity prediction models. This data is also used to estimate the intensity of cyclone in the advanced Dvorak technique (ADT), and in the estimation of radius of maximum winds (Rmax) of TC which is an essential input parameter for the prediction of storm surge associated to the cyclones. The different patterns of cloud structure during the intensification stage, eye-wall formation and dissipation have been discussed. The early identification of these features helps in predicting the rapid intensification of TC which in turn improves the intensity predictions.

  14. Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation

    PubMed Central

    Mourad, Raphaël; Cuvier, Olivier

    2016-01-01

    Recent advances in long-range Hi-C contact mapping have revealed the importance of the 3D structure of chromosomes in gene expression. A current challenge is to identify the key molecular drivers of this 3D structure. Several genomic features, such as architectural proteins and functional elements, were shown to be enriched at topological domain borders using classical enrichment tests. Here we propose multiple logistic regression to identify those genomic features that positively or negatively influence domain border establishment or maintenance. The model is flexible, and can account for statistical interactions among multiple genomic features. Using both simulated and real data, we show that our model outperforms enrichment test and non-parametric models, such as random forests, for the identification of genomic features that influence domain borders. Using Drosophila Hi-C data at a very high resolution of 1 kb, our model suggests that, among architectural proteins, BEAF-32 and CP190 are the main positive drivers of 3D domain borders. In humans, our model identifies well-known architectural proteins CTCF and cohesin, as well as ZNF143 and Polycomb group proteins as positive drivers of domain borders. The model also reveals the existence of several negative drivers that counteract the presence of domain borders including P300, RXRA, BCL11A and ELK1. PMID:27203237

  15. The 3D Structure of the Proton

    NASA Astrophysics Data System (ADS)

    Kaiser, Ralf

    2012-09-01

    When Rutherford, Geiger and Marsden discovered the atomic nucleus in 1909 in Manchester, they at the same time also laid the foundations for the most successful method to study the structure of nuclei and nucleons. They found a point-like scattering centre inside the atom and identified it with the atomic nucleus and the theoretical description of this process has been known as Rutherford scattering ever since. The deviation between the theoretical description for a point-like scattering centre and experimental data has since been used to reveal information about the structure of the nucleus as well as the nucleon. There has been a continuous development from Hofstadters experiments in the 1950s, over the SLAC experiments in the 60s and 70s to the the HERA experiments at DESY and the experimental programme at Jeffersonlab. In this paper I am presenting the most recent results in Deeply Virtual Compton Scattering from the Hermes experiment at DESY, taken with a high density unpolarised target and a recoil detector in 2006/7.

  16. 3D Animations for Exploring Nucleon Structure

    NASA Astrophysics Data System (ADS)

    Gorman, Waverly; Burkardt, Matthias

    2016-09-01

    Over the last few years many intuitive pictures have been developed for the interpretation of electron hadron scattering experiments, such as a mechanism for transverse single-spin asymmetries in semi-inclusive deep-inelastic scattering experiments. While Dr. Burkardt's pictures have been helpful for many researchers in the field, they are still difficult to visualize for broader audiences since they rely mostly on 2-dimensional static images. In order to make more accessible for a broader audience what can be learned from Jefferson Lab experiments, we have started to work on developing 3-dimensional animations for these processes. The goal is to enable the viewer to repeatedly look at the same microscopic mechanism for a specific reaction, with the viewpoint of the observer changing. This should help an audience that is not so familiar with these reactions to better understand what can be learned from various experiments at Jefferson Lab aimed at exploring the nucleon structure. Jefferson Lab Minority/Female Undergraduate Research Assistantship.

  17. 3D ultrasound image segmentation using multiple incomplete feature sets

    NASA Astrophysics Data System (ADS)

    Fan, Liexiang; Herrington, David M.; Santago, Peter, II

    1999-05-01

    We use three features, the intensity, texture and motion to obtain robust results for segmentation of intracoronary ultrasound images. Using a parameterized equation to describe the lumen-plaque and media-adventitia boundaries, we formulate the segmentation as a parameter estimation through a cost functional based on the posterior probability, which can handle the incompleteness of the features in ultrasound images by employing outlier detection.

  18. Preliminary investigations on 3D PIC simulation of DPHC structure using NEPTUNE3D code

    NASA Astrophysics Data System (ADS)

    Zhao, Hailong; Dong, Ye; Zhou, Haijing; Zou, Wenkang; Wang, Qiang

    2016-10-01

    Cubic region (34cm × 34cm × 18cm) including the double post-hole convolute (DPHC) structure was chosen to perform a series of fully 3D PIC simulations using NEPTUNE3D codes, massive data ( 200GB) could be acquired and solved in less than 5 hours. Cold-chamber tests were performed during which only cathode electron emission was considered without temperature rise or ion emission, current loss efficiency was estimated by comparisons between output magnetic field profiles with or without electron emission. PIC simulation results showed three stages of current transforming process with election emission in DPHC structure, the maximum ( 20%) current loss was 437kA at 15ns, while only 0.46% 0.48% was lost when driving current reached its peak. DPHC structure proved valuable functions during energy transform process in PTS facility, and NEPTUNE3D provided tools to explore this sophisticated physics. Project supported by the National Natural Science Foundation of China, Grant No. 11571293, 11505172.

  19. Combination of 3D skin surface texture features and 2D ABCD features for improved melanoma diagnosis.

    PubMed

    Ding, Yi; John, Nigel W; Smith, Lyndon; Sun, Jiuai; Smith, Melvyn

    2015-10-01

    Two-dimensional asymmetry, border irregularity, colour variegation and diameter (ABCD) features are important indicators currently used for computer-assisted diagnosis of malignant melanoma (MM); however, they often prove to be insufficient to make a convincing diagnosis. Previous work has demonstrated that 3D skin surface normal features in the form of tilt and slant pattern disruptions are promising new features independent from the existing 2D ABCD features. This work investigates that whether improved lesion classification can be achieved by combining the 3D features with the 2D ABCD features. Experiments using a nonlinear support vector machine classifier show that many combinations of the 2D ABCD features and the 3D features can give substantially better classification accuracy than using (1) single features and (2) many combinations of the 2D ABCD features. The best 2D and 3D feature combination includes the overall 3D skin surface disruption, the asymmetry and all the three colour channel features. It gives an overall 87.8 % successful classification, which is better than the best single feature with 78.0 % and the best 2D feature combination with 83.1 %. These demonstrate that (1) the 3D features have additive values to improve the existing lesion classification and (2) combining the 3D feature with all the 2D features does not lead to the best lesion classification. The two ABCD features not selected by the best 2D and 3D combination, namely (1) the border feature and (2) the diameter feature, were also studied in separate experiments. It found that inclusion of either feature in the 2D and 3D combination can successfully classify 3 out of 4 lesion groups. The only one group not accurately classified by either feature can be classified satisfactorily by the other. In both cases, they have shown better classification performances than those without the 3D feature in the combinations. This further demonstrates that (1) the 3D feature can be used to

  20. Dual multispectral and 3D structured light laparoscope

    NASA Astrophysics Data System (ADS)

    Clancy, Neil T.; Lin, Jianyu; Arya, Shobhit; Hanna, George B.; Elson, Daniel S.

    2015-03-01

    Intraoperative feedback on tissue function, such as blood volume and oxygenation would be useful to the surgeon in cases where current clinical practice relies on subjective measures, such as identification of ischaemic bowel or tissue viability during anastomosis formation. Also, tissue surface profiling may be used to detect and identify certain pathologies, as well as diagnosing aspects of tissue health such as gut motility. In this paper a dual modality laparoscopic system is presented that combines multispectral reflectance and 3D surface imaging. White light illumination from a xenon source is detected by a laparoscope-mounted fast filter wheel camera to assemble a multispectral image (MSI) cube. Surface shape is then calculated using a spectrally-encoded structured light (SL) pattern detected by the same camera and triangulated using an active stereo technique. Images of porcine small bowel were acquired during open surgery. Tissue reflectance spectra were acquired and blood volume was calculated at each spatial pixel across the bowel wall and mesentery. SL features were segmented and identified using a `normalised cut' algoritm and the colour vector of each spot. Using the 3D geometry defined by the camera coordinate system the multispectral data could be overlaid onto the surface mesh. Dual MSI and SL imaging has the potential to provide augmented views to the surgeon supplying diagnostic information related to blood supply health and organ function. Future work on this system will include filter optimisation to reduce noise in tissue optical property measurement, and minimise spot identification errors in the SL pattern.

  1. Kernel regression based feature extraction for 3D MR image denoising.

    PubMed

    López-Rubio, Ezequiel; Florentín-Núñez, María Nieves

    2011-08-01

    Kernel regression is a non-parametric estimation technique which has been successfully applied to image denoising and enhancement in recent times. Magnetic resonance 3D image denoising has two features that distinguish it from other typical image denoising applications, namely the tridimensional structure of the images and the nature of the noise, which is Rician rather than Gaussian or impulsive. Here we propose a principled way to adapt the general kernel regression framework to this particular problem. Our noise removal system is rooted on a zeroth order 3D kernel regression, which computes a weighted average of the pixels over a regression window. We propose to obtain the weights from the similarities among small sized feature vectors associated to each pixel. In turn, these features come from a second order 3D kernel regression estimation of the original image values and gradient vectors. By considering directional information in the weight computation, this approach substantially enhances the performance of the filter. Moreover, Rician noise level is automatically estimated without any need of human intervention, i.e. our method is fully automated. Experimental results over synthetic and real images demonstrate that our proposal achieves good performance with respect to the other MRI denoising filters being compared.

  2. 3-D visualization of geologic structures and processes

    NASA Astrophysics Data System (ADS)

    Pflug, R.; Klein, H.; Ramshorn, Ch.; Genter, M.; Stärk, A.

    Interactive 3-D computer graphics techniques are used to visualize geologic structures and simulated geologic processes. Geometric models that serve as input to 3-D viewing programs are generated from contour maps, from serial sections, or directly from simulation program output. Choice of viewing parameters strongly affects the perception of irregular surfaces. An interactive 3-D rendering program and its graphical user interface provide visualization tools for structural geology, seismic interpretation, and visual post-processing of simulations. Dynamic display of transient ground-water simulations and sedimentary process simulations can visualize processes developing through time.

  3. 3D-2D ultrasound feature-based registration for navigated prostate biopsy: a feasibility study.

    PubMed

    Selmi, Sonia Y; Promayon, Emmanuel; Troccaz, Jocelyne

    2016-08-01

    The aim of this paper is to describe a 3D-2D ultrasound feature-based registration method for navigated prostate biopsy and its first results obtained on patient data. A system combining a low-cost tracking system and a 3D-2D registration algorithm was designed. The proposed 3D-2D registration method combines geometric and image-based distances. After extracting features from ultrasound images, 3D and 2D features within a defined distance are matched using an intensity-based function. The results are encouraging and show acceptable errors with simulated transforms applied on ultrasound volumes from real patients.

  4. Finding Organized Structures in 3-D LADAR Data

    DTIC Science & Technology

    2004-12-01

    work exists also on how to extract planar and linear objects from scattered 3-D point clouds , see for example [5], [6]. Methods were even proposed to...of structure detection and segmentation from 3-D point clouds collected from a single sensor location or integrated from multiple locations. In [2...primitives to point clouds are difficult to use practically for large data sets containing multiple complex structures, in opposition to multiple planar

  5. Evaluation of 3D Printer Accuracy in Producing Fractal Structure.

    PubMed

    Kikegawa, Kana; Takamatsu, Kyuuichirou; Kawakami, Masaru; Furukawa, Hidemitsu; Mayama, Hiroyuki; Nonomura, Yoshimune

    2017-01-01

    Hierarchical structures, also known as fractal structures, exhibit advantageous material properties, such as water- and oil-repellency as well as other useful optical characteristics, owing to its self-similarity. Various methods have been developed for producing hierarchical geometrical structures. Recently, fractal structures have been manufactured using a 3D printing technique that involves computer-aided design data. In this study, we confirmed the accuracy of geometrical structures when Koch curve-like fractal structures with zero to three generations were printed using a 3D printer. The fractal dimension was analyzed using a box-counting method. This analysis indicated that the fractal dimension of the third generation hierarchical structure was approximately the same as that of the ideal Koch curve. These findings demonstrate that the design and production of fractal structures can be controlled using a 3D printer. Although the interior angle deviated from the ideal value, the side length could be precisely controlled.

  6. Direct-Write 3D Nanoprinting of Plasmonic Structures

    DOE PAGES

    Winkler, Robert; Schmidt, Franz-Philipp; Karl-Franzens Univ.; ...

    2016-11-23

    During the past decade, significant progress has been made in the field of resonant optics ranging from fundamental aspects to concrete applications. And while several techniques have been introduced for the fabrication of highly defined metallic nanostructures, the synthesis of complex, free-standing three-dimensional (3D) structures is still an intriguing, but so far intractable, challenge. Here, we demonstrate a 3D direct-write synthesis approach that addresses this challenge. Specifically, we succeeded in the direct-write fabrication of 3D nanoarchitectures via electron-stimulated reactions, which are applicable on virtually any material and surface morphology. Furthermore, by that, complex 3D nanostructures composed of highly compact, puremore » gold can be fabricated, which reveal strong plasmonic activity and pave the way for a new generation of 3D nanoplasmonic architectures that can be printed on-demand.« less

  7. Direct-Write 3D Nanoprinting of Plasmonic Structures.

    PubMed

    Winkler, Robert; Schmidt, Franz-Philipp; Haselmann, Ulrich; Fowlkes, Jason D; Lewis, Brett B; Kothleitner, Gerald; Rack, Philip D; Plank, Harald

    2017-03-08

    During the past decade, significant progress has been made in the field of resonant optics ranging from fundamental aspects to concrete applications. While several techniques have been introduced for the fabrication of highly defined metallic nanostructures, the synthesis of complex, free-standing three-dimensional (3D) structures is still an intriguing, but so far intractable, challenge. In this study, we demonstrate a 3D direct-write synthesis approach that addresses this challenge. Specifically, we succeeded in the direct-write fabrication of 3D nanoarchitectures via electron-stimulated reactions, which are applicable on virtually any material and surface morphology. By that, complex 3D nanostructures composed of highly compact, pure gold can be fabricated, which reveal strong plasmonic activity and pave the way for a new generation of 3D nanoplasmonic architectures that can be printed on-demand.

  8. Direct-Write 3D Nanoprinting of Plasmonic Structures

    SciTech Connect

    Winkler, Robert; Schmidt, Franz-Philipp; Haselmann, Ulrich; Fowlkes, Jason D.; Lewis, Brett B.; Kothleitner, Gerald; Rack, Philip D.; Plank, Harald

    2016-11-23

    During the past decade, significant progress has been made in the field of resonant optics ranging from fundamental aspects to concrete applications. And while several techniques have been introduced for the fabrication of highly defined metallic nanostructures, the synthesis of complex, free-standing three-dimensional (3D) structures is still an intriguing, but so far intractable, challenge. Here, we demonstrate a 3D direct-write synthesis approach that addresses this challenge. Specifically, we succeeded in the direct-write fabrication of 3D nanoarchitectures via electron-stimulated reactions, which are applicable on virtually any material and surface morphology. Furthermore, by that, complex 3D nanostructures composed of highly compact, pure gold can be fabricated, which reveal strong plasmonic activity and pave the way for a new generation of 3D nanoplasmonic architectures that can be printed on-demand.

  9. 3D-Fun: predicting enzyme function from structure.

    PubMed

    von Grotthuss, Marcin; Plewczynski, Dariusz; Vriend, Gert; Rychlewski, Leszek

    2008-07-01

    The 'omics' revolution is causing a flurry of data that all needs to be annotated for it to become useful. Sequences of proteins of unknown function can be annotated with a putative function by comparing them with proteins of known function. This form of annotation is typically performed with BLAST or similar software. Structural genomics is nowadays also bringing us three dimensional structures of proteins with unknown function. We present here software that can be used when sequence comparisons fail to determine the function of a protein with known structure but unknown function. The software, called 3D-Fun, is implemented as a server that runs at several European institutes and is freely available for everybody at all these sites. The 3D-Fun servers accept protein coordinates in the standard PDB format and compare them with all known protein structures by 3D structural superposition using the 3D-Hit software. If structural hits are found with proteins with known function, these are listed together with their function and some vital comparison statistics. This is conceptually very similar in 3D to what BLAST does in 1D. Additionally, the superposition results are displayed using interactive graphics facilities. Currently, the 3D-Fun system only predicts enzyme function but an expanded version with Gene Ontology predictions will be available soon. The server can be accessed at http://3dfun.bioinfo.pl/ or at http://3dfun.cmbi.ru.nl/.

  10. Differentiating bladder carcinoma from bladder wall using 3D textural features: an initial study

    NASA Astrophysics Data System (ADS)

    Xu, Xiaopan; Zhang, Xi; Liu, Yang; Tian, Qiang; Zhang, Guopeng; Lu, Hongbing

    2016-03-01

    Differentiating bladder tumors from wall tissues is of critical importance for the detection of invasion depth and cancer staging. The textural features embedded in bladder images have demonstrated their potentials in carcinomas detection and classification. The purpose of this study was to investigate the feasibility of differentiating bladder carcinoma from bladder wall using three-dimensional (3D) textural features extracted from MR bladder images. The widely used 2D Tamura features were firstly wholly extended to 3D, and then different types of 3D textural features including 3D features derived from gray level co-occurrence matrices (GLCM) and grey level-gradient co-occurrence matrix (GLGCM), as well as 3D Tamura features, were extracted from 23 volumes of interest (VOIs) of bladder tumors and 23 VOIs of patients' bladder wall. Statistical results show that 30 out of 47 features are significantly different between cancer tissues and wall tissues. Using these features with significant differences between these two types of tissues, classification performance with a supported vector machine (SVM) classifier demonstrates that the combination of three types of selected 3D features outperform that of using only one type of features. All the observations demonstrate that significant textural differences exist between carcinomatous tissues and bladder wall, and 3D textural analysis may be an effective way for noninvasive staging of bladder cancer.

  11. Formal representation of 3D structural geological models

    NASA Astrophysics Data System (ADS)

    Wang, Zhangang; Qu, Honggang; Wu, Zixing; Yang, Hongjun; Du, Qunle

    2016-05-01

    The development and widespread application of geological modeling methods has increased demands for the integration and sharing services of three dimensional (3D) geological data. However, theoretical research in the field of geological information sciences is limited despite the widespread use of Geographic Information Systems (GIS) in geology. In particular, fundamental research on the formal representations and standardized spatial descriptions of 3D structural models is required. This is necessary for accurate understanding and further applications of geological data in 3D space. In this paper, we propose a formal representation method for 3D structural models using the theory of point set topology, which produces a mathematical definition for the major types of geological objects. The spatial relationships between geologic boundaries, structures, and units are explained in detail using the 9-intersection model. Reasonable conditions for describing the topological space of 3D structural models are also provided. The results from this study can be used as potential support for the standardized representation and spatial quality evaluation of 3D structural models, as well as for specific needs related to model-based management, query, and analysis.

  12. Toward mobile 3D visualization for structural biologists.

    PubMed

    Tanramluk, Duangrudee; Akavipat, Ruj; Charoensawan, Varodom

    2013-12-01

    Technological advances in crystallography have led to the ever-rapidly increasing number of biomolecular structures deposited in public repertoires. This undoubtedly shifts the bottleneck of structural biology research from obtaining high-quality structures to data analysis and interpretation. The recently available glasses-free autostereoscopic laptop offers an unprecedented opportunity to visualize and study 3D structures using a much more affordable, and for the first time, portable device. Together with a gamepad re-programmed for 3D structure controlling, we describe how the gaming technologies can deliver the output 3D images for high-quality viewing, comparable to that of a passive stereoscopic system, and can give the user more control and flexibility than the conventional controlling setup using only a mouse and a keyboard.

  13. Medical image retrieval system using multiple features from 3D ROIs

    NASA Astrophysics Data System (ADS)

    Lu, Hongbing; Wang, Weiwei; Liao, Qimei; Zhang, Guopeng; Zhou, Zhiming

    2012-02-01

    Compared to a retrieval using global image features, features extracted from regions of interest (ROIs) that reflect distribution patterns of abnormalities would benefit more for content-based medical image retrieval (CBMIR) systems. Currently, most CBMIR systems have been designed for 2D ROIs, which cannot reflect 3D anatomical features and region distribution of lesions comprehensively. To further improve the accuracy of image retrieval, we proposed a retrieval method with 3D features including both geometric features such as Shape Index (SI) and Curvedness (CV) and texture features derived from 3D Gray Level Co-occurrence Matrix, which were extracted from 3D ROIs, based on our previous 2D medical images retrieval system. The system was evaluated with 20 volume CT datasets for colon polyp detection. Preliminary experiments indicated that the integration of morphological features with texture features could improve retrieval performance greatly. The retrieval result using features extracted from 3D ROIs accorded better with the diagnosis from optical colonoscopy than that based on features from 2D ROIs. With the test database of images, the average accuracy rate for 3D retrieval method was 76.6%, indicating its potential value in clinical application.

  14. 3D annotation and manipulation of medical anatomical structures

    NASA Astrophysics Data System (ADS)

    Vitanovski, Dime; Schaller, Christian; Hahn, Dieter; Daum, Volker; Hornegger, Joachim

    2009-02-01

    Although the medical scanners are rapidly moving towards a three-dimensional paradigm, the manipulation and annotation/labeling of the acquired data is still performed in a standard 2D environment. Editing and annotation of three-dimensional medical structures is currently a complex task and rather time-consuming, as it is carried out in 2D projections of the original object. A major problem in 2D annotation is the depth ambiguity, which requires 3D landmarks to be identified and localized in at least two of the cutting planes. Operating directly in a three-dimensional space enables the implicit consideration of the full 3D local context, which significantly increases accuracy and speed. A three-dimensional environment is as well more natural optimizing the user's comfort and acceptance. The 3D annotation environment requires the three-dimensional manipulation device and display. By means of two novel and advanced technologies, Wii Nintendo Controller and Philips 3D WoWvx display, we define an appropriate 3D annotation tool and a suitable 3D visualization monitor. We define non-coplanar setting of four Infrared LEDs with a known and exact position, which are tracked by the Wii and from which we compute the pose of the device by applying a standard pose estimation algorithm. The novel 3D renderer developed by Philips uses either the Z-value of a 3D volume, or it computes the depth information out of a 2D image, to provide a real 3D experience without having some special glasses. Within this paper we present a new framework for manipulation and annotation of medical landmarks directly in three-dimensional volume.

  15. 3D Ultrasonic Wave Simulations for Structural Health Monitoring

    NASA Technical Reports Server (NTRS)

    Campbell, Leckey Cara A/; Miler, Corey A.; Hinders, Mark K.

    2011-01-01

    Structural health monitoring (SHM) for the detection of damage in aerospace materials is an important area of research at NASA. Ultrasonic guided Lamb waves are a promising SHM damage detection technique since the waves can propagate long distances. For complicated flaw geometries experimental signals can be difficult to interpret. High performance computing can now handle full 3-dimensional (3D) simulations of elastic wave propagation in materials. We have developed and implemented parallel 3D elastodynamic finite integration technique (3D EFIT) code to investigate ultrasound scattering from flaws in materials. EFIT results have been compared to experimental data and the simulations provide unique insight into details of the wave behavior. This type of insight is useful for developing optimized experimental SHM techniques. 3D EFIT can also be expanded to model wave propagation and scattering in anisotropic composite materials.

  16. 3D Wilson cycle: structural inheritance and subduction polarity reversals

    NASA Astrophysics Data System (ADS)

    Beaussier, Stephane; Gerya, Taras; Burg, Jean-Pierre

    2016-04-01

    Many orogenies display along-strike variations in their orogenic wedge geometry. For instance, the Alps is an example of lateral changes in the subducting lithosphere polarity. High resolution tomography has shown that the southeast dipping European lithosphere is separated from the northeast dipping Adriatic lithosphere by a narrow transition zone at about the "Judicarian" line (Kissling et al. 2006). The formation of such 3D variations remains conjectural. We investigate the conditions that can spontaneously induce such lithospheric structures, and intend to identify the main parameters controlling their formation and geometry. Using the 3D thermo-mechanical code, I3ELVIS (Gerya and Yuen 2007) we modelled a Wilson cycle starting from a continental lithosphere in an extensional setting resulting in continental breakup and oceanic spreading. At a later stage, divergence is gradually reversed to convergence, which induce subduction of the oceanic lithosphere formed during oceanic spreading. In this model, all lateral and longitudinal structures of the lithospheres are generated self-consistently, and are consequences of the initial continental structure, tectono-magmatic inheritance, and material rheology. Our numerical simulations point out the control of rheological parameters defining the brittle/plastic yielding conditions for the lithosphere. Formation of several opposing domains of opposing subduction polarity is facilitated by wide and weak oceanic lithospheres. Furthermore, contrasts of strength between the continental and oceanic lithosphere, as well as the angle between the plate suture and the shortening direction have a second order effect on the lateral geometry of the subduction zone. In our numerical experiments systematic lateral changes in the subduction lithosphere polarity during subduction initiation form spontaneously suggesting intrinsic physical origin of this phenomenon. Further studies are necessary to understand why this feature, observed

  17. 3D WHOLE-PROMINENCE FINE STRUCTURE MODELING

    SciTech Connect

    Gunár, Stanislav; Mackay, Duncan H.

    2015-04-20

    We present the first 3D whole-prominence fine structure model. The model combines a 3D magnetic field configuration of an entire prominence obtained from nonlinear force-free field simulations, with a detailed description of the prominence plasma. The plasma is located in magnetic dips in hydrostatic equilibrium and is distributed along multiple fine structures within the 3D magnetic model. Through the use of a novel radiative transfer visualization technique for the Hα line such plasma-loaded magnetic field model produces synthetic images of the modeled prominence comparable with high-resolution observations. This allows us for the first time to use a single technique to consistently study, in both emission on the limb and absorption against the solar disk, the fine structures of prominences/filaments produced by a magnetic field model.

  18. Facial expression identification using 3D geometric features from Microsoft Kinect device

    NASA Astrophysics Data System (ADS)

    Han, Dongxu; Al Jawad, Naseer; Du, Hongbo

    2016-05-01

    Facial expression identification is an important part of face recognition and closely related to emotion detection from face images. Various solutions have been proposed in the past using different types of cameras and features. Microsoft Kinect device has been widely used for multimedia interactions. More recently, the device has been increasingly deployed for supporting scientific investigations. This paper explores the effectiveness of using the device in identifying emotional facial expressions such as surprise, smile, sad, etc. and evaluates the usefulness of 3D data points on a face mesh structure obtained from the Kinect device. We present a distance-based geometric feature component that is derived from the distances between points on the face mesh and selected reference points in a single frame. The feature components extracted across a sequence of frames starting and ending by neutral emotion represent a whole expression. The feature vector eliminates the need for complex face orientation correction, simplifying the feature extraction process and making it more efficient. We applied the kNN classifier that exploits a feature component based similarity measure following the principle of dynamic time warping to determine the closest neighbors. Preliminary tests on a small scale database of different facial expressions show promises of the newly developed features and the usefulness of the Kinect device in facial expression identification.

  19. Automated 3D structure composition for large RNAs

    PubMed Central

    Popenda, Mariusz; Szachniuk, Marta; Antczak, Maciej; Purzycka, Katarzyna J.; Lukasiak, Piotr; Bartol, Natalia; Blazewicz, Jacek; Adamiak, Ryszard W.

    2012-01-01

    Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues. PMID:22539264

  20. Automated 3D structure composition for large RNAs.

    PubMed

    Popenda, Mariusz; Szachniuk, Marta; Antczak, Maciej; Purzycka, Katarzyna J; Lukasiak, Piotr; Bartol, Natalia; Blazewicz, Jacek; Adamiak, Ryszard W

    2012-08-01

    Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues.

  1. Designing 3D Structure by 5-7 Kirigami

    NASA Astrophysics Data System (ADS)

    Gong, Xingting; Cho, Yigil; Castle, Toen; Sussman, Daniel; Kamien, Randall

    2015-03-01

    The purpose of this talk is to explore how one can create 3D structures from 2D materials through the art of kirigami. Kirigami expands upon origami by allowing not only folds, but also cuts, into materials. If we take an incompressible material such as paper and remove a hole from it, the paper will buckle into the third dimension once that hole is sealed in order to relieve strain. Thus, orienting cuts and folds in certain places throughout a sheet of paper can influence its ``pop-up,'' 3D structure. To narrow down the inverse design problem, we confined ourselves to making only one kind of cut (which we call the ``5-7 cut'') on a honeycomb grid, and we show how this single cut can give rise to arbitrarily complex three dimensional structures. A simple set of rules exists: (a) one 5-7 cut divides the material into 2 sections which can choose to pop-up or down independently of each other, (b) rows of uniform cuts must pop up or down in unison, giving (nearly) arbitrary 2D structure, and (c) the 5-7 cuts can be arranged in various ways to create 6 basic pop-up ``modes,'' which can then be arranged to give (nearly) arbitrary 3D structure. These simple rules allow a framework for designing targeted 3D structure from an initial 2D sheet of material. This work was supported by NSF EFRI-ODISSEI Grant EFRI 13-31583.

  2. Airborne LIDAR and high resolution satellite data for rapid 3D feature extraction

    NASA Astrophysics Data System (ADS)

    Jawak, S. D.; Panditrao, S. N.; Luis, A. J.

    2014-11-01

    . The CHM or the normalized DSM represents the absolute height of all aboveground urban features relative to the ground. After normalization, the elevation value of a point indicates the height from the ground to the point. The above-ground points were used for tree feature and building footprint extraction. In individual tree extraction, first and last return point clouds were used along with the bare earth and building footprint models discussed above. In this study, scene dependent extraction criteria were employed to improve the 3D feature extraction process. LiDAR-based refining/ filtering techniques used for bare earth layer extraction were crucial for improving the subsequent 3D features (tree and building) feature extraction. The PAN-sharpened WV-2 image (with 0.5 m spatial resolution) was used to assess the accuracy of LiDAR-based 3D feature extraction. Our analysis provided an accuracy of 98 % for tree feature extraction and 96 % for building feature extraction from LiDAR data. This study could extract total of 15143 tree features using CHM method, out of which total of 14841 were visually interpreted on PAN-sharpened WV-2 image data. The extracted tree features included both shadowed (total 13830) and non-shadowed (total 1011). We note that CHM method could overestimate total of 302 tree features, which were not observed on the WV-2 image. One of the potential sources for tree feature overestimation was observed in case of those tree features which were adjacent to buildings. In case of building feature extraction, the algorithm could extract total of 6117 building features which were interpreted on WV-2 image, even capturing buildings under the trees (total 605) and buildings under shadow (total 112). Overestimation of tree and building features was observed to be limiting factor in 3D feature extraction process. This is due to the incorrect filtering of point cloud in these areas. One of the potential sources of overestimation was the man-made structures

  3. Coherent structures in 3D viscous time-periodic flow

    NASA Astrophysics Data System (ADS)

    Znaien, J. G.; Speetjens, M. F. M.; Trieling, R. R.; Clercx, H. J. H.

    2010-11-01

    Periodically driven laminar flows occur in many industrial processes from food-mixing devices to micro-mixer in lab-on-a-chip systems. The present study is motivated by better understanding fundamental transport phenomena in three-dimensional viscous time-periodic flows. Both numerical simulation and three-dimensional Particle Tracking Velocimetry measurements are performed to investigate the 3D advection of a passive scalar in a lid-driven cylindrical cavity flow. The flow is forced by a time-periodic in-plane motion of one endwall via a given forcing protocol. We concentrate on the formation and interaction of coherent structures due to fluid inertia, which play an important role in 3D mixing by geometrically determining the tracer transport. The disintegration of these structures by fluid inertia reflects an essentially 3D route to chaos. Data from tracking experiments of small particles will be compared with predictions from numerical simulations on transport of passive tracers.

  4. 3D genome structure modeling by Lorentzian objective function.

    PubMed

    Trieu, Tuan; Cheng, Jianlin

    2016-11-29

    The 3D structure of the genome plays a vital role in biological processes such as gene interaction, gene regulation, DNA replication and genome methylation. Advanced chromosomal conformation capture techniques, such as Hi-C and tethered conformation capture, can generate chromosomal contact data that can be used to computationally reconstruct 3D structures of the genome. We developed a novel restraint-based method that is capable of reconstructing 3D genome structures utilizing both intra-and inter-chromosomal contact data. Our method was robust to noise and performed well in comparison with a panel of existing methods on a controlled simulated data set. On a real Hi-C data set of the human genome, our method produced chromosome and genome structures that are consistent with 3D FISH data and known knowledge about the human chromosome and genome, such as, chromosome territories and the cluster of small chromosomes in the nucleus center with the exception of the chromosome 18. The tool and experimental data are available at https://missouri.box.com/v/LorDG.

  5. Coarse-grained modeling of RNA 3D structure.

    PubMed

    Dawson, Wayne K; Maciejczyk, Maciej; Jankowska, Elzbieta J; Bujnicki, Janusz M

    2016-07-01

    Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result.

  6. RNA and protein 3D structure modeling: similarities and differences.

    PubMed

    Rother, Kristian; Rother, Magdalena; Boniecki, Michał; Puton, Tomasz; Bujnicki, Janusz M

    2011-09-01

    In analogy to proteins, the function of RNA depends on its structure and dynamics, which are encoded in the linear sequence. While there are numerous methods for computational prediction of protein 3D structure from sequence, there have been very few such methods for RNA. This review discusses template-based and template-free approaches for macromolecular structure prediction, with special emphasis on comparison between the already tried-and-tested methods for protein structure modeling and the very recently developed "protein-like" modeling methods for RNA. We highlight analogies between many successful methods for modeling of these two types of biological macromolecules and argue that RNA 3D structure can be modeled using "protein-like" methodology. We also highlight the areas where the differences between RNA and proteins require the development of RNA-specific solutions.

  7. Strategies to reconstruct 3D Coffea arabica L. plant structure.

    PubMed

    Matsunaga, Fabio Takeshi; Tosti, Jonas Barbosa; Androcioli-Filho, Armando; Brancher, Jacques Duílio; Costes, Evelyne; Rakocevic, Miroslava

    2016-01-01

    Accurate model of structural elements is necessary to model the foliage and fruit distributions in cultivated plants, both of them being key parameters for yield prediction. However, the level of details in architectural data collection could vary, simplifying the data collection when plants get older and because of the high time cost required. In the present study, we aimed at reconstructing and analyzing plant structure, berry distributions and yield in Coffea arabica (Arabica coffee), by using both detailed or partial morphological information and probabilistic functions. Different datasets of coffee plant architectures were available with different levels of detail depending on the tree age. Three scales of decomposition-plant, axes and metamers were used reconstruct the plant architectures. CoffePlant3D, a software which integrates a series of mathematical, computational and statistical methods organized in three newly developed modules, AmostraCafe3D, VirtualCafe3D and Cafe3D, was developed to accurately reconstruct coffee plants in 3D, whatever the level of details available. The number of metamers of the 2nd order axes was shown to be linearly proportional to that of the orthotropic trunk, and the number of berries per metamer was modeled as a Gaussian function within a specific zone along the plagiotropic axes. This ratio of metamer emission rhythm between the orthotropic trunk and plagiotropic axes represents the pillar of botanical events in the C. arabica development and was central in our modeling approach, especially to reconstruct missing data. The methodology proposed for reconstructing coffee plants under the CoffePlant3D was satisfactorily validated across dataset available and could be performed for any other Arabica coffee variety.

  8. 3D-profile measurement of advanced semiconductor features by reference metrology

    NASA Astrophysics Data System (ADS)

    Takamasu, Kiyoshi; Iwaki, Yuuki; Takahashi, Satoru; Kawada, Hiroki; Ikota, Masami; Lorusso, Gian F.; Horiguchi, Naoto

    2016-03-01

    A method of sub-nanometer uncertainty for the 3D-profile measurement using TEM (Transmission Electron Microscope) images is proposed to standardize 3D-profile measurement through reference metrology. The proposed method has been validated for profiles of Si lines, photoresist features and advanced-FinFET (Fin-shaped Field-Effect Transistor) features in our previous investigations. However, efficiency of 3D-profile measurement using TEM is limited by measurement time including processing of the sample. In this article, we demonstrate a novel on-wafer 3D-profile metrology as "FIB-to-CDSEM method" with FIB (Focused Ion Beam) slope cut and CD-SEM (Critical Dimension Secondary Electron Microscope) measuring. Using the method, a few micrometer wide on a wafer is coated and cut by 45 degree slope using FIB tool. Then, the wafer is transferred to CD-SEM to measure the cross section image by top down CD-SEM measurement. We apply FIB-to-CDSEM method to CMOS sensor device. 3D-profile and 3D-profile parameters such as top line width and side wall angles of CMOS sensor device are evaluated. The 3D-profile parameters also are measured by TEM images as reference metrology. We compare the 3D-profile parameters by TEM method and FIB-to-CDSEM method. The average values and correlations on the wafer are agreed well between TEM and FIB-to- CDSEM methods.

  9. Instability and Wave Propagation in Structured 3D Composites

    NASA Astrophysics Data System (ADS)

    Kaynia, Narges; Fang, Nicholas X.; Boyce, Mary C.

    2014-03-01

    Many structured composites found in nature possess undulating and wrinkled interfacial layers that regulate mechanical, chemical, acoustic, adhesive, thermal, electrical and optical functions of the material. This research focused on the complex instability and wrinkling pattern arising in 3D structured composites and the effect of the buckling pattern on the overall structural response. The 3D structured composites consisted of stiffer plates supported by soft matrix on both sides. Compression beyond the critical strain led to complex buckling patterns in the initially straight plates. The motivation of our work is to elaborate the formation of a system of prescribed periodic scatterers (metamaterials) due to buckling, and their effect to interfere wave propagation through the metamaterial structures. Such metamaterials made from elastomers enable large reversible deformation and, as a result, significant changes of the wave propagation properties. We developed analytical and finite element models to capture various aspects of the instability mechanism. Mechanical experiments were designed to further explore the modeling results. The ability to actively alter the 3D composite structure can enable on-demand tunability of many different functions, such as active control of wave propagation to create band-gaps and waveguides.

  10. Real-time structured light intraoral 3D measurement pipeline

    NASA Astrophysics Data System (ADS)

    Gheorghe, Radu; Tchouprakov, Andrei; Sokolov, Roman

    2013-02-01

    Computer aided design and manufacturing (CAD/CAM) is increasingly becoming a standard feature and service provided to patients in dentist offices and denture manufacturing laboratories. Although the quality of the tools and data has slowly improved in the last years, due to various surface measurement challenges, practical, accurate, invivo, real-time 3D high quality data acquisition and processing still needs improving. Advances in GPU computational power have allowed for achieving near real-time 3D intraoral in-vivo scanning of patient's teeth. We explore in this paper, from a real-time perspective, a hardware-software-GPU solution that addresses all the requirements mentioned before. Moreover we exemplify and quantify the hard and soft deadlines required by such a system and illustrate how they are supported in our implementation.

  11. 3D printing meets computational astrophysics: deciphering the structure of η Carinae's inner colliding winds

    NASA Astrophysics Data System (ADS)

    Madura, T. I.; Clementel, N.; Gull, T. R.; Kruip, C. J. H.; Paardekooper, J.-P.

    2015-06-01

    We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (≳120 M⊙), highly eccentric (e ˜ 0.9) binary star system η Carinae. We demonstrate the methodology used to incorporate 3D interactive figures into a PDF (Portable Document Format) journal publication and the benefits of using 3D visualization and 3D printing as tools to analyse data from multidimensional numerical simulations. Using a consumer-grade 3D printer (MakerBot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics simulations of η Carinae's inner (r ˜ 110 au) wind-wind collision interface at multiple orbital phases. The 3D prints and visualizations reveal important, previously unknown `finger-like' structures at orbital phases shortly after periastron (φ ˜ 1.045) that protrude radially outwards from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. thin-shell, Rayleigh-Taylor) that arise at the interface between the radiatively cooled layer of dense post-shock primary-star wind and the fast (3000 km s-1), adiabatic post-shock companion-star wind. The success of our work and easy identification of previously unrecognized physical features highlight the important role 3D printing and interactive graphics can play in the visualization and understanding of complex 3D time-dependent numerical simulations of astrophysical phenomena.

  12. 3D printed components with ultrasonically arranged microscale structure

    NASA Astrophysics Data System (ADS)

    Llewellyn-Jones, Thomas M.; Drinkwater, Bruce W.; Trask, Richard S.

    2016-02-01

    This paper shows the first application of in situ manipulation of discontinuous fibrous structure mid-print, within a 3D printed polymeric composite architecture. Currently, rapid prototyping methods (fused filament fabrication, stereolithography) are gaining increasing popularity within the engineering commnity to build structural components. Unfortunately, the full potential of these components is limited by the mechanical properties of the materials used. The aim of this study is to create and demonstrate a novel method to instantaneously orient micro-scale glass fibres within a selectively cured photocurable resin system, using ultrasonic forces to align the fibres in the desired 3D architecture. To achieve this we have mounted a switchable, focused laser module on the carriage of a three-axis 3D printing stage, above an in-house ultrasonic alignment rig containing a mixture of photocurable resin and discontinuous 14 μm diameter glass fibre reinforcement(50 μm length). In our study, a suitable print speed of 20 mm s-1 was used, which is comparable to conventional additive layer techniques. We show the ability to construct in-plane orthogonally aligned sections printed side by side, where the precise orientation of the configurations is controlled by switching the ultrasonic standing wave profile mid-print. This approach permits the realisation of complex fibrous architectures within a 3D printed landscape. The versatile nature of the ultrasonic manipulation technique also permits a wide range of particle types (diameters, aspect ratios and functions) and architectures (in-plane, and out-plane) to be patterned, leading to the creation of a new generation of fibrous reinforced composites for 3D printing.

  13. Fluorescence in situ hybridization applications for super-resolution 3D structured illumination microscopy.

    PubMed

    Markaki, Yolanda; Smeets, Daniel; Cremer, Marion; Schermelleh, Lothar

    2013-01-01

    Fluorescence in situ hybridization on three-dimensionally preserved cells (3D-FISH) is an efficient tool to analyze the subcellular localization and spatial arrangement of targeted DNA sequences and RNA transcripts at the single cell level. 3D reconstructions from serial optical sections obtained by confocal laser scanning microscopy (CLSM) have long been considered the gold standard for 3D-FISH analyses. Recent super-resolution techniques circumvent the diffraction-limit of optical resolution and have defined a new state-of-the-art in bioimaging. Three-dimensional structured illumination microscopy (3D-SIM) represents one of these technologies. Notably, 3D-SIM renders an eightfold improved volumetric resolution over conventional imaging, and allows the simultaneous visualization of differently labeled target structures. These features make this approach highly attractive for the analysis of spatial relations and substructures of nuclear targets that escape detection by conventional light microscopy. Here, we focus on the application of 3D-SIM for the visualization of subnuclear 3D-FISH preparations. In comparison with conventional fluorescence microscopy, the quality of 3D-SIM data is dependent to a much greater extent on the optimal sample preparation, labeling and acquisition conditions. We describe typical problems encountered with super-resolution imaging of in situ hybridizations in mammalian tissue culture cells and provide optimized DNA-/(RNA)-FISH protocols including combinations with immunofluorescence staining (Immuno-FISH) and DNA replication labeling using click chemistry.

  14. Advancements in 3D Structural Analysis of Geothermal Systems

    SciTech Connect

    Siler, Drew L; Faulds, James E; Mayhew, Brett; McNamara, David

    2013-06-23

    Robust geothermal activity in the Great Basin, USA is a product of both anomalously high regional heat flow and active fault-controlled extension. Elevated permeability associated with some fault systems provides pathways for circulation of geothermal fluids. Constraining the local-scale 3D geometry of these structures and their roles as fluid flow conduits is crucial in order to mitigate both the costs and risks of geothermal exploration and to identify blind (no surface expression) geothermal resources. Ongoing studies have indicated that much of the robust geothermal activity in the Great Basin is associated with high density faulting at structurally complex fault intersection/interaction areas, such as accommodation/transfer zones between discrete fault systems, step-overs or relay ramps in fault systems, intersection zones between faults with different strikes or different senses of slip, and horse-tailing fault terminations. These conceptualized models are crucial for locating and characterizing geothermal systems in a regional context. At the local scale, however, pinpointing drilling targets and characterizing resource potential within known or probable geothermal areas requires precise 3D characterization of the system. Employing a variety of surface and subsurface data sets, we have conducted detailed 3D geologic analyses of two Great Basin geothermal systems. Using EarthVision (Dynamic Graphics Inc., Alameda, CA) we constructed 3D geologic models of both the actively producing Brady’s geothermal system and a ‘greenfield’ geothermal prospect at Astor Pass, NV. These 3D models allow spatial comparison of disparate data sets in 3D and are the basis for quantitative structural analyses that can aid geothermal resource assessment and be used to pinpoint discrete drilling targets. The relatively abundant data set at Brady’s, ~80 km NE of Reno, NV, includes 24 wells with lithologies interpreted from careful analysis of cuttings and core, a 1

  15. The 3-D inelastic analyses for computational structural mechanics

    NASA Technical Reports Server (NTRS)

    Hopkins, D. A.; Chamis, C. C.

    1989-01-01

    The 3-D inelastic analysis method is a focused program with the objective to develop computationally effective analysis methods and attendant computer codes for three-dimensional, nonlinear time and temperature dependent problems present in the hot section of turbojet engine structures. Development of these methods was a major part of the Hot Section Technology (HOST) program over the past five years at Lewis Research Center.

  16. 3D reconstruction methods of coronal structures by radio observations

    NASA Technical Reports Server (NTRS)

    Aschwanden, Markus J.; Bastian, T. S.; White, Stephen M.

    1992-01-01

    The ability to carry out the three dimensional (3D) reconstruction of structures in the solar corona would represent a major advance in the study of the physical properties in active regions and in flares. Methods which allow a geometric reconstruction of quasistationary coronal structures (for example active region loops) or dynamic structures (for example flaring loops) are described: stereoscopy of multi-day imaging observations by the VLA (Very Large Array); tomography of optically thin emission (in radio or soft x-rays); multifrequency band imaging by the VLA; and tracing of magnetic field lines by propagating electron beams.

  17. Robust affine-invariant feature points matching for 3D surface reconstruction of complex landslide scenes

    NASA Astrophysics Data System (ADS)

    Stumpf, André; Malet, Jean-Philippe; Allemand, Pascal; Skupinski, Grzegorz; Deseilligny, Marc-Pierrot

    2013-04-01

    Multi-view stereo surface reconstruction from dense terrestrial photographs is being increasingly applied for geoscience applications such as quantitative geomorphology, and a number of different software solution and processing streamlines have been suggested. For image matching, camera self-calibration and bundle block adjustment, most approaches make use of scale-invariant feature transform (SIFT) to identify homologous points in multiple images. SIFT-like point matching is robust to apparent translation, rotation, and scaling of objects in multiple viewing geometries but the number of correctly identified matching points typically declines drastically with increasing angles between the viewpoints. For the application of multi-view stereo of complex landslide scenes, the viewing geometry is often constrained by the local topography and barriers such as rocks and vegetation occluding the target. Under such conditions it is not uncommon to encounter view angle differences of > 30% that hinder the image matching and eventually prohibit the joint estimation of the camera parameters from all views. Recently an affine invariant extension of the SIFT detector (ASIFT) has been demonstrated to provide more robust matches when large view-angle differences become an issue. In this study the ASIFT detector was adopted to detect homologous points in terrestrial photographs preceding 3D reconstruction of different parts (main scarp, toe) of the Super-Sauze landslide (Southern French Alps). 3D surface models for different time periods and different parts of the landslide were derived using the multi-view stereo framework implemented in MicMac (©IGN). The obtained 3D models were compared with reconstructions using the traditional SIFT detectors as well as alternative structure-from-motion implementations. An estimate of the absolute accuracy of the photogrammetric models was obtained through co-registration and comparison with high-resolution terrestrial LiDAR scans.

  18. Cancer3D: understanding cancer mutations through protein structures.

    PubMed

    Porta-Pardo, Eduard; Hrabe, Thomas; Godzik, Adam

    2015-01-01

    The new era of cancer genomics is providing us with extensive knowledge of mutations and other alterations in cancer. The Cancer3D database at http://www.cancer3d.org gives an open and user-friendly way to analyze cancer missense mutations in the context of structures of proteins in which they are found. The database also helps users analyze the distribution patterns of the mutations as well as their relationship to changes in drug activity through two algorithms: e-Driver and e-Drug. These algorithms use knowledge of modular structure of genes and proteins to separately study each region. This approach allows users to find novel candidate driver regions or drug biomarkers that cannot be found when similar analyses are done on the whole-gene level. The Cancer3D database provides access to the results of such analyses based on data from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE). In addition, it displays mutations from over 14,700 proteins mapped to more than 24,300 structures from PDB. This helps users visualize the distribution of mutations and identify novel three-dimensional patterns in their distribution.

  19. Synthesis, structure and properties of a 3D acentric coordination polymer with noninterpenetrated (10,3)-d topology

    NASA Astrophysics Data System (ADS)

    Lun, Huijie; Li, Xuefei; Wang, Xiao; Li, Haiyan; Li, Yamin; Bai, Yan

    2017-01-01

    A new coordination polymer, {[Mn(HPIDC)(H2O)]·2H2O}n (1) (H3PIDC = 2-(pyridin-4-yl)-1H-imidazole-4,5-dicarboxylic acid), has been obtained by hydrothermal method and structurally characterized by X-ray single crystal diffraction, elemental analysis and thermogravimetric analysis (TGA). X-ray single crystal diffraction reveals that compound 1 crystallizing in acentric Pna21 space group, exhibits an ultimate racemic three-dimension framework with rare noninterpenetrated (10,3)-d (or utp) topology due to the alternate array of left- and right-handed helixes. Moreover, compound 1 also features ferroelectric, nonlinear optical (NLO) and antiferromagnetic behaviors.

  20. Feature relevance assessment for the semantic interpretation of 3D point cloud data

    NASA Astrophysics Data System (ADS)

    Weinmann, M.; Jutzi, B.; Mallet, C.

    2013-10-01

    The automatic analysis of large 3D point clouds represents a crucial task in photogrammetry, remote sensing and computer vision. In this paper, we propose a new methodology for the semantic interpretation of such point clouds which involves feature relevance assessment in order to reduce both processing time and memory consumption. Given a standard benchmark dataset with 1.3 million 3D points, we first extract a set of 21 geometric 3D and 2D features. Subsequently, we apply a classifier-independent ranking procedure which involves a general relevance metric in order to derive compact and robust subsets of versatile features which are generally applicable for a large variety of subsequent tasks. This metric is based on 7 different feature selection strategies and thus addresses different intrinsic properties of the given data. For the example of semantically interpreting 3D point cloud data, we demonstrate the great potential of smaller subsets consisting of only the most relevant features with 4 different state-of-the-art classifiers. The results reveal that, instead of including as many features as possible in order to compensate for lack of knowledge, a crucial task such as scene interpretation can be carried out with only few versatile features and even improved accuracy.

  1. Morphological features of the macerated cranial bones registered by the 3D vision system for potential use in forensic anthropology.

    PubMed

    Skrzat, Janusz; Sioma, Andrzej; Kozerska, Magdalena

    2013-01-01

    In this paper we present potential usage of the 3D vision system for registering features of the macerated cranial bones. Applied 3D vision system collects height profiles of the object surface and from that data builds a three-dimensional image of the surface. This method appeared to be accurate enough to capture anatomical details of the macerated bones. With the aid of the 3D vision system we generated images of the surface of the human calvaria which was used for testing the system. Performed reconstruction visualized the imprints of the dural vascular system, cranial sutures, and the three-layer structure of the cranial bones observed in the cross-section. We figure out that the 3D vision system may deliver data which can enhance estimation of sex from the osteological material.

  2. Dynactin 3D structure: implications for assembly and dynein binding.

    PubMed

    Imai, Hiroshi; Narita, Akihiro; Maéda, Yuichiro; Schroer, Trina A

    2014-09-23

    The multisubunit protein complex, dynactin, is an essential component of the cytoplasmic dynein motor. High-resolution structural work on dynactin and the dynein/dynactin supercomplex has been limited to small subunits and recombinant fragments that do not report fully on either ≈1MDa assembly. In the present study, we used negative-stain electron microscopy and image analysis based on random conical tilt reconstruction to obtain a three-dimensional (3D) structure of native vertebrate dynactin. The 35-nm-long dynactin molecule has a V-shaped shoulder at one end and a flattened tip at the other end, both offset relative to the long axis of the actin-related protein (Arp) backbone. The shoulder projects dramatically away from the Arp filament core in a way that cannot be appreciated in two-dimensional images, which has implications for the mechanism of dynein binding. The 3D structure allows the helical parameters of the entire Arp filament core, which includes the actin capping protein, CP, to be determined for the first time. This structure exhibits near identity to F-actin and can be well fitted into the dynactin envelope. Molecular fitting of modeled CP-Arp polymers into the envelope shows that the filament contains between 7 and 9 Arp protomers and is capped at both ends. In the 7 Arp model, which agrees best with measured Arp stoichiometry and other structural information, actin capping protein (CP) is not present at the distal tip of the structure, unlike what is seen in the other models. The 3D structure suggests a mechanism for dynactin assembly and length specification.

  3. Myosin filament 3D structure in mammalian cardiac muscle☆

    PubMed Central

    AL-Khayat, Hind A.; Morris, Edward P.; Kensler, Robert W.; Squire, John M.

    2008-01-01

    A number of cardiac myopathies (e.g. familial hypertrophic cardiomyopathy and dilated cardiomyopathy) are linked to mutations in cardiac muscle myosin filament proteins, including myosin and myosin binding protein C (MyBP-C). To understand the myopathies it is necessary to know the normal 3D structure of these filaments. We have carried out 3D single particle analysis of electron micrograph images of negatively stained isolated myosin filaments from rabbit cardiac muscle. Single filament images were aligned and divided into segments about 2 × 430 Å long, each of which was treated as an independent ‘particle’. The resulting 40 Å resolution 3D reconstruction showed both axial and azimuthal (no radial) myosin head perturbations within the 430 Å repeat, with successive crown rotations of approximately 60°, 60° and 0°, rather than the regular 40° for an unperturbed helix. However, it is shown that the projecting density peaks appear to start at low radius from origins closer to those expected for an unperturbed helical filament, and that the azimuthal perturbation especially increases with radius. The head arrangements in rabbit cardiac myosin filaments are very similar to those in fish skeletal muscle myosin filaments, suggesting a possible general structural theme for myosin filaments in all vertebrate striated muscles (skeletal and cardiac). PMID:18472277

  4. Uniform Local Binary Pattern Based Texture-Edge Feature for 3D Human Behavior Recognition.

    PubMed

    Ming, Yue; Wang, Guangchao; Fan, Chunxiao

    2015-01-01

    With the rapid development of 3D somatosensory technology, human behavior recognition has become an important research field. Human behavior feature analysis has evolved from traditional 2D features to 3D features. In order to improve the performance of human activity recognition, a human behavior recognition method is proposed, which is based on a hybrid texture-edge local pattern coding feature extraction and integration of RGB and depth videos information. The paper mainly focuses on background subtraction on RGB and depth video sequences of behaviors, extracting and integrating historical images of the behavior outlines, feature extraction and classification. The new method of 3D human behavior recognition has achieved the rapid and efficient recognition of behavior videos. A large number of experiments show that the proposed method has faster speed and higher recognition rate. The recognition method has good robustness for different environmental colors, lightings and other factors. Meanwhile, the feature of mixed texture-edge uniform local binary pattern can be used in most 3D behavior recognition.

  5. Manufacturing of a 3D complex hyperstable Cesic structure

    NASA Astrophysics Data System (ADS)

    Kroedel, Matthias; Courteau, Pascal; Poupinet, Anne; Sarri, Giuseppe

    2007-09-01

    Global astrometry requires extremely stable materials for instrument structures, such as optical benches. Cesic®, developed by ECM and Thales Alenia Space for mirrors and high stability structures, offers an excellent compromise in terms of structural strength, stability and very high lightweight capability, with a coefficient of thermal expansion that is virtually zero at cryogenic T°. The High-Stability Optical Bench (HSOB) GAIA study, realized by Thales Alenia Space under ESA contract, aimed to design, develop and test a full-scale representative of the HSOB bench, made entirely of Cesic®. The bench has been equipped with SAGEIS-CSO laser metrology system MOUSE1, a Michelson interferometer composed of integrated optics with nm-resolution. The HSOB bench has been submitted to a homogeneous T° step under vacuum to characterize 3-D expansion behavior of its two arms. The quite negligible interarm differential, measured with a nm-range reproducibility, demonstrates that a complete 3-D structure made of Cesic® has the same CTE homogeneity as do characterization samples, fully in line with the stringent GAIA requirements (1ppm at 120K). This demonstrates that Cesic® properties at cryogenic temperatures are fully appropriate to the manufacturing of complex highly stable optical structures. This successful study confirms ECM's and Thales Alenia Space's ability to design and manufacture monolithic lightweight highly stable optical structures, based on inner-cell triangular design made possible by the unique Cesic® manufacturing process.

  6. 3D variational brain tumor segmentation on a clustered feature set

    NASA Astrophysics Data System (ADS)

    Popuri, Karteek; Cobzas, Dana; Jagersand, Martin; Shah, Sirish L.; Murtha, Albert

    2009-02-01

    Tumor segmentation from MRI data is a particularly challenging and time consuming task. Tumors have a large diversity in shape and appearance with intensities overlapping the normal brain tissues. In addition, an expanding tumor can also deflect and deform nearby tissue. Our work addresses these last two difficult problems. We use the available MRI modalities (T1, T1c, T2) and their texture characteristics to construct a multi-dimensional feature set. Further, we extract clusters which provide a compact representation of the essential information in these features. The main idea in this paper is to incorporate these clustered features into the 3D variational segmentation framework. In contrast to the previous variational approaches, we propose a segmentation method that evolves the contour in a supervised fashion. The segmentation boundary is driven by the learned inside and outside region voxel probabilities in the cluster space. We incorporate prior knowledge about the normal brain tissue appearance, during the estimation of these region statistics. In particular, we use a Dirichlet prior that discourages the clusters in the ventricles to be in the tumor and hence better disambiguate the tumor from brain tissue. We show the performance of our method on real MRI scans. The experimental dataset includes MRI scans, from patients with difficult instances, with tumors that are inhomogeneous in appearance, small in size and in proximity to the major structures in the brain. Our method shows good results on these test cases.

  7. Automatic structural matching of 3D image data

    NASA Astrophysics Data System (ADS)

    Ponomarev, Svjatoslav; Lutsiv, Vadim; Malyshev, Igor

    2015-10-01

    A new image matching technique is described. It is implemented as an object-independent hierarchical structural juxtaposition algorithm based on an alphabet of simple object-independent contour structural elements. The structural matching applied implements an optimized method of walking through a truncated tree of all possible juxtapositions of two sets of structural elements. The algorithm was initially developed for dealing with 2D images such as the aerospace photographs, and it turned out to be sufficiently robust and reliable for matching successfully the pictures of natural landscapes taken in differing seasons from differing aspect angles by differing sensors (the visible optical, IR, and SAR pictures, as well as the depth maps and geographical vector-type maps). At present (in the reported version), the algorithm is enhanced based on additional use of information on third spatial coordinates of observed points of object surfaces. Thus, it is now capable of matching the images of 3D scenes in the tasks of automatic navigation of extremely low flying unmanned vehicles or autonomous terrestrial robots. The basic principles of 3D structural description and matching of images are described, and the examples of image matching are presented.

  8. Automating the determination of 3D protein structure

    SciTech Connect

    Rayl, K.D.

    1993-12-31

    The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.

  9. An endoscopic 3D scanner based on structured light.

    PubMed

    Schmalz, Christoph; Forster, Frank; Schick, Anton; Angelopoulou, Elli

    2012-07-01

    We present a new endoscopic 3D scanning system based on Single Shot Structured Light. The proposed design makes it possible to build an extremely small scanner. The sensor head contains a catadioptric camera and a pattern projection unit. The paper describes the working principle and calibration procedure of the sensor. The prototype sensor head has a diameter of only 3.6mm and a length of 14mm. It is mounted on a flexible shaft. The scanner is designed for tubular cavities and has a cylindrical working volume of about 30mm length and 30mm diameter. It acquires 3D video at 30 frames per second and typically generates approximately 5000 3D points per frame. By design, the resolution varies over the working volume, but is generally better than 200μm. A prototype scanner has been built and is evaluated in experiments with phantoms and biological samples. The recorded average error on a known test object was 92μm.

  10. Gene3D: modelling protein structure, function and evolution.

    PubMed

    Yeats, Corin; Maibaum, Michael; Marsden, Russell; Dibley, Mark; Lee, David; Addou, Sarah; Orengo, Christine A

    2006-01-01

    The Gene3D release 4 database and web portal (http://cathwww.biochem.ucl.ac.uk:8080/Gene3D) provide a combined structural, functional and evolutionary view of the protein world. It is focussed on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species. The protein sequences have also been clustered into whole-chain families so as to aid functional prediction. The structural annotation is generated using HMM models based on the CATH domain families; CATH is a repository for manually deduced protein domains. Amongst the changes from the last publication are: the addition of over 100 genomes and the UniProt sequence database, domain data from Pfam, metabolic pathway and functional data from COGs, KEGG and GO, and protein-protein interaction data from MINT and BIND. The website has been rebuilt to allow more sophisticated querying and the data returned is presented in a clearer format with greater functionality. Furthermore, all data can be downloaded in a simple XML format, allowing users to carry out complex investigations at their own computers.

  11. Water linked 3D coordination polymers: Syntheses, structures and applications

    NASA Astrophysics Data System (ADS)

    Singh, Suryabhan; Bhim, Anupam

    2016-12-01

    Three new coordination polymers (CPs) based on Cd and Pb, [Cd(OBA)(μ-H2O)(H2O)]n1, [Pb(OBA)(μ-H2O)]n2 [where OBA=4,4'-Oxybis(benzoate)] and [Pb(SDBA)(H2O)]n.1/4DMF 3 (SDBA=4,4'-Sulfonyldibenzoate), have been synthesized and characterized. The single crystal structural studies reveal that CPs 1 and 2 have three dimensional structure. A water molecule bridges two metal centres which appears to the responsible for the dimensionality increase from 2D to 3D. Compound 3 has a supramolecular 3D structure involving water molecule and hydrogen bonds. A structural transformation is observed when 3 was heated at 100 °C or kept in methanol, forming [Pb(SDBA)]n4. Compound 4 is used as supporting matrix for palladium nanoparticles, PdNPs@4. The PdNPs@4 exhibits good catalytic activity toward the reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) in the presence of NaBH4 at room temperature. Luminescence studies revealed that all CPs could be an effective sensor for nitroaromatic explosives.

  12. Computerized lung nodule detection using 3D feature extraction and learning based algorithms.

    PubMed

    Ozekes, Serhat; Osman, Onur

    2010-04-01

    In this paper, a Computer Aided Detection (CAD) system based on three-dimensional (3D) feature extraction is introduced to detect lung nodules. First, eight directional search was applied in order to extract regions of interests (ROIs). Then, 3D feature extraction was performed which includes 3D connected component labeling, straightness calculation, thickness calculation, determining the middle slice, vertical and horizontal widths calculation, regularity calculation, and calculation of vertical and horizontal black pixel ratios. To make a decision for each ROI, feed forward neural networks (NN), support vector machines (SVM), naive Bayes (NB) and logistic regression (LR) methods were used. These methods were trained and tested via k-fold cross validation, and results were compared. To test the performance of the proposed system, 11 cases, which were taken from Lung Image Database Consortium (LIDC) dataset, were used. ROC curves were given for all methods and 100% detection sensitivity was reached except naive Bayes.

  13. Analytical and numerical investigations on the accuracy and robustness of geometric features extracted from 3D point cloud data

    NASA Astrophysics Data System (ADS)

    Dittrich, André; Weinmann, Martin; Hinz, Stefan

    2017-04-01

    In photogrammetry, remote sensing, computer vision and robotics, a topic of major interest is represented by the automatic analysis of 3D point cloud data. This task often relies on the use of geometric features amongst which particularly the ones derived from the eigenvalues of the 3D structure tensor (e.g. the three dimensionality features of linearity, planarity and sphericity) have proven to be descriptive and are therefore commonly involved for classification tasks. Although these geometric features are meanwhile considered as standard, very little attention has been paid to their accuracy and robustness. In this paper, we hence focus on the influence of discretization and noise on the most commonly used geometric features. More specifically, we investigate the accuracy and robustness of the eigenvalues of the 3D structure tensor and also of the features derived from these eigenvalues. Thereby, we provide both analytical and numerical considerations which clearly reveal that certain features are more susceptible to discretization and noise whereas others are more robust.

  14. Complete Tem-Tomography: 3D Structure of Gems Cluster

    NASA Technical Reports Server (NTRS)

    Matsuno, J.; Miyake, A.; Tsuchiyama, A.; Messenger, S.; Nakamura-Messenger, K.

    2015-01-01

    GEMS (glass with embedded metal and sulfide) grains in interplanetary dust particles (IDPs) are considered to be one of the ubiquitous and fundamental building blocks of solids in the Solar System. They have been considered to be interstellar silicate dust that survived various metamorphism or alteration processes in the protoplanetary disk but the elemental and isotopic composition measurements suggest that most of them have been formed in the protoplanetary disk as condensates from high temperature gas. This formation model is also supported by the formation of GEMS-like grains with respect to the size, mineral assemblage, texture and infrared spectrum by condensation experiments from mean GEMS composition materials. Previous GEMS studies were performed only with 2D observation by transmission electron microscopy (TEM) or scanning TEM (STEM). However, the 3D shape and structure of GEMS grains and the spatial distribution of Fe/FeS's has critical information about their formation and origin. Recently, the 3D structure of GEMS grains in ultrathin sections of cluster IDPs was revealed by electron tomography using a TEM/STEM (JEM-2100F, JEOL). However, CT images of thin sections mounted on Cu grids acquired by conventional TEM-tomography are limited to low tilt angles (e. g., less than absolute value of 75 deg. In fact, previous 3D TEM observations of GEMS were affected by some artifacts related to the limited tilt range in the TEM used. Complete tomographic images should be acquired by rotating the sample tilt angle over a range of more than absolute value of 80 deg otherwise the CT images lose their correct structures. In order to constrain the origin and formation process of GEMS grains more clearly, we performed complete electron tomography for GEMS grains. Here we report the sample preparation method we have developed for this study, and the preliminary results.

  15. RELAP5-3D Code Includes Athena Features and Models

    SciTech Connect

    Richard A. Riemke; Cliff B. Davis; Richard R. Schultz

    2006-07-01

    Version 2.3 of the RELAP5-3D computer program includes all features and models previously available only in the ATHENA version of the code. These include the addition of new working fluids (i.e., ammonia, blood, carbon dioxide, glycerol, helium, hydrogen, lead-bismuth, lithium, lithium-lead, nitrogen, potassium, sodium, and sodium-potassium) and a magnetohydrodynamic model that expands the capability of the code to model many more thermal-hydraulic systems. In addition to the new working fluids along with the standard working fluid water, one or more noncondensable gases (e.g., air, argon, carbon dioxide, carbon monoxide, helium, hydrogen, krypton, nitrogen, oxygen, sf6, xenon) can be specified as part of the vapor/gas phase of the working fluid. These noncondensable gases were in previous versions of RELAP5- 3D. Recently four molten salts have been added as working fluids to RELAP5-3D Version 2.4, which has had limited release. These molten salts will be in RELAP5-3D Version 2.5, which will have a general release like RELAP5-3D Version 2.3. Applications that use these new features and models are discussed in this paper.

  16. Characterizing 3D Vegetation Structure from Space: Mission Requirements

    NASA Technical Reports Server (NTRS)

    Hall, Forrest G.; Bergen, Kathleen; Blair, James B.; Dubayah, Ralph; Houghton, Richard; Hurtt, George; Kellndorfer, Josef; Lefsky, Michael; Ranson, Jon; Saatchi, Sasan; Shugart, H. H.; Wickland, Diane

    2012-01-01

    Human and natural forces are rapidly modifying the global distribution and structure of terrestrial ecosystems on which all of life depends, altering the global carbon cycle, affecting our climate now and for the foreseeable future, causing steep reductions in species diversity, and endangering Earth s sustainability. To understand changes and trends in terrestrial ecosystems and their functioning as carbon sources and sinks, and to characterize the impact of their changes on climate, habitat and biodiversity, new space assets are urgently needed to produce high spatial resolution global maps of the three-dimensional (3D) structure of vegetation, its biomass above ground, the carbon stored within and the implications for atmospheric green house gas concentrations and climate. These needs were articulated in a 2007 National Research Council (NRC) report (NRC, 2007) recommending a new satellite mission, DESDynI, carrying an L-band Polarized Synthetic Aperture Radar (Pol-SAR) and a multi-beam lidar (Light RAnging And Detection) operating at 1064 nm. The objectives of this paper are to articulate the importance of these new, multi-year, 3D vegetation structure and biomass measurements, to briefly review the feasibility of radar and lidar remote sensing technology to meet these requirements, to define the data products and measurement requirements, and to consider implications of mission durations. The paper addresses these objectives by synthesizing research results and other input from a broad community of terrestrial ecology, carbon cycle, and remote sensing scientists and working groups. We conclude that: (1) current global biomass and 3-D vegetation structure information is unsuitable for both science and management and policy. The only existing global datasets of biomass are approximations based on combining land cover type and representative carbon values, instead of measurements of actual biomass. Current measurement attempts based on radar and multispectral

  17. Process monitor of 3D-device features by using FIB and CD-SEM

    NASA Astrophysics Data System (ADS)

    Kawada, Hiroki; Ikota, Masami; Sakai, Hideo; Torikawa, Shota; Tomimatsu, Satoshi; Onishi, Tsuyoshi

    2016-03-01

    For yield improvement of 3D-device manufacturing, metrology for the variability of individual device-features is on hot issue. Transmission Electron Microscope (TEM) can be used for monitoring the individual cross-section. However, efficiency of process monitoring is limited by the speed of measurement including preparation of lamella sample. In this work we demonstrate speedy 3D-profile measurement of individual line-features without the lamella sampling. For instance, we make a-few-micrometer-wide and 45-degree-descending slope in dense line-features by using Focused Ion Beam (FIB) tool capable of 300mm-wafer. On the descending slope, obliquely cut cross-section of the line features appears. Then, we transfer the wafer to Critical-Dimension Secondary Electron Microscope (CDSEM) to measure the oblique cross-section in normal top-down view. As the descending angle is 45 degrees, the oblique cross-section looks like a cross-section normal to the wafer surface. For every single line-features the 3D dimensions are measured. To the reference metrology of the Scanning TEM (STEM), nanometric linearity and precision are confirmed for the height and the width under the hard mask of the line features. Without cleaving wafer the 60 cells on the wafer can be measured in 3 hours, which allows us of near-line process monitor of in-wafer uniformity.

  18. The malarial drug target Plasmodium falciparum 1-deoxy-D-xylulose-5-phosphate reductoisomerase (PfDXR): development of a 3-D model for identification of novel, structural and functional features and for inhibitor screening.

    PubMed

    Goble, Jessica L; Adendorff, Matthew R; de Beer, Tjaart A P; Stephens, Linda L; Blatch, Gregory L

    2010-01-01

    A three-dimensional model of the malarial drug target protein PfDXR was generated, and validated using structure-checking programs and protein docking studies. Structural and functional features unique to PfDXR were identified using the model and comparative sequence analyses with apicomplexan and non-apicomplexan DXR proteins. Furthermore, we have used the model to develop an efficient approach to screen for potential tool compounds for use in the rational design of novel DXR inhibitors.

  19. Simulation approach of atomic layer deposition in large 3D structures

    NASA Astrophysics Data System (ADS)

    Schwille, Matthias C.; Barth, Jonas; Schössler, Timo; Schön, Florian; Bartha, Johann W.; Oettel, Martin

    2017-04-01

    We present a new simulation method predicting thicknesses of thin films obtained by atomic layer deposition in high aspect ratio 3D geometries as they appear in MEMS manufacturing. The method features a Monte-Carlo computation of film deposition in free molecular flow, as well as in the Knudsen and diffusive gas regime, applicable for large structures. We compare our approach to analytic and simulation results from the literature. The capability of the method is demonstrated by a comparison to experimental film thicknesses in a large 3D structure. Finally, the feasability to extract process parameters, i.e. sticking coefficients is shown.

  20. Protein 3D structure computed from evolutionary sequence variation.

    PubMed

    Marks, Debora S; Colwell, Lucy J; Sheridan, Robert; Hopf, Thomas A; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

    2011-01-01

    The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing.In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy.We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues, including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7-4.8 Å C(α)-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein structures

  1. Efficient global wave propagation adapted to 3-D structural complexity: a pseudospectral/spectral-element approach

    NASA Astrophysics Data System (ADS)

    Leng, Kuangdai; Nissen-Meyer, Tarje; van Driel, Martin

    2016-12-01

    We present a new, computationally efficient numerical method to simulate global seismic wave propagation in realistic 3-D Earth models. We characterize the azimuthal dependence of 3-D wavefields in terms of Fourier series, such that the 3-D equations of motion reduce to an algebraic system of coupled 2-D meridian equations, which is then solved by a 2-D spectral element method (SEM). Computational efficiency of such a hybrid method stems from lateral smoothness of 3-D Earth models and axial singularity of seismic point sources, which jointly confine the Fourier modes of wavefields to a few lower orders. We show novel benchmarks for global wave solutions in 3-D structures between our method and an independent, fully discretized 3-D SEM with remarkable agreement. Performance comparisons are carried out on three state-of-the-art tomography models, with seismic period ranging from 34 s down to 11 s. It turns out that our method has run up to two orders of magnitude faster than the 3-D SEM, featured by a computational advantage expanding with seismic frequency.

  2. 3D Printing of Hierarchical Silk Fibroin Structures.

    PubMed

    Sommer, Marianne R; Schaffner, Manuel; Carnelli, Davide; Studart, André R

    2016-12-21

    Like many other natural materials, silk is hierarchically structured from the amino acid level up to the cocoon or spider web macroscopic structures. Despite being used industrially in a number of applications, hierarchically structured silk fibroin objects with a similar degree of architectural control as in natural structures have not been produced yet due to limitations in fabrication processes. In a combined top-down and bottom-up approach, we exploit the freedom in macroscopic design offered by 3D printing and the template-guided assembly of ink building blocks at the meso- and nanolevel to fabricate hierarchical silk porous materials with unprecedented structural control. Pores with tunable sizes in the range 40-350 μm are generated by adding sacrificial organic microparticles as templates to a silk fibroin-based ink. Commercially available wax particles or monodisperse polycaprolactone made by microfluidics can be used as microparticle templates. Since closed pores are generated after template removal, an ultrasonication treatment can optionally be used to achieve open porosity. Such pore templating particles can be further modified with nanoparticles to create a hierarchical template that results in porous structures with a defined nanotopography on the pore walls. The hierarchically porous silk structures obtained with this processing technique can potentially be utilized in various application fields from structural materials to thermal insulation to tissue engineering scaffolds.

  3. Diagnosis and control of 3D elastic mechanical structures

    NASA Astrophysics Data System (ADS)

    Krajcin, Idriz; Soeffker, Dirk

    2005-05-01

    In this paper, a model-based approach for fault detection and vibration control of flexible structures is proposed and applied to 3D-structures. Faults like cracks or impacts acting on a flexible structure are considered as unknown inputs acting on the structure. The Proportional-Integral-Observer (PI-Observer) is used to estimate the system states as well as unknown inputs acting on a system. Also the effects of structural changes are understood as external effects (related to the unchanged structure) and are considered as fictitious external forces or moments. The paper deals with the design of the PI-Observer for practical applications when measurement noise and model uncertainties are present and shows its performance in experimental results. As examples, impacts acting upon a one side clamped elastic beam and on a thin plate structure are estimated using displacement or strain measurements. To control the vibration of the flexible plate, two piezoelectric patches bonded on the structure are used as actuators. The control algorithm introduced in this contribution contains a state feedback control and additionally a disturbance rejection. The disturbances are estimated using the PI-Observer. Experimental results show the performance and the robustness properties of the control strategy for the vibration control of a very thin plate.

  4. Computerized lung cancer malignancy level analysis using 3D texture features

    NASA Astrophysics Data System (ADS)

    Sun, Wenqing; Huang, Xia; Tseng, Tzu-Liang; Zhang, Jianying; Qian, Wei

    2016-03-01

    Based on the likelihood of malignancy, the nodules are classified into five different levels in Lung Image Database Consortium (LIDC) database. In this study, we tested the possibility of using threedimensional (3D) texture features to identify the malignancy level of each nodule. Five groups of features were implemented and tested on 172 nodules with confident malignancy levels from four radiologists. These five feature groups are: grey level co-occurrence matrix (GLCM) features, local binary pattern (LBP) features, scale-invariant feature transform (SIFT) features, steerable features, and wavelet features. Because of the high dimensionality of our proposed features, multidimensional scaling (MDS) was used for dimension reduction. RUSBoost was applied for our extracted features for classification, due to its advantages in handling imbalanced dataset. Each group of features and the final combined features were used to classify nodules highly suspicious for cancer (level 5) and moderately suspicious (level 4). The results showed that the area under the curve (AUC) and accuracy are 0.7659 and 0.8365 when using the finalized features. These features were also tested on differentiating benign and malignant cases, and the reported AUC and accuracy were 0.8901 and 0.9353.

  5. Quantitative analysis and feature recognition in 3-D microstructural data sets

    NASA Astrophysics Data System (ADS)

    Lewis, A. C.; Suh, C.; Stukowski, M.; Geltmacher, A. B.; Spanos, G.; Rajan, K.

    2006-12-01

    A three-dimensional (3-D) reconstruction of an austenitic stainless-steel microstructure was used as input for an image-based finite-element model to simulate the anisotropic elastic mechanical response of the microstructure. The quantitative data-mining and data-warehousing techniques used to correlate regions of high stress with critical microstructural features are discussed. Initial analysis of elastic stresses near grain boundaries due to mechanical loading revealed low overall correlation with their location in the microstructure. However, the use of data-mining and feature-tracking techniques to identify high-stress outliers revealed that many of these high-stress points are generated near grain boundaries and grain edges (triple junctions). These techniques also allowed for the differentiation between high stresses due to boundary conditions of the finite volume reconstructed, and those due to 3-D microstructural features.

  6. Automatic feature detection for 3D surface reconstruction from HDTV endoscopic videos

    NASA Astrophysics Data System (ADS)

    Groch, Anja; Baumhauer, Matthias; Meinzer, Hans-Peter; Maier-Hein, Lena

    2010-02-01

    A growing number of applications in the field of computer-assisted laparoscopic interventions depend on accurate and fast 3D surface acquisition. The most commonly applied methods for 3D reconstruction of organ surfaces from 2D endoscopic images involve establishment of correspondences in image pairs to allow for computation of 3D point coordinates via triangulation. The popular feature-based approach for correspondence search applies a feature descriptor to compute high-dimensional feature vectors describing the characteristics of selected image points. Correspondences are established between image points with similar feature vectors. In a previous study, the performance of a large set of state-of-the art descriptors for the use in minimally invasive surgery was assessed. However, standard Phase Alternating Line (PAL) endoscopic images were utilized for this purpose. In this paper, we apply some of the best performing feature descriptors to in-vivo PAL endoscopic images as well as to High Definition Television (HDTV) endoscopic images of the same scene and show that the quality of the correspondences can be increased significantly when using high resolution images.

  7. 3D flexible NiTi-braided elastomer composites for smart structure applications

    NASA Astrophysics Data System (ADS)

    Heller, L.; Vokoun, D.; Šittner, P.; Finckh, H.

    2012-04-01

    While outstanding functional properties of thin NiTi wires are nowadays well recognized and beneficially utilized in medical NiTi devices, development of 2D/3D wire structures made out of these NiTi wires remains challenging and mostly unexplored. The research is driven by the idea of creating novel 2D/3D smart structures which inherit the functional properties of NiTi wires and actively utilize geometrical deformations within the structure to create new/improved functional properties. Generally, textile technology provides attractive processing methods for manufacturing 2D/3D smart structures made out of NiTi wires. Such structures may be beneficially combined with soft elastomers to create smart deformable composites. Following this route, we carried out experimental work focused on development of 3D flexible NiTi-braided elastomer composites involving their design, laboratory manufacture and thermomechanical testing. We describe the manufacturing technology and structural properties of these composites; and perform thermomechanical tests on the composites, focusing particularly on quasistatic tensile properties, energy absorption, damping and actuation under tensile loading. Functional thermomechanical properties of the composites are discussed with regard to the mechanical properties of the components and architecture of the composites. It is found that the composites indeed inherit all important features of the thermomechanical behavior of NiTi wires but, due to their internal architecture, outperform single NiTi wires in some features such as the magnitude of recoverable strain, superelastic damping capacity and thermally induced actuation strain.

  8. Definition of subsurface stratigraphy, structure and rock properties from 3-D seismic data

    NASA Astrophysics Data System (ADS)

    Hart, Bruce S.

    1999-10-01

    This paper summarizes how three-dimensional (3-D) seismic technology is being used, primarily in the petroleum industry, to define subsurface structure, stratigraphy and rock properties. A 3-D seismic data volume: (a) provides a more accurate image of the subsurface than can be obtained with 2-D seismic methods; (b) is continuous, and so has a much greater spatial sampling than is obtained with 2-D seismic or other subsurface data (e.g., wells); and (c) can be viewed and interpreted interactively from a variety of perspectives, thus enhancing the interpreter's ability to generate an accurate description of subsurface features of interest. Seismic interpretation was once the almost exclusive realm of geophysicists, however, most 3-D seismic interpretation today is conducted by multidisciplinary teams that integrate geophysical, geological, petrophysical and engineering data and concepts into the 3-D seismic interpretation. These factors, plus proper survey design, help to increase the chances of success of a 3-D seismic interpretation project. Although there are cases where the technology is not appropriate or cannot be applied (for economic reasons or otherwise), the general success of 3-D seismic has led it to become a mainstay of the petroleum industry. The approach and technology, first developed in that industry, have potential applications in other applied and fundamental earth science disciplines, including mining, environmental geology, structural geology and stratigraphy.

  9. Proteins without unique 3D structures: biotechnological applications of intrinsically unstable/disordered proteins.

    PubMed

    Uversky, Vladimir N

    2015-03-01

    Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) are functional proteins or regions that do not have unique 3D structures under functional conditions. Therefore, from the viewpoint of their lack of stable 3D structure, IDPs/IDPRs are inherently unstable. As much as structure and function of normal ordered globular proteins are determined by their amino acid sequences, the lack of unique 3D structure in IDPs/IDPRs and their disorder-based functionality are also encoded in the amino acid sequences. Because of their specific sequence features and distinctive conformational behavior, these intrinsically unstable proteins or regions have several applications in biotechnology. This review introduces some of the most characteristic features of IDPs/IDPRs (such as peculiarities of amino acid sequences of these proteins and regions, their major structural features, and peculiar responses to changes in their environment) and describes how these features can be used in the biotechnology, for example for the proteome-wide analysis of the abundance of extended IDPs, for recombinant protein isolation and purification, as polypeptide nanoparticles for drug delivery, as solubilization tools, and as thermally sensitive carriers of active peptides and proteins.

  10. POISs3: A 3D poisson smoother of structured grids

    NASA Astrophysics Data System (ADS)

    Lehtimaeki, R.

    Flow solvers based on solving Navier-Stokes or Euler equations generally need a computational grid to represent the domain of the flow. A structured computational grid can be efficiently produced by algebraic methods like transfinite interpolation. Unfortunately, algebraic methods propagate all kinds of unsmoothness of the boundary into the field. Unsmoothness of the grid, in turn, can result in inaccuracy in the flow solver. In the present work a 3D elliptic grid smoother was developed. The smoother is based on solving three Poisson equations, one for each curvilinear direction. The Poisson equations formed in the physical region are first transformed to the computational (rectilinear) region. The resulting equations form a system of three coupled elliptic quasi-linear partial differential equations in the computational domain. A short review of the Poisson method is presented. The regularity of a grid cell is studied and a skewness value is developed.

  11. Prediction of spin-dependent electronic structure in 3d-transition-metal doped antimonene

    NASA Astrophysics Data System (ADS)

    Yang, L. F.; Song, Y.; Mi, W. B.; Wang, X. C.

    2016-07-01

    We investigate the geometric structure and electronic and magnetic properties of 3d-transition-metal atom doped antimonene using spin-polarized first-principles calculations. Strong orbital hybridization exhibits between 3d-transition-metal and Sb atoms, where covalent bonds form in antimonene. A spin-polarized semiconducting state appears in Cr-doped antimonene, while half-metallic states appear by doping Ti, V, and Mn. These findings indicate that once combined with doping states, the bands of antimonene systems offer a variety of features. Specific dopants lead to half-metallic characters with high spin polarization that has potential application in spintronics.

  12. Multifunctional 3D printing of heterogeneous hydrogel structures.

    PubMed

    Nadernezhad, Ali; Khani, Navid; Skvortsov, Gözde Akdeniz; Toprakhisar, Burak; Bakirci, Ezgi; Menceloglu, Yusuf; Unal, Serkan; Koc, Bahattin

    2016-09-15

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing.

  13. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

    The properties of molecules derive in part from their structures. Because of the importance of understanding molecular structures various methodologies, ranging from first principles to empirical technique, were developed for computing the structure of molecules. For large molecules such as polymer model compounds, the structural information is difficult to comprehend by examining tabulated data. Therefore, a molecular graphics display system, called MOLDS, was developed to help interpret the data. MOLDS is a menu-driven program developed to run on the LADC SNS computer systems. This program can read a data file generated by the modeling programs or data can be entered using the keyboard. MOLDS has the following capabilities: draws the 3-D representation of a molecule using stick, ball and ball, or space filled model from Cartesian coordinates, draws different perspective views of the molecule; rotates the molecule on the X, Y, Z axis or about some arbitrary line in space, zooms in on a small area of the molecule in order to obtain a better view of a specific region; and makes hard copy representation of molecules on a graphic printer. In addition, MOLDS can be easily updated and readily adapted to run on most computer systems.

  14. Multifunctional 3D printing of heterogeneous hydrogel structures

    NASA Astrophysics Data System (ADS)

    Nadernezhad, Ali; Khani, Navid; Skvortsov, Gözde Akdeniz; Toprakhisar, Burak; Bakirci, Ezgi; Menceloglu, Yusuf; Unal, Serkan; Koc, Bahattin

    2016-09-01

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing.

  15. Multifunctional 3D printing of heterogeneous hydrogel structures

    PubMed Central

    Nadernezhad, Ali; Khani, Navid; Skvortsov, Gözde Akdeniz; Toprakhisar, Burak; Bakirci, Ezgi; Menceloglu, Yusuf; Unal, Serkan; Koc, Bahattin

    2016-01-01

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing. PMID:27630079

  16. 3D Printing Meets Computational Astrophysics: Deciphering the Structure of Eta Carinae’s Colliding Winds Using 3D Prints of Smoothed Particle Hydrodynamics Simulations

    NASA Astrophysics Data System (ADS)

    Madura, Thomas; Gull, Theodore R.; Clementel, Nicola; Paardekooper, Jan-Pieter; Kruip, Chael; Corcoran, Michael F.; Hamaguchi, Kenji; Teodoro, Mairan

    2015-01-01

    We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (>120 MSun), highly eccentric (e ~ 0.9) binary Eta Carinae. Using a consumer-grade 3D printer (Makerbot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics simulations of Eta Carinae's inner (r ~110 AU) wind-wind collision interface at multiple orbital phases. These 3D prints reveal important, previously unknown 'finger-like' structures at orbital phases shortly after periastron (φ ~1.045) that protrude radially outward from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. Rayleigh-Taylor) that arise at the interface between the radiatively-cooled layer of dense post-shock primary-star wind and the hot, adiabatic post-shock companion-star wind. The success of our work and easy identification of previously unknown physical features highlight the important role 3D printing can play in the visualization and understanding of complex 3D time-dependent numerical simulations of astrophysical phenomena.

  17. Proteopedia: Exciting Advances in the 3D Encyclopedia of Biomolecular Structure

    NASA Astrophysics Data System (ADS)

    Prilusky, Jaime; Hodis, Eran; Sussman, Joel L.

    Proteopedia is a collaborative, 3D web-encyclopedia of protein, nucleic acid and other structures. Proteopedia ( http://www.proteopedia.org ) presents 3D biomolecule structures in a broadly accessible manner to a diverse scientific audience through easy-to-use molecular visualization tools integrated into a wiki environment that anyone with a user account can edit. We describe recent advances in the web resource in the areas of content and software. In terms of content, we describe a large growth in user-added content as well as improvements in automatically-generated content for all PDB entry pages in the resource. In terms of software, we describe new features ranging from the capability to create pages hidden from public view to the capability to export pages for offline viewing. New software features also include an improved file-handling system and availability of biological assemblies of protein structures alongside their asymmetric units.

  18. 3D printing technology using high viscous materials - Synthesis of functional materials and fabrication of 3D metal structure

    NASA Astrophysics Data System (ADS)

    Hong, Seongik

    In the 3D printing technology, the research for using various materials has been performing. In this research work, 3D printable high viscous materials are suggested as one of the solutions for problems in the traditional 3D printing technology. First, Cu-Ag coreshell was synthesized as a functional material. In terms of the reaction rate, reaction rate limiting step was defined as a fundamental research, and then prepared Cu-Ag coreshell was printed and analyzed. Second, the high viscous Cu paste was prepared and then metal 3D printed structure was fabricated by using new printing method. In the synthesis of Cu-Ag coreshell, different sizes of Cu particle, 2μm and 100nm were used, and when 2μm Cu was applied, the reaction rate was limited by film diffusion control. However, when 100nm Cu was applied, reaction rate was controlled by CuO film and the rate of the reaction, which includes removing CuO film in the solution, is limited by chemical reaction control. The shape of Cu-Ag particle is spherical in the 2μm Cu condition and dendrite shape in the 100nm Cu condition respectively. The conductivity of Cu-Ag coreshell paste increased as increasing content of coreshell particle in the paste and sintering temperature. In order to print high viscous metal paste, the high viscous Cu paste was printed by using screw extruder, and the viscosity of Cu paste was measured as a fundamental research. As increasing wt.% of Cu in the paste, the viscosity also increased. In addition, the shrinkage factor was reduced by increasing wt.% of Cu in the paste. An optimized printing condition for the high viscous material was obtained, and by using this condition, 3D metal structure was fabricated. The final product was heat treated and polished. Through these processes, a fine quality of metal 3D structure was printed.

  19. 3D Imaging with Structured Illumination for Advanced Security Applications

    SciTech Connect

    Birch, Gabriel Carisle; Dagel, Amber Lynn; Kast, Brian A.; Smith, Collin S.

    2015-09-01

    Three-dimensional (3D) information in a physical security system is a highly useful dis- criminator. The two-dimensional data from an imaging systems fails to provide target dis- tance and three-dimensional motion vector, which can be used to reduce nuisance alarm rates and increase system effectiveness. However, 3D imaging devices designed primarily for use in physical security systems are uncommon. This report discusses an architecture favorable to physical security systems; an inexpensive snapshot 3D imaging system utilizing a simple illumination system. The method of acquiring 3D data, tests to understand illumination de- sign, and software modifications possible to maximize information gathering capability are discussed.

  20. Parameterization of 3D brain structures for statistical shape analysis

    NASA Astrophysics Data System (ADS)

    Zhu, Litao; Jiang, Tianzi

    2004-05-01

    Statistical Shape Analysis (SSA) is a powerful tool for noninvasive studies of pathophysiology and diagnosis of brain diseases. It also provides a shape constraint for the segmentation of brain structures. There are two key problems in SSA: the representation of shapes and their alignments. The widely used parameterized representations are obtained by preserving angles or areas and the alignments of shapes are achieved by rotating parameter net. However, representations preserving angles or areas do not really guarantee the anatomical correspondence of brain structures. In this paper, we incorporate shape-based landmarks into parameterization of banana-like 3D brain structures to address this problem. Firstly, we get the triangulated surface of the object and extract two landmarks from the mesh, i.e. the ends of the banana-like object. Then the surface is parameterized by creating a continuous and bijective mapping from the surface to a spherical surface based on a heat conduction model. The correspondence of shapes is achieved by mapping the two landmarks to the north and south poles of the sphere and using an extracted origin orientation to select the dateline during parameterization. We apply our approach to the parameterization of lateral ventricle and a multi-resolution shape representation is obtained by using the Discrete Fourier Transform.

  1. The 3D structure of Coronal Mass Ejections

    NASA Astrophysics Data System (ADS)

    Patsourakos, Spiros

    2016-07-01

    Coronal Mass Ejections (CMEs) represent one of the most powerful energy release phenomena in the entire solar system and are a major driver of space weather. Prior to 2006, our observational access to CMEs was limited to single viewpoint remote sensing observations in the inner/outer corona, and in-situ observations further away, e.g. at 1 AU. Taking all these factors together, turned out to be a major obstacle in our understanding and characterizing of the 3D structure and evolution of CMEs. The situation improved dramatically with the availability of multi-viewpoint imaging observations of CMEs, all way through from the Sun to 1 AU, from the STEREO mission since 2006, combined with observations from other missions (SOHO, Hinode, SDO, IRIS). With this talk we will discuss several key recent results in CME science resulting from the analysis of multi-viewpoint observations. This includes: (1) shape and structure; (2) kinematics and energetics; (3) trajectories, deflections and rotations; (4) arrival times and velocities at 1 AU; (5) magnetic field structure; (6) relationships with coronal and interplanetary shocks and solar energetic particles. The implications of these results in terms of CME theories and models will be also addressed. We will conclude with a discussion of important open issues in our understanding of CMEs and how these could be addressed with upcoming (Solar Orbiter, Solar Probe Plus) and under-study missions (e.g., L5).

  2. Improved hybrid optimization algorithm for 3D protein structure prediction.

    PubMed

    Zhou, Changjun; Hou, Caixia; Wei, Xiaopeng; Zhang, Qiang

    2014-07-01

    A new improved hybrid optimization algorithm - PGATS algorithm, which is based on toy off-lattice model, is presented for dealing with three-dimensional protein structure prediction problems. The algorithm combines the particle swarm optimization (PSO), genetic algorithm (GA), and tabu search (TS) algorithms. Otherwise, we also take some different improved strategies. The factor of stochastic disturbance is joined in the particle swarm optimization to improve the search ability; the operations of crossover and mutation that are in the genetic algorithm are changed to a kind of random liner method; at last tabu search algorithm is improved by appending a mutation operator. Through the combination of a variety of strategies and algorithms, the protein structure prediction (PSP) in a 3D off-lattice model is achieved. The PSP problem is an NP-hard problem, but the problem can be attributed to a global optimization problem of multi-extremum and multi-parameters. This is the theoretical principle of the hybrid optimization algorithm that is proposed in this paper. The algorithm combines local search and global search, which overcomes the shortcoming of a single algorithm, giving full play to the advantage of each algorithm. In the current universal standard sequences, Fibonacci sequences and real protein sequences are certified. Experiments show that the proposed new method outperforms single algorithms on the accuracy of calculating the protein sequence energy value, which is proved to be an effective way to predict the structure of proteins.

  3. 3D Seismic Imaging over a Potential Collapse Structure

    NASA Astrophysics Data System (ADS)

    Gritto, Roland; O'Connell, Daniel; Elobaid Elnaiem, Ali; Mohamed, Fathelrahman; Sadooni, Fadhil

    2016-04-01

    The Middle-East has seen a recent boom in construction including the planning and development of complete new sub-sections of metropolitan areas. Before planning and construction can commence, however, the development areas need to be investigated to determine their suitability for the planned project. Subsurface parameters such as the type of material (soil/rock), thickness of top soil or rock layers, depth and elastic parameters of basement, for example, comprise important information needed before a decision concerning the suitability of the site for construction can be made. A similar problem arises in environmental impact studies, when subsurface parameters are needed to assess the geological heterogeneity of the subsurface. Environmental impact studies are typically required for each construction project, particularly for the scale of the aforementioned building boom in the Middle East. The current study was conducted in Qatar at the location of a future highway interchange to evaluate a suite of 3D seismic techniques in their effectiveness to interrogate the subsurface for the presence of karst-like collapse structures. The survey comprised an area of approximately 10,000 m2 and consisted of 550 source- and 192 receiver locations. The seismic source was an accelerated weight drop while the geophones consisted of 3-component 10 Hz velocity sensors. At present, we analyzed over 100,000 P-wave phase arrivals and performed high-resolution 3-D tomographic imaging of the shallow subsurface. Furthermore, dispersion analysis of recorded surface waves will be performed to obtain S-wave velocity profiles of the subsurface. Both results, in conjunction with density estimates, will be utilized to determine the elastic moduli of the subsurface rock layers.

  4. CARd-3D: Carbon Distribution in 3D Structure Program for Globular Proteins.

    PubMed

    Ekambaram, Rajasekaran; Kannaiyan, Akila; Marimuthu, Vijayasarathy; Swaminathan, Vinobha Chinnaiah; Renganathan, Senthil; Perumal, Ananda Gopu

    2014-01-01

    Spatial arrangement of carbon in protein structure is analyzed here. Particularly, the carbon fractions around individual atoms are compared. It is hoped that it follows the principle of 31.45% carbon around individual atoms. The results reveal that globular protein's atoms follow this principle. A comparative study on monomer versus dimer reveal that carbon is better distributed in dimeric form than in its monomeric form. Similar study on solid versus liquid structures reveals that the liquid (NMR) structure has better carbon distribution over the corresponding solid (X-Ray) structure. The carbon fraction distributions in fiber and toxin protein are compared. Fiber proteins follow the principle of carbon fraction distribution. At the same time it has another broad spectrum of carbon distribution than in globular proteins. The toxin protein follows an abnormal carbon fraction distribution. The carbon fraction distribution plays an important role in deciding the structure and shape of proteins. It is hoped to help in understanding the protein folding and function.

  5. Validate and update of 3D urban features using multi-source fusion

    NASA Astrophysics Data System (ADS)

    Arrington, Marcus; Edwards, Dan; Sengers, Arjan

    2012-06-01

    As forecast by the United Nations in May 2007, the population of the world transitioned from a rural to an urban demographic majority with more than half living in urban areas.1 Modern urban environments are complex 3- dimensional (3D) landscapes with 4-dimensional patterns of activity that challenge various traditional 1-dimensional and 2-dimensional sensors to accurately sample these man-made terrains. Depending on geographic location, data resulting from LIDAR, multi-spectral, electro-optical, thermal, ground-based static and mobile sensors may be available with multiple collects along with more traditional 2D GIS features. Reconciling differing data sources over time to correctly portray the dynamic urban landscape raises significant fusion and representational challenges particularly as higher levels of spatial resolution are available and expected by users. This paper presents a framework for integrating the imperfect answers of our differing sensors and data sources into a powerful representation of the complex urban environment. A case study is presented involving the integration of temporally diverse 2D, 2.5D and 3D spatial data sources over Kandahar, Afghanistan. In this case study we present a methodology for validating and augmenting 2D/2.5D urban feature and attribute data with LIDAR to produce validated 3D objects. We demonstrate that nearly 15% of buildings in Kandahar require understanding nearby vegetation before 3-D validation can be successful. We also address urban temporal change detection at the object level. Finally we address issues involved with increased sampling resolution since urban features are rarely simple cubes but in the case of Kandahar involve balconies, TV dishes, rooftop walls, small rooms, and domes among other things.

  6. The 3D Attenuation Structure of Deception Island (Antarctica)

    NASA Astrophysics Data System (ADS)

    Prudencio, J.; De Siena, L.; Ibáñez, J. M.; Del Pezzo, E.; García-Yeguas, A.; Díaz-Moreno, A.

    2015-05-01

    The seismic and volcanological structure of Deception Island (Antarctica) is an intense focus topic in Volcano Geophysics. The interpretations given by scientists on the origin, nature, and location of the structures buried under the island strongly diverge. We present a high-resolution 3D P-wave attenuation tomography model obtained by using the coda normalization method on 20,293 high-quality waveforms produced by active sources. The checkerboard and synthetic anomaly tests guarantee the reproduction of the input anomalies under the island down to a depth of 4 km. The results, once compared with our current knowledge on the geological, geochemical, and geophysical structure of the region, depict Deception as a piecemeal caldera structure coming out of the Bransfield Trough. High-attenuation anomalies contouring the northeastern emerged caldera rim correlate with the locations of sediments. In our interpretation, the main attenuation contrast, which appears under the collapsed southeastern caldera rim, is related to the deeper feeding systems. A unique P-wave high-attenuation spherical-like anomaly in the inner bay extends between depths of 1 and 3 km. The northern contour of the anomaly coincides with the calderic rim both at 1 and 2 km, while smaller anomalies connect it with deeper structures below 3 km, dipping toward the Bransfield Trough. In our interpretation, the large upper anomaly is caused by a high-temperature shallow (1-3 km deep) geothermal system, located beneath the sediment-filled bay in the collapsed blocks and heated by smaller, deeper contributions of molten materials (magma) rising from southeast.

  7. 3D structures of membrane proteins from genomic sequencing

    PubMed Central

    Hopf, Thomas A.; Colwell, Lucy J.; Sheridan, Robert; Rost, Burkhard; Sander, Chris; Marks, Debora S.

    2012-01-01

    Summary We show that amino acid co-variation in proteins, extracted from the evolutionary sequence record, can be used to fold transmembrane proteins. We use this technique to predict previously unknown, 3D structures for 11 transmembrane proteins (with up to 14 helices) from their sequences alone. The prediction method (EVfold_membrane), applies a maximum entropy approach to infer evolutionary co-variation in pairs of sequence positions within a protein family and then generates all-atom models with the derived pairwise distance constraints. We benchmark the approach with blinded, de novo computation of known transmembrane protein structures from 23 families, demonstrating unprecedented accuracy of the method for large transmembrane proteins. We show how the method can predict oligomerization, functional sites, and conformational changes in transmembrane proteins. With the rapid rise in large-scale sequencing, more accurate and more comprehensive information on evolutionary constraints can be decoded from genetic variation, greatly expanding the repertoire of transmembrane proteins amenable to modelling by this method. PMID:22579045

  8. Pack Aluminization Synthesis of Superalloy 3D Woven and 3D Braided Structures

    NASA Astrophysics Data System (ADS)

    Erdeniz, Dinc; Levinson, Amanda J.; Sharp, Keith W.; Rowenhorst, David J.; Fonda, Richard W.; Dunand, David C.

    2015-01-01

    Micro-architectured, precipitation-strengthened structures were created in a new process combining weaving, gas-phase alloying, diffusion, and precipitation. First, high-ductility Ni-20 wt pct Cr wires with 202 μm diameter were braided, or non-crimp orthogonal woven, into three-dimensional structures. Second, these structures were vapor-phase alloyed with Al at 1273 K (1000 °C) by pack cementation, creating uniform NiAl coatings on the wires when using a retort. Also, solid-state bonding was achieved at wire intersections, where two wires were sufficiently close to each other, as determined via optical and X-ray tomographic microscopy. Third, the NiAl-coated wires were fully homogenized and aged to form γ' precipitates distributed in a γ matrix phase, the same microstructure providing strength in nickel-based superalloys. The resulting structures—consisting of wires (i) woven in a controlled three-dimensional architecture, (ii) bonded at contact points and (iii) strengthened by γ' precipitates—are expected to show high strength at ambient and elevated temperatures, low density, and high permeability which is useful for active cooling.

  9. 3D printed low-loss THz waveguide based on Kagome photonic crystal structure.

    PubMed

    Yang, Jing; Zhao, Jiayu; Gong, Cheng; Tian, Haolin; Sun, Lu; Chen, Ping; Lin, Lie; Liu, Weiwei

    2016-10-03

    A low-loss hollow core terahertz waveguide based on Kagome photonic crystal structure has been designed and fabricated by 3D printing. The 3D printed waveguide has been characterized by using THz time-domain spectroscopy. The results demonstrate that the obtained waveguide features average power propagation loss of 0.02 cm-1 for 0.2-1.0 THz (the minimum is about 0.002 cm-1 at 0.75 THz). More interesting, it could be simply mechanically spliced without any additional alignment, while maintaining the excellent performance. The 3D printing technique will be a promising solution to fabricate Kagome THz waveguide with well controllable characteristics and low cost.

  10. Recognizing Objects in 3D Point Clouds with Multi-Scale Local Features

    PubMed Central

    Lu, Min; Guo, Yulan; Zhang, Jun; Ma, Yanxin; Lei, Yinjie

    2014-01-01

    Recognizing 3D objects from point clouds in the presence of significant clutter and occlusion is a highly challenging task. In this paper, we present a coarse-to-fine 3D object recognition algorithm. During the phase of offline training, each model is represented with a set of multi-scale local surface features. During the phase of online recognition, a set of keypoints are first detected from each scene. The local surfaces around these keypoints are further encoded with multi-scale feature descriptors. These scene features are then matched against all model features to generate recognition hypotheses, which include model hypotheses and pose hypotheses. Finally, these hypotheses are verified to produce recognition results. The proposed algorithm was tested on two standard datasets, with rigorous comparisons to the state-of-the-art algorithms. Experimental results show that our algorithm was fully automatic and highly effective. It was also very robust to occlusion and clutter. It achieved the best recognition performance on all of these datasets, showing its superiority compared to existing algorithms. PMID:25517694

  11. Recognizing objects in 3D point clouds with multi-scale local features.

    PubMed

    Lu, Min; Guo, Yulan; Zhang, Jun; Ma, Yanxin; Lei, Yinjie

    2014-12-15

    Recognizing 3D objects from point clouds in the presence of significant clutter and occlusion is a highly challenging task. In this paper, we present a coarse-to-fine 3D object recognition algorithm. During the phase of offline training, each model is represented with a set of multi-scale local surface features. During the phase of online recognition, a set of keypoints are first detected from each scene. The local surfaces around these keypoints are further encoded with multi-scale feature descriptors. These scene features are then matched against all model features to generate recognition hypotheses, which include model hypotheses and pose hypotheses. Finally, these hypotheses are verified to produce recognition results. The proposed algorithm was tested on two standard datasets, with rigorous comparisons to the state-of-the-art algorithms. Experimental results show that our algorithm was fully automatic and highly effective. It was also very robust to occlusion and clutter. It achieved the best recognition performance on all of these datasets, showing its superiority compared to existing algorithms.

  12. 3D Soil Images Structure Quantification using Relative Entropy

    NASA Astrophysics Data System (ADS)

    Tarquis, A. M.; Gonzalez-Nieto, P. L.; Bird, N. R. A.

    2012-04-01

    Soil voids manifest the cumulative effect of local pedogenic processes and ultimately influence soil behavior - especially as it pertains to aeration and hydrophysical properties. Because of the relatively weak attenuation of X-rays by air, compared with liquids or solids, non-disruptive CT scanning has become a very attractive tool for generating three-dimensional imagery of soil voids. One of the main steps involved in this analysis is the thresholding required to transform the original (greyscale) images into the type of binary representation (e.g., pores in white, solids in black) needed for fractal analysis or simulation with Lattice-Boltzmann models (Baveye et al., 2010). The objective of the current work is to apply an innovative approach to quantifying soil voids and pore networks in original X-ray CT imagery using Relative Entropy (Bird et al., 2006; Tarquis et al., 2008). These will be illustrated using typical imagery representing contrasting soil structures. Particular attention will be given to the need to consider the full 3D context of the CT imagery, as well as scaling issues, in the application and interpretation of this index.

  13. Slat Cove Unsteadiness Effect of 3D Flow Structures

    NASA Technical Reports Server (NTRS)

    Choudhari, Meelan M.; Khorrami, Mehdi R.

    2006-01-01

    Previous studies have indicated that 2D, time accurate computations based on a pseudo-laminar zonal model of the slat cove region (within the framework of the Reynolds-Averaged Navier-Stokes equations) are inadequate for predicting the full unsteady dynamics of the slat cove flow field. Even though such computations could capture the large-scale, unsteady vorticity structures in the slat cove region without requiring any external forcing, the simulated vortices were excessively strong and the recirculation zone was unduly energetic in comparison with the PIV measurements for a generic high-lift configuration. To resolve this discrepancy and to help enable physics based predictions of slat aeroacoustics, the present paper is focused on 3D simulations of the slat cove flow over a computational domain of limited spanwise extent. Maintaining the pseudo-laminar approach, current results indicate that accounting for the three-dimensionality of flow fluctuations leads to considerable improvement in the accuracy of the unsteady, nearfield solution. Analysis of simulation data points to the likely significance of turbulent fluctuations near the reattachment region toward the generation of broadband slat noise. The computed acoustic characteristics (in terms of the frequency spectrum and spatial distribution) within short distances from the slat resemble the previously reported, subscale measurements of slat noise.

  14. 3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures

    PubMed Central

    Wang, Jian; Zhao, Yunjie; Zhu, Chunyan; Xiao, Yi

    2015-01-01

    Model evaluation is a necessary step for better prediction and design of 3D RNA structures. For proteins, this has been widely studied and the knowledge-based statistical potential has been proved to be one of effective ways to solve this problem. Currently, a few knowledge-based statistical potentials have also been proposed to evaluate predicted models of RNA tertiary structures. The benchmark tests showed that they can identify the native structures effectively but further improvements are needed to identify near-native structures and those with non-canonical base pairs. Here, we present a novel knowledge-based potential, 3dRNAscore, which combines distance-dependent and dihedral-dependent energies. The benchmarks on different testing datasets all show that 3dRNAscore are more efficient than existing evaluation methods in recognizing native state from a pool of near-native states of RNAs as well as in ranking near-native states of RNA models. PMID:25712091

  15. Comparison of 2D and 3D wavelet features for TLE lateralization

    NASA Astrophysics Data System (ADS)

    Jafari-Khouzani, Kourosh; Soltanian-Zadeh, Hamid; Elisevich, Kost; Patel, Suresh

    2004-04-01

    Intensity and volume features of the hippocampus from MR images of the brain are known to be useful in detecting the abnormality and consequently candidacy of the hippocampus for temporal lobe epilepsy surgery. However, currently, intracranial EEG exams are required to determine the abnormal hippocampus. These exams are lengthy, painful and costly. The aim of this study is to evaluate texture characteristics of the hippocampi from MR images to help physicians determine the candidate hippocampus for surgery. We studied the MR images of 20 epileptic patients. Intracranial EEG results as well as surgery outcome were used as gold standard. The hippocampi were manually segmented by an expert from T1-weighted MR images. Then the segmented regions were mapped on the corresponding FLAIR images for texture analysis. We calculate the average energy features from 2D wavelet transform of each slice of hippocampus as well as the energy features produced by 3D wavelet transform of the whole hippocampus volume. The 2D wavelet transform is calculated both from the original slices as well as from the slices perpendicular to the principal axis of the hippocampus. In order to calculate the 3D wavelet transform we first rotate each hippocampus to fit it in a rectangular prism and then fill the empty area by extrapolating the intensity values. We combine the resulting features with volume feature and compare their ability to distinguish between normal and abnormal hippocampi using linear classifier and fuzzy c-means clustering algorithm. Experimental results show that the texture features can correctly classify the hippocampi.

  16. Visual Object Recognition with 3D-Aware Features in KITTI Urban Scenes

    PubMed Central

    Yebes, J. Javier; Bergasa, Luis M.; García-Garrido, Miguel Ángel

    2015-01-01

    Driver assistance systems and autonomous robotics rely on the deployment of several sensors for environment perception. Compared to LiDAR systems, the inexpensive vision sensors can capture the 3D scene as perceived by a driver in terms of appearance and depth cues. Indeed, providing 3D image understanding capabilities to vehicles is an essential target in order to infer scene semantics in urban environments. One of the challenges that arises from the navigation task in naturalistic urban scenarios is the detection of road participants (e.g., cyclists, pedestrians and vehicles). In this regard, this paper tackles the detection and orientation estimation of cars, pedestrians and cyclists, employing the challenging and naturalistic KITTI images. This work proposes 3D-aware features computed from stereo color images in order to capture the appearance and depth peculiarities of the objects in road scenes. The successful part-based object detector, known as DPM, is extended to learn richer models from the 2.5D data (color and disparity), while also carrying out a detailed analysis of the training pipeline. A large set of experiments evaluate the proposals, and the best performing approach is ranked on the KITTI website. Indeed, this is the first work that reports results with stereo data for the KITTI object challenge, achieving increased detection ratios for the classes car and cyclist compared to a baseline DPM. PMID:25903553

  17. Human Sinoatrial Node Structure: 3D Microanatomy of Sinoatrial Conduction Pathways

    PubMed Central

    Csepe, Thomas A.; Zhao, Jichao; Hansen, Brian J.; Li, Ning; Sul, Lidiya V.; Lim, Praise; Wang, Yufeng; Simonetti, Orlando P.; Kilic, Ahmet; Mohler, Peter J.; Janssen, Paul ML.; Fedorov, Vadim V.

    2016-01-01

    Introduction Despite a century of extensive study on the human sinoatrial node (SAN), the structure-to-function features of specialized SAN conduction pathways (SACP) are still unknown and debated. We report a new method for direct analysis of the SAN microstructure in optically-mapped human hearts with and without clinical history of SAN dysfunction. Methods Two explanted donor human hearts were coronary-perfused and optically-mapped. Structural analyses of histological sections parallel to epicardium (~13-21μm intervals) were integrated with optical maps to create 3D computational reconstructions of the SAN complex. High-resolution fiber fields were obtained using 3D Eigen-analysis of the structure tensor, and used to analyze SACP microstructure with a fiber-tracking approach. Results Optical mapping revealed normal SAN activation of the atria through a lateral SACP proximal to the crista terminalis in Heart #1 but persistent SAN exit block in diseased Heart #2. 3D structural analysis displayed a functionally-observed SAN border composed of fibrosis, fat, and/or discontinuous fibers between SAN and atria, which was only crossed by several branching myofiber tracts in SACP regions. Computational 3D fiber-tracking revealed that myofiber tracts of SACPs created continuous connections between SAN #1 and atria, but in SAN #2, SACP region myofiber tracts were discontinuous due to fibrosis and fat. Conclusions We developed a new integrative functional, structural and computational approach that allowed for the resolution of the specialized 3D microstructure of human SACPs for the first time. Application of this integrated approach will shed new light on the role of the specialized SAN microanatomy in maintaining sinus rhythm. PMID:26743207

  18. ProSAT+: visualizing sequence annotations on 3D structure.

    PubMed

    Stank, Antonia; Richter, Stefan; Wade, Rebecca C

    2016-08-01

    PRO: tein S: tructure A: nnotation T: ool-plus (ProSAT(+)) is a new web server for mapping protein sequence annotations onto a protein structure and visualizing them simultaneously with the structure. ProSAT(+) incorporates many of the features of the preceding ProSAT and ProSAT2 tools but also provides new options for the visualization and sharing of protein annotations. Data are extracted from the UniProt KnowledgeBase, the RCSB PDB and the PDBe SIFTS resource, and visualization is performed using JSmol. User-defined sequence annotations can be added directly to the URL, thus enabling visualization and easy data sharing. ProSAT(+) is available at http://prosat.h-its.org.

  19. A tetraphenylethylene core-based 3D structure small molecular acceptor enabling efficient non-fullerene organic solar cells.

    PubMed

    Liu, Yuhang; Mu, Cheng; Jiang, Kui; Zhao, Jingbo; Li, Yunke; Zhang, Lu; Li, Zhengke; Lai, Joshua Yuk Lin; Hu, Huawei; Ma, Tingxuan; Hu, Rongrong; Yu, Demei; Huang, Xuhui; Tang, Ben Zhong; Yan, He

    2015-02-01

    A tetraphenylethylene core-based small molecular acceptor with a unique 3D molecular structure is developed. Bulk-heterojunction blend films with a small feature size (≈20 nm) are obtained, which lead to non-fullerene organic solar cells (OSCs) with 5.5% power conversion efficiency. The work provides a new molecular design approach to efficient non-fullerene OSCs based on 3D-structured small-molecule acceptors.

  20. The Wavelet Element Method. Part 2; Realization and Additional Features in 2D and 3D

    NASA Technical Reports Server (NTRS)

    Canuto, Claudio; Tabacco, Anita; Urban, Karsten

    1998-01-01

    The Wavelet Element Method (WEM) provides a construction of multiresolution systems and biorthogonal wavelets on fairly general domains. These are split into subdomains that are mapped to a single reference hypercube. Tensor products of scaling functions and wavelets defined on the unit interval are used on the reference domain. By introducing appropriate matching conditions across the interelement boundaries, a globally continuous biorthogonal wavelet basis on the general domain is obtained. This construction does not uniquely define the basis functions but rather leaves some freedom for fulfilling additional features. In this paper we detail the general construction principle of the WEM to the 1D, 2D and 3D cases. We address additional features such as symmetry, vanishing moments and minimal support of the wavelet functions in each particular dimension. The construction is illustrated by using biorthogonal spline wavelets on the interval.

  1. 3-D Radar Imaging Reveals Deep Structures and Buried Craters Within the Martian Polar Caps

    NASA Astrophysics Data System (ADS)

    Putzig, N. E.; Foss, F. J., II; Campbell, B. A.; Phillips, R. J.; Smith, I. B.

    2015-12-01

    We use Shallow Radar (SHARAD) observations on thousands of orbital passes by the Mars Reconnaissance Orbiter to produce fully imaged 3-D data volumes encompassing both polar ice caps of Mars. Greatly clarifying the view of subsurface features, a completed volume for Planum Boreum provides new constraints on the nature and timing of emplacement of the northern polar deposits and their relationship to climate. The standard method of mapping subsurface features with single-pass 2-D radargrams has been very fruitful (see Brothers et al. 2015, JGR 120 in press, and references therein), but a full assessment of internal structures has been hindered by interfering off-nadir echoes from spiral troughs and other variable topography prevalent on both caps. By assembling the SHARAD radargrams into a volume and applying a 3-D imaging process (migration) borrowed from seismic processing techniques, we enhance the signal-to-noise ratio while repositioning the echoes to their proper locations, thereby unraveling the interference. As part of the process, we correct ionospheric distortions and delays of the radar echoes (Campbell et al. 2014, IEEE GRSL 11 #3). Interfaces painstakingly mapped in radargrams (e.g., the basal-unit surface, a buried chasma) are clearly visible in the 3-D volume, and new features are revealed. Structures may now be mapped through trough-rich regions, including a widespread sequence that provides corroborative evidence of recent ice ages (Smith et al. 2015, LPSC XLVI #2574). Distinctive radar signatures associated with known, partially buried craters also occur elsewhere in the volume but without surface expression. Presumably, these are fully buried craters that may provide a new means to estimate the age of the deposits. Preliminary work for Planum Australe demonstrates that the 3-D processing currently underway will illuminate deep structures that are broadly obfuscated in 2-D radargrams by a shallow scatterer (Campbell et al. 2015, LPSC XLVI #2366).

  2. Generation of 3-D surface maps in waste storage silos using a structured light source

    NASA Technical Reports Server (NTRS)

    Burks, B. L.; Rowe, J. C.; Dinkins, M. A.; Christensen, B.; Selleck, C.; Jacoboski, D.; Markus, R.

    1992-01-01

    Surface contours inside the large waste storage tanks typical of the Department of Energy (DOE) complex are, in general, highly irregular. In addition to pipes and other pieces of equipment in the tanks, the surfaces may have features such as mounds, fissures, crystalline structures, and mixed solid and liquid forms. Prior to remediation activities, it will be necessary to characterize the waste to determine the most effective remediation approaches. Surface contour data will be required both prior to and during remediation. The use is described of a structured light source to generate 3-D surface contour maps of the interior of waste storage silos at the Feed Materials Production Center at Fernald, OH. The landscape inside these large waste storage tanks bears a strong resemblance to some of the landscapes that might be encountered during lunar or planetary exploration. Hence, these terrestrial 3-D mapping techniques may be directly applicable to extraterrestrial exploration. In further development, it will be demonstrated that these 3-D data can be used for robotic task planning just as 3-D surface contour data of a satellite could be used to plan maintenance tasks for a space-based servicing robot.

  3. 3D facial expression recognition using maximum relevance minimum redundancy geometrical features

    NASA Astrophysics Data System (ADS)

    Rabiu, Habibu; Saripan, M. Iqbal; Mashohor, Syamsiah; Marhaban, Mohd Hamiruce

    2012-12-01

    In recent years, facial expression recognition (FER) has become an attractive research area, which besides the fundamental challenges, it poses, finds application in areas, such as human-computer interaction, clinical psychology, lie detection, pain assessment, and neurology. Generally the approaches to FER consist of three main steps: face detection, feature extraction and expression recognition. The recognition accuracy of FER hinges immensely on the relevance of the selected features in representing the target expressions. In this article, we present a person and gender independent 3D facial expression recognition method, using maximum relevance minimum redundancy geometrical features. The aim is to detect a compact set of features that sufficiently represents the most discriminative features between the target classes. Multi-class one-against-one SVM classifier was employed to recognize the seven facial expressions; neutral, happy, sad, angry, fear, disgust, and surprise. The average recognition accuracy of 92.2% was recorded. Furthermore, inter database homogeneity was investigated between two independent databases the BU-3DFE and UPM-3DFE the results showed a strong homogeneity between the two databases.

  4. 3D-2D Deformable Image Registration Using Feature-Based Nonuniform Meshes

    PubMed Central

    Guo, Xiaohu; Cai, Yiqi; Yang, Yin; Wang, Jing; Jia, Xun

    2016-01-01

    By using prior information of planning CT images and feature-based nonuniform meshes, this paper demonstrates that volumetric images can be efficiently registered with a very small portion of 2D projection images of a Cone-Beam Computed Tomography (CBCT) scan. After a density field is computed based on the extracted feature edges from planning CT images, nonuniform tetrahedral meshes will be automatically generated to better characterize the image features according to the density field; that is, finer meshes are generated for features. The displacement vector fields (DVFs) are specified at the mesh vertices to drive the deformation of original CT images. Digitally reconstructed radiographs (DRRs) of the deformed anatomy are generated and compared with corresponding 2D projections. DVFs are optimized to minimize the objective function including differences between DRRs and projections and the regularity. To further accelerate the above 3D-2D registration, a procedure to obtain good initial deformations by deforming the volume surface to match 2D body boundary on projections has been developed. This complete method is evaluated quantitatively by using several digital phantoms and data from head and neck cancer patients. The feature-based nonuniform meshing method leads to better results than either uniform orthogonal grid or uniform tetrahedral meshes. PMID:27019849

  5. 3D-2D Deformable Image Registration Using Feature-Based Nonuniform Meshes.

    PubMed

    Zhong, Zichun; Guo, Xiaohu; Cai, Yiqi; Yang, Yin; Wang, Jing; Jia, Xun; Mao, Weihua

    2016-01-01

    By using prior information of planning CT images and feature-based nonuniform meshes, this paper demonstrates that volumetric images can be efficiently registered with a very small portion of 2D projection images of a Cone-Beam Computed Tomography (CBCT) scan. After a density field is computed based on the extracted feature edges from planning CT images, nonuniform tetrahedral meshes will be automatically generated to better characterize the image features according to the density field; that is, finer meshes are generated for features. The displacement vector fields (DVFs) are specified at the mesh vertices to drive the deformation of original CT images. Digitally reconstructed radiographs (DRRs) of the deformed anatomy are generated and compared with corresponding 2D projections. DVFs are optimized to minimize the objective function including differences between DRRs and projections and the regularity. To further accelerate the above 3D-2D registration, a procedure to obtain good initial deformations by deforming the volume surface to match 2D body boundary on projections has been developed. This complete method is evaluated quantitatively by using several digital phantoms and data from head and neck cancer patients. The feature-based nonuniform meshing method leads to better results than either uniform orthogonal grid or uniform tetrahedral meshes.

  6. Computerized 3-D reconstruction of complicated anatomical structure

    NASA Astrophysics Data System (ADS)

    Andreasen, Arne; Drewes, Asbjorn M.; Assentoft, Joergen E.

    1992-06-01

    In the study of the rabbit hippocampal region, images of 430 serial sections were aligned by a `parameter-shift' algorithm. The resulting 3-D matrix represents a fixed and stained but `whole' rabbit brain. From this virtual object the slice procedure, displacement, and re- alignment could be computer simulated and the artifacts associated with these procedures estimated.

  7. Postprocessing techniques for 3D non-linear structures

    NASA Technical Reports Server (NTRS)

    Gallagher, Richard S.

    1987-01-01

    How graphics postprocessing techniques are currently used to examine the results of 3-D nonlinear analyses, some new techniques which take advantage of recent technology, and how these results relate to both the finite element model and its geometric parent are reviewed.

  8. Multi-resolution Gabor wavelet feature extraction for needle detection in 3D ultrasound

    NASA Astrophysics Data System (ADS)

    Pourtaherian, Arash; Zinger, Svitlana; Mihajlovic, Nenad; de With, Peter H. N.; Huang, Jinfeng; Ng, Gary C.; Korsten, Hendrikus H. M.

    2015-12-01

    Ultrasound imaging is employed for needle guidance in various minimally invasive procedures such as biopsy guidance, regional anesthesia and brachytherapy. Unfortunately, a needle guidance using 2D ultrasound is very challenging, due to a poor needle visibility and a limited field of view. Nowadays, 3D ultrasound systems are available and more widely used. Consequently, with an appropriate 3D image-based needle detection technique, needle guidance and interventions may significantly be improved and simplified. In this paper, we present a multi-resolution Gabor transformation for an automated and reliable extraction of the needle-like structures in a 3D ultrasound volume. We study and identify the best combination of the Gabor wavelet frequencies. High precision in detecting the needle voxels leads to a robust and accurate localization of the needle for the intervention support. Evaluation in several ex-vivo cases shows that the multi-resolution analysis significantly improves the precision of the needle voxel detection from 0.23 to 0.32 at a high recall rate of 0.75 (gain 40%), where a better robustness and confidence were confirmed in the practical experiments.

  9. Analysis of the 3D Structure and Velocity of a CME on 2 January 2008

    NASA Astrophysics Data System (ADS)

    López, F. M.; Cremades, H.

    We perform an analysis of the 3D structure and velocity of a CME (coronal mass ejection) ejected on 2 January 2008. The event was imaged by both STEREO A and B spacecraft (mutual separation of ˜44°), providing polarized images of the event from two different points of view. To obtain information on the 3D structure of the CME from polarized images, a polarization technique (Moran & Davila, Science 305, 66, 2003) is applied. Aided by this method, we have constructed topographical maps which show the height of the various event features from the plane of the sky (i.e. toward or away from the observer) and have dinamically analyzed and compared the real and projected on the plane of the sky velocities.

  10. Fragment-based strategy for structural optimization in combination with 3D-QSAR.

    PubMed

    Yuan, Haoliang; Tai, Wenting; Hu, Shihe; Liu, Haichun; Zhang, Yanmin; Yao, Sihui; Ran, Ting; Lu, Shuai; Ke, Zhipeng; Xiong, Xiao; Xu, Jinxing; Chen, Yadong; Lu, Tao

    2013-10-01

    Fragment-based drug design has emerged as an important methodology for lead discovery and drug design. Different with other studies focused on fragment library design and active fragment identification, a fragment-based strategy was developed in combination with three-dimensional quantitative structure-activity relationship (3D-QSAR) for structural optimization in this study. Based on a validated scaffold or fragment hit, a series of structural optimization was conducted to convert it to lead compounds, including 3D-QSAR modelling, active site analysis, fragment-based structural optimization and evaluation of new molecules. 3D-QSAR models and active site analysis provided sufficient information for confirming the SAR and pharmacophoric features for fragments. This strategy was evaluated through the structural optimization on a c-Met inhibitor scaffold 5H-benzo[4,5]cyclohepta[1,2-b]pyridin-5-one, which resulted in an c-Met inhibitor with high inhibitory activity. Our study suggested the effectiveness of this fragment-based strategy and the druggability of our newly explored active region. The reliability of this strategy indicated it could also be applied to facilitate lead optimization of other targets.

  11. Fragment-based strategy for structural optimization in combination with 3D-QSAR

    NASA Astrophysics Data System (ADS)

    Yuan, Haoliang; Tai, Wenting; Hu, Shihe; Liu, Haichun; Zhang, Yanmin; Yao, Sihui; Ran, Ting; Lu, Shuai; Ke, Zhipeng; Xiong, Xiao; Xu, Jinxing; Chen, Yadong; Lu, Tao

    2013-10-01

    Fragment-based drug design has emerged as an important methodology for lead discovery and drug design. Different with other studies focused on fragment library design and active fragment identification, a fragment-based strategy was developed in combination with three-dimensional quantitative structure-activity relationship (3D-QSAR) for structural optimization in this study. Based on a validated scaffold or fragment hit, a series of structural optimization was conducted to convert it to lead compounds, including 3D-QSAR modelling, active site analysis, fragment-based structural optimization and evaluation of new molecules. 3D-QSAR models and active site analysis provided sufficient information for confirming the SAR and pharmacophoric features for fragments. This strategy was evaluated through the structural optimization on a c-Met inhibitor scaffold 5H-benzo[4,5]cyclohepta[1,2-b]pyridin-5-one, which resulted in an c-Met inhibitor with high inhibitory activity. Our study suggested the effectiveness of this fragment-based strategy and the druggability of our newly explored active region. The reliability of this strategy indicated it could also be applied to facilitate lead optimization of other targets.

  12. Colloidal and polyelectrolyte inks for direct-write assembly of 3D periodic structures

    NASA Astrophysics Data System (ADS)

    Gratson, Gregory Michael

    Novel inks were developed for the direct-write assembly of 3D periodic structures with varying feature size. Specifically, two ink designs were pursued: (1) a model colloidal ink (feature size > 100 mum) and (2) a polyelectrolyte ink (feature size ˜ 1 mum). The rheological properties of both inks were specifically tailored for our direct-write assembly process, which involves ink deposition through a fine scale nozzle that is robotically controlled using a 3-axis stage. Central to this approach is the design of inks that are capable of flowing through deposition nozzles of varying size and then "setting" immediately to facilitate shape retention of the deposited features. In addition, the inks must contain a high solid volume fraction to minimize drying-induced shrinkage after assembly is complete. First, a model colloidal ink based on monodisperse silica microspheres was designed for 3D periodic structures. These colloidal inks suffer difficulties (e.g., nozzle clogging) when used to fabricate structures with feature sizes below ˜ 100 mum, so a different ink design was pursued based on polyelectrolyte complexes. These inks rapidly solidified upon deposition into an IPA/water coagulation reservoir, and the exact coagulation mechanism depended strongly on reservoir composition. The water/IPA ratio in the reservoir (83--88 % IPA) was carefully tailored to produce filaments that could maintain their shape while spanning unsupported regions in the structure, yet were flexible enough to adhere to the substrate or underlying layers. Several micro-periodic structures of varying design were fabricated, revealing the facile nature of our approach. 3D micro-periodic scaffolds were used to create photonic crystals with high refractive index contrast. Silica chemical vapor deposition was performed under ambient conditions to produce a thin inorganic layer around the polymer, which facilitated further high-temperature steps. The polymer was removed through burnout at 475

  13. Feature extraction from 3D lidar point clouds using image processing methods

    NASA Astrophysics Data System (ADS)

    Zhu, Ling; Shortridge, Ashton; Lusch, David; Shi, Ruoming

    2011-10-01

    Airborne LiDAR data have become cost-effective to produce at local and regional scales across the United States and internationally. These data are typically collected and processed into surface data products by contractors for state and local communities. Current algorithms for advanced processing of LiDAR point cloud data are normally implemented in specialized, expensive software that is not available for many users, and these users are therefore unable to experiment with the LiDAR point cloud data directly for extracting desired feature classes. The objective of this research is to identify and assess automated, readily implementable GIS procedures to extract features like buildings, vegetated areas, parking lots and roads from LiDAR data using standard image processing tools, as such tools are relatively mature with many effective classification methods. The final procedure adopted employs four distinct stages. First, interpolation is used to transfer the 3D points to a high-resolution raster. Raster grids of both height and intensity are generated. Second, multiple raster maps - a normalized surface model (nDSM), difference of returns, slope, and the LiDAR intensity map - are conflated to generate a multi-channel image. Third, a feature space of this image is created. Finally, supervised classification on the feature space is implemented. The approach is demonstrated in both a conceptual model and on a complex real-world case study, and its strengths and limitations are addressed.

  14. Evaluation of feature-based 3-d registration of probabilistic volumetric scenes

    NASA Astrophysics Data System (ADS)

    Restrepo, Maria I.; Ulusoy, Ali O.; Mundy, Joseph L.

    2014-12-01

    Automatic estimation of the world surfaces from aerial images has seen much attention and progress in recent years. Among current modeling technologies, probabilistic volumetric models (PVMs) have evolved as an alternative representation that can learn geometry and appearance in a dense and probabilistic manner. Recent progress, in terms of storage and speed, achieved in the area of volumetric modeling, opens the opportunity to develop new frameworks that make use of the PVM to pursue the ultimate goal of creating an entire map of the earth, where one can reason about the semantics and dynamics of the 3-d world. Aligning 3-d models collected at different time-instances constitutes an important step for successful fusion of large spatio-temporal information. This paper evaluates how effectively probabilistic volumetric models can be aligned using robust feature-matching techniques, while considering different scenarios that reflect the kind of variability observed across aerial video collections from different time instances. More precisely, this work investigates variability in terms of discretization, resolution and sampling density, errors in the camera orientation, and changes in illumination and geographic characteristics. All results are given for large-scale, outdoor sites. In order to facilitate the comparison of the registration performance of PVMs to that of other 3-d reconstruction techniques, the registration pipeline is also carried out using Patch-based Multi-View Stereo (PMVS) algorithm. Registration performance is similar for scenes that have favorable geometry and the appearance characteristics necessary for high quality reconstruction. In scenes containing trees, such as a park, or many buildings, such as a city center, registration performance is significantly more accurate when using the PVM.

  15. Generated 3D-common feature hypotheses using the HipHop method for developing new topoisomerase I inhibitors.

    PubMed

    Ataei, Sanaz; Yilmaz, Serap; Ertan-Bolelli, Tugba; Yildiz, Ilkay

    2015-07-01

    The continued interest in designing novel topoisomerase I (Topo I) inhibitors and the lack of adequate ligand-based computer-aided drug discovery efforts combined with the drawbacks of structure-based design prompted us to explore the possibility of developing ligand-based three-dimensional (3D) pharmacophore(s). This approach avoids the pitfalls of structure-based techniques because it only focuses on common features among known ligands; furthermore, the pharmacophore model can be used as 3D search queries to discover new Topo I inhibitory scaffolds. In this article, we employed the HipHop module using Discovery Studio to construct plausible binding hypotheses for clinically used Topo I inhibitors, such as camptothecin, topotecan, belotecan, and SN-38, which is an active metabolite of irinotecan. The docked pose of topotecan was selected as a reference compound. The first hypothesis (Hypo 01) among the obtained 10 hypotheses was chosen for further analysis. Hypo 01 had six features, which were two hydrogen-bond acceptors, one hydrogen-bond donor, one hydrophob aromatic and one hydrophob aliphatic, and one ring aromatic. Our obtained hypothesis was checked by using some of the aromathecin derivatives which were published for their Topo I inhibitory potency. Moreover, five structures were found to be possible anti-Topo I compounds from the DruglikeDiverse database. From this research, it can be suggested that our model could be useful for further studies in order to design new potent Topo I-targeting antitumor drugs.

  16. Surface feature based classification of plant organs from 3D laserscanned point clouds for plant phenotyping

    PubMed Central

    2013-01-01

    Background Laserscanning recently has become a powerful and common method for plant parameterization and plant growth observation on nearly every scale range. However, 3D measurements with high accuracy, spatial resolution and speed result in a multitude of points that require processing and analysis. The primary objective of this research has been to establish a reliable and fast technique for high throughput phenotyping using differentiation, segmentation and classification of single plants by a fully automated system. In this report, we introduce a technique for automated classification of point clouds of plants and present the applicability for plant parameterization. Results A surface feature histogram based approach from the field of robotics was adapted to close-up laserscans of plants. Local geometric point features describe class characteristics, which were used to distinguish among different plant organs. This approach has been proven and tested on several plant species. Grapevine stems and leaves were classified with an accuracy of up to 98%. The proposed method was successfully transferred to 3D-laserscans of wheat plants for yield estimation. Wheat ears were separated with an accuracy of 96% from other plant organs. Subsequently, the ear volume was calculated and correlated to the ear weight, the kernel weights and the number of kernels. Furthermore the impact of the data resolution was evaluated considering point to point distances between 0.3 and 4.0 mm with respect to the classification accuracy. Conclusion We introduced an approach using surface feature histograms for automated plant organ parameterization. Highly reliable classification results of about 96% for the separation of grapevine and wheat organs have been obtained. This approach was found to be independent of the point to point distance and applicable to multiple plant species. Its reliability, flexibility and its high order of automation make this method well suited for the demands of

  17. Functional classification of protein 3D structures from predicted local interaction sites.

    PubMed

    Parasuram, Ramya; Lee, Joslynn S; Yin, Pengcheng; Somarowthu, Srinivas; Ondrechen, Mary Jo

    2010-12-01

    A new approach to the functional classification of protein 3D structures is described with application to some examples from structural genomics. This approach is based on functional site prediction with THEMATICS and POOL. THEMATICS employs calculated electrostatic potentials of the query structure. POOL is a machine learning method that utilizes THEMATICS features and has been shown to predict accurate, precise, highly localized interaction sites. Extension to the functional classification of structural genomics proteins is now described. Predicted functionally important residues are structurally aligned with those of proteins with previously characterized biochemical functions. A 3D structure match at the predicted local functional site then serves as a more reliable predictor of biochemical function than an overall structure match. Annotation is confirmed for a structural genomics protein with the ribulose phosphate binding barrel (RPBB) fold. A putative glucoamylase from Bacteroides fragilis (PDB ID 3eu8) is shown to be in fact probably not a glucoamylase. Finally a structural genomics protein from Streptomyces coelicolor annotated as an enoyl-CoA hydratase (PDB ID 3g64) is shown to be misannotated. Its predicted active site does not match the well-characterized enoyl-CoA hydratases of similar structure but rather bears closer resemblance to those of a dehalogenase with similar fold.

  18. Vertical Corner Feature Based Precise Vehicle Localization Using 3D LIDAR in Urban Area.

    PubMed

    Im, Jun-Hyuck; Im, Sung-Hyuck; Jee, Gyu-In

    2016-08-10

    Tall buildings are concentrated in urban areas. The outer walls of buildings are vertically erected to the ground and almost flat. Therefore, the vertical corners that meet the vertical planes are present everywhere in urban areas. These corners act as convenient landmarks, which can be extracted by using the light detection and ranging (LIDAR) sensor. A vertical corner feature based precise vehicle localization method is proposed in this paper and implemented using 3D LIDAR (Velodyne HDL-32E). The vehicle motion is predicted by accumulating the pose increment output from the iterative closest point (ICP) algorithm based on the geometric relations between the scan data of the 3D LIDAR. The vertical corner is extracted using the proposed corner extraction method. The vehicle position is then corrected by matching the prebuilt corner map with the extracted corner. The experiment was carried out in the Gangnam area of Seoul, South Korea. In the experimental results, the maximum horizontal position error is about 0.46 m and the 2D Root Mean Square (RMS) horizontal error is about 0.138 m.

  19. Vertical Corner Feature Based Precise Vehicle Localization Using 3D LIDAR in Urban Area

    PubMed Central

    Im, Jun-Hyuck; Im, Sung-Hyuck; Jee, Gyu-In

    2016-01-01

    Tall buildings are concentrated in urban areas. The outer walls of buildings are vertically erected to the ground and almost flat. Therefore, the vertical corners that meet the vertical planes are present everywhere in urban areas. These corners act as convenient landmarks, which can be extracted by using the light detection and ranging (LIDAR) sensor. A vertical corner feature based precise vehicle localization method is proposed in this paper and implemented using 3D LIDAR (Velodyne HDL-32E). The vehicle motion is predicted by accumulating the pose increment output from the iterative closest point (ICP) algorithm based on the geometric relations between the scan data of the 3D LIDAR. The vertical corner is extracted using the proposed corner extraction method. The vehicle position is then corrected by matching the prebuilt corner map with the extracted corner. The experiment was carried out in the Gangnam area of Seoul, South Korea. In the experimental results, the maximum horizontal position error is about 0.46 m and the 2D Root Mean Square (RMS) horizontal error is about 0.138 m. PMID:27517936

  20. Face recognition based on matching of local features on 3D dynamic range sequences

    NASA Astrophysics Data System (ADS)

    Echeagaray-Patrón, B. A.; Kober, Vitaly

    2016-09-01

    3D face recognition has attracted attention in the last decade due to improvement of technology of 3D image acquisition and its wide range of applications such as access control, surveillance, human-computer interaction and biometric identification systems. Most research on 3D face recognition has focused on analysis of 3D still data. In this work, a new method for face recognition using dynamic 3D range sequences is proposed. Experimental results are presented and discussed using 3D sequences in the presence of pose variation. The performance of the proposed method is compared with that of conventional face recognition algorithms based on descriptors.

  1. Bispectrum feature extraction of gearbox faults based on nonnegative Tucker3 decomposition with 3D calculations

    NASA Astrophysics Data System (ADS)

    Wang, Haijun; Xu, Feiyun; Zhao, Jun'ai; Jia, Minping; Hu, Jianzhong; Huang, Peng

    2013-11-01

    Nonnegative Tucker3 decomposition(NTD) has attracted lots of attentions for its good performance in 3D data array analysis. However, further research is still necessary to solve the problems of overfitting and slow convergence under the anharmonic vibration circumstance occurred in the field of mechanical fault diagnosis. To decompose a large-scale tensor and extract available bispectrum feature, a method of conjugating Choi-Williams kernel function with Gauss-Newton Cartesian product based on nonnegative Tucker3 decomposition(NTD_EDF) is investigated. The complexity of the proposed method is reduced from o( n N lg n) in 3D spaces to o( R 1 R 2 nlg n) in 1D vectors due to its low rank form of the Tucker-product convolution. Meanwhile, a simultaneously updating algorithm is given to overcome the overfitting, slow convergence and low efficiency existing in the conventional one-by-one updating algorithm. Furthermore, the technique of spectral phase analysis for quadratic coupling estimation is used to explain the feature spectrum extracted from the gearbox fault data by the proposed method in detail. The simulated and experimental results show that the sparser and more inerratic feature distribution of basis images can be obtained with core tensor by the NTD_EDF method compared with the one by the other methods in bispectrum feature extraction, and a legible fault expression can also be performed by power spectral density(PSD) function. Besides, the deviations of successive relative error(DSRE) of NTD_EDF achieves 81.66 dB against 15.17 dB by beta-divergences based on NTD(NTD_Beta) and the time-cost of NTD_EDF is only 129.3 s, which is far less than 1 747.9 s by hierarchical alternative least square based on NTD (NTD_HALS). The NTD_EDF method proposed not only avoids the data overfitting and improves the computation efficiency but also can be used to extract more inerratic and sparser bispectrum features of the gearbox fault.

  2. Registration of Feature-Poor 3D Measurements from Fringe Projection

    PubMed Central

    von Enzberg, Sebastian; Al-Hamadi, Ayoub; Ghoneim, Ahmed

    2016-01-01

    We propose a novel method for registration of partly overlapping three-dimensional surface measurements for stereo-based optical sensors using fringe projection. Based on two-dimensional texture matching, it allows global registration of surfaces with poor and ambiguous three-dimensional features, which are common to surface inspection applications. No prior information about relative sensor position is necessary, which makes our approach suitable for semi-automatic and manual measurement. The algorithm is robust and works with challenging measurements, including uneven illumination, surfaces with specular reflection as well as sparsely textured surfaces. We show that precisions of 1 mm and below can be achieved along the surfaces, which is necessary for further local 3D registration. PMID:26927106

  3. A new 3D texture feature based computer-aided diagnosis approach to differentiate pulmonary nodules

    NASA Astrophysics Data System (ADS)

    Han, Fangfang; Wang, Huafeng; Song, Bowen; Zhang, Guopeng; Lu, Hongbing; Moore, William; Zhao, Hong; Liang, Zhengrong

    2013-02-01

    To distinguish malignant pulmonary nodules from benign ones is of much importance in computer-aided diagnosis of lung diseases. Compared to many previous methods which are based on shape or growth assessing of nodules, this proposed three-dimensional (3D) texture feature based approach extracted fifty kinds of 3D textural features from gray level, gradient and curvature co-occurrence matrix, and more derivatives of the volume data of the nodules. To evaluate the presented approach, the Lung Image Database Consortium public database was downloaded. Each case of the database contains an annotation file, which indicates the diagnosis results from up to four radiologists. In order to relieve partial-volume effect, interpolation process was carried out to those volume data with image slice thickness more than 1mm, and thus we had categorized the downloaded datasets to five groups to validate the proposed approach, one group of thickness less than 1mm, two types of thickness range from 1mm to 1.25mm and greater than 1.25mm (each type contains two groups, one with interpolation and the other without). Since support vector machine is based on statistical learning theory and aims to learn for predicting future data, so it was chosen as the classifier to perform the differentiation task. The measure on the performance was based on the area under the curve (AUC) of Receiver Operating Characteristics. From 284 nodules (122 malignant and 162 benign ones), the validation experiments reported a mean of 0.9051 and standard deviation of 0.0397 for the AUC value on average over 100 randomizations.

  4. Fast 3D elastic micro-seismic source location using new GPU features

    NASA Astrophysics Data System (ADS)

    Xue, Qingfeng; Wang, Yibo; Chang, Xu

    2016-12-01

    In this paper, we describe new GPU features and their applications in passive seismic - micro-seismic location. Locating micro-seismic events is quite important in seismic exploration, especially when searching for unconventional oil and gas resources. Different from the traditional ray-based methods, the wave equation method, such as the method we use in our paper, has a remarkable advantage in adapting to low signal-to-noise ratio conditions and does not need a person to select the data. However, because it has a conspicuous deficiency due to its computation cost, these methods are not widely used in industrial fields. To make the method useful, we implement imaging-like wave equation micro-seismic location in a 3D elastic media and use GPU to accelerate our algorithm. We also introduce some new GPU features into the implementation to solve the data transfer and GPU utilization problems. Numerical and field data experiments show that our method can achieve a more than 30% performance improvement in GPU implementation just by using these new features.

  5. Feature-constrained surface reconstruction approach for point cloud data acquired with 3D laser scanner

    NASA Astrophysics Data System (ADS)

    Wang, Yongbo; Sheng, Yehua; Lu, Guonian; Tian, Peng; Zhang, Kai

    2008-04-01

    Surface reconstruction is an important task in the field of 3d-GIS, computer aided design and computer graphics (CAD & CG), virtual simulation and so on. Based on available incremental surface reconstruction methods, a feature-constrained surface reconstruction approach for point cloud is presented. Firstly features are extracted from point cloud under the rules of curvature extremes and minimum spanning tree. By projecting local sample points to the fitted tangent planes and using extracted features to guide and constrain the process of local triangulation and surface propagation, topological relationship among sample points can be achieved. For the constructed models, a process named consistent normal adjustment and regularization is adopted to adjust normal of each face so that the correct surface model is achieved. Experiments show that the presented approach inherits the convenient implementation and high efficiency of traditional incremental surface reconstruction method, meanwhile, it avoids improper propagation of normal across sharp edges, which means the applicability of incremental surface reconstruction is greatly improved. Above all, appropriate k-neighborhood can help to recognize un-sufficient sampled areas and boundary parts, the presented approach can be used to reconstruct both open and close surfaces without additional interference.

  6. 3-D modeling useful tool for planning. [mapping groundwater and soil pollution and subsurface features

    SciTech Connect

    Calmbacher, C.W. )

    1992-12-01

    Visualizing and delineating subsurface geological features, groundwater contaminant plumes, soil contamination, geological faults, shears and other features can prove invaluable to environmental consultants, engineers, geologists and hydrogeologists. Three-dimensional modeling is useful for a variety of applications from planning remediation to site planning design. The problem often is figuring out how to convert drilling logs, map lists or contaminant levels from soil and groundwater into a 3-D model. Three-dimensional subsurface modeling is not a new requirement, but a flexible, easily applied method of developing such models has not always been readily available. LYNX Geosystems Inc. has developed the Geoscience Modeling System (GMS) in answer to the needs of those regularly having to do three-dimensional geostatistical modeling. The GMS program has been designed to allow analysis, interpretation and visualization of complex geological features and soil and groundwater contamination. This is a powerful program driven by a 30 volume modeling technology engine. Data can be entered, stored, manipulated and analyzed in ways that will present very few limitations to the user. The program has selections for Geoscience Data Management, Geoscience Data Analysis, Geological Modeling (interpretation and analysis), Geostatistical Modeling and an optional engineering component.

  7. Photopolymerization of 3D conductive polypyrrole structures via digital light processing

    NASA Astrophysics Data System (ADS)

    Price, Aaron D.

    2016-04-01

    The intrinsically conductive polymer polypyrrole is conventionally synthesized as monolithic films that exhibit significant actuation strains when subjected to an applied electric potential. Though numerous linear and bending actuators based on polypyrrole films have been investigated, the limitations inherent to planar film geometries inhibit the realization of more complex behaviours. Hence, three-dimensional polypyrrole structures are sought to greatly expand the potential applications for conductive polymer actuators. This research aims to develop a novel additive manufacturing method for the fabrication of three-dimensional structures of conductive polypyrrole. In this investigation, radiation-curing techniques are employed by means of digital light processing (DLP) technology. DLP is an additive manufacturing technique where programmed light patterns emitted from a dedicated source are used to selectively cure a specially formulated polymer resin. Successive curing operations lead to a layered 3D structure into which fine features may be incorporated. Energy dispersive spectroscopy (EDS) is subsequently employed to examine the unique microstructural features of the resultant 3D printed polymer morphology in order to elucidate the nature of the conductivity. These polymer microstructures are highly desirable since actuation response times are highly dependent on ion transport distances, and hence the ability to fabricate fine features offers a potential mechanism to improve actuator performance.

  8. Development of the Improving Process for the 3D Printed Structure

    NASA Astrophysics Data System (ADS)

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-01

    The authors focus on the Fused Deposition Modeling (FDM) 3D printer because the FDM 3D printer can print the utility resin material. It can print with low cost and therefore it is the most suitable for home 3D printer. The FDM 3D printer has the problem that it produces layer grooves on the surface of the 3D printed structure. Therefore the authors developed the 3D-Chemical Melting Finishing (3D-CMF) for removing layer grooves. In this method, a pen-style device is filled with a chemical able to dissolve the materials used for building 3D printed structures. By controlling the behavior of this pen-style device, the convex parts of layer grooves on the surface of the 3D printed structure are dissolved, which, in turn, fills the concave parts. In this study it proves the superiority of the 3D-CMF than conventional processing for the 3D printed structure. It proves utilizing the evaluation of the safety, selectively and stability. It confirms the improving of the 3D-CMF and it is confirmed utilizing the data of the surface roughness precision and the observation of the internal state and the evaluation of the mechanical characteristics.

  9. Development of the Improving Process for the 3D Printed Structure

    PubMed Central

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-01

    The authors focus on the Fused Deposition Modeling (FDM) 3D printer because the FDM 3D printer can print the utility resin material. It can print with low cost and therefore it is the most suitable for home 3D printer. The FDM 3D printer has the problem that it produces layer grooves on the surface of the 3D printed structure. Therefore the authors developed the 3D-Chemical Melting Finishing (3D-CMF) for removing layer grooves. In this method, a pen-style device is filled with a chemical able to dissolve the materials used for building 3D printed structures. By controlling the behavior of this pen-style device, the convex parts of layer grooves on the surface of the 3D printed structure are dissolved, which, in turn, fills the concave parts. In this study it proves the superiority of the 3D-CMF than conventional processing for the 3D printed structure. It proves utilizing the evaluation of the safety, selectively and stability. It confirms the improving of the 3D-CMF and it is confirmed utilizing the data of the surface roughness precision and the observation of the internal state and the evaluation of the mechanical characteristics. PMID:28054558

  10. Development of the Improving Process for the 3D Printed Structure.

    PubMed

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-05

    The authors focus on the Fused Deposition Modeling (FDM) 3D printer because the FDM 3D printer can print the utility resin material. It can print with low cost and therefore it is the most suitable for home 3D printer. The FDM 3D printer has the problem that it produces layer grooves on the surface of the 3D printed structure. Therefore the authors developed the 3D-Chemical Melting Finishing (3D-CMF) for removing layer grooves. In this method, a pen-style device is filled with a chemical able to dissolve the materials used for building 3D printed structures. By controlling the behavior of this pen-style device, the convex parts of layer grooves on the surface of the 3D printed structure are dissolved, which, in turn, fills the concave parts. In this study it proves the superiority of the 3D-CMF than conventional processing for the 3D printed structure. It proves utilizing the evaluation of the safety, selectively and stability. It confirms the improving of the 3D-CMF and it is confirmed utilizing the data of the surface roughness precision and the observation of the internal state and the evaluation of the mechanical characteristics.

  11. A 3D model describing the initial structure of an artificial hydrological catchment

    NASA Astrophysics Data System (ADS)

    Maurer, T.; Schneider, A.; Buczko, U.; Gerke, H. H.

    2009-04-01

    The initial development stages of artificially constructed hydrologic catchments are characterized by the absence of vegetation, soil organic matter and soil horizons. This results in increased surface runoff and favors erosion processes that dominate the initial phase. Hydraulic conditions on artificial catchments thus are governed by rapidly changing surface structures as well as by the primary internal structural framework. Contemporary hydrological modeling does not consider any dynamic change of relevant structural features but rather assumes a stable, invariant landscape. The objective of this study was the digital visualization and quantitative description of the initial state and its early structural dynamics, exemplified for the small artificial hydrological catchment "Huehnerwasser" near Cottbus, Germany. Photogrammetric surveys of surface and internal structural units (clay basis liner) during the construction phase provided spatially and temporally resolved data for digital elevation models (DEM). Interpolated physical and chemical soil properties obtained at a borehole grid (e.g., texture) are used for the visualization of spatial distribution of relevant (hydraulic) parameters. The data are merged in a database and visualized in the 3D-GIS application GoCAD. The specific technological construction processes determines the internal structure of the artificial catchment. Resulting differences in bulk density and texture are supposed to have considerable impact on hydraulic properties. A structure generator program was implemented to reproduce the initial structure of the sediment layer as closely as possible. Results of the digital structure generation are checked with non-invasive geophysical measurements, on-site bore holes data and off-site 2D vertical spoil exploration. The accuracy of structure generator results will be compared with predictions of different interpolation methods. Thus, the structure model will serve as a basis for deriving the 3D

  12. 3D structure and conductive thermal field of the Upper Rhine Graben

    NASA Astrophysics Data System (ADS)

    Freymark, Jessica; Sippel, Judith; Scheck-Wenderoth, Magdalena; Bär, Kristian; Stiller, Manfred; Fritsche, Johann-Gerhard; Kracht, Matthias

    2016-04-01

    The Upper Rhine Graben (URG) was formed as part of the European Cenozoic Rift System in a complex extensional setting. At present-day, it has a large socioeconomic relevance as it provides a great potential for geothermal energy production in Germany and France. For the utilisation of this energy resource it is crucial to understand the structure and the observed temperature anomalies in the rift basin. In the framework of the EU-funded "IMAGE" project (Integrated Methods for Advanced Geothermal Exploration), we apply a data-driven numerical modelling approach to quantify the processes and properties controlling the spatial distribution of subsurface temperatures. Typically, reservoir-scale numerical models are developed for predictions on the subsurface hydrothermal conditions and for reducing the risk of drilling non-productive geothermal wells. One major problem related to such models is setting appropriate boundary conditions that define, for instance, how much heat enters the reservoir from greater depths. Therefore, we first build a regional lithospheric-scale 3D structural model, which covers not only the entire URG but also adjacent geological features like the Black Forest and the Vosges Mountains. In particular, we use a multidisciplinary dataset (e.g. well data, seismic reflection data, existing structural models, gravity) to construct the geometries of the sediments, the crust and the lithospheric mantle that control the spatial distribution of thermal conductivity and radiogenic heat production and hence temperatures. By applying a data-based and lithology-dependent parameterisation of this lithospheric-scale 3D structural model and a 3D finite element method, we calculate the steady-state conductive thermal field for the entire region. Available measured temperatures (down to depths of up to 5 km) are considered to validate the 3D thermal model. We present major characteristics of the lithospheric-scale 3D structural model and results of the 3D

  13. Building a 3D Virtual Liver: Methods for Simulating Blood Flow and Hepatic Clearance on 3D Structures

    PubMed Central

    Rezania, Vahid; Tuszynski, Jack

    2016-01-01

    In this paper, we develop a spatio-temporal modeling approach to describe blood and drug flow, as well as drug uptake and elimination, on an approximation of the liver. Extending on previously developed computational approaches, we generate an approximation of a liver, which consists of a portal and hepatic vein vasculature structure, embedded in the surrounding liver tissue. The vasculature is generated via constrained constructive optimization, and then converted to a spatial grid of a selected grid size. Estimates for surrounding upscaled lobule tissue properties are then presented appropriate to the same grid size. Simulation of fluid flow and drug metabolism (hepatic clearance) are completed using discretized forms of the relevant convective-diffusive-reactive partial differential equations for these processes. This results in a single stage, uniformly consistent method to simulate equations for blood and drug flow, as well as drug metabolism, on a 3D structure representative of a liver. PMID:27649537

  14. The RCSB protein data bank: integrative view of protein, gene and 3D structural information.

    PubMed

    Rose, Peter W; Prlić, Andreas; Altunkaya, Ali; Bi, Chunxiao; Bradley, Anthony R; Christie, Cole H; Costanzo, Luigi Di; Duarte, Jose M; Dutta, Shuchismita; Feng, Zukang; Green, Rachel Kramer; Goodsell, David S; Hudson, Brian; Kalro, Tara; Lowe, Robert; Peisach, Ezra; Randle, Christopher; Rose, Alexander S; Shao, Chenghua; Tao, Yi-Ping; Valasatava, Yana; Voigt, Maria; Westbrook, John D; Woo, Jesse; Yang, Huangwang; Young, Jasmine Y; Zardecki, Christine; Berman, Helen M; Burley, Stephen K

    2017-01-04

    The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a 'Structural View of Biology.' Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive.

  15. Minimizing camera-eye optical aberrations during the 3D reconstruction of retinal structures

    NASA Astrophysics Data System (ADS)

    Aldana-Iuit, Javier; Martinez-Perez, M. Elena; Espinosa-Romero, Arturo; Diaz-Uribe, Rufino

    2010-05-01

    3D reconstruction of blood vessels is a powerful visualization tool for physicians, since it allows them to refer to qualitative representation of their subject of study. In this paper we propose a 3D reconstruction method of retinal vessels from fundus images. The reconstruction method propose herein uses images of the same retinal structure in epipolar geometry. Images are preprocessed by RISA system for segmenting blood vessels and obtaining feature points for correspondences. The correspondence points process is solved using correlation. The LMedS analysis and Graph Transformation Matching algorithm are used for outliers suppression. Camera projection matrices are computed with the normalized eight point algorithm. Finally, we retrieve 3D position of the retinal tree points by linear triangulation. In order to increase the power of visualization, 3D tree skeletons are represented by surfaces via generalized cylinders whose radius correspond to morphological measurements obtained by RISA. In this paper the complete calibration process including the fundus camera and the optical properties of the eye, the so called camera-eye system is proposed. On one hand, the internal parameters of the fundus camera are obtained by classical algorithms using a reference pattern. On the other hand, we minimize the undesirable efects of the aberrations induced by the eyeball optical system assuming that contact enlarging lens corrects astigmatism, spherical and coma aberrations are reduced changing the aperture size and eye refractive errors are suppressed adjusting camera focus during image acquisition. Evaluation of two self-calibration proposals and results of 3D blood vessel surface reconstruction are presented.

  16. 1d, 2d, and 3d periodic structures: Electromagnetic characterization, design, and measurement

    NASA Astrophysics Data System (ADS)

    Brockett, Timothy John

    Periodic structures have many useful applications in electromagnetics including phased arrays, frequency selective surfaces, and absorbing interfaces. Their unique properties can be used to provide increased performance in antenna gain, electromagnetic propagation, and electromagnetic absorption. In antenna arrays, repeating elements create a larger eective aperture, increasing the gain of the antenna and the ability to scan the direction of the main beam. Three-dimensional periodic structures, such as an array of shaped pillars such as columns, cones, or prisms have the potential of improving electromagnetic absorption, improving performance in applications such as solar cell eciency and absorbing interfaces. Furthermore, research into periodic structures is a continuing endeavor where novel approaches and analysis in appropriate applications can be sought. This dissertation will address the analysis, diagnostics, and enhancement of 1D, 2D, and 3D periodic structures for antenna array applications and solar cell technology. In particular, a unique approach to array design will be introduced to prevent the appearance of undesirable grating lobes in large antenna arrays that employ subarrays. This approach, named the distortion diagnostic procedure, can apply directly to 1D and 2D periodic structures in the form of planar antenna arrays. Interesting corollaries included here are developments in millimeter-wave antenna measurements including spiral planar scanning, phaseless measurements, and addressing antennas that feature an internal source. Finally, analysis and enhancement of 3D periodic structures in nanostructure photovoltaic arrays and absorbing interfaces will be examined for their behavior and basic operation in regards to improved absorption of electromagnetic waves.

  17. Superpose3D: A Local Structural Comparison Program That Allows for User-Defined Structure Representations

    PubMed Central

    Gherardini, Pier Federico; Ausiello, Gabriele; Helmer-Citterich, Manuela

    2010-01-01

    Local structural comparison methods can be used to find structural similarities involving functional protein patches such as enzyme active sites and ligand binding sites. The outcome of such analyses is critically dependent on the representation used to describe the structure. Indeed different categories of functional sites may require the comparison program to focus on different characteristics of the protein residues. We have therefore developed superpose3D, a novel structural comparison software that lets users specify, with a powerful and flexible syntax, the structure description most suited to the requirements of their analysis. Input proteins are processed according to the user's directives and the program identifies sets of residues (or groups of atoms) that have a similar 3D position in the two structures. The advantages of using such a general purpose program are demonstrated with several examples. These test cases show that no single representation is appropriate for every analysis, hence the usefulness of having a flexible program that can be tailored to different needs. Moreover we also discuss how to interpret the results of a database screening where a known structural motif is searched against a large ensemble of structures. The software is written in C++ and is released under the open source GPL license. Superpose3D does not require any external library, runs on Linux, Mac OSX, Windows and is available at http://cbm.bio.uniroma2.it/superpose3D. PMID:20700534

  18. 3D Geo-Structures Visualization Education Project (3dgeostructuresvis.ucdavis.edu)

    NASA Astrophysics Data System (ADS)

    Billen, M. I.

    2014-12-01

    Students of field-based geology must master a suite of challenging skills from recognizing rocks, to measuring orientations of features in the field, to finding oneself (and the outcrop) on a map and placing structural information on maps. Students must then synthesize this information to derive meaning from the observations and ultimately to determine the three-dimensional (3D) shape of the deformed structures and their kinematic history. Synthesizing this kind of information requires sophisticated visualizations skills in order to extrapolate observations into the subsurface or missing (eroded) material. The good news is that students can learn 3D visualization skills through practice, and virtual tools can help provide some of that practice. Here I present a suite of learning modules focused at developing students' ability to imagine (visualize) complex 3D structures and their exposure through digital topographic surfaces. Using the software 3DVisualizer, developed by KeckCAVES (keckcaves.org) we have developed visualizations of common geologic structures (e.g., syncline, dipping fold) in which the rock is represented by originally flat-lying layers of sediment, each with a different color, which have been subsequently deformed. The exercises build up in complexity, first focusing on understanding the structure in 3D (penetrative understanding), and then moving to the exposure of the structure at a topographic surface. Individual layers can be rendered as a transparent feature to explore how the layer extends above and below the topographic surface (e.g., to follow an eroded fold limb across a valley). The exercises are provided using either movies of the visualization (which can also be used for examples during lectures), or the data and software can be downloaded to allow for more self-driven exploration and learning. These virtual field models and exercises can be used as "practice runs" before going into the field, as make-up assignments, as a field

  19. 3D reconstruction of the Shigella T3SS transmembrane regions reveals 12-fold symmetry and novel features throughout

    PubMed Central

    Hodgkinson, Julie L.; Horsley, Ashley; Stabat, David; Simon, Martha; Johnson, Steven; da Fonseca, Paula C. A.; Morris, Edward P.; Wall, Joseph S.; Lea, Susan M.; Blocker, Ariel J.

    2009-01-01

    Type III secretion systems (T3SSs) mediate bacterial protein translocation into eukaryotic cells, a process essential for virulence of many Gram-negative pathogens. They are composed of a cytoplasmic secretion machinery and a base bridging both bacterial membranes into which a hollow, external needle is embedded. When isolated, the latter two parts are termed ‘needle complex’ (NC). Incomplete understanding of NC structure hampers studies of T3SS function. To estimate the stoichiometry of its components, the mass f its sub-domains was measured by scanning transmission electron microscopy (STEM). Subunit symmetries were determined by analysis of top and side views within negatively stained samples in low dose transmission electron microscopy (TEM). Application of 12-fold symmetry allowed generation of a 21-25Å resolution three-dimensional (3D) reconstruction of the NC base, revealing many new features and permitting tentative docking of the crystal structure of EscJ, an inner membrane component. PMID:19396171

  20. Genome3D: exploiting structure to help users understand their sequences

    PubMed Central

    Lewis, Tony E.; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L.; Buchan, Daniel W.A.; Chothia, Cyrus; Cozzetto, Domenico; Dana, José M.; Filippis, Ioannis; Gough, Julian; Jones, David T.; Kelley, Lawrence A.; Kleywegt, Gerard J.; Minneci, Federico; Mistry, Jaina; Murzin, Alexey G.; Ochoa-Montaño, Bernardo; Oates, Matt E.; Punta, Marco; Rackham, Owen J.L.; Stahlhacke, Jonathan; Sternberg, Michael J.E.; Velankar, Sameer; Orengo, Christine

    2015-01-01

    Genome3D (http://www.genome3d.eu) is a collaborative resource that provides predicted domain annotations and structural models for key sequences. Since introducing Genome3D in a previous NAR paper, we have substantially extended and improved the resource. We have annotated representatives from Pfam families to improve coverage of diverse sequences and added a fast sequence search to the website to allow users to find Genome3D-annotated sequences similar to their own. We have improved and extended the Genome3D data, enlarging the source data set from three model organisms to 10, and adding VIVACE, a resource new to Genome3D. We have analysed and updated Genome3D's SCOP/CATH mapping. Finally, we have improved the superposition tools, which now give users a more powerful interface for investigating similarities and differences between structural models. PMID:25348407

  1. Determining the 3-D structure and motion of objects using a scanning laser range sensor

    NASA Astrophysics Data System (ADS)

    Nandhakumar, N.; Smith, Philip W.

    1993-12-01

    In order for the EVAHR robot to autonomously track and grasp objects, its vision system must be able to determine the 3-D structure and motion of an object from a sequence of sensory images. This task is accomplished by the use of a laser radar range sensor which provides dense range maps of the scene. Unfortunately, the currently available laser radar range cameras use a sequential scanning approach which complicates image analysis. Although many algorithms have been developed for recognizing objects from range images, none are suited for use with single beam, scanning, time-of-flight sensors because all previous algorithms assume instantaneous acquisition of the entire image. This assumption is invalid since the EVAHR robot is equipped with a sequential scanning laser range sensor. If an object is moving while being imaged by the device, the apparent structure of the object can be significantly distorted due to the significant non-zero delay time between sampling each image pixel. If an estimate of the motion of the object can be determined, this distortion can be eliminated; but, this leads to the motion-structure paradox - most existing algorithms for 3-D motion estimation use the structure of objects to parameterize their motions. The goal of this research is to design a rigid-body motion recovery technique which overcomes this limitation. The method being developed is an iterative, linear, feature-based approach which uses the non-zero image acquisition time constraint to accurately recover the motion parameters from the distorted structure of the 3-D range maps. Once the motion parameters are determined, the structural distortion in the range images is corrected.

  2. Histo-anatomic 3D printing of dental structures.

    PubMed

    Schweiger, J; Beuer, F; Stimmelmayr, M; Edelhoff, D; Magne, P; Güth, J F

    2016-11-04

    The creation of dental restorations with natural appearance and biomechanics represents a major challenge for the restorative team. The manufacturing-process of high-aesthetic restorations from tooth-coloured restorative materials is currently dominated by manual manufacturing procedures and the outcome is highly dependent on the knowledge and skills of the performing dental technician. On the other hand, due to the simplicity of the manufacturing process, CAD/CAM restorations from different material classes gain more and more acceptance in the daily routine. Multi-layered restorations show significant aesthetic advantages versus monolithic ones, but are difficult to fabricate using digital technologies. The key element for the successful automated digital fabrication of aesthetic anterior restorations seems to be the form of the individual dentine core as defined by dentine enamel junction (DEJ) covered by a more transparent layer of material imitating the enamel layer to create the outer enamel surface (OES). This article describes the possibilities and technologies available for so-called '4D-printing'. It introduces the digital manufacturing process of multilayered anterior teeth using 3D multipart printing, taking the example of manufacturing replicas of extracted intact natural teeth.

  3. Disulfide Connectivity Prediction Based on Modelled Protein 3D Structural Information and Random Forest Regression.

    PubMed

    Yu, Dong-Jun; Li, Yang; Hu, Jun; Yang, Xibei; Yang, Jing-Yu; Shen, Hong-Bin

    2015-01-01

    Disulfide connectivity is an important protein structural characteristic. Accurately predicting disulfide connectivity solely from protein sequence helps to improve the intrinsic understanding of protein structure and function, especially in the post-genome era where large volume of sequenced proteins without being functional annotated is quickly accumulated. In this study, a new feature extracted from the predicted protein 3D structural information is proposed and integrated with traditional features to form discriminative features. Based on the extracted features, a random forest regression model is performed to predict protein disulfide connectivity. We compare the proposed method with popular existing predictors by performing both cross-validation and independent validation tests on benchmark datasets. The experimental results demonstrate the superiority of the proposed method over existing predictors. We believe the superiority of the proposed method benefits from both the good discriminative capability of the newly developed features and the powerful modelling capability of the random forest. The web server implementation, called TargetDisulfide, and the benchmark datasets are freely available at: http://csbio.njust.edu.cn/bioinf/TargetDisulfide for academic use.

  4. Learning the 3-D structure of objects from 2-D views depends on shape, not format

    PubMed Central

    Tian, Moqian; Yamins, Daniel; Grill-Spector, Kalanit

    2016-01-01

    Humans can learn to recognize new objects just from observing example views. However, it is unknown what structural information enables this learning. To address this question, we manipulated the amount of structural information given to subjects during unsupervised learning by varying the format of the trained views. We then tested how format affected participants' ability to discriminate similar objects across views that were rotated 90° apart. We found that, after training, participants' performance increased and generalized to new views in the same format. Surprisingly, the improvement was similar across line drawings, shape from shading, and shape from shading + stereo even though the latter two formats provide richer depth information compared to line drawings. In contrast, participants' improvement was significantly lower when training used silhouettes, suggesting that silhouettes do not have enough information to generate a robust 3-D structure. To test whether the learned object representations were format-specific or format-invariant, we examined if learning novel objects from example views transfers across formats. We found that learning objects from example line drawings transferred to shape from shading and vice versa. These results have important implications for theories of object recognition because they suggest that (a) learning the 3-D structure of objects does not require rich structural cues during training as long as shape information of internal and external features is provided and (b) learning generates shape-based object representations independent of the training format. PMID:27153196

  5. Semiautomatic approaches to account for 3-D distortion of the electric field from local, near-surface structures in 3-D resistivity inversions of 3-D regional magnetotelluric data

    USGS Publications Warehouse

    Rodriguez, Brian D.

    2017-03-31

    This report summarizes the results of three-dimensional (3-D) resistivity inversion simulations that were performed to account for local 3-D distortion of the electric field in the presence of 3-D regional structure, without any a priori information on the actual 3-D distribution of the known subsurface geology. The methodology used a 3-D geologic model to create a 3-D resistivity forward (“known”) model that depicted the subsurface resistivity structure expected for the input geologic configuration. The calculated magnetotelluric response of the modeled resistivity structure was assumed to represent observed magnetotelluric data and was subsequently used as input into a 3-D resistivity inverse model that used an iterative 3-D algorithm to estimate 3-D distortions without any a priori geologic information. A publicly available inversion code, WSINV3DMT, was used for all of the simulated inversions, initially using the default parameters, and subsequently using adjusted inversion parameters. A semiautomatic approach of accounting for the static shift using various selections of the highest frequencies and initial models was also tested. The resulting 3-D resistivity inversion simulation was compared to the “known” model and the results evaluated. The inversion approach that produced the lowest misfit to the various local 3-D distortions was an inversion that employed an initial model volume resistivity that was nearest to the maximum resistivities in the near-surface layer.

  6. Air-structured optical fiber drawn from a 3D-printed preform.

    PubMed

    Cook, Kevin; Canning, John; Leon-Saval, Sergio; Reid, Zane; Hossain, Md Arafat; Comatti, Jade-Edouard; Luo, Yanhua; Peng, Gang-Ding

    2015-09-01

    A structured optical fiber is drawn from a 3D-printed structured preform. Preforms containing a single ring of holes around the core are fabricated using filament made from a modified butadiene polymer. More broadly, 3D printers capable of processing soft glasses, silica, and other materials are likely to come on line in the not-so-distant future. 3D printing of optical preforms signals a new milestone in optical fiber manufacture.

  7. Lightweight NiFe2O4 with controllable 3D network structure and enhanced microwave absorbing properties

    PubMed Central

    Wang, Fen; Wang, Xing; Zhu, Jianfeng; Yang, Haibo; Kong, Xingang; Liu, Xiao

    2016-01-01

    3D network structure NiFe2O4 was successfully synthesized by a templated salt precipitation method using PMMA colloid crystal as templates. The morphology, phase composition and microwave absorbing properties of as-prepared samples were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), vector network analyzer (VNA), and so on. The results revealed that the 3D network structure was configurated with smooth spherical walls composed of NiFe2O4 nanocrystals and their pore diameters being in the range of 80–250 nm. The microwave absorption properties of the 3D network structure NiFe2O4 were crucially determined by the special structure. The synergy of intrinsic magnetic loss of magnetic NiFe2O4 and the interfacial polarization enhanced by 3D network structure and the interaction of multiple mechanisms endowed the sample with the feature of strong absorption, broad bandwidth and lightweight. There is more than one valley in the reflection loss curves and the maximum reflection loss is 27.5 dB with a bandwidth of 4 GHz. Moreover, the 3D network structure NiFe2O4 show a greater reflection loss with the same thickness comparing to the ordinary NiFe2O4 nanoparticles, which could achieve the feature of lightweight of the microwave absorbing materials. PMID:27897209

  8. Lightweight NiFe2O4 with controllable 3D network structure and enhanced microwave absorbing properties

    NASA Astrophysics Data System (ADS)

    Wang, Fen; Wang, Xing; Zhu, Jianfeng; Yang, Haibo; Kong, Xingang; Liu, Xiao

    2016-11-01

    3D network structure NiFe2O4 was successfully synthesized by a templated salt precipitation method using PMMA colloid crystal as templates. The morphology, phase composition and microwave absorbing properties of as-prepared samples were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), vector network analyzer (VNA), and so on. The results revealed that the 3D network structure was configurated with smooth spherical walls composed of NiFe2O4 nanocrystals and their pore diameters being in the range of 80–250 nm. The microwave absorption properties of the 3D network structure NiFe2O4 were crucially determined by the special structure. The synergy of intrinsic magnetic loss of magnetic NiFe2O4 and the interfacial polarization enhanced by 3D network structure and the interaction of multiple mechanisms endowed the sample with the feature of strong absorption, broad bandwidth and lightweight. There is more than one valley in the reflection loss curves and the maximum reflection loss is 27.5 dB with a bandwidth of 4 GHz. Moreover, the 3D network structure NiFe2O4 show a greater reflection loss with the same thickness comparing to the ordinary NiFe2O4 nanoparticles, which could achieve the feature of lightweight of the microwave absorbing materials.

  9. Lightweight NiFe2O4 with controllable 3D network structure and enhanced microwave absorbing properties.

    PubMed

    Wang, Fen; Wang, Xing; Zhu, Jianfeng; Yang, Haibo; Kong, Xingang; Liu, Xiao

    2016-11-29

    3D network structure NiFe2O4 was successfully synthesized by a templated salt precipitation method using PMMA colloid crystal as templates. The morphology, phase composition and microwave absorbing properties of as-prepared samples were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), vector network analyzer (VNA), and so on. The results revealed that the 3D network structure was configurated with smooth spherical walls composed of NiFe2O4 nanocrystals and their pore diameters being in the range of 80-250 nm. The microwave absorption properties of the 3D network structure NiFe2O4 were crucially determined by the special structure. The synergy of intrinsic magnetic loss of magnetic NiFe2O4 and the interfacial polarization enhanced by 3D network structure and the interaction of multiple mechanisms endowed the sample with the feature of strong absorption, broad bandwidth and lightweight. There is more than one valley in the reflection loss curves and the maximum reflection loss is 27.5 dB with a bandwidth of 4 GHz. Moreover, the 3D network structure NiFe2O4 show a greater reflection loss with the same thickness comparing to the ordinary NiFe2O4 nanoparticles, which could achieve the feature of lightweight of the microwave absorbing materials.

  10. Optimal design of a new 3D haptic gripper for telemanipulation, featuring magnetorheological fluid brakes

    NASA Astrophysics Data System (ADS)

    Nguyen, Q. H.; Choi, S. B.; Lee, Y. S.; Han, M. S.

    2013-01-01

    In this research work, a new configuration of a 3D haptic gripper for telemanipulation is proposed and optimally designed. The proposed haptic gripper, featuring three magnetorheological fluid brakes (MRBs), reflects the rolling torque, the grasping force and the approach force from the slave manipulator to the master operator. After describing the operational principle of the haptic gripper, an optimal design of the MRBs for the gripper is performed. The purpose of the optimization problem is to find the most compact MRB that can provide a required braking torque/force to the master operator while the off-state torque/force is kept as small as possible. In the optimal design, different types of MRBs and different MR fluids (MRFs) are considered. In order to obtain the optimal solution of the MRBs, an optimization approach based on finite element analysis (FEA) integrated with an optimization tool is used. The optimal solutions of the MRBs are then obtained and the optimized MRBs for the haptic gripper are identified. In addition, discussions on the optimal solutions and performance of the optimized MRBs are given.

  11. 3D-printed paper spray ionization cartridge with fast wetting and continuous solvent supply features.

    PubMed

    Salentijn, Gert I J; Permentier, Hjalmar P; Verpoorte, Elisabeth

    2014-12-02

    We report the development of a 3D-printed cartridge for paper spray ionization (PSI) that can be used almost immediately after solvent introduction in a dedicated reservoir and allows prolonged spray generation from a paper tip. The fast wetting feature described in this work is based on capillary action through paper and movement of fluid between paper and the cartridge material (polylactic acid, PLA). The influence of solvent composition, PLA conditioning of the cartridge with isopropanol, and solvent volume introduced into the reservoir have been investigated with relation to wetting time and the amount of solvent consumed for wetting. Spray has been demonstrated with this cartridge for tens of minutes, without any external pumping. It is shown that fast wetting and spray generation can easily be achieved using a number of solvent mixtures commonly used for PSI. The PSI cartridge was applied to the analysis of lidocaine from a paper tip using different solvent mixtures, and to the analysis of lidocaine from a serum sample. Finally, a demonstration of online paper chromatography-mass spectrometry is given.

  12. Using "click-e-bricks" to make 3D elastomeric structures.

    PubMed

    Morin, Stephen A; Shevchenko, Yanina; Lessing, Joshua; Kwok, Sen Wai; Shepherd, Robert F; Stokes, Adam A; Whitesides, George M

    2014-09-10

    Soft, 3D elastomeric structures and composite structures are easy to fabricate using click-e-bricks, and the internal architecture of these structures together with the capabilities built into the bricks themselves provide mechanical, optical, electrical, and fluidic functions.

  13. Characterizing 3D RNA structure by single molecule FRET.

    PubMed

    Stephenson, James D; Kenyon, Julia C; Symmons, Martyn F; Lever, Andrew M L

    2016-07-01

    The importance of elucidating the three dimensional structures of RNA molecules is becoming increasingly clear. However, traditional protein structural techniques such as NMR and X-ray crystallography have several important drawbacks when probing long RNA molecules. Single molecule Förster resonance energy transfer (smFRET) has emerged as a useful alternative as it allows native sequences to be probed in physiological conditions and allows multiple conformations to be probed simultaneously. This review serves to describe the method of generating a three dimensional RNA structure from smFRET data from the biochemical probing of the secondary structure to the computational refinement of the final model.

  14. Partial order optimum likelihood (POOL): maximum likelihood prediction of protein active site residues using 3D Structure and sequence properties.

    PubMed

    Tong, Wenxu; Wei, Ying; Murga, Leonel F; Ondrechen, Mary Jo; Williams, Ronald J

    2009-01-01

    A new monotonicity-constrained maximum likelihood approach, called Partial Order Optimum Likelihood (POOL), is presented and applied to the problem of functional site prediction in protein 3D structures, an important current challenge in genomics. The input consists of electrostatic and geometric properties derived from the 3D structure of the query protein alone. Sequence-based conservation information, where available, may also be incorporated. Electrostatics features from THEMATICS are combined with multidimensional isotonic regression to form maximum likelihood estimates of probabilities that specific residues belong to an active site. This allows likelihood ranking of all ionizable residues in a given protein based on THEMATICS features. The corresponding ROC curves and statistical significance tests demonstrate that this method outperforms prior THEMATICS-based methods, which in turn have been shown previously to outperform other 3D-structure-based methods for identifying active site residues. Then it is shown that the addition of one simple geometric property, the size rank of the cleft in which a given residue is contained, yields improved performance. Extension of the method to include predictions of non-ionizable residues is achieved through the introduction of environment variables. This extension results in even better performance than THEMATICS alone and constitutes to date the best functional site predictor based on 3D structure only, achieving nearly the same level of performance as methods that use both 3D structure and sequence alignment data. Finally, the method also easily incorporates such sequence alignment data, and when this information is included, the resulting method is shown to outperform the best current methods using any combination of sequence alignments and 3D structures. Included is an analysis demonstrating that when THEMATICS features, cleft size rank, and alignment-based conservation scores are used individually or in combination

  15. The radiological feature of anterior occiput-to-axis screw fixation as it guides the screw trajectory on 3D printed models: a feasibility study on 3D images and 3D printed models.

    PubMed

    Wu, Ai-Min; Wang, Sheng; Weng, Wan-Qing; Shao, Zhen-Xuan; Yang, Xin-Dong; Wang, Jian-Shun; Xu, Hua-Zi; Chi, Yong-Long

    2014-12-01

    Anterior occiput-to-axis screw fixation is more suitable than a posterior approach for some patients with a history of posterior surgery. The complex osseous anatomy between the occiput and the axis causes a high risk of injury to neurological and vascular structures, and it is important to have an accurate screw trajectory to guide anterior occiput-to-axis screw fixation. Thirty computed tomography (CT) scans of upper cervical spines were obtained for three-dimensional (3D) reconstruction. Cylinders (1.75 mm radius) were drawn to simulate the trajectory of an anterior occiput-to-axis screw. The imitation screw was adjusted to 4 different angles and measured, as were the values of the maximized anteroposterior width and the left-right width of the occiput (C0) to the C1 and C1 to C2 joints. Then, the 3D models were printed, and an angle guide device was used to introduce the screws into the 3D models referring to the angles calculated from the 3D images. We found the screw angle ranged from α1 (left: 4.99±4.59°; right: 4.28±5.45°) to α2 (left: 20.22±3.61°; right: 19.63±4.94°); on the lateral view, the screw angle ranged from β1 (left: 13.13±4.93°; right: 11.82±5.64°) to β2 (left: 34.86±6.00°; right: 35.01±5.77°). No statistically significant difference was found between the data of the left and right sides. On the 3D printed models, all of the anterior occiput-to-axis screws were successfully introduced, and none of them penetrated outside of the cortex; the mean α4 was 12.00±4.11 (left) and 12.25±4.05 (right), and the mean β4 was 23.44±4.21 (left) and 22.75±4.41 (right). No significant difference was found between α4 and β4 on the 3D printed models and α3 and β3 calculated from the 3D digital images of the left and right sides. Aided with the angle guide device, we could achieve an optimal screw trajectory for anterior occiput-to-axis screw fixation on 3D printed C0 to C2 models.

  16. SAFAS: Unifying Form and Structure through Interactive 3D Simulation

    ERIC Educational Resources Information Center

    Polys, Nicholas F.; Bacim, Felipe; Setareh, Mehdi; Jones, Brett D.

    2015-01-01

    There has been a significant gap between the tools used for the design of a building's architectural form and those that evaluate the structural physics of that form. Seeking to bring the perspectives of visual design and structural engineering closer together, we developed and evaluated a design tool for students and practitioners to explore the…

  17. The 3D Structure of the Galactic Bulge

    NASA Astrophysics Data System (ADS)

    Zoccali, Manuela; Valenti, Elena

    2016-06-01

    We review the observational evidences concerning the three-dimensional structure of the Galactic bulge. Although the inner few kpc of our Galaxy are normally referred to as the bulge, all the observations demonstrate that this region is dominated by a bar, i.e., the bulge is a bar. The bar has a boxy/peanut (X-shaped) structure in its outer regions, while it seems to become less and less elongated in its innermost region. A thinner and longer structure departing from the main bar has also been found, although the observational evidences that support the scenario of two separate structures has been recently challenged. Metal-poor stars ([Fe/H] ≲ -0.5 dex) trace a different structure, and also have different kinematics.

  18. Comparative 3D genome structure analysis of the fission and the budding yeast.

    PubMed

    Gong, Ke; Tjong, Harianto; Zhou, Xianghong Jasmine; Alber, Frank

    2015-01-01

    We studied the 3D structural organization of the fission yeast genome, which emerges from the tethering of heterochromatic regions in otherwise randomly configured chromosomes represented as flexible polymer chains in an nuclear environment. This model is sufficient to explain in a statistical manner many experimentally determined distinctive features of the fission yeast genome, including chromatin interaction patterns from Hi-C experiments and the co-locations of functionally related and co-expressed genes, such as genes expressed by Pol-III. Our findings demonstrate that some previously described structure-function correlations can be explained as a consequence of random chromatin collisions driven by a few geometric constraints (mainly due to centromere-SPB and telomere-NE tethering) combined with the specific gene locations in the chromosome sequence. We also performed a comparative analysis between the fission and budding yeast genome structures, for which we previously detected a similar organizing principle. However, due to the different chromosome sizes and numbers, substantial differences are observed in the 3D structural genome organization between the two species, most notably in the nuclear locations of orthologous genes, and the extent of nuclear territories for genes and chromosomes. However, despite those differences, remarkably, functional similarities are maintained, which is evident when comparing spatial clustering of functionally related genes in both yeasts. Functionally related genes show a similar spatial clustering behavior in both yeasts, even though their nuclear locations are largely different between the yeast species.

  19. Gene3D: Structural Assignment for Whole Genes and Genomes Using the CATH Domain Structure Database

    PubMed Central

    Buchan, Daniel W.A.; Shepherd, Adrian J.; Lee, David; Pearl, Frances M.G.; Rison, Stuart C.G.; Thornton, Janet M.; Orengo, Christine A.

    2002-01-01

    We present a novel web-based resource, Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, the functional Dictionary of Homologous Superfamilies (DHS) and PDBsum. Currently Gene3D provides annotation for 36 complete genomes (two eukaryotes, six archaea, and 28 bacteria). On average, between 30% and 40% of the genes of a given genome can be structurally annotated. Matches to structural domains are found using the profile-based method (PSI-BLAST). and a novel protocol, DRange, is used to resolve conflicts in matches involving different homologous superfamilies. PMID:11875040

  20. Topology-based Simplification for Feature Extraction from 3D Scalar Fields

    SciTech Connect

    Gyulassy, A; Natarajan, V; Pascucci, V; Bremer, P; Hamann, B

    2005-10-13

    This paper describes a topological approach for simplifying continuous functions defined on volumetric domains. We present a combinatorial algorithm that simplifies the Morse-Smale complex by repeated application of two atomic operations that removes pairs of critical points. The Morse-Smale complex is a topological data structure that provides a compact representation of gradient flows between critical points of a function. Critical points paired by the Morse-Smale complex identify topological features and their importance. The simplification procedure leaves important critical points untouched, and is therefore useful for extracting desirable features. We also present a visualization of the simplified topology.

  1. The 3D structures of VDAC represent a native conformation

    PubMed Central

    Hiller, Sebastian; Abramson, Jeff; Mannella, Carmen; Wagner, Gerhard; Zeth, Kornelius

    2010-01-01

    The most abundant protein of the mitochondrial outer membrane is the voltage-dependent anion channel (VDAC), which facilitates the exchange of ions and molecules between mitochondria and cytosol and is regulated by interactions with other proteins and small molecules. VDAC has been extensively studied for more than three decades, and last year three independent investigations revealed a structure of VDAC-1 exhibiting 19 transmembrane β-strands, constituting a unique structural class of β-barrel membrane proteins. Here, we provide a historical perspective on VDAC research and give an overview of the experimental design used to obtain these structures. Furthermore, we validate the protein refolding approach and summarize biochemical and biophysical evidence that links the 19-stranded structure to the native form of VDAC. PMID:20708406

  2. Three-dimensional measurement of small inner surface profiles using feature-based 3-D panoramic registration

    NASA Astrophysics Data System (ADS)

    Gong, Yuanzheng; Seibel, Eric J.

    2017-01-01

    Rapid development in the performance of sophisticated optical components, digital image sensors, and computer abilities along with decreasing costs has enabled three-dimensional (3-D) optical measurement to replace more traditional methods in manufacturing and quality control. The advantages of 3-D optical measurement, such as noncontact, high accuracy, rapid operation, and the ability for automation, are extremely valuable for inline manufacturing. However, most of the current optical approaches are eligible for exterior instead of internal surfaces of machined parts. A 3-D optical measurement approach is proposed based on machine vision for the 3-D profile measurement of tiny complex internal surfaces, such as internally threaded holes. To capture the full topographic extent (peak to valley) of threads, a side-view commercial rigid scope is used to collect images at known camera positions and orientations. A 3-D point cloud is generated with multiview stereo vision using linear motion of the test piece, which is repeated by a rotation to form additional point clouds. Registration of these point clouds into a complete reconstruction uses a proposed automated feature-based 3-D registration algorithm. The resulting 3-D reconstruction is compared with x-ray computed tomography to validate the feasibility of our proposed method for future robotically driven industrial 3-D inspection.

  3. Three-dimensional measurement of small inner surface profiles using feature-based 3-D panoramic registration

    PubMed Central

    Gong, Yuanzheng; Seibel, Eric J.

    2017-01-01

    Rapid development in the performance of sophisticated optical components, digital image sensors, and computer abilities along with decreasing costs has enabled three-dimensional (3-D) optical measurement to replace more traditional methods in manufacturing and quality control. The advantages of 3-D optical measurement, such as noncontact, high accuracy, rapid operation, and the ability for automation, are extremely valuable for inline manufacturing. However, most of the current optical approaches are eligible for exterior instead of internal surfaces of machined parts. A 3-D optical measurement approach is proposed based on machine vision for the 3-D profile measurement of tiny complex internal surfaces, such as internally threaded holes. To capture the full topographic extent (peak to valley) of threads, a side-view commercial rigid scope is used to collect images at known camera positions and orientations. A 3-D point cloud is generated with multiview stereo vision using linear motion of the test piece, which is repeated by a rotation to form additional point clouds. Registration of these point clouds into a complete reconstruction uses a proposed automated feature-based 3-D registration algorithm. The resulting 3-D reconstruction is compared with x-ray computed tomography to validate the feasibility of our proposed method for future robotically driven industrial 3-D inspection. PMID:28286351

  4. 3D bioprinting matrices with controlled pore structure and release function guide in vitro self-organization of sweat gland.

    PubMed

    Liu, Nanbo; Huang, Sha; Yao, Bin; Xie, Jiangfan; Wu, Xu; Fu, Xiaobing

    2016-10-03

    3D bioprinting matrices are novel platforms for tissue regeneration. Tissue self-organization is a critical process during regeneration that implies the features of organogenesis. However, it is not clear from the current evidences whether 3D printed construct plays a role in guiding tissue self-organization in vitro. Based on our previous study, we bioprinted a 3D matrix as the restrictive niche for direct sweat gland differentiation of epidermal progenitors by different pore structure (300-μm or 400-μm nozzle diameters printed) and reported a long-term gradual transition of differentiated cells into glandular morphogenesis occurs within the 3D construct in vitro. At the initial 14-day culture, an accelerated cell differentiation was achieved with inductive cues released along with gelatin reduction. After protein release completed, the 3D construct guide the self-organized formation of sweat gland tissues, which is similar to that of the natural developmental process. However, glandular morphogenesis was only observed in 300-μm-printed constructs. In the absence of 3D architectural support, glandular morphogenesis was not occurred. This striking finding made us to identify a previously unknown role of the 3D-printed structure in glandular tissue regeneration, and this self-organizing strategy can be applied to forming other tissues in vitro.

  5. 3D bioprinting matrices with controlled pore structure and release function guide in vitro self-organization of sweat gland

    PubMed Central

    Liu, Nanbo; Huang, Sha; Yao, Bin; Xie, Jiangfan; Wu, Xu; Fu, Xiaobing

    2016-01-01

    3D bioprinting matrices are novel platforms for tissue regeneration. Tissue self-organization is a critical process during regeneration that implies the features of organogenesis. However, it is not clear from the current evidences whether 3D printed construct plays a role in guiding tissue self-organization in vitro. Based on our previous study, we bioprinted a 3D matrix as the restrictive niche for direct sweat gland differentiation of epidermal progenitors by different pore structure (300-μm or 400-μm nozzle diameters printed) and reported a long-term gradual transition of differentiated cells into glandular morphogenesis occurs within the 3D construct in vitro. At the initial 14-day culture, an accelerated cell differentiation was achieved with inductive cues released along with gelatin reduction. After protein release completed, the 3D construct guide the self-organized formation of sweat gland tissues, which is similar to that of the natural developmental process. However, glandular morphogenesis was only observed in 300-μm–printed constructs. In the absence of 3D architectural support, glandular morphogenesis was not occurred. This striking finding made us to identify a previously unknown role of the 3D-printed structure in glandular tissue regeneration, and this self-organizing strategy can be applied to forming other tissues in vitro. PMID:27694985

  6. MUFOLD: A new solution for protein 3D structure prediction.

    PubMed

    Zhang, Jingfen; Wang, Qingguo; Barz, Bogdan; He, Zhiquan; Kosztin, Ioan; Shang, Yi; Xu, Dong

    2010-04-01

    There have been steady improvements in protein structure prediction during the past 2 decades. However, current methods are still far from consistently predicting structural models accurately with computing power accessible to common users. Toward achieving more accurate and efficient structure prediction, we developed a number of novel methods and integrated them into a software package, MUFOLD. First, a systematic protocol was developed to identify useful templates and fragments from Protein Data Bank for a given target protein. Then, an efficient process was applied for iterative coarse-grain model generation and evaluation at the Calpha or backbone level. In this process, we construct models using interresidue spatial restraints derived from alignments by multidimensional scaling, evaluate and select models through clustering and static scoring functions, and iteratively improve the selected models by integrating spatial restraints and previous models. Finally, the full-atom models were evaluated using molecular dynamics simulations based on structural changes under simulated heating. We have continuously improved the performance of MUFOLD by using a benchmark of 200 proteins from the Astral database, where no template with >25% sequence identity to any target protein is included. The average root-mean-square deviation of the best models from the native structures is 4.28 A, which shows significant and systematic improvement over our previous methods. The computing time of MUFOLD is much shorter than many other tools, such as Rosetta. MUFOLD demonstrated some success in the 2008 community-wide experiment for protein structure prediction CASP8.

  7. Structured light imaging system for structural and optical characterization of 3D tissue-simulating phantoms

    NASA Astrophysics Data System (ADS)

    Liu, Songde; Smith, Zach; Xu, Ronald X.

    2016-10-01

    There is a pressing need for a phantom standard to calibrate medical optical devices. However, 3D printing of tissue-simulating phantom standard is challenged by lacking of appropriate methods to characterize and reproduce surface topography and optical properties accurately. We have developed a structured light imaging system to characterize surface topography and optical properties (absorption coefficient and reduced scattering coefficient) of 3D tissue-simulating phantoms. The system consisted of a hyperspectral light source, a digital light projector (DLP), a CMOS camera, two polarizers, a rotational stage, a translation stage, a motion controller, and a personal computer. Tissue-simulating phantoms with different structural and optical properties were characterized by the proposed imaging system and validated by a standard integrating sphere system. The experimental results showed that the proposed system was able to achieve pixel-level optical properties with a percentage error of less than 11% for absorption coefficient and less than 7% for reduced scattering coefficient for phantoms without surface curvature. In the meanwhile, 3D topographic profile of the phantom can be effectively reconstructed with an accuracy of less than 1% deviation error. Our study demonstrated that the proposed structured light imaging system has the potential to characterize structural profile and optical properties of 3D tissue-simulating phantoms.

  8. Subtractive 3D Printing of Optically Active Diamond Structures

    NASA Astrophysics Data System (ADS)

    Martin, Aiden A.; Toth, Milos; Aharonovich, Igor

    2014-05-01

    Controlled fabrication of semiconductor nanostructures is an essential step in engineering of high performance photonic and optoelectronic devices. Diamond in particular has recently attracted considerable attention as a promising platform for quantum technologies, photonics and high resolution sensing applications. Here we demonstrate the fabrication of optically active, functional diamond structures using gas-mediated electron beam induced etching (EBIE). The technique achieves dry chemical etching at room temperature through the dissociation of surface-adsorbed H2O molecules by energetic electrons in a water vapor environment. Parallel processing is possible by electron flood exposure and the use of an etch mask, while high resolution, mask-free, iterative editing is demonstrated by direct write etching of inclined facets of diamond microparticles. The realized structures demonstrate the potential of EBIE for the fabrication of optically active structures in diamond.

  9. Study on embedding fiber Bragg grating sensor into the 3D printing structure for health monitoring

    NASA Astrophysics Data System (ADS)

    Li, Ruiya; Tan, Yuegang; Zhou, Zude; Fang, Liang; Chen, Yiyang

    2016-10-01

    3D printing technology is a rapidly developing manufacturing technology, which is known as a core technology in the third industrial revolution. With the continuous improvement of the application of 3D printing products, the health monitoring of the 3D printing structure is particularly important. Fiber Bragg grating (FBG) sensing technology is a new type of optical sensing technology with unique advantages comparing to traditional sensing technology, and it has great application prospects in structural health monitoring. In this paper, the FBG sensors embedded in the internal structure of the 3D printing were used to monitor the static and dynamic strain variation of 3D printing structure during loading process. The theoretical result and experimental result has good consistency and the characteristic frequency detected by FBG sensor is consistent with the testing results of traditional accelerator in the dynamic experiment. The results of this paper preliminary validate that FBG embedded in the 3D printing structure can effectively detecting the static and dynamic stain change of the 3D printing structure, which provide some guidance for the health monitoring of 3D printing structure.

  10. Delineation of nuclear structures in 3D multicellular systems

    SciTech Connect

    2013-09-13

    A pipeline, implemented within the Insight Segmentation and Registration Toolkit (ITK) and The Visualization Toolkit (VTK) framework, to delineate each nucleus and to profile morphometric and colony organization. At an abstract level, our approach is an extension of a previously developed method for monolayer call structure models.

  11. Spectrally encoded fiber-based structured lighting probe for intraoperative 3D imaging

    PubMed Central

    Clancy, Neil T.; Stoyanov, Danail; Maier-Hein, Lena; Groch, Anja; Yang, Guang-Zhong; Elson, Daniel S.

    2011-01-01

    Three dimensional quantification of organ shape and structure during minimally invasive surgery (MIS) could enhance precision by allowing the registration of multi-modal or pre-operative image data (US/MRI/CT) with the live optical image. Structured illumination is one technique to obtain 3D information through the projection of a known pattern onto the tissue, although currently these systems tend to be used only for macroscopic imaging or open procedures rather than in endoscopy. To account for occlusions, where a projected feature may be hidden from view and/or confused with a neighboring point, a flexible multispectral structured illumination probe has been developed that labels each projected point with a specific wavelength using a supercontinuum laser. When imaged by a standard endoscope camera they can then be segmented using their RGB values, and their 3D coordinates calculated after camera calibration. The probe itself is sufficiently small (1.7 mm diameter) to allow it to be used in the biopsy channel of commonly used medical endoscopes. Surgical robots could therefore also employ this technology to solve navigation and visualization problems in MIS, and help to develop advanced surgical procedures such as natural orifice translumenal endoscopic surgery. PMID:22076272

  12. Robotic extrusion processes for direct ink writing of 3D conductive polyaniline structures

    NASA Astrophysics Data System (ADS)

    Holness, F. Benjamin; Price, Aaron D.

    2016-04-01

    The intractable nature of intrinsically conductive polymers (ICP) leads to practical limitations in the fabrication of ICP-based transducers having complex three-dimensional geometries. Conventional ICP device fabrication processes have focused primarily on thin-film deposition techniques; therefore this study explores novel additive manufacturing processes specifically developed for ICP with the ultimate goal of increasing the functionality of ICP sensors and actuators. Herein we employ automated polymer paste extrusion processes for the direct ink writing of 3D conductive polyaniline (PANI) structures. Realization of these structures is enabled through a modified fused filament fabrication delta robot equipped with an integrated polymer paste extruder. This unique robot-controlled additive manufacturing platform is capable of fabricating high-resolution 3D conductive PANI and has been utilized to produce structures with a minimum feature size of 1.5 mm. The required processability of PANI is achieved by means of a counter-ion induced thermal doping method. Using this method, a viscous paste is formulated as the extrudate and a thermo-chemical treatment is applied post extrusion to finalize the complexation.

  13. 3D P-wave Velocity Structure Beneath the Eastern Canadian Shield and Northern Appalachian Region

    NASA Astrophysics Data System (ADS)

    Villemaire, M.; Darbyshire, F. A.; Bastow, I. D.

    2010-12-01

    Previous seismic studies of the upper mantle of the Canadian Shield have indicated some low-velocity anomalies within the cratonic lithosphere in the Abitibi-Grenville region. The lack of seismograph station coverage to the east and south-east of the studied area prevented definition of the 3D geometry of these anomalies. Adding new stations from the province of Quebec and from the northeastern United States allows us to carry out new studies of the P-wave velocity structure of the upper mantle, in order to better understand the complexity of the region and the interaction of the lithosphere with possible thermal anomalies in the underlying mantle. We analysed teleseismic P wave arrivals from almost 200 earthquakes, recorded at 45 stations deployed across the provinces of Quebec and Ontario and across the northeastern US. The relative arrival times of teleseismic P waves across the array were measured using the cross-correlation method of VanDecar & Crosson (1990). The travel time data were then inverted to estimate the 3D P-wave velocity structure beneath the region, using the least-squares tomographic inversion code of VanDecar (1991). The model shows some interesting features. We see a diffuse low-velocity structure beneath New-England that extends to at least 500 km depth, and that may be related to the Appalachian Mountain belt. There is also a linear low-velocity structure, flanked by higher velocities, perpendicular to the Grenville Front, and along the Ottawa Valley. We interpret this feature as a mantle signature of the Great Meteor Hotspot track. We have looked for systematic differences between the mantle underlying the Archean Superior craton and the Proterozoic Grenville Province but did not find a significant difference in the upper mantle. We investigate the role of thermal and compositional effects to interpret the velocity models and to relate the patterns of the anomalies to past and present tectonic structures.

  14. Imaging solar coronal magnetic structures in 3D

    NASA Astrophysics Data System (ADS)

    Cartledge, N. P.

    The study of solar coronal structures and, in particular prominences, is a key part of understanding the highly complex physical mechanisms occurring in the Sun's atmosphere. Solar prominences are important in their own right and some of the most puzzling questions in solar theory have arisen through their study. For example, how do they form and how is their mass continuously replenished? How can the magnetic field provide their continuous support against gravity over time periods of several months? How can such cool, dense material exist in thermal equilibrium in the surrounding coronal environment? Why do they erupt? A study of their structure and that of the surrounding medium is important in determining the nature of the coronal plasma and magnetic field. Also, prominences are closely associated with other key phenomena such as coronal mass ejections and eruptive solar flares which occur as a prominence loses equilibrium and rises from the solar surface. Our current understanding of these fascinating structures is extremely limited and we know very little about their basic global structure. In fact, recent prominence observations have caused our basic paradigms to be challenged (Priest, 1996) and so we must set up new models in order to gain even a fundamental understanding. Prominences are highly nonlinear, three-dimensional structures. Large feet (or barbs) reach out from the main body of a prominence and reach down to the photosphere where the dense material continuously drains away. These provide a real clue to the three-dimensional nature of the coronal field and its relation to the photospheric field. It is important, therefore, to make stereographic observations of prominences in order to gain a basic understanding of their essentially three-dimensional nature and attempt to formulate new paradigms for their structure and evolution. There is no doubt that the study of prominences in three dimensions is a crucial exercise if we are to develop a better

  15. Rapid Prototyping across the Spectrum: RF to Optical 3D Electromagnetic Structures

    DTIC Science & Technology

    2015-11-17

    fabricated using 3D printer . The fill factor decreases radially outwards and the voids are visible in the unit cells as you approach the periphery of the...with thin walls) [29]. Figure 6: Examples of lenses fabricated with AM (a) GRIN lens fabricated using 3D printer . The fill factor decreases...AFRL-RW-EG-TP-2015-002 Rapid Prototyping across the Spectrum: RF to Optical 3D Electromagnetic Structures Jeffery W. Allen Monica S. Allen Brett

  16. 3D Printing for Spacecraft Multi-Functional Structures

    NASA Astrophysics Data System (ADS)

    Roddy, P. A.; Huang, C. Y.; Lyke, J.; Baur, J.; Durstock, M.; MacDonald, E.

    2013-12-01

    Three-dimensional printing, more formally Additive Manufacturing (AM), is being explored by groups worldwide for use in space missions, but we recognize the amazing potential of this emerging technology to produce space weather environmental sensors at costs commensurate with declining research budgets. We present here a plan to go substantially beyond the novelty stage of this technology by developing a foundation for using AM in high-assurance space system missions. Our two-pronged approach involves (1) a disciplined investigation of material properties and reliability (electrical, mechanical, radiation) of AM and (2) the extension of this knowledge to make complex structures that can exploit the advantages of AM. We address the design, manufacture, and optimization of multifunctional space structures using multi-physics design methods, integrated computational models, and AM. Integrated multifunctional structures have significant advantage in flexibility, size, weight, and power in comparison to formally attached elements, but their design and fabrication can be complex. The complexity and range in element shape, processing method, material properties and vehicle integration make this an ideal problem to advance the current state of the art methods for multiphysics mechanism design and strengthening AM processing science.

  17. Code System for Analysis of 3-D Reinforced Concrete Structures.

    SciTech Connect

    ANDERSON, C. A.

    1999-11-22

    Version 00 NONSAP-C is a finite element program for determining the static and dynamic response of three-dimensional reinforced concrete structures. Long-term, or creep, behavior of concrete structures can also be analyzed. Nonlinear constitutive relations for concrete under short-term loads are incorporated in two time-independent models, a variable-modulus approach with orthotropic behavior induced in the concrete due to the development of different tangent moduli in different directions and an elastic-plastic model in which the concrete is assumed to be a continuous, isotropic, and linearly elastic-plastic strain-hardening-fracture material. A viscoelastic constitutive model for long-term thermal creep of concrete is included. Three-dimensional finite elements available in NONSAP-C include a truss element, a multinode tendon element for prestressed and post tensioned concrete structures, an elastic-plastic membrane element to represent the behavior of cavity liners, and a general isoparametric element with a variable number of nodes for analysis of solids and thick shells.

  18. Classification of lung nodules in diagnostic CT: an approach based on 3D vascular features, nodule density distribution, and shape features

    NASA Astrophysics Data System (ADS)

    Lo, Shih-Chung B.; Hsu, Li-Yueh; Freedman, Matthew T.; Lure, Yuan Ming F.; Zhao, Hui

    2003-05-01

    We have developed various segmentation and analysis methods for the quantification of lung nodules in thoracic CT. Our methods include the enhancement of lung structures followed by a series of segmentation methods to extract the nodule and to form 3D configuration at an area of interest. The vascular index, aspect ratio, circularity, irregularity, extent, compactness, and convexity were also computed as shape features for quantifying the nodule boundary. The density distribution of the nodule was modeled based on its internal homogeneity and/or heterogeneity. We also used several density related features including entropy, difference entropy as well as other first and second order moments. We have collected 48 cases of lung nodules scanned by thin-slice diagnostic CT. Of these cases, 24 are benign and 24 are malignant. A jackknife experiment was performed using a standard back-propagation neural network as the classifier. The LABROC result showed that the Az of this preliminary study is 0.89.

  19. Topologic connection between 2-D layered structures and 3-D diamond structures for conventional semiconductors

    PubMed Central

    Wang, Jianwei; Zhang, Yong

    2016-01-01

    When coming to identify new 2D materials, our intuition would suggest us to look from layered instead of 3D materials. However, since graphite can be hypothetically derived from diamond by stretching it along its [111] axis, many 3D materials can also potentially be explored as new candidates for 2D materials. Using a density functional theory, we perform a systematic study over the common Group IV, III–V, and II–VI semiconductors along different deformation paths to reveal new structures that are topologically connected to but distinctly different from the 3D parent structure. Specifically, we explore two major phase transition paths, originating respectively from wurtzite and NiAs structure, by applying compressive and tensile strain along the symmetry axis, and calculating the total energy changes to search for potential metastable states, as well as phonon spectra to examine the structural stability. Each path is found to further split into two branches under tensile strain–low buckled and high buckled structures, which respectively lead to a low and high buckled monolayer structure. Most promising new layered or planar structures identified include BeO, GaN, and ZnO on the tensile strain side, Ge, Si, and GaP on the compressive strain side. PMID:27090430

  20. Structural 3d Monitoring Using a New Sinusoidal Fitting Adjustment

    NASA Astrophysics Data System (ADS)

    Detchev, I.; Habib, A.; Lichti, D.; El-Badry, M.

    2016-06-01

    Digital photogrammetric systems combined with image processing techniques have been used for structural monitoring purposes for more than a decade. For applications requiring sub-millimetre level precision, the use of off-the-shelf DSLR cameras is a suitable choice, especially when the low cost of the involved sensors is a priority. The disadvantage in the use of entry level DSLRs is that there is a trade-off between frame rate and burst rate - a high frame rate is either not available or it cannot be sustained long enough. This problem must be overcome when monitoring a structural element undergoing a dynamic test, where a range of loads are cycled through multiple times a second. In order to estimate deflections during such a scenario, this paper proposes a new least-squares adjustment for sinusoidal fitting. The new technique is capable of processing multiple back-to-back bursts of data within the same adjustment, which synthetically increases the de-facto temporal resolution of the system. The paper describes a beam deformation test done in a structures laboratory. The experimental results were assessed in terms of both their precision and accuracy. The new method increased the effective sampling frequency three-fold, which improved the standard deviations of the estimated parameters with up to two orders of magnitude. A residual RMSE as low as 30 μm was attained, and likewise the RMSE of the computed amplitudes between the photogrammetric system and the control laser transducers was as small as 34 μm.

  1. Small-angle scattering and 3D structure interpretation.

    PubMed

    Trewhella, Jill

    2016-10-01

    This review focuses on advances in the application of solution small-angle scattering (SAS) in structural analysis of biomolecules and the complexes they form. Examples highlighted illustrate the unique contribution of SAS, using both X-rays and neutrons, in hybrid or integrative modelling methods. The increased information content when neutron scattering with contrast variation is used is a particular focus. Finally, progress toward an agreed reporting framework, the development of open data and model archives, and the importance of these initiatives is covered.

  2. Efficient 3D texture feature extraction from CT images for computer-aided diagnosis of pulmonary nodules

    NASA Astrophysics Data System (ADS)

    Han, Fangfang; Wang, Huafeng; Song, Bowen; Zhang, Guopeng; Lu, Hongbing; Moore, William; Liang, Zhengrong; Zhao, Hong

    2014-03-01

    Texture feature from chest CT images for malignancy assessment of pulmonary nodules has become an un-ignored and efficient factor in Computer-Aided Diagnosis (CADx). In this paper, we focus on extracting as fewer as needed efficient texture features, which can be combined with other classical features (e.g. size, shape, growing rate, etc.) for assisting lung nodule diagnosis. Based on a typical calculation algorithm of texture features, namely Haralick features achieved from the gray-tone spatial-dependence matrices, we calculated two dimensional (2D) and three dimensional (3D) Haralick features from the CT images of 905 nodules. All of the CT images were downloaded from the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI), which is the largest public chest database. 3D Haralick feature model of thirteen directions contains more information from the relationships on the neighbor voxels of different slices than 2D features from only four directions. After comparing the efficiencies of 2D and 3D Haralick features applied on the diagnosis of nodules, principal component analysis (PCA) algorithm was used to extract as fewer as needed efficient texture features. To achieve an objective assessment of the texture features, the support vector machine classifier was trained and tested repeatedly for one hundred times. And the statistical results of the classification experiments were described by an average receiver operating characteristic (ROC) curve. The mean value (0.8776) of the area under the ROC curves in our experiments can show that the two extracted 3D Haralick projected features have the potential to assist the classification of benign and malignant nodules.

  3. Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

    PubMed Central

    Lewis, Tony E.; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L.; Buchan, Daniel W.A.; Chothia, Cyrus; Cuff, Alison; Dana, Jose M.; Filippis, Ioannis; Gough, Julian; Hunter, Sarah; Jones, David T.; Kelley, Lawrence A.; Kleywegt, Gerard J.; Minneci, Federico; Mitchell, Alex; Murzin, Alexey G.; Ochoa-Montaño, Bernardo; Rackham, Owen J. L.; Smith, James; Sternberg, Michael J. E.; Velankar, Sameer; Yeats, Corin; Orengo, Christine

    2013-01-01

    Genome3D, available at http://www.genome3d.eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence–structure–function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural domains (structural annotations) and their 3D structures (structural models). Structural annotations and 3D model predictions are currently available for three model genomes (Homo sapiens, E. coli and baker’s yeast), and the project will extend to other genomes in the near future. As these resources exploit different strategies for predicting structures, the main aim of Genome3D is to enable comparisons between all the resources so that biologists can see where predictions agree and are therefore more trusted. Furthermore, as these methods differ in whether they build their predictions using CATH or SCOP, Genome3D also contains the first official mapping between these two databases. This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs). PMID:23203986

  4. Nano-Structural Elucidation in Carbon Black Loaded NR Vulcanizate by 3D-TEM and In Situ WAXD Measurements

    SciTech Connect

    Ikeda,Y.; Kato, A.; Shimanuki, J.; Kohjiya, S.; Tosaka, M.; Poompradub, S.; Toki, S.; Hsiao, B.

    2007-01-01

    Three dimensional (3D) visualization of nanometer structure of carbon black dispersion in rubbery matrix has successfully been studied and reported in this paper. Use of 3D-TEM, which is computerized tomography combined with transmission electron microscopy (TEM), enabled us to reconstruct 3D images of carbon black aggregates in natural rubber (NR) matrix. The TEM measurements were conducted by a bright-field method on thin samples without any electron staining. The sample was subject to uni-axial tilting (+65 degree to -65 degree with 2 degree increment) in the sample chamber, and 66 TEM images were taken on each sample. These TEM images were used for computerized tomography to reconstruct the 3D image. This technique is designated as 3D-TEM. The nano-structural features observed by 3D-TEM were in conformity with the electron-conductivity results, and the percolation behavior was recognized. These results were further supplemented by in situ wide-angle X-ray diffraction (WAXD), i.e., simultaneous WAXD and tensile measurements on the sample to observe the strain-induced crystallization in NR vulcanizate. Upon tensile elongation, the crystallization was clearly observed in WAXD in the presence of carbon black, and it contributed to the tensile properties. In order to understand the performances of filled NR vulcanizates, it surely is necessary to know the structural states of the mixed nano-filler and the crystallites produced upon elongation.

  5. 3D nano-structures for laser nano-manipulation

    PubMed Central

    Seniutinas, Gediminas; Gervinskas, Gediminas; Brasselet, Etienne; Juodkazis, Saulius

    2013-01-01

    Summary The resputtering of gold films from nano-holes defined in a sacrificial PMMA mask, which was made by electron beam lithography, was carried out with a dry plasma etching tool in order to form well-like structures with a high aspect ratio (height/width ≈ 3–4) at the rims of the nano-holes. The extraordinary transmission through the patterns of such nano-wells was investigated experimentally and numerically. By doing numerical simulations of 50-nm and 100-nm diameter polystyrene beads in water and air, we show the potential of such patterns for self-induced back-action (SIBA) trapping. The best trapping conditions were found to be a trapping force of 2 pN/W/μm2 (numerical result) exerted on a 50-nm diameter bead in water. The simulations were based on the analytical Lorentz force model. PMID:24062979

  6. 3-D Structure of Sunspots using Imaging Spectroscopy

    NASA Technical Reports Server (NTRS)

    Balasubramaniam, K. S.; Gary, G. Allen; Reardon, K.

    2006-01-01

    We use the Interferometric BIdimensional Spectrometer (IBIS) of the INAF/Arcetri Astrophysical Observatory and installed at the National Solar Observatory (NSO) Dunn Solar Telescope, to understand the structure of sunspots. Using the spectral lines FeI 6301.5 A, FeII 7224.4 A, and CaII 8542.6 A, we examine the spectroscopic variation of sunspot penumbral and umbral structures at the heights of formation of these lines. These high resolution observations were acquired on 2004 July 30-31, of active region NOAA 10654, using the high order NSO adaptive optics system. We map the spatio-temporal variation of Doppler signatures in these spectral lines, from the photosphere to the chromosphere. From a 70-minute temporal average of individual 32-second cadence Doppler observations we find that the averaged velocities decrease with height, about 3.5 times larger in the deeper photosphere (FeII 7224.4 A; height-of-formation approx. 50 km) than in the upper photosphere FeI 6301.5 A; height-of-formation approx. 350 km), There is a remarkable coherence of Doppler signals over the height difference of 300 km. From a high-speed animation of the Doppler sequence we find evidence for what appears to be ejection of high speed gas concentrations from edges of penumbral filaments into the surrounding granular photosphere. The Evershed flow persists a few arcseconds beyond the traditionally demarcated penumbra-granulation boundary. We present these and other results and discuss the implications of these measurements for sunspot models.

  7. Fabrication of 2D and 3D photonic structures using laser lithography

    NASA Astrophysics Data System (ADS)

    Gaso, P.; Jandura, D.; Pudis, D.

    2016-12-01

    In this paper we demonstrate possibilities of three-dimensional (3D) printing technology based on two photon polymerization. We used three-dimensional dip-in direct-laser-writing (DLW) optical lithography to fabricate 2D and 3D optical structures for optoelectronics and for optical sensing applications. DLW lithography allows us use a non conventional way how to couple light into the waveguide structure. We prepared ring resonator and we investigated its transmission spectral characteristic. We present 3D inverse opal structure from its design to printing and scanning electron microscope (SEM) imaging. Finally, SEM images of some prepared photonic crystal structures were performed.

  8. Stress Recovery and Error Estimation for 3-D Shell Structures

    NASA Technical Reports Server (NTRS)

    Riggs, H. R.

    2000-01-01

    The C1-continuous stress fields obtained from finite element analyses are in general lower- order accurate than are the corresponding displacement fields. Much effort has focussed on increasing their accuracy and/or their continuity, both for improved stress prediction and especially error estimation. A previous project developed a penalized, discrete least squares variational procedure that increases the accuracy and continuity of the stress field. The variational problem is solved by a post-processing, 'finite-element-type' analysis to recover a smooth, more accurate, C1-continuous stress field given the 'raw' finite element stresses. This analysis has been named the SEA/PDLS. The recovered stress field can be used in a posteriori error estimators, such as the Zienkiewicz-Zhu error estimator or equilibrium error estimators. The procedure was well-developed for the two-dimensional (plane) case involving low-order finite elements. It has been demonstrated that, if optimal finite element stresses are used for the post-processing, the recovered stress field is globally superconvergent. Extension of this work to three dimensional solids is straightforward. Attachment: Stress recovery and error estimation for shell structure (abstract only). A 4-node, shear-deformable flat shell element developed via explicit Kirchhoff constraints (abstract only). A novel four-node quadrilateral smoothing element for stress enhancement and error estimation (abstract only).

  9. 3D-Printed Broadband Dielectric Tube Terahertz Waveguide with Anti-Reflection Structure

    NASA Astrophysics Data System (ADS)

    Vogt, Dominik Walter; Leonhardt, Rainer

    2016-11-01

    We demonstrate broadband, low loss, and close-to-zero dispersion guidance of terahertz (THz) radiation in a dielectric tube with an anti-reflection structure (AR-tube waveguide) in the frequency range from 0.2 to 1.0 THz. The anti-reflection structure (ARS) consists of close-packed cones in a hexagonal lattice arranged on the outer surface of the tube cladding. The feature size of the ARS is in the order of the wavelength between 0.2 and 1.0 THz. The waveguides are fabricated with the versatile and cost efficient 3D-printing method. Terahertz time-domain spectroscopy (THz-TDS) measurements as well as 3D finite-difference time-domain simulations (FDTD) are performed to extensively characterize the AR-tube waveguides. Spectrograms, attenuation spectra, effective phase refractive indices, and the group-velocity dispersion parameters β 2 of the AR-tube waveguides are presented. Both the experimental and numerical results confirm the extended bandwidth and smaller group-velocity dispersion of the AR-tube waveguide compared to a low loss plain dielectric tube THz waveguide. The AR-tube waveguide prototypes show an attenuation spectrum close to the theoretical limit given by the infinite cladding tube waveguide.

  10. Using 3D visualization and seismic attributes to improve structural and stratigraphic resolution of reservoirs

    SciTech Connect

    Kerr, J. ); Jones, G.L. )

    1996-01-01

    Recent advances in hardware and software have given the interpreter and engineer new ways to view 3D seismic data and well bore information. Recent papers have also highlighted the use of various statistics and seismic attributes. By combining new 3D rendering technologies with recent trends in seismic analysis, the interpreter can improve the structural and stratigraphic resolution of hydrocarbon reservoirs. This paper gives several examples using 3D visualization to better define both the structural and stratigraphic aspects of several different structural types from around the world. Statistics, 3D visualization techniques and rapid animation are used to show complex faulting and detailed channel systems. These systems would be difficult to map using either 2D or 3D data with conventional interpretation techniques.

  11. Using 3D visualization and seismic attributes to improve structural and stratigraphic resolution of reservoirs

    SciTech Connect

    Kerr, J.; Jones, G.L.

    1996-12-31

    Recent advances in hardware and software have given the interpreter and engineer new ways to view 3D seismic data and well bore information. Recent papers have also highlighted the use of various statistics and seismic attributes. By combining new 3D rendering technologies with recent trends in seismic analysis, the interpreter can improve the structural and stratigraphic resolution of hydrocarbon reservoirs. This paper gives several examples using 3D visualization to better define both the structural and stratigraphic aspects of several different structural types from around the world. Statistics, 3D visualization techniques and rapid animation are used to show complex faulting and detailed channel systems. These systems would be difficult to map using either 2D or 3D data with conventional interpretation techniques.

  12. A 3-D fluorescence imaging system incorporating structured illumination technology

    NASA Astrophysics Data System (ADS)

    Antos, L.; Emord, P.; Luquette, B.; McGee, B.; Nguyen, D.; Phipps, A.; Phillips, D.; Helguera, M.

    2010-02-01

    A currently available 2-D high-resolution, optical molecular imaging system was modified by the addition of a structured illumination source, OptigridTM, to investigate the feasibility of providing depth resolution along the optical axis. The modification involved the insertion of the OptigridTM and a lens in the path between the light source and the image plane, as well as control and signal processing software. Projection of the OptigridTM onto the imaging surface at an angle, was resolved applying the Scheimpflug principle. The illumination system implements modulation of the light source and provides a framework for capturing depth resolved mages. The system is capable of in-focus projection of the OptigridTM at different spatial frequencies, and supports the use of different lenses. A calibration process was developed for the system to achieve consistent phase shifts of the OptigridTM. Post-processing extracted depth information using depth modulation analysis using a phantom block with fluorescent sheets at different depths. An important aspect of this effort was that it was carried out by a multidisciplinary team of engineering and science students as part of a capstone senior design program. The disciplines represented are mechanical engineering, electrical engineering and imaging science. The project was sponsored by a financial grant from New York State with equipment support from two industrial concerns. The students were provided with a basic imaging concept and charged with developing, implementing, testing and validating a feasible proof-of-concept prototype system that was returned to the originator of the concept for further evaluation and characterization.

  13. The 3D velocity structure beneath Iceland: Identifying melt pathways

    NASA Astrophysics Data System (ADS)

    Allen, R.

    2003-04-01

    The integration of various seismic datasets, recorded by the broadband HOTSPOT network deployed across Iceland, provides one of the highest resolution studies of the crust and mantle structure associated with a plume-ridge system. The mantle P- and S-velocity models (ICEMAN), derived from teleseismic body-wave and surface wave analysis, show a vertical, cylindrical low velocity anomaly ˜200 km in diameter extending from ˜400 km, the maximum depth of resolution, up to ˜200 km above which low velocity material is present beneath all of Iceland. The maximum P- and S-velocity anomalies of -2% and -4% respectively are found beneath the northwestern edge of Vatnajokull. The crustal S-velocity model (ICECRTb) is constrained by local surface waves, refraction experiments and receiver functions, and shows significant variation in crustal thickness. The thinnest, ˜15 km, crust is found around coastal regions, the thickest crust is beneath northwestern Vatnajokull where it reaches a thickness of 45 km. Within this thick crustal root is a vertical low velocity anomaly connecting the core of the mantle anomaly to horizontal low velocity regions that extend along the western and eastern volcanic zones but not the northern volcanic zone. These crustal low velocity zones are interpreted as regions through which melt is fed from the mantle to shallow magma chambers beneath the rift zones, where crustal formation occurs. The pipework between the core of the mantle anomaly and the southern rift zones is responsible for ˜30 km thick crust. Its absence to the north results in relatively thin, ˜20 km thick, crust.

  14. Electrodeposition-based 3D Printing of Metallic Microarchitectures with Controlled Internal Structures.

    PubMed

    Seol, Seung Kwon; Kim, Daeho; Lee, Sanghyeon; Kim, Jung Hyun; Chang, Won Suk; Kim, Ji Tae

    2015-08-26

    3D printing of metallic microarchitectures with controlled internal structures is realized at room temperature in ambient air conditions by the manipulation of metal ion concentration and pulsed electric potentials in the electrolyte meniscus during the meniscus-guided electrodeposition. Precise control of the printing nozzle enables the drawing of complex 3D microarchitectures with well-defined geometries and positions.

  15. Searching protein 3-D structures for optimal structure alignment using intelligent algorithms and data structures.

    PubMed

    Novosád, Tomáš; Snášel, Václav; Abraham, Ajith; Yang, Jack Y

    2010-11-01

    In this paper, we present a novel algorithm for measuring protein similarity based on their 3-D structure (protein tertiary structure). The algorithm used a suffix tree for discovering common parts of main chains of all proteins appearing in the current research collaboratory for structural bioinformatics protein data bank (PDB). By identifying these common parts, we build a vector model and use some classical information retrieval (IR) algorithms based on the vector model to measure the similarity between proteins--all to all protein similarity. For the calculation of protein similarity, we use term frequency × inverse document frequency ( tf × idf ) term weighing schema and cosine similarity measure. The goal of this paper is to introduce new protein similarity metric based on suffix trees and IR methods. Whole current PDB database was used to demonstrate very good time complexity of the algorithm as well as high precision. We have chosen the structural classification of proteins (SCOP) database for verification of the precision of our algorithm because it is maintained primarily by humans. The next success of this paper would be the ability to determine SCOP categories of proteins not included in the latest version of the SCOP database (v. 1.75) with nearly 100% precision.

  16. Locally adaptive 2D-3D registration using vascular structure model for liver catheterization.

    PubMed

    Kim, Jihye; Lee, Jeongjin; Chung, Jin Wook; Shin, Yeong-Gil

    2016-03-01

    Two-dimensional-three-dimensional (2D-3D) registration between intra-operative 2D digital subtraction angiography (DSA) and pre-operative 3D computed tomography angiography (CTA) can be used for roadmapping purposes. However, through the projection of 3D vessels, incorrect intersections and overlaps between vessels are produced because of the complex vascular structure, which makes it difficult to obtain the correct solution of 2D-3D registration. To overcome these problems, we propose a registration method that selects a suitable part of a 3D vascular structure for a given DSA image and finds the optimized solution to the partial 3D structure. The proposed algorithm can reduce the registration errors because it restricts the range of the 3D vascular structure for the registration by using only the relevant 3D vessels with the given DSA. To search for the appropriate 3D partial structure, we first construct a tree model of the 3D vascular structure and divide it into several subtrees in accordance with the connectivity. Then, the best matched subtree with the given DSA image is selected using the results from the coarse registration between each subtree and the vessels in the DSA image. Finally, a fine registration is conducted to minimize the difference between the selected subtree and the vessels of the DSA image. In experimental results obtained using 10 clinical datasets, the average distance errors in the case of the proposed method were 2.34±1.94mm. The proposed algorithm converges faster and produces more correct results than the conventional method in evaluations on patient datasets.

  17. 3D WHOLE-PROMINENCE FINE STRUCTURE MODELING. II. PROMINENCE EVOLUTION

    SciTech Connect

    Gunár, Stanislav; Mackay, Duncan H.

    2015-10-20

    We use the new three-dimensional (3D) whole-prominence fine structure model to study the evolution of prominences and their fine structures in response to changes in the underlying photospheric magnetic flux distribution. The applied model combines a detailed 3D prominence magnetic field configuration with a realistic description of the prominence plasma distributed along multiple fine structures. In addition, we utilize an approximate Hα visualization technique to study the evolution of the visible cool prominence plasma both in emission (prominence) and absorption (filament). We show that the initial magnetic field configuration of the modeled prominence is significantly disturbed by the changing position of a single polarity of a magnetic bipole as the bipole is advected toward the main body of the filament. This leads to the creation of a barb, which becomes the dominant feature visible in the synthetic Hα images of both the prominence and filament views. The evolution of the bipole also creates conditions that lead to the disappearance and reappearance of large portions of the main body. We also show that an arch-like region containing a dark void (a bubble) can be naturally produced in the synthetic prominence Hα images. While not visible in terms of the magnetic field lines, it is due to a lack of Hα emission from low-pressure, low-density plasma located in shallow magnetic dips lying along the lines of sight intersecting the dark void. In addition, a quasi-vertical small-scale feature consisting of short and deep dips, piled one above the other, is produced.

  18. 3D lidar imaging for detecting and understanding plant responses and canopy structure.

    PubMed

    Omasa, Kenji; Hosoi, Fumiki; Konishi, Atsumi

    2007-01-01

    Understanding and diagnosing plant responses to stress will benefit greatly from three-dimensional (3D) measurement and analysis of plant properties because plant responses are strongly related to their 3D structures. Light detection and ranging (lidar) has recently emerged as a powerful tool for direct 3D measurement of plant structure. Here the use of 3D lidar imaging to estimate plant properties such as canopy height, canopy structure, carbon stock, and species is demonstrated, and plant growth and shape responses are assessed by reviewing the development of lidar systems and their applications from the leaf level to canopy remote sensing. In addition, the recent creation of accurate 3D lidar images combined with natural colour, chlorophyll fluorescence, photochemical reflectance index, and leaf temperature images is demonstrated, thereby providing information on responses of pigments, photosynthesis, transpiration, stomatal opening, and shape to environmental stresses; these data can be integrated with 3D images of the plants using computer graphics techniques. Future lidar applications that provide more accurate dynamic estimation of various plant properties should improve our understanding of plant responses to stress and of interactions between plants and their environment. Moreover, combining 3D lidar with other passive and active imaging techniques will potentially improve the accuracy of airborne and satellite remote sensing, and make it possible to analyse 3D information on ecophysiological responses and levels of various substances in agricultural and ecological applications and in observations of the global biosphere.

  19. Biomineralized 3-D Nanoparticle Assemblies with Micro-to-Nanoscale Features and Tailored Chemistries

    DTIC Science & Technology

    2008-01-07

    Sandhage, “3-D Microparticles of BaTiO3 and Zn2SiO4 via the Chemical ( Sol - Gel , Acetate Precursor, or Hydrothermal) Conversion of Biologically (Diatom...Sandhage, “ Sol - Gel Synthesis on Self-Replicating Single-Cell Scaffolds: Applying Complex Chemistries to Nature’s 3-D Nanostructured Templates,” Chem. Comm...Prescribed by ANSI Std. Z39.18 Adobe Professional 7.0 PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ORGANIZATION. 3. DATES COVERED (From - To) 5b. GRANT

  20. Computing 3-D structure of rigid objects using stereo and motion

    NASA Technical Reports Server (NTRS)

    Nguyen, Thinh V.

    1987-01-01

    Work performed as a step toward an intelligent automatic machine vision system for 3-D imaging is discussed. The problem considered is the quantitative 3-D reconstruction of rigid objects. Motion and stereo are the two clues considered in this system. The system basically consists of three processes: the low level process to extract image features, the middle level process to establish the correspondence in the stereo (spatial) and motion (temporal) modalities, and the high level process to compute the 3-D coordinates of the corner points by integrating the spatial and temporal correspondences.

  1. Recovery and Visualization of 3D Structure of Chromosomes from Tomographic Reconstruction Images

    NASA Astrophysics Data System (ADS)

    Babu, Sabarish; Liao, Pao-Chuan; Shin, Min C.; Tsap, Leonid V.

    2006-12-01

    The objectives of this work include automatic recovery and visualization of a 3D chromosome structure from a sequence of 2D tomographic reconstruction images taken through the nucleus of a cell. Structure is very important for biologists as it affects chromosome functions, behavior of the cell, and its state. Analysis of chromosome structure is significant in the detection of diseases, identification of chromosomal abnormalities, study of DNA structural conformation, in-depth study of chromosomal surface morphology, observation of in vivo behavior of the chromosomes over time, and in monitoring environmental gene mutations. The methodology incorporates thresholding based on a histogram analysis with a polyline splitting algorithm, contour extraction via active contours, and detection of the 3D chromosome structure by establishing corresponding regions throughout the slices. Visualization using point cloud meshing generates a 3D surface. The 3D triangular mesh of the chromosomes provides surface detail and allows a user to interactively analyze chromosomes using visualization software.

  2. Design of novel 3D gene activated PEG scaffolds with ordered pore structure.

    PubMed

    Orsi, Silvia; Guarnieri, Daniela; Netti, Paolo A

    2010-03-01

    The ability to genetically modify cells seeded inside synthetic hydrogel scaffolds offers a suitable approach to induce and control tissue repair and regeneration guiding cell fate. In fact the transfected cells can act as local in vivo bioreactor, secreting plasmid encoded proteins that augment tissue regeneration processes. We have realized a DNA bioactivated high porous poly(ethylene glycol) (PEG) matrix by polyethyleneimine (PEI)/DNA complexes adsorption. As the design of the microarchitectural features of a scaffold also contributes to promote and influence cell fate, we appropriately designed the inner structure of gene activated PEG hydrogels by gelatine microparticles templating. Microarchitectural properties of the scaffold were analysed by scanning electron microscopy. 3D cell migration and transfection were monitored through time-lapse videomicroscopy and confocal laser scanning microscopy.

  3. Integration of a 3D perspective view in the navigation display: featuring pilot's mental model

    NASA Astrophysics Data System (ADS)

    Ebrecht, L.; Schmerwitz, S.

    2015-05-01

    Synthetic vision systems (SVS) appear as spreading technology in the avionic domain. Several studies prove enhanced situational awareness when using synthetic vision. Since the introduction of synthetic vision a steady change and evolution started concerning the primary flight display (PFD) and the navigation display (ND). The main improvements of the ND comprise the representation of colored ground proximity warning systems (EGPWS), weather radar, and TCAS information. Synthetic vision seems to offer high potential to further enhance cockpit display systems. Especially, concerning the current trend having a 3D perspective view in a SVS-PFD while leaving the navigational content as well as methods of interaction unchanged the question arouses if and how the gap between both displays might evolve to a serious problem. This issue becomes important in relation to the transition and combination of strategic and tactical flight guidance. Hence, pros and cons of 2D and 3D views generally as well as the gap between the egocentric perspective 3D view of the PFD and the exocentric 2D top and side view of the ND will be discussed. Further a concept for the integration of a 3D perspective view, i.e., bird's eye view, in synthetic vision ND will be presented. The combination of 2D and 3D views in the ND enables a better correlation of the ND and the PFD. Additionally, this supports the building of pilot's mental model. The authors believe it will improve the situational and spatial awareness. It might prove to further raise the safety margin when operating in mountainous areas.

  4. Laser direct writing 3D structures for microfluidic channels: flow meter and mixer

    NASA Astrophysics Data System (ADS)

    Lin, Chih-Lang; Liu, Yi-Jui; Lin, Zheng-Da; Wu, Bo-Long; Lee, Yi-Hsiung; Shin, Chow-Shing; Baldeck, Patrice L.

    2015-03-01

    The 3D laser direct-writing technology is aimed at the modeling of arbitrary three-dimensional (3D) complex microstructures by scanning a laser-focusing point along predetermined trajectories. Through the perspective technique, the details of designed 3D structures can be properly fabricated in a microchannel. This study introduces a direct reading flow meter and a 3D passive mixer fabricated by laser direct writing for microfluidic applications. The flow meter consists of two rod-shaped springs, a pillar, an anchor, and a wedge-shaped indicator, installed inside a microfluidic channel. The indicator is deflected by the flowing fluid while restrained by the spring to establish an equilibrium indication according to the flow rate. The measurement is readily carried out by optical microscopy observation. The 3D passive Archimedes-screw-shaped mixer is designed to disturb the laminar flow 3D direction for enhancing the mixing efficiency. The simulation results indicate that the screw provides 3D disturbance of streamlines in the microchannel. The mixing demonstration for fluids flowing in the micrchannel approximately agrees with the simulation result. Thanks to the advantage of the laser direct writing technology, this study performs the ingenious applications of 3D structures for microchannels.

  5. A Novel Medical Freehand Sketch 3D Model Retrieval Method by Dimensionality Reduction and Feature Vector Transformation.

    PubMed

    Jing, Zhang; Sheng, Kang Bao

    2015-01-01

    To assist physicians to quickly find the required 3D model from the mass medical model, we propose a novel retrieval method, called DRFVT, which combines the characteristics of dimensionality reduction (DR) and feature vector transformation (FVT) method. The DR method reduces the dimensionality of feature vector; only the top M low frequency Discrete Fourier Transform coefficients are retained. The FVT method does the transformation of the original feature vector and generates a new feature vector to solve the problem of noise sensitivity. The experiment results demonstrate that the DRFVT method achieves more effective and efficient retrieval results than other proposed methods.

  6. A Novel Medical Freehand Sketch 3D Model Retrieval Method by Dimensionality Reduction and Feature Vector Transformation

    PubMed Central

    Jing, Zhang; Sheng, Kang Bao

    2016-01-01

    To assist physicians to quickly find the required 3D model from the mass medical model, we propose a novel retrieval method, called DRFVT, which combines the characteristics of dimensionality reduction (DR) and feature vector transformation (FVT) method. The DR method reduces the dimensionality of feature vector; only the top M low frequency Discrete Fourier Transform coefficients are retained. The FVT method does the transformation of the original feature vector and generates a new feature vector to solve the problem of noise sensitivity. The experiment results demonstrate that the DRFVT method achieves more effective and efficient retrieval results than other proposed methods. PMID:27293478

  7. 3D Printers Can Provide an Added Dimension for Teaching Structure-Energy Relationships

    ERIC Educational Resources Information Center

    Blauch, David N.; Carroll, Felix A.

    2014-01-01

    A 3D printer is used to prepare a variety of models representing potential energy as a function of two geometric coordinates. These models facilitate the teaching of structure-energy relationships in molecular conformations and in chemical reactions.

  8. A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures

    PubMed Central

    Li, Haotian; Huang, Yangyu

    2017-01-01

    Computational prediction of RNA-protein complex 3D structures includes two basic steps: one is sampling possible structures and another is scoring the sampled structures to pick out the correct one. At present, constructing accurate scoring functions is still not well solved and the performances of the scoring functions usually depend on used benchmarks. Here we propose a pair-conformation-dependent scoring function, 3dRPC-Score, for 3D RNA-protein complex structure prediction by considering the nucleotide-residue pairs having the same energy if their conformations are similar, instead of the distance-only dependence of the most existing scoring functions. Benchmarking shows that 3dRPC-Score has a consistent performance in three test sets. PMID:28358834

  9. A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures.

    PubMed

    Li, Haotian; Huang, Yangyu; Xiao, Yi

    2017-01-01

    Computational prediction of RNA-protein complex 3D structures includes two basic steps: one is sampling possible structures and another is scoring the sampled structures to pick out the correct one. At present, constructing accurate scoring functions is still not well solved and the performances of the scoring functions usually depend on used benchmarks. Here we propose a pair-conformation-dependent scoring function, 3dRPC-Score, for 3D RNA-protein complex structure prediction by considering the nucleotide-residue pairs having the same energy if their conformations are similar, instead of the distance-only dependence of the most existing scoring functions. Benchmarking shows that 3dRPC-Score has a consistent performance in three test sets.

  10. A 3D acquisition system combination of structured-light scanning and shape from silhouette

    NASA Astrophysics Data System (ADS)

    Sun, Changku; Tao, Li; Wang, Peng; He, Li

    2006-05-01

    A robust and accurate three dimensional (3D) acquisition system is presented, which is a combination of structured-light scanning and shape from silhouette. Using common world coordinate system, two groups of point data can be integrated into the final complete 3D model without any integration and registration algorithm. The mathematics model of structured-light scanning is described in detail, and the shape from silhouette algorithm is introduced as well. The complete 3D model of a cup with a handle is obtained successfully by the proposed technique. At last the measurement on a ball bearing is performed, with the measurement precision better than 0.15 mm.

  11. Automatic Segmentation of Lung Carcinoma Using 3D Texture Features in 18-FDG PET/CT.

    PubMed

    Markel, Daniel; Caldwell, Curtis; Alasti, Hamideh; Soliman, Hany; Ung, Yee; Lee, Justin; Sun, Alexander

    2013-01-01

    Target definition is the largest source of geometric uncertainty in radiation therapy. This is partly due to a lack of contrast between tumor and healthy soft tissue for computed tomography (CT) and due to blurriness, lower spatial resolution, and lack of a truly quantitative unit for positron emission tomography (PET). First-, second-, and higher-order statistics, Tamura, and structural features were characterized for PET and CT images of lung carcinoma and organs of the thorax. A combined decision tree (DT) with K-nearest neighbours (KNN) classifiers as nodes containing combinations of 3 features were trained and used for segmentation of the gross tumor volume. This approach was validated for 31 patients from two separate institutions and scanners. The results were compared with thresholding approaches, the fuzzy clustering method, the 3-level fuzzy locally adaptive Bayesian algorithm, the multivalued level set algorithm, and a single KNN using Hounsfield units and standard uptake value. The results showed the DTKNN classifier had the highest sensitivity of 73.9%, second highest average Dice coefficient of 0.607, and a specificity of 99.2% for classifying voxels when using a probabilistic ground truth provided by simultaneous truth and performance level estimation using contours drawn by 3 trained physicians.

  12. Automatic Segmentation of Lung Carcinoma Using 3D Texture Features in 18-FDG PET/CT

    PubMed Central

    Markel, Daniel; Caldwell, Curtis; Alasti, Hamideh; Soliman, Hany; Ung, Yee; Lee, Justin; Sun, Alexander

    2013-01-01

    Target definition is the largest source of geometric uncertainty in radiation therapy. This is partly due to a lack of contrast between tumor and healthy soft tissue for computed tomography (CT) and due to blurriness, lower spatial resolution, and lack of a truly quantitative unit for positron emission tomography (PET). First-, second-, and higher-order statistics, Tamura, and structural features were characterized for PET and CT images of lung carcinoma and organs of the thorax. A combined decision tree (DT) with K-nearest neighbours (KNN) classifiers as nodes containing combinations of 3 features were trained and used for segmentation of the gross tumor volume. This approach was validated for 31 patients from two separate institutions and scanners. The results were compared with thresholding approaches, the fuzzy clustering method, the 3-level fuzzy locally adaptive Bayesian algorithm, the multivalued level set algorithm, and a single KNN using Hounsfield units and standard uptake value. The results showed the DTKNN classifier had the highest sensitivity of 73.9%, second highest average Dice coefficient of 0.607, and a specificity of 99.2% for classifying voxels when using a probabilistic ground truth provided by simultaneous truth and performance level estimation using contours drawn by 3 trained physicians. PMID:23533750

  13. 2D and 3D reconstruction and geomechanical characterization of kilometre-scale complex folded structures

    NASA Astrophysics Data System (ADS)

    Zanchi, Andrea; Agliardi, Federico; Crosta, Giovanni B.; Villa, Alberto; Bistacchi, Andrea; Iudica, Gaetano

    2015-04-01

    points based on their normal vector orientations to identify and map bedding and fractures. Combined stereographic analysis of bedding orientations and use of filters allowed the quantification of fold hinge and limb geometries and their 3D reconstruction in GOCAD. Fracture patterns derived from points clouds and field data allowed identifying different geomechanical domains associated to the folded structure. Our results encourage the integrated analysis of high-resolution point clouds and detailed structural and geomechanical field data as inputs to the 3D geometrical reconstruction and modelling of folded rock masses. Validation of virtual outcrop reconstructions through a comparison with field structural measurements suggests that very precise geometrical constraints can be obtained by TLS on geological bodies with complex geometrical features. However, additional constraints on TLS survey layout design are required to optimise the reconstruction and distinction of specific structural elements associated to folding as bedding and fold-related fracture systems.

  14. Effect of 3d doping on the electronic structure of BaFe2As2

    SciTech Connect

    McLeod, John A.; Buling, A.; Green, R.J.; Boyko, T.D.; Skorikov, N.A.; Kurmaev, E.Z.; Neumann, M.; Finkelstein, L.D.; Ni, Ni; Thaler, Alexander; Budko, Serguei L.; Canfield, Paul; Moewes, A.

    2012-04-25

    The electronic structure of BaFe2As2 doped with Co, Ni and Cu has been studied by a variety of experimental and theoretical methods, but a clear picture of the dopant 3d states has not yet emerged. Herein we provide experimental evidence of the distribution of Co, Ni and Cu 3d states in the valence band. We conclude that the Co and Ni 3d states provide additional free carriers to the Fermi level, while the Cu 3d states are found at the bottom of the valence band in a localized 3d10 shell. These findings help shed light on why superconductivity can occur in BaFe2As2 doped with Co and Ni but not Cu.

  15. 3D finite-difference modeling algorithm and anomaly features of ZTEM

    NASA Astrophysics Data System (ADS)

    Wang, Tao; Tan, Han-Dong; Li, Zhi-Qiang; Wang, Kun-Peng; Hu, Zhi-Ming; Zhang, Xing-Dong

    2016-09-01

    The Z-Axis tipper electromagnetic (ZTEM) technique is based on a frequency-domain airborne electromagnetic system that measures the natural magnetic field. A survey area was divided into several blocks by using the Maxwell's equations, and the magnetic components at the center of each edge of the grid cell are evaluated by applying the staggered-grid finite-difference method. The tipper and its divergence are derived to complete the 3D ZTEM forward modeling algorithm. A synthetic model is then used to compare the responses with those of 2D finite-element forward modeling to verify the accuracy of the algorithm. ZTEM offers high horizontal resolution to both simple and complex distributions of conductivity. This work is the theoretical foundation for the interpretation of ZTEM data and the study of 3D ZTEM inversion.

  16. Segmentation of vascular structures and hematopoietic cells in 3D microscopy images and quantitative analysis

    NASA Astrophysics Data System (ADS)

    Mu, Jian; Yang, Lin; Kamocka, Malgorzata M.; Zollman, Amy L.; Carlesso, Nadia; Chen, Danny Z.

    2015-03-01

    In this paper, we present image processing methods for quantitative study of how the bone marrow microenvironment changes (characterized by altered vascular structure and hematopoietic cell distribution) caused by diseases or various factors. We develop algorithms that automatically segment vascular structures and hematopoietic cells in 3-D microscopy images, perform quantitative analysis of the properties of the segmented vascular structures and cells, and examine how such properties change. In processing images, we apply local thresholding to segment vessels, and add post-processing steps to deal with imaging artifacts. We propose an improved watershed algorithm that relies on both intensity and shape information and can separate multiple overlapping cells better than common watershed methods. We then quantitatively compute various features of the vascular structures and hematopoietic cells, such as the branches and sizes of vessels and the distribution of cells. In analyzing vascular properties, we provide algorithms for pruning fake vessel segments and branches based on vessel skeletons. Our algorithms can segment vascular structures and hematopoietic cells with good quality. We use our methods to quantitatively examine the changes in the bone marrow microenvironment caused by the deletion of Notch pathway. Our quantitative analysis reveals property changes in samples with deleted Notch pathway. Our tool is useful for biologists to quantitatively measure changes in the bone marrow microenvironment, for developing possible therapeutic strategies to help the bone marrow microenvironment recovery.

  17. The RCSB protein data bank: integrative view of protein, gene and 3D structural information

    PubMed Central

    Rose, Peter W.; Prlić, Andreas; Altunkaya, Ali; Bi, Chunxiao; Bradley, Anthony R.; Christie, Cole H.; Costanzo, Luigi Di; Duarte, Jose M.; Dutta, Shuchismita; Feng, Zukang; Green, Rachel Kramer; Goodsell, David S.; Hudson, Brian; Kalro, Tara; Lowe, Robert; Peisach, Ezra; Randle, Christopher; Rose, Alexander S.; Shao, Chenghua; Tao, Yi-Ping; Valasatava, Yana; Voigt, Maria; Westbrook, John D.; Woo, Jesse; Yang, Huangwang; Young, Jasmine Y.; Zardecki, Christine; Berman, Helen M.; Burley, Stephen K.

    2017-01-01

    The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a ‘Structural View of Biology.’ Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive. PMID:27794042

  18. Deformable registration of 3D vessel structures to a single projection image

    NASA Astrophysics Data System (ADS)

    Zikic, Darko; Groher, Martin; Khamene, Ali; Navab, Nassir

    2008-03-01

    Alignment of angiographic preoperative 3D scans to intraoperative 2D projections is an important issue for 3D depth perception and navigation during interventions. Currently, in a setting where only one 2D projection is available, methods employing a rigid transformation model present the state of the art for this problem. In this work, we introduce a method capable of deformably registering 3D vessel structures to a respective single projection of the scene. Our approach addresses the inherent ill-posedness of the problem by incorporating a priori knowledge about the vessel structures into the formulation. We minimize the distance between the 2D points and corresponding projected 3D points together with regularization terms encoding the properties of length preservation of vessel structures and smoothness of deformation. We demonstrate the performance and accuracy of the proposed method by quantitative tests on synthetic examples as well as real angiographic scenes.

  19. Recovery and Visualization of 3D Structure of Chromosomes from Tomographic Reconstruction Images

    SciTech Connect

    Babu, S; Liao, P; Shin, M C; Tsap, L V

    2004-04-28

    The objectives of this work include automatic recovery and visualization of a 3D chromosome structure from a sequence of 2D tomographic reconstruction images taken through the nucleus of a cell. Structure is very important for biologists as it affects chromosome functions, behavior of the cell and its state. Chromosome analysis is significant in the detection of deceases and in monitoring environmental gene mutations. The algorithm incorporates thresholding based on a histogram analysis with a polyline splitting algorithm, contour extraction via active contours, and detection of the 3D chromosome structure by establishing corresponding regions throughout the slices. Visualization using point cloud meshing generates a 3D surface. The 3D triangular mesh of the chromosomes provides surface detail and allows a user to interactively analyze chromosomes using visualization software.

  20. A 3-D crustal velocity structure across the Variscides of southwest Ireland

    NASA Astrophysics Data System (ADS)

    Landes, M.; Readman, P. W.; O'Reilly, B. M.; Shannon, P. M.

    2003-04-01

    In the VARNET-96 experiment three seismic refraction profiles were acquired to examine the crustal structure in the south-west of Ireland. The shotpoint geometry allowed for both in-line and off-line fan shot recordings on the three profiles. Results of 3-D inversion modelling illustrate that there is pervasive lateral heterogeneity of the sedimentary and crustal velocity structure south of the Shannon Estuary. Palaeozoic strata at the south coast are about 5-6 km thick associated with the sedimentary infill of the Munster and South Munster Basins. To the north, shallow upper crust in the vicinity of the Killarney-Mallow Fault Zone is followed by a 3-4 km thick sedimentary succession in the Dingle-Shannon Basin. A zone of high-velocity upper crust (6.4-6.6 km/s) beneath the South Munster Basin correlates with a gravity high between the Kenmare-Killarney and the Leinster Granite gravity lows. Other high-velocity zones beneath Dingle Bay and the Kenmare River region may be associated with the deep traces of the Killarney-Mallow Fault Zone and the Cork-Kenmare Line. The 3-D velocity model was taken as a basis for the computation of PmP reflected arrivals from the crust-mantle boundary. The Moho depth varies from 28-29 km at the south coast to 32-33 km beneath the Dingle-Shannon Basin. Pervasive Variscan deformation appears to be confined to the sedimentary and upper crustal structure thus supporting a thin-skinned tectonic model for Variscan deformation. Deep-crustal variations only occur where they can be correlated with major tectonic features such as the Caledonian Iapetus Suture near the Shannon Estuary. The shallowing of the Moho towards the coast may result from Mesozoic crustal extension in the adjacent offshore sedimentary basins.

  1. Multi-sourced, 3D geometric characterization of volcanogenic karst features: Integrating lidar, sonar, and geophysical datasets (Invited)

    NASA Astrophysics Data System (ADS)

    Sharp, J. M.; Gary, M. O.; Reyes, R.; Halihan, T.; Fairfield, N.; Stone, W. C.

    2009-12-01

    Karstic aquifers can form very complex hydrogeological systems and 3-D mapping has been difficult, but Lidar, phased array sonar, and improved earth resistivity techniques show promise in this and in linking metadata to models. Zacatón, perhaps the Earth’s deepest cenote, has a sub-aquatic void space exceeding 7.5 x 106 cubic m3. It is the focus of this study which has created detailed 3D maps of the system. These maps include data from above and beneath the the water table and within the rock matrix to document the extent of the immense karst features and to interpret the geologic processes that formed them. Phase 1 used high resolution (20 mm) Lidar scanning of surficial features of four large cenotes. Scan locations, selected to achieve full feature coverage once registered, were established atop surface benchmarks with UTM coordinates established using GPS and Total Stations. The combined datasets form a geo-registered mesh of surface features down to water level in the cenotes. Phase 2 conducted subsurface imaging using Earth Resistivity Imaging (ERI) geophysics. ERI identified void spaces isolated from open flow conduits. A unique travertine morphology exists in which some cenotes are dry or contain shallow lakes with flat travertine floors; some water-filled cenotes have flat floors without the cone of collapse material; and some have collapse cones. We hypothesize that the floors may have large water-filled voids beneath them. Three separate flat travertine caps were imaged: 1) La Pilita, which is partially open, exposing cap structure over a deep water-filled shaft; 2) Poza Seca, which is dry and vegetated; and 3) Tule, which contains a shallow (<1 m) lake. A fourth line was run adjacent to cenote Verde. La Pilita ERI, verified by SCUBA, documented the existence of large water-filled void zones ERI at Poza Seca showed a thin cap overlying a conductive zone extending to at least 25 m depth beneath the cap with no lower boundary of this zone evident

  2. Contribution of 3D inversion of Electrical Resistivity Tomography data applied to volcanic structures

    NASA Astrophysics Data System (ADS)

    Portal, Angélie; Fargier, Yannick; Lénat, Jean-François; Labazuy, Philippe

    2016-04-01

    The electrical resistivity tomography (ERT) method, initially developed for environmental and engineering exploration, is now commonly used for geological structures imaging. Such structures can present complex characteristics that conventional 2D inversion processes cannot perfectly integrate. Here we present a new 3D inversion algorithm named EResI, firstly developed for levee investigation, and presently applied to the study of a complex lava dome (the Puy de Dôme volcano, France). EResI algorithm is based on a conventional regularized Gauss-Newton inversion scheme and a 3D non-structured discretization of the model (double grid method based on tetrahedrons). This discretization allows to accurately model the topography of investigated structure (without a mesh deformation procedure) and also permits a precise location of the electrodes. Moreover, we demonstrate that a complete 3D unstructured discretization limits the number of inversion cells and is better adapted to the resolution capacity of tomography than a structured discretization. This study shows that a 3D inversion with a non-structured parametrization has some advantages compared to classical 2D inversions. The first advantage comes from the fact that a 2D inversion leads to artefacts due to 3D effects (3D topography, 3D internal resistivity). The second advantage comes from the fact that the capacity to experimentally align electrodes along an axis (for 2D surveys) depends on the constrains on the field (topography...). In this case, a 2D assumption induced by 2.5D inversion software prevents its capacity to model electrodes outside this axis leading to artefacts in the inversion result. The last limitation comes from the use of mesh deformation techniques used to accurately model the topography in 2D softwares. This technique used for structured discretization (Res2dinv) is prohibed for strong topography (>60 %) and leads to a small computational errors. A wide geophysical survey was carried out

  3. 3D high-resolution two-photon crosslinked hydrogel structures for biological studies.

    PubMed

    Brigo, Laura; Urciuolo, Anna; Giulitti, Stefano; Giustina, Gioia Della; Tromayer, Maximilian; Liska, Robert; Elvassore, Nicola; Brusatin, Giovanna

    2017-03-25

    Hydrogels are widely used as matrices for cell growth due to the their tuneable chemical and physical properties, which mimic the extracellular matrix of natural tissue. The microfabrication of hydrogels into arbitrarily complex 3D structures is becoming essential for numerous biological applications, and in particular for investigating the correlation between cell shape and cell function in a 3D environment. Micrometric and sub-micrometric resolution hydrogel scaffolds are required to deeply investigate molecular mechanisms behind cell-matrix interaction and downstream cellular processes. We report the design and development of high resolution 3D gelatin hydrogel woodpile structures by two-photon crosslinking. Hydrated structures of lateral linewidth down to 0.5 µm, lateral and axial resolution down to a few µm are demonstrated. According to the processing parameters, different degrees of polymerization are obtained, resulting in hydrated scaffolds of variable swelling and deformation. The 3D hydrogels are biocompatible and promote cell adhesion and migration. Interestingly, according to the polymerization degree, 3D hydrogel woodpile structures show variable extent of cell adhesion and invasion. Human BJ cell lines show capability of deforming 3D micrometric resolved hydrogel structures.

  4. Atlas and feature based 3D pathway visualization enhancement for skull base pre-operative fast planning from head CT

    NASA Astrophysics Data System (ADS)

    Aghdasi, Nava; Li, Yangming; Berens, Angelique; Moe, Kris S.; Bly, Randall A.; Hannaford, Blake

    2015-03-01

    Minimally invasive neuroendoscopic surgery provides an alternative to open craniotomy for many skull base lesions. These techniques provides a great benefit to the patient through shorter ICU stays, decreased post-operative pain and quicker return to baseline function. However, density of critical neurovascular structures at the skull base makes planning for these procedures highly complex. Furthermore, additional surgical portals are often used to improve visualization and instrument access, which adds to the complexity of pre-operative planning. Surgical approach planning is currently limited and typically involves review of 2D axial, coronal, and sagittal CT and MRI images. In addition, skull base surgeons manually change the visualization effect to review all possible approaches to the target lesion and achieve an optimal surgical plan. This cumbersome process relies heavily on surgeon experience and it does not allow for 3D visualization. In this paper, we describe a rapid pre-operative planning system for skull base surgery using the following two novel concepts: importance-based highlight and mobile portal. With this innovation, critical areas in the 3D CT model are highlighted based on segmentation results. Mobile portals allow surgeons to review multiple potential entry portals in real-time with improved visualization of critical structures located inside the pathway. To achieve this we used the following methods: (1) novel bone-only atlases were manually generated, (2) orbits and the center of the skull serve as features to quickly pre-align the patient's scan with the atlas, (3) deformable registration technique was used for fine alignment, (4) surgical importance was assigned to each voxel according to a surgical dictionary, and (5) pre-defined transfer function was applied to the processed data to highlight important structures. The proposed idea was fully implemented as independent planning software and additional

  5. 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

  6. Edge structure preserving 3D image denoising by local surface approximation.

    PubMed

    Qiu, Peihua; Mukherjee, Partha Sarathi

    2012-08-01

    In various applications, including magnetic resonance imaging (MRI) and functional MRI (fMRI), 3D images are becoming increasingly popular. To improve the reliability of subsequent image analyses, 3D image denoising is often a necessary preprocessing step, which is the focus of the current paper. In the literature, most existing image denoising procedures are for 2D images. Their direct extensions to 3D cases generally cannot handle 3D images efficiently because the structure of a typical 3D image is substantially more complicated than that of a typical 2D image. For instance, edge locations are surfaces in 3D cases which would be much more challenging to handle compared to edge curves in 2D cases. We propose a novel 3D image denoising procedure in this paper, based on local approximation of the edge surfaces using a set of surface templates. An important property of this method is that it can preserve edges and major edge structures (e.g., intersections of two edge surfaces and pointed corners). Numerical studies show that it works well in various applications.

  7. Vascular Structure Identification in Intraoperative 3D Contrast-Enhanced Ultrasound Data

    PubMed Central

    Ilunga-Mbuyamba, Elisee; Avina-Cervantes, Juan Gabriel; Lindner, Dirk; Cruz-Aceves, Ivan; Arlt, Felix; Chalopin, Claire

    2016-01-01

    In this paper, a method of vascular structure identification in intraoperative 3D Contrast-Enhanced Ultrasound (CEUS) data is presented. Ultrasound imaging is commonly used in brain tumor surgery to investigate in real time the current status of cerebral structures. The use of an ultrasound contrast agent enables to highlight tumor tissue, but also surrounding blood vessels. However, these structures can be used as landmarks to estimate and correct the brain shift. This work proposes an alternative method for extracting small vascular segments close to the tumor as landmark. The patient image dataset involved in brain tumor operations includes preoperative contrast T1MR (cT1MR) data and 3D intraoperative contrast enhanced ultrasound data acquired before (3D-iCEUSstart) and after (3D-iCEUSend) tumor resection. Based on rigid registration techniques, a preselected vascular segment in cT1MR is searched in 3D-iCEUSstart and 3D-iCEUSend data. The method was validated by using three similarity measures (Normalized Gradient Field, Normalized Mutual Information and Normalized Cross Correlation). Tests were performed on data obtained from ten patients overcoming a brain tumor operation and it succeeded in nine cases. Despite the small size of the vascular structures, the artifacts in the ultrasound images and the brain tissue deformations, blood vessels were successfully identified. PMID:27070610

  8. Structure of Pseudoknot PK26 Shows 3D Domain Swapping in an RNA

    NASA Technical Reports Server (NTRS)

    Lietzke, Susan E; Barnes, Cindy L.

    1998-01-01

    3D domain swapping provides a facile pathway for the evolution of oligomeric proteins and allosteric mechanisms and a means for using monomer-oligomer equilibria to regulate biological activity. The term "3D domain swapping" describes the exchange of identical domains between two protein monomers to create an oligomer. 3D domain swapping has, so far, only been recognized in proteins. In this study, the structure of the pseudoknot PK26 is reported and it is a clear example of 3D domain swapping in RNA. PK26 was chosen for study because RNA pseudoknots are required structures in several biological processes and they arise frequently in in vitro selection experiments directed against protein targets. PK26 specifically inhibits HIV-1 reverse transcriptase with nanomolar affinity. We have now determined the 3.1 A resolution crystal structure of PK26 and find that it forms a 3D domain swapped dimer. PK26 shows extensive base pairing between and within strands. Formation of the dimer requires the linker region between the pseudoknot folds to adopt a unique conformation that allows a base within a helical stem to skip one base in the stacking register. Rearrangement of the linker would permit a monomeric pseudoknot to form. This structure shows how RNA can use 3D domain swapping to build large scale oligomers like the putative hexamer in the packaging RNA of bacteriophage Phi29.

  9. Interpretation and mapping of geological features using mobile devices for 3D outcrop modelling

    NASA Astrophysics Data System (ADS)

    Buckley, Simon J.; Kehl, Christian; Mullins, James R.; Howell, John A.

    2016-04-01

    Advances in 3D digital geometric characterisation have resulted in widespread adoption in recent years, with photorealistic models utilised for interpretation, quantitative and qualitative analysis, as well as education, in an increasingly diverse range of geoscience applications. Topographic models created using lidar and photogrammetry, optionally combined with imagery from sensors such as hyperspectral and thermal cameras, are now becoming commonplace in geoscientific research. Mobile devices (tablets and smartphones) are maturing rapidly to become powerful field computers capable of displaying and interpreting 3D models directly in the field. With increasingly high-quality digital image capture, combined with on-board sensor pose estimation, mobile devices are, in addition, a source of primary data, which can be employed to enhance existing geological models. Adding supplementary image textures and 2D annotations to photorealistic models is therefore a desirable next step to complement conventional field geoscience. This contribution reports on research into field-based interpretation and conceptual sketching on images and photorealistic models on mobile devices, motivated by the desire to utilise digital outcrop models to generate high quality training images (TIs) for multipoint statistics (MPS) property modelling. Representative training images define sedimentological concepts and spatial relationships between elements in the system, which are subsequently modelled using artificial learning to populate geocellular models. Photorealistic outcrop models are underused sources of quantitative and qualitative information for generating TIs, explored further in this research by linking field and office workflows through the mobile device. Existing textured models are loaded to the mobile device, allowing rendering in a 3D environment. Because interpretation in 2D is more familiar and comfortable for users, the developed application allows new images to be captured

  10. A 3-D Puzzle Approach to Building Protein-DNA Structures.

    PubMed

    Hinton, Deborah M

    2017-02-02

    Despite recent advances in structural analysis, it is still challenging to obtain a high resolution structure for a complex of RNA polymerase, transcriptional factors, and DNA. However, using biochemical constraints, 3-D printed models of available structures, and computer modeling, one can build biologically relevant models of such supramolecular complexes.

  11. Laser fabrication of 2D and 3D metal nanoparticle structures and arrays.

    PubMed

    Kuznetsov, A I; Kiyan, R; Chichkov, B N

    2010-09-27

    A novel method for fabrication of 2D and 3D metal nanoparticle structures and arrays is proposed. This technique is based on laser-induced transfer of molten metal nanodroplets from thin metal films. Metal nanoparticles are produced by solidification of these nanodroplets. The size of the transferred nanoparticles can be controllably changed in the range from 180 nm to 1500 nm. Several examples of complex 2D and 3D microstructures generated form gold nanoparticles are demonstrated.

  12. 3D and 4D atlas system of living human body structure.

    PubMed

    Suzuki, N; Takatsu, A; Hattori, A; Ezumi, T; Oda, S; Yanai, T; Tominaga, H

    1998-01-01

    A reference system for accessing anatomical information from a complete 3D structure of the whole body "living human", including 4D cardiac dynamics, was reconstructed with 3D and 4D data sets obtained from normal volunteers. With this system, we were able to produce a human atlas in which sectional images can be accessed from any part of the human body interactively by real-time image generation.

  13. Cryogenic optical localization provides 3D protein structure data with Angstrom resolution.

    PubMed

    Weisenburger, Siegfried; Boening, Daniel; Schomburg, Benjamin; Giller, Karin; Becker, Stefan; Griesinger, Christian; Sandoghdar, Vahid

    2017-02-01

    We introduce Cryogenic Optical Localization in 3D (COLD), a method to localize multiple fluorescent sites within a single small protein with Angstrom resolution. We demonstrate COLD by determining the conformational state of the cytosolic Per-ARNT-Sim domain from the histidine kinase CitA of Geobacillus thermodenitrificans and resolving the four biotin sites of streptavidin. COLD provides quantitative 3D information about small- to medium-sized biomolecules on the Angstrom scale and complements other techniques in structural biology.

  14. Linear-time protein 3-D structure searching with insertions and deletions

    PubMed Central

    2010-01-01

    Background Two biomolecular 3-D structures are said to be similar if the RMSD (root mean square deviation) between the two molecules' sequences of 3-D coordinates is less than or equal to some given constant bound. Tools for searching for similar structures in biomolecular 3-D structure databases are becoming increasingly important in the structural biology of the post-genomic era. Results We consider an important, fundamental problem of reporting all substructures in a 3-D structure database of chain molecules (such as proteins) which are similar to a given query 3-D structure, with consideration of indels (i.e., insertions and deletions). This problem has been believed to be very difficult but its exact computational complexity has not been known. In this paper, we first prove that the problem in unbounded dimensions is NP-hard. We then propose a new algorithm that dramatically improves the average-case time complexity of the problem in 3-D in case the number of indels k is bounded by a constant. Our algorithm solves the above problem for a query of size m and a database of size N in average-case O(N) time, whereas the time complexity of the previously best algorithm was O(Nmk+1). Conclusions Our results show that although the problem of searching for similar structures in a database based on the RMSD measure with indels is NP-hard in the case of unbounded dimensions, it can be solved in 3-D by a simple average-case linear time algorithm when the number of indels is bounded by a constant. PMID:20047663

  15. Automatic segmentation and 3D feature extraction of protein aggregates in Caenorhabditis elegans

    NASA Astrophysics Data System (ADS)

    Rodrigues, Pedro L.; Moreira, António H. J.; Teixeira-Castro, Andreia; Oliveira, João; Dias, Nuno; Rodrigues, Nuno F.; Vilaça, João L.

    2012-03-01

    In the last years, it has become increasingly clear that neurodegenerative diseases involve protein aggregation, a process often used as disease progression readout and to develop therapeutic strategies. This work presents an image processing tool to automatic segment, classify and quantify these aggregates and the whole 3D body of the nematode Caenorhabditis Elegans. A total of 150 data set images, containing different slices, were captured with a confocal microscope from animals of distinct genetic conditions. Because of the animals' transparency, most of the slices pixels appeared dark, hampering their body volume direct reconstruction. Therefore, for each data set, all slices were stacked in one single 2D image in order to determine a volume approximation. The gradient of this image was input to an anisotropic diffusion algorithm that uses the Tukey's biweight as edge-stopping function. The image histogram median of this outcome was used to dynamically determine a thresholding level, which allows the determination of a smoothed exterior contour of the worm and the medial axis of the worm body from thinning its skeleton. Based on this exterior contour diameter and the medial animal axis, random 3D points were then calculated to produce a volume mesh approximation. The protein aggregations were subsequently segmented based on an iso-value and blended with the resulting volume mesh. The results obtained were consistent with qualitative observations in literature, allowing non-biased, reliable and high throughput protein aggregates quantification. This may lead to a significant improvement on neurodegenerative diseases treatment planning and interventions prevention.

  16. Tailored complex 3D vortex lattice structures by perturbed multiples of three-plane waves.

    PubMed

    Xavier, Jolly; Vyas, Sunil; Senthilkumaran, Paramasivam; Joseph, Joby

    2012-04-20

    As three-plane waves are the minimum number required for the formation of vortex-embedded lattice structures by plane wave interference, we present our experimental investigation on the formation of complex 3D photonic vortex lattice structures by a designed superposition of multiples of phase-engineered three-plane waves. The unfolding of the generated complex photonic lattice structures with higher order helical phase is realized by perturbing the superposition of a relatively phase-encoded, axially equidistant multiple of three noncoplanar plane waves. Through a programmable spatial light modulator assisted single step fabrication approach, the unfolded 3D vortex lattice structures are experimentally realized, well matched to our computer simulations. The formation of higher order intertwined helices embedded in these 3D spiraling vortex lattice structures by the superposition of the multiples of phase-engineered three-plane waves interference is also studied.

  17. Building Proteins in a Day: Efficient 3D Molecular Structure Estimation with Electron Cryomicroscopy.

    PubMed

    Punjani, Ali; Brubaker, Marcus A; Fleet, David J

    2017-04-01

    Discovering the 3D atomic-resolution structure of molecules such as proteins and viruses is one of the foremost research problems in biology and medicine. Electron Cryomicroscopy (cryo-EM) is a promising vision-based technique for structure estimation which attempts to reconstruct 3D atomic structures from a large set of 2D transmission electron microscope images. This paper presents a new Bayesian framework for cryo-EM structure estimation that builds on modern stochastic optimization techniques to allow one to scale to very large datasets. We also introduce a novel Monte-Carlo technique that reduces the cost of evaluating the objective function during optimization by over five orders of magnitude. The net result is an approach capable of estimating 3D molecular structure from large-scale datasets in about a day on a single CPU workstation.

  18. The 3D Structure of the Binding Pocket of the Human Oxytocin Receptor for Benzoxazine Antagonists, Determined by Molecular Docking, Scoring Functions and 3D-QSAR Methods

    NASA Astrophysics Data System (ADS)

    Jójárt, Balázs; Martinek, Tamás A.; Márki, Árpád

    2005-05-01

    Molecular docking and 3D-QSAR studies were performed to determine the binding mode for a series of benzoxazine oxytocin antagonists taken from the literature. Structural hypotheses were generated by docking the most active molecule to the rigid receptor by means of AutoDock 3.05. The cluster analysis yielded seven possible binding conformations. These structures were refined by using constrained simulated annealing, and the further ligands were aligned in the refined receptor by molecular docking. A good correlation was found between the estimated Δ G bind and the p K i values for complex F. The Connolly-surface analysis, CoMFA and CoMSIA models q CoMFA 2 = 0.653, q CoMSA 2 = 0.630 and r pred,CoMFA 2 = 0.852 , r pred,CoMSIA 2 = 0.815) confirmed the scoring function results. The structural features of the receptor-ligand complex and the CoMFA and CoMSIA fields are in closely connected. These results suggest that receptor-ligand complex F is the most likely binding hypothesis for the studied benzoxazine analogs.

  19. Single cell detection using 3D magnetic rolled-up structures.

    PubMed

    Ger, Tzong-Rong; Huang, Hao-Ting; Huang, Chen-Yu; Lai, Mei-Feng

    2013-11-07

    A 3D rolled-up structure made of a SiO2 layer and a fishbone-like magnetic thin film was proposed here as a biosensor. The magnetoresistance (MR) measurement results of the sensor suggest that the presence of the stray field, which is induced by the magnetic nanoparticles, significantly increased the switching field. Comparing the performance of the 2D sensor and 3D sensor designed in this study, the response in switching field variation was 12.14% in the 2D sensor and 62.55% in the 3D sensor. The response in MR ratio variation was 4.55% in the 2D sensor and 82.32% in the 3D sensor. In addition, the design of the 3D sensor structure also helped to attract and trap a single magnetic cell due to its stronger stray field compared with the 2D structure. The 3D magnetic biosensor designed here can provide important information for future biochip research and applications.

  20. Stereomicroscopic 3D-pattern profiling of murine and human intestinal inflammation reveals unique structural phenotypes

    PubMed Central

    Rodriguez-Palacios, Alex; Kodani, Tomohiro; Kaydo, Lindsey; Pietropaoli, Davide; Corridoni, Daniele; Howell, Scott; Katz, Jeffry; Xin, Wei; Pizarro, Theresa T.; Cominelli, Fabio

    2015-01-01

    Histology is fundamental to assess two-dimensional intestinal inflammation; however, inflammatory bowel diseases (IBDs) are often indistinguishable microscopically on the basis of mucosal biopsies. Here, we use stereomicroscopy (SM) to rapidly profile the entire intestinal topography and assess inflammation. We examine the mucosal surface of >700 mice (encompassing >16 strains and various IBD-models), create a profiling catalogue of 3D-stereomicroscopic abnormalities and demonstrate that mice with comparable histological scores display unique sub-clusters of 3D-structure-patterns of IBD pathology, which we call 3D-stereoenterotypes, and which are otherwise indiscernible histologically. We show that two ileal IBD-stereoenterotypes (‘cobblestones' versus ‘villous mini-aggregation') cluster separately within two distinct mouse lines of spontaneous ileitis, suggesting that host genetics drive unique and divergent inflammatory 3D-structural patterns in the gut. In humans, stereomicroscopy reveals ‘liquefaction' lesions and hierarchical fistulous complexes, enriched with clostridia/segmented filamentous bacteria, running under healthy mucosa in Crohn's disease. We suggest that stereomicroscopic (3D-SMAPgut) profiling can be easily implemented and enable the comprehensive study of inflammatory 3D structures, genetics and flora in IBD. PMID:26154811

  1. Gene3D: structural assignments for the biologist and bioinformaticist alike

    PubMed Central

    Buchan, Daniel W. A.; Rison, Stuart C. G.; Bray, James E.; Lee, David; Pearl, Frances; Thornton, Janet M.; Orengo, Christine A.

    2003-01-01

    The Gene3D database (http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/) provides structural assignments for genes within complete genomes. These are available via the internet from either the World Wide Web or FTP. Assignments are made using PSI-BLAST and subsequently processed using the DRange protocol. The DRange protocol is an empirically benchmarked method for assessing the validity of structural assignments made using sequence searching methods where appropriate assignment statistics are collected and made available. Gene3D links assignments to their appropriate entries in relevent structural and classification resources (PDBsum, CATH database and the Dictionary of Homologous Superfamilies). Release 2.0 of Gene3D includes 62 genomes, 2 eukaryotes, 10 archaea and 40 bacteria. Currently, structural assignments can be made for between 30 and 40 percent of any given genome. In any genome, around half of those genes assigned a structural domain are assigned a single domain and the other half of the genes are assigned multiple structural domains. Gene3D is linked to the CATH database and is updated with each new update of CATH. PMID:12520054

  2. 3D structure and dynamics of prominences in IRIS-Hinode collaborative observations

    NASA Astrophysics Data System (ADS)

    Okamoto, J.; De Pontieu, B.; Tarbell, T. D.; Title, A. M.

    2013-12-01

    A new solar physics satellite, Interface Region Imaging Spectrograph (IRIS), was launched on June 27, 2013. IRIS obtains UV spectra and images with high spatial resolution (0.33 arcsec) and high time cadence (1 sec / slit) of the chromosphere and transition region of the Sun. The chromosphere is located between the photosphere and the corona. Recently, the Hinode satellite has revealed that the chromosphere is highly active and suggested that it is a very important region in terms of energy deposit and transfer for coronal heating and solar wind acceleration. However, we cannot have further chromospheric information by Hinode because the Hinode Solar Optical Telescope has only a filtergraph for chromospheric observations. Now we have IRIS. IRIS performs spectroscopic observations to get the missing physical quantities of the dynamic chromosphere. Moreover, IRIS and Hinode is the most powerful collaboration to understand chromospheric activities. Hinode observes extremely high-cadence (1.6 sec) and high-spatial (0.2 arcsec) 2-D images, while IRIS measures line-of-sight velocity and Doppler width of fine structures with temperature dependence. This combination provides information about 3-D structures and dynamic phenomena of chromospheric features. Here we focus on prominence observations performed by IRIS and Hinode, and introduce the initial results of prominence dynamics and magnetic structures such as helical configurations, propagating waves and their damping mechanisms, and formation processes.

  3. Online 3D Ear Recognition by Combining Global and Local Features

    PubMed Central

    Liu, Yahui; Zhang, Bob; Lu, Guangming; Zhang, David

    2016-01-01

    The three-dimensional shape of the ear has been proven to be a stable candidate for biometric authentication because of its desirable properties such as universality, uniqueness, and permanence. In this paper, a special laser scanner designed for online three-dimensional ear acquisition was described. Based on the dataset collected by our scanner, two novel feature classes were defined from a three-dimensional ear image: the global feature class (empty centers and angles) and local feature class (points, lines, and areas). These features are extracted and combined in an optimal way for three-dimensional ear recognition. Using a large dataset consisting of 2,000 samples, the experimental results illustrate the effectiveness of fusing global and local features, obtaining an equal error rate of 2.2%. PMID:27935955

  4. Classification of Informal Settlements Through the Integration of 2d and 3d Features Extracted from Uav Data

    NASA Astrophysics Data System (ADS)

    Gevaert, C. M.; Persello, C.; Sliuzas, R.; Vosselman, G.

    2016-06-01

    Unmanned Aerial Vehicles (UAVs) are capable of providing very high resolution and up-to-date information to support informal settlement upgrading projects. In order to provide accurate basemaps, urban scene understanding through the identification and classification of buildings and terrain is imperative. However, common characteristics of informal settlements such as small, irregular buildings with heterogeneous roof material and large presence of clutter challenge state-of-the-art algorithms. Especially the dense buildings and steeply sloped terrain cause difficulties in identifying elevated objects. This work investigates how 2D radiometric and textural features, 2.5D topographic features, and 3D geometric features obtained from UAV imagery can be integrated to obtain a high classification accuracy in challenging classification problems for the analysis of informal settlements. It compares the utility of pixel-based and segment-based features obtained from an orthomosaic and DSM with point-based and segment-based features extracted from the point cloud to classify an unplanned settlement in Kigali, Rwanda. Findings show that the integration of 2D and 3D features leads to higher classification accuracies.

  5. 3D-printing and mechanics of bio-inspired articulated and multi-material structures.

    PubMed

    Porter, Michael M; Ravikumar, Nakul; Barthelat, Francois; Martini, Roberto

    2016-12-21

    3D-printing technologies allow researchers to build simplified physical models of complex biological systems to more easily investigate their mechanics. In recent years, a number of 3D-printed structures inspired by the dermal armors of various fishes have been developed to study their multiple mechanical functionalities, including flexible protection, improved hydrodynamics, body support, or tail prehensility. Natural fish armors are generally classified according to their shape, material and structural properties as elasmoid scales, ganoid scales, placoid scales, carapace scutes, or bony plates. Each type of dermal armor forms distinct articulation patterns that facilitate different functional advantages. In this paper, we highlight recent studies that developed 3D-printed structures not only to inform the design and application of some articulated and multi-material structures, but also to explain the mechanics of the natural biological systems they mimic.

  6. Lithographically-generated 3D lamella layers and their structural color.

    PubMed

    Zhang, Sichao; Chen, Yifang; Lu, Bingrui; Liu, Jianpeng; Shao, Jinhai; Xu, Chen

    2016-04-28

    Inspired by the structural color from the multilayer nanophotonic structures in Morpho butterfly wing scales, 3D lamellae layers in dielectric polymers (polymethyl methacrylate, PMMA) with n ∼ 1.5 were designed and fabricated by standard top-down electron beam lithography with one-step exposure followed by an alternating development/dissolution process of PMMA/LOR (lift-off resist) multilayers. This work offers direct proof of the structural blue/green color via lithographically-replicated PMMA/air multilayers, analogous to those in real Morpho butterfly wings. The success of nanolithography in this work for the 3D lamellae structures in dielectric polymers not only enables us to gain deeper insight into the mysterious blue color of the Morpho butterfly wings, but also breaks through the bottleneck in technical development toward broad applications in gas/liquid sensors, 3D meta-materials, coloring media, and infrared imaging devices, etc.

  7. Lithographically-generated 3D lamella layers and their structural color

    NASA Astrophysics Data System (ADS)

    Zhang, Sichao; Chen, Yifang; Lu, Bingrui; Liu, Jianpeng; Shao, Jinhai; Xu, Chen

    2016-04-01

    Inspired by the structural color from the multilayer nanophotonic structures in Morpho butterfly wing scales, 3D lamellae layers in dielectric polymers (polymethyl methacrylate, PMMA) with n ~ 1.5 were designed and fabricated by standard top-down electron beam lithography with one-step exposure followed by an alternating development/dissolution process of PMMA/LOR (lift-off resist) multilayers. This work offers direct proof of the structural blue/green color via lithographically-replicated PMMA/air multilayers, analogous to those in real Morpho butterfly wings. The success of nanolithography in this work for the 3D lamellae structures in dielectric polymers not only enables us to gain deeper insight into the mysterious blue color of the Morpho butterfly wings, but also breaks through the bottleneck in technical development toward broad applications in gas/liquid sensors, 3D meta-materials, coloring media, and infrared imaging devices, etc.

  8. 3-D seismic velocity and attenuation structures in the geothermal field

    SciTech Connect

    Nugraha, Andri Dian; Syahputra, Ahmad; Fatkhan,; Sule, Rachmat

    2013-09-09

    We conducted delay time tomography to determine 3-D seismic velocity structures (Vp, Vs, and Vp/Vs ratio) using micro-seismic events in the geothermal field. The P-and S-wave arrival times of these micro-seismic events have been used as input for the tomographic inversion. Our preliminary seismic velocity results show that the subsurface condition of geothermal field can be fairly delineated the characteristic of reservoir. We then extended our understanding of the subsurface physical properties through determining of attenuation structures (Qp, Qs, and Qs/Qp ratio) using micro-seismic waveform. We combined seismic velocities and attenuation structures to get much better interpretation of the reservoir characteristic. Our preliminary attanuation structures results show reservoir characterization can be more clearly by using the 3-D attenuation model of Qp, Qs, and Qs/Qp ratio combined with 3-D seismic velocity model of Vp, Vs, and Vp/Vs ratio.

  9. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

    PubMed

    Ishikawa, Takashi

    2013-01-01

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

  10. Neural coding of 3D features of objects for hand action in the parietal cortex of the monkey.

    PubMed Central

    Sakata, H; Taira, M; Kusunoki, M; Murata, A; Tanaka, Y; Tsutsui, K

    1998-01-01

    In our previous studies of hand manipulation task-related neurons, we found many neurons of the parietal association cortex which responded to the sight of three-dimensional (3D) objects. Most of the task-related neurons in the AIP area (the lateral bank of the anterior intraparietal sulcus) were visually responsive and half of them responded to objects for manipulation. Most of these neurons were selective for the 3D features of the objects. More recently, we have found binocular visual neurons in the lateral bank of the caudal intraparietal sulcus (c-IPS area) that preferentially respond to a luminous bar or place at a particular orientation in space. We studied the responses of axis-orientation selective (AOS) neurons and surface-orientation selective (SOS) neurons in this area with stimuli presented on a 3D computer graphics display. The AOS neurons showed a stronger response to elongated stimuli and showed tuning to the orientation of the longitudinal axis. Many of them preferred a tilted stimulus in depth and appeared to be sensitive to orientation disparity and/or width disparity. The SOS neurons showed a stronger response to a flat than to an elongated stimulus and showed tuning to the 3D orientation of the surface. Their responses increased with the width or length of the stimulus. A considerable number of SOS neurons responded to a square in a random dot stereogram and were tuned to orientation in depth, suggesting their sensitivity to the gradient of disparity. We also found several SOS neurons that responded to a square with tilted or slanted contours, suggesting their sensitivity to orientation disparity and/or width disparity. Area c-IPS is likely to send visual signals of the 3D features of an object to area AIP for the visual guidance of hand actions. PMID:9770229

  11. System for conveyor belt part picking using structured light and 3D pose estimation

    NASA Astrophysics Data System (ADS)

    Thielemann, J.; Skotheim, Ø.; Nygaard, J. O.; Vollset, T.

    2009-01-01

    Automatic picking of parts is an important challenge to solve within factory automation, because it can remove tedious manual work and save labor costs. One such application involves parts that arrive with random position and orientation on a conveyor belt. The parts should be picked off the conveyor belt and placed systematically into bins. We describe a system that consists of a structured light instrument for capturing 3D data and robust methods for aligning an input 3D template with a 3D image of the scene. The method uses general and robust pre-processing steps based on geometric primitives that allow the well-known Iterative Closest Point algorithm to converge quickly and robustly to the correct solution. The method has been demonstrated for localization of car parts with random position and orientation. We believe that the method is applicable for a wide range of industrial automation problems where precise localization of 3D objects in a scene is needed.

  12. 3D printing of weft knitted textile based structures by selective laser sintering of nylon powder

    NASA Astrophysics Data System (ADS)

    Beecroft, M.

    2016-07-01

    3D printing is a form of additive manufacturing whereby the building up of layers of material creates objects. The selective laser sintering process (SLS) uses a laser beam to sinter powdered material to create objects. This paper builds upon previous research into 3D printed textile based material exploring the use of SLS using nylon powder to create flexible weft knitted structures. The results show the potential to print flexible textile based structures that exhibit the properties of traditional knitted textile structures along with the mechanical properties of the material used, whilst describing the challenges regarding fineness of printing resolution. The conclusion highlights the potential future development and application of such pieces.

  13. An efficient finite-element algorithm for 3D layered complex structure modelling.

    PubMed

    Sahalos, J N; Kyriacou, G A; Vafiadis, E

    1994-05-01

    In this paper an efficient finite-element method (FEM) algorithm for complicated three-dimensional (3D) layered type models has been developed. Its unique feature is that it can handle, with memory requirements within the abilities of a simple PC, arbitrarily shaped 3D elements. This task is achieved by storing only the non-zero coefficients of the sparse FEM system of equations. The algorithm is applied to the solution of the Laplace equation in models with up to 79 layers of trilinear general hexahedron elements. The system of equations is solved with the Gauss-Seidel iterative technique.

  14. A synergistic approach to the design, fabrication and evaluation of 3D printed micro and nano featured scaffolds for vascularized bone tissue repair

    PubMed Central

    Holmes, Benjamin; Bulusu, Kartik; Plesniak, Michael; Zhang, Lijie Grace

    2016-01-01

    3D bioprinting has begun to show great promise in advancing the development of functional tissue/organ replacements. However, to realize the true potential of 3D bioprinted tissues for clinical use requires the fabrication of an interconnected and effective vascular network. Solving this challenge is critical, as human tissue relies on an adequate network of blood vessels to transport oxygen, nutrients, other chemicals, biological factors and waste, in and out of the tissue. Here, we have successfully designed and printed a series of novel 3D bone scaffolds with both bone formation supporting structures and highly interconnected 3D microvascular mimicking channels, for efficient and enhanced osteogenic bone regeneration as well as vascular cell growth. Using a chemical functionalization process, we have conjugated our samples with nano hydroxyapatite (nHA), for the creation of novel micro and nano featured devices for vascularized bone growth. We evaluated our scaffolds with mechanical testing, hydrodynamic measurements and in vitro human mesenchymal stem cell (hMSC) adhesion (4 h), proliferation (1, 3 and 5 d) and osteogenic differentiation (1, 2 and 3 weeks). These tests confirmed bone-like physical properties and vascular-like flow profiles, as well as demonstrated enhanced hMSC adhesion, proliferation and osteogenic differentiation. Additional in vitro experiments with human umbilical vein endothelial cells also demonstrated improved vascular cell growth, migration and organization on micro-nano featured scaffolds. PMID:26758780

  15. A synergistic approach to the design, fabrication and evaluation of 3D printed micro and nano featured scaffolds for vascularized bone tissue repair.

    PubMed

    Holmes, Benjamin; Bulusu, Kartik; Plesniak, Michael; Zhang, Lijie Grace

    2016-02-12

    3D bioprinting has begun to show great promise in advancing the development of functional tissue/organ replacements. However, to realize the true potential of 3D bioprinted tissues for clinical use requires the fabrication of an interconnected and effective vascular network. Solving this challenge is critical, as human tissue relies on an adequate network of blood vessels to transport oxygen, nutrients, other chemicals, biological factors and waste, in and out of the tissue. Here, we have successfully designed and printed a series of novel 3D bone scaffolds with both bone formation supporting structures and highly interconnected 3D microvascular mimicking channels, for efficient and enhanced osteogenic bone regeneration as well as vascular cell growth. Using a chemical functionalization process, we have conjugated our samples with nano hydroxyapatite (nHA), for the creation of novel micro and nano featured devices for vascularized bone growth. We evaluated our scaffolds with mechanical testing, hydrodynamic measurements and in vitro human mesenchymal stem cell (hMSC) adhesion (4 h), proliferation (1, 3 and 5 d) and osteogenic differentiation (1, 2 and 3 weeks). These tests confirmed bone-like physical properties and vascular-like flow profiles, as well as demonstrated enhanced hMSC adhesion, proliferation and osteogenic differentiation. Additional in vitro experiments with human umbilical vein endothelial cells also demonstrated improved vascular cell growth, migration and organization on micro-nano featured scaffolds.

  16. A synergistic approach to the design, fabrication and evaluation of 3D printed micro and nano featured scaffolds for vascularized bone tissue repair

    NASA Astrophysics Data System (ADS)

    Holmes, Benjamin; Bulusu, Kartik; Plesniak, Michael; Zhang, Lijie Grace

    2016-02-01

    3D bioprinting has begun to show great promise in advancing the development of functional tissue/organ replacements. However, to realize the true potential of 3D bioprinted tissues for clinical use requires the fabrication of an interconnected and effective vascular network. Solving this challenge is critical, as human tissue relies on an adequate network of blood vessels to transport oxygen, nutrients, other chemicals, biological factors and waste, in and out of the tissue. Here, we have successfully designed and printed a series of novel 3D bone scaffolds with both bone formation supporting structures and highly interconnected 3D microvascular mimicking channels, for efficient and enhanced osteogenic bone regeneration as well as vascular cell growth. Using a chemical functionalization process, we have conjugated our samples with nano hydroxyapatite (nHA), for the creation of novel micro and nano featured devices for vascularized bone growth. We evaluated our scaffolds with mechanical testing, hydrodynamic measurements and in vitro human mesenchymal stem cell (hMSC) adhesion (4 h), proliferation (1, 3 and 5 d) and osteogenic differentiation (1, 2 and 3 weeks). These tests confirmed bone-like physical properties and vascular-like flow profiles, as well as demonstrated enhanced hMSC adhesion, proliferation and osteogenic differentiation. Additional in vitro experiments with human umbilical vein endothelial cells also demonstrated improved vascular cell growth, migration and organization on micro-nano featured scaffolds.

  17. 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine.

    PubMed

    McGuire, Ross; Verhoeven, Stefan; Vass, Márton; Vriend, Gerrit; de Esch, Iwan J P; Lusher, Scott J; Leurs, Rob; Ridder, Lars; Kooistra, Albert J; Ritschel, Tina; de Graaf, Chris

    2017-02-27

    3D-e-Chem-VM is an open source, freely available Virtual Machine ( http://3d-e-chem.github.io/3D-e-Chem-VM/ ) that integrates cheminformatics and bioinformatics tools for the analysis of protein-ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools that can analyze and combine small molecule and protein structural information in a graphical programming environment. New chemical and biological data analytics tools and workflows have been developed for the efficient exploitation of structural and pharmacological protein-ligand interaction data from proteomewide databases (e.g., ChEMBLdb and PDB), as well as customized information systems focused on, e.g., G protein-coupled receptors (GPCRdb) and protein kinases (KLIFS). The integrated structural cheminformatics research infrastructure compiled in the 3D-e-Chem-VM enables the design of new approaches in virtual ligand screening (Chemdb4VS), ligand-based metabolism prediction (SyGMa), and structure-based protein binding site comparison and bioisosteric replacement for ligand design (KRIPOdb).

  18. Characterisation of the surface structure of 3D printed scaffolds for cell infiltration and surgical suturing.

    PubMed

    Ruiz-Cantu, Laura; Gleadall, Andrew; Faris, Callum; Segal, Joel; Shakesheff, Kevin; Yang, Jing

    2016-03-01

    3D printing is of great interest for tissue engineering scaffolds due to the ability to form complex geometries and control internal structures, including porosity and pore size. The porous structure of scaffolds plays an important role in cell ingrowth and nutrition infusion. Although the internal porosity and pore size of 3D printed scaffolds have been frequently studied, the surface porosity and pore size, which are critical for cell infiltration and mass transport, have not been investigated. The surface geometry can differ considerably from the internal scaffold structure depending on the 3D printing process. It is vital to be able to control the surface geometry of scaffolds as well as the internal structure to fabricate optimal architectures. This work presents a method to control the surface porosity and pore size of 3D printed scaffolds. Six scaffold designs have been printed with surface porosities ranging from 3% to 21%. We have characterised the overall scaffold porosity and surface porosity using optical microscopy and microCT. It has been found that surface porosity has a significant impact on cell infiltration and proliferation. In addition, the porosity of the surface has been found to have an effect on mechanical properties and on the forces required to penetrate the scaffold with a surgical suturing needle. To the authors' knowledge, this study is the first to investigate the surface geometry of extrusion-based 3D printed scaffolds and demonstrates the importance of surface geometry in cell infiltration and clinical manipulation.

  19. Novel scanning electron microscopy methods for analyzing the 3D structure of the Golgi apparatus.

    PubMed

    Koga, Daisuke; Ushiki, Tatsuo; Watanabe, Tsuyoshi

    2017-01-01

    The structure of the Golgi apparatus has been extensively examined by light and electron microscopy, but details of its three-dimensional (3D) structure have remained unclear because of the technical limitations of conventional microscopy techniques. To overcome this problem, we have developed several novel scanning electron microscopy (SEM) methods for observing the 3D structure of subcellular organelles including the Golgi apparatus: (1) an osmium maceration method that facilitates SEM observation of membranous organelles, including the Golgi apparatus, by selectively removing soluble cytoplasmic proteins, (2) an osmium impregnation/maceration method that combines an osmium impregnation method with the osmium maceration method to determine the polarity of the Golgi apparatus by SEM, (3) a correlative light and SEM method that combines a cryosectioning technique with the osmium maceration method to enable correlation of the immunocytochemical distribution of molecules with the 3D ultrastructure of the Golgi apparatus, and (4) array tomography based on the systematic collection and integration of SEM images of serial ultrathin sections on glass slides for revealing the 3D ultrastructure of the entire Golgi apparatus. Together, the novel SEM techniques listed above can reveal the complete 3D structure of the Golgi apparatus in different cell types.

  20. 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine

    PubMed Central

    2017-01-01

    3D-e-Chem-VM is an open source, freely available Virtual Machine (http://3d-e-chem.github.io/3D-e-Chem-VM/) that integrates cheminformatics and bioinformatics tools for the analysis of protein–ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools that can analyze and combine small molecule and protein structural information in a graphical programming environment. New chemical and biological data analytics tools and workflows have been developed for the efficient exploitation of structural and pharmacological protein–ligand interaction data from proteomewide databases (e.g., ChEMBLdb and PDB), as well as customized information systems focused on, e.g., G protein-coupled receptors (GPCRdb) and protein kinases (KLIFS). The integrated structural cheminformatics research infrastructure compiled in the 3D-e-Chem-VM enables the design of new approaches in virtual ligand screening (Chemdb4VS), ligand-based metabolism prediction (SyGMa), and structure-based protein binding site comparison and bioisosteric replacement for ligand design (KRIPOdb). PMID:28125221

  1. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

    PubMed Central

    Hayat, Sikander; Sander, Chris; Marks, Debora S.

    2015-01-01

    Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand–strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases. PMID:25858953

  2. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences.

    PubMed

    Hayat, Sikander; Sander, Chris; Marks, Debora S; Elofsson, Arne

    2015-04-28

    Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand-strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases.

  3. Fabrication of scalable and structured tissue engineering scaffolds using water dissolvable sacrificial 3D printed moulds.

    PubMed

    Mohanty, Soumyaranjan; Larsen, Layla Bashir; Trifol, Jon; Szabo, Peter; Burri, Harsha Vardhan Reddy; Canali, Chiara; Dufva, Marin; Emnéus, Jenny; Wolff, Anders

    2015-10-01

    One of the major challenges in producing large scale engineered tissue is the lack of ability to create large highly perfused scaffolds in which cells can grow at a high cell density and viability. Here, we explore 3D printed polyvinyl alcohol (PVA) as a sacrificial mould in a polymer casting process. The PVA mould network defines the channels and is dissolved after curing the polymer casted around it. The printing parameters determined the PVA filament density in the sacrificial structure and this density resulted in different stiffness of the corresponding elastomer replica. It was possible to achieve 80% porosity corresponding to about 150 cm(2)/cm(3) surface to volume ratio. The process is easily scalable as demonstrated by fabricating a 75 cm(3) scaffold with about 16,000 interconnected channels (about 1m(2) surface area) and with a channel to channel distance of only 78 μm. To our knowledge this is the largest scaffold ever to be produced with such small feature sizes and with so many structured channels. The fabricated scaffolds were applied for in-vitro culturing of hepatocytes over a 12-day culture period. Smaller scaffolds (6×4 mm) were tested for cell culturing and could support homogeneous cell growth throughout the scaffold. Presumably, the diffusion of oxygen and nutrient throughout the channel network is rapid enough to support cell growth. In conclusion, the described process is scalable, compatible with cell culture, rapid, and inexpensive.

  4. 3D Modelling of Inaccessible Areas using UAV-based Aerial Photography and Structure from Motion

    NASA Astrophysics Data System (ADS)

    Obanawa, Hiroyuki; Hayakawa, Yuichi; Gomez, Christopher

    2014-05-01

    In hardly accessible areas, the collection of 3D point-clouds using TLS (Terrestrial Laser Scanner) can be very challenging, while airborne equivalent would not give a correct account of subvertical features and concave geometries like caves. To solve such problem, the authors have experimented an aerial photography based SfM (Structure from Motion) technique on a 'peninsular-rock' surrounded on three sides by the sea at a Pacific coast in eastern Japan. The research was carried out using UAS (Unmanned Aerial System) combined with a commercial small UAV (Unmanned Aerial Vehicle) carrying a compact camera. The UAV is a DJI PHANTOM: the UAV has four rotors (quadcopter), it has a weight of 1000 g, a payload of 400 g and a maximum flight time of 15 minutes. The camera is a GoPro 'HERO3 Black Edition': resolution 12 million pixels; weight 74 g; and 0.5 sec. interval-shot. The 3D model has been constructed by digital photogrammetry using a commercial SfM software, Agisoft PhotoScan Professional®, which can generate sparse and dense point-clouds, from which polygonal models and orthophotographs can be calculated. Using the 'flight-log' and/or GCPs (Ground Control Points), the software can generate digital surface model. As a result, high-resolution aerial orthophotographs and a 3D model were obtained. The results have shown that it was possible to survey the sea cliff and the wave cut-bench, which are unobservable from land side. In details, we could observe the complexity of the sea cliff that is nearly vertical as a whole while slightly overhanging over the thinner base. The wave cut bench is nearly flat and develops extensively at the base of the cliff. Although there are some evidences of small rockfalls at the upper part of the cliff, there is no evidence of very recent activity, because no fallen rock exists on the wave cut bench. This system has several merits: firstly lower cost than the existing measuring methods such as manned-flight survey and aerial laser

  5. Optimization of a 3D Dynamic Culturing System for In Vitro Modeling of Frontotemporal Neurodegeneration-Relevant Pathologic Features.

    PubMed

    Tunesi, Marta; Fusco, Federica; Fiordaliso, Fabio; Corbelli, Alessandro; Biella, Gloria; Raimondi, Manuela T

    2016-01-01

    Frontotemporal lobar degeneration (FTLD) is a severe neurodegenerative disorder that is diagnosed with increasing frequency in clinical setting. Currently, no therapy is available and in addition the molecular basis of the disease are far from being elucidated. Consequently, it is of pivotal importance to develop reliable and cost-effective in vitro models for basic research purposes and drug screening. To this respect, recent results in the field of Alzheimer's disease have suggested that a tridimensional (3D) environment is an added value to better model key pathologic features of the disease. Here, we have tried to add complexity to the 3D cell culturing concept by using a microfluidic bioreactor, where cells are cultured under a continuous flow of medium, thus mimicking the interstitial fluid movement that actually perfuses the body tissues, including the brain. We have implemented this model using a neuronal-like cell line (SH-SY5Y), a widely exploited cell model for neurodegenerative disorders that shows some basic features relevant for FTLD modeling, such as the release of the FTLD-related protein progranulin (PRGN) in specific vesicles (exosomes). We have efficiently seeded the cells on 3D scaffolds, optimized a disease-relevant oxidative stress experiment (by targeting mitochondrial function that is one of the possible FTLD-involved pathological mechanisms) and evaluated cell metabolic activity in dynamic culture in comparison to static conditions, finding that SH-SY5Y cells cultured in 3D scaffold are susceptible to the oxidative damage triggered by a mitochondrial-targeting toxin (6-OHDA) and that the same cells cultured in dynamic conditions kept their basic capacity to secrete PRGN in exosomes once recovered from the bioreactor and plated in standard 2D conditions. We think that a further improvement of our microfluidic system may help in providing a full device where assessing basic FTLD-related features (including PRGN dynamic secretion) that may be

  6. Efficient feature-based 2D/3D registration of transesophageal echocardiography to x-ray fluoroscopy for cardiac interventions

    NASA Astrophysics Data System (ADS)

    Hatt, Charles R.; Speidel, Michael A.; Raval, Amish N.

    2014-03-01

    We present a novel 2D/ 3D registration algorithm for fusion between transesophageal echocardiography (TEE) and X-ray fluoroscopy (XRF). The TEE probe is modeled as a subset of 3D gradient and intensity point features, which facilitates efficient 3D-to-2D perspective projection. A novel cost-function, based on a combination of intensity and edge features, evaluates the registration cost value without the need for time-consuming generation of digitally reconstructed radiographs (DRRs). Validation experiments were performed with simulations and phantom data. For simulations, in silica XRF images of a TEE probe were generated in a number of different pose configurations using a previously acquired CT image. Random misregistrations were applied and our method was used to recover the TEE probe pose and compare the result to the ground truth. Phantom experiments were performed by attaching fiducial markers externally to a TEE probe, imaging the probe with an interventional cardiac angiographic x-ray system, and comparing the pose estimated from the external markers to that estimated from the TEE probe using our algorithm. Simulations found a 3D target registration error of 1.08(1.92) mm for biplane (monoplane) geometries, while the phantom experiment found a 2D target registration error of 0.69mm. For phantom experiments, we demonstrated a monoplane tracking frame-rate of 1.38 fps. The proposed feature-based registration method is computationally efficient, resulting in near real-time, accurate image based registration between TEE and XRF.

  7. 3D topography of biologic tissue by multiview imaging and structured light illumination

    NASA Astrophysics Data System (ADS)

    Liu, Peng; Zhang, Shiwu; Xu, Ronald

    2014-02-01

    Obtaining three-dimensional (3D) information of biologic tissue is important in many medical applications. This paper presents two methods for reconstructing 3D topography of biologic tissue: multiview imaging and structured light illumination. For each method, the working principle is introduced, followed by experimental validation on a diabetic foot model. To compare the performance characteristics of these two imaging methods, a coordinate measuring machine (CMM) is used as a standard control. The wound surface topography of the diabetic foot model is measured by multiview imaging and structured light illumination methods respectively and compared with the CMM measurements. The comparison results show that the structured light illumination method is a promising technique for 3D topographic imaging of biologic tissue.

  8. Structure-From-Motion in 3D Space Using 2D Lidars

    PubMed Central

    Choi, Dong-Geol; Bok, Yunsu; Kim, Jun-Sik; Shim, Inwook; Kweon, In So

    2017-01-01

    This paper presents a novel structure-from-motion methodology using 2D lidars (Light Detection And Ranging). In 3D space, 2D lidars do not provide sufficient information for pose estimation. For this reason, additional sensors have been used along with the lidar measurement. In this paper, we use a sensor system that consists of only 2D lidars, without any additional sensors. We propose a new method of estimating both the 6D pose of the system and the surrounding 3D structures. We compute the pose of the system using line segments of scan data and their corresponding planes. After discarding the outliers, both the pose and the 3D structures are refined via nonlinear optimization. Experiments with both synthetic and real data show the accuracy and robustness of the proposed method. PMID:28165372

  9. 3D modelling of facade features on large sites acquired by vehicle based laser scanning

    NASA Astrophysics Data System (ADS)

    Boulaassal, H.; Landes, T.; Grussenmeyer, P.

    2011-12-01

    Mobile mapping laser scanning systems have become more and more widespread for the acquisition of millions of 3D points on large and geometrically complex urban sites. Vehicle-based Laser Scanning (VLS) systems travel many kilometers while acquiring raw point clouds which are registered in real time in a common coordinate system. Improvements of the acquisition steps as well as the automatic processing of the collected point clouds are still a conundrum for researchers. This paper shows some results obtained by application, on mobile laser scanner data, of segmentation and reconstruction algorithms intended initially to generate individual vector facade models using stationary Terrestrial Laser Scanner (TLS) data. The operating algorithms are adapted so as to take into account characteristics of VLS data. The intrinsic geometry of a point cloud as well as the relative geometry between registered point clouds are different from that obtained by a static TLS. The amount of data provided by this acquisition technique is another issue. Such particularities should be taken into consideration while processing this type of point clouds. The segmentation of VLS data is carried out based on an adaptation of RANSAC algorithm. Edge points of each element are extracted by applying a second algorithm. Afterwards, the vector models of each facade element are reconstructed. In order to validate the results, large samples with different characteristics have been introduced in the developed processing chain. The limitations as well as the capabilities of each process will be emphasized in terms of geometry and processing time.

  10. Visualizing and Tracking Evolving Features in 3D Unstructured and Adaptive Datasets

    SciTech Connect

    Silver, D.; Zabusky, N.

    2002-08-01

    The massive amounts of time-varying datasets being generated demand new visualization and quantification techniques. Visualization alone is not sufficient. Without proper measurement information/computations real science cannot be done. Our focus is this work was to combine visualization with quantification of the data to allow for advanced querying and searching. As part of this proposal, we have developed a feature extraction adn tracking methodology which allows researcher to identify features of interest and follow their evolution over time. The implementation is distributed and operates over data In-situ: where it is stored and when it was computed.

  11. 3D multi-layered fibrous cellulose structure using an electrohydrodynamic process for tissue engineering.

    PubMed

    Kim, Minseong; Kim, GeunHyung

    2015-11-01

    Micro/nanofibrous structures have been applied widely in various tissue-engineering applications because the topological structures are similar to the extracellular matrix (ECM), which encourages a high degree of cell adhesion and growth. However, it has been difficult to produce a three-dimensional (3D) fibrous structure using controllable macro-pores. Recently, cellulose has been considered a high-potential natural-origin biomaterial, but its use in 3D biomedical structures has been limited due to its narrow processing window. Here, we suggest a new 3D cellulose scaffold consisting of multi-layered struts made of submicron-sized entangled fibers that were fabricated using an electrohydrodynamic direct jet (EHDJ) process that is spin-printing. By optimizing processing conditions (electric field strength, cellulose feeding rate, and distance between nozzle and target), we can achieve a multi-layered cellulose structure consisting of the cylindrically entangled cellulose fibers. To compare the properties of the fabricated 3D cellulose structure, we used a PCL fibrous scaffold, which has a similar fibrous morphology and pore geometry, as a control. The physical and in vitro biocompatibilities of both fibrous scaffolds were assessed using human dermal fibroblasts, and the cellulose structure showed higher cell adhesion and metabolic activities compared with the control. These results suggest the EHDJ process to be an effective fabricating tool for tissue engineering and the cellulose scaffold has high potential as a tissue regenerative material.

  12. Enhanced genome annotation using structural profiles in the program 3D-PSSM.

    PubMed

    Kelley, L A; MacCallum, R M; Sternberg, M J

    2000-06-02

    A method (three-dimensional position-specific scoring matrix, 3D-PSSM) to recognise remote protein sequence homologues is described. The method combines the power of multiple sequence profiles with knowledge of protein structure to provide enhanced recognition and thus functional assignment of newly sequenced genomes. The method uses structural alignments of homologous proteins of similar three-dimensional structure in the structural classification of proteins (SCOP) database to obtain a structural equivalence of residues. These equivalences are used to extend multiply aligned sequences obtained by standard sequence searches. The resulting large superfamily-based multiple alignment is converted into a PSSM. Combined with secondary structure matching and solvation potentials, 3D-PSSM can recognise structural and functional relationships beyond state-of-the-art sequence methods. In a cross-validated benchmark on 136 homologous relationships unambiguously undetectable by position-specific iterated basic local alignment search tool (PSI-Blast), 3D-PSSM can confidently assign 18 %. The method was applied to the remaining unassigned regions of the Mycoplasma genitalium genome and an additional 13 regions were assigned with 95 % confidence. 3D-PSSM is available to the community as a web server: http://www.bmm.icnet.uk/servers/3dpssm

  13. Structure light telecentric stereoscopic vision 3D measurement system based on Scheimpflug condition

    NASA Astrophysics Data System (ADS)

    Mei, Qing; Gao, Jian; Lin, Hui; Chen, Yun; Yunbo, He; Wang, Wei; Zhang, Guanjin; Chen, Xin

    2016-11-01

    We designed a new three-dimensional (3D) measurement system for micro components: a structure light telecentric stereoscopic vision 3D measurement system based on the Scheimpflug condition. This system creatively combines the telecentric imaging model and the Scheimpflug condition on the basis of structure light stereoscopic vision, having benefits of a wide measurement range, high accuracy, fast speed, and low price. The system measurement range is 20 mm×13 mm×6 mm, the lateral resolution is 20 μm, and the practical vertical resolution reaches 2.6 μm, which is close to the theoretical value of 2 μm and well satisfies the 3D measurement needs of micro components such as semiconductor devices, photoelectron elements, and micro-electromechanical systems. In this paper, we first introduce the principle and structure of the system and then present the system calibration and 3D reconstruction. We then present an experiment that was performed for the 3D reconstruction of the surface topography of a wafer, followed by a discussion. Finally, the conclusions are presented.

  14. Towards an efficient compression of 3D coordinates of macromolecular structures

    PubMed Central

    Valasatava, Yana; Bradley, Anthony R.; Rose, Alexander S.; Duarte, Jose M.; Prlić, Andreas

    2017-01-01

    The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the visualization of large molecular complexes and enable new and scalable means for data analysis. We evaluated a series of compression techniques for coordinates of 3D macromolecular structures and identified the best performing approaches. By balancing compression efficiency in terms of the decompression speed and compression ratio, and code complexity, our results provide the foundation for a novel standard to represent macromolecular coordinates in a compact and useful file format. PMID:28362865

  15. Towards an efficient compression of 3D coordinates of macromolecular structures.

    PubMed

    Valasatava, Yana; Bradley, Anthony R; Rose, Alexander S; Duarte, Jose M; Prlić, Andreas; Rose, Peter W

    2017-01-01

    The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the visualization of large molecular complexes and enable new and scalable means for data analysis. We evaluated a series of compression techniques for coordinates of 3D macromolecular structures and identified the best performing approaches. By balancing compression efficiency in terms of the decompression speed and compression ratio, and code complexity, our results provide the foundation for a novel standard to represent macromolecular coordinates in a compact and useful file format.

  16. Local-global alignment for finding 3D similarities in protein structures

    DOEpatents

    Zemla, Adam T.

    2011-09-20

    A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

  17. Obtaining 3d models of surface snow and ice features (penitentes) with a Xbox Kinect

    NASA Astrophysics Data System (ADS)

    Nicholson, Lindsey; Partan, Benjamin; Pętlicki, Michał; MacDonell, Shelley

    2014-05-01

    Penitentes are snow or ice spikes that can reach several metres in height. They are a common feature of snow and ice surfaces in the semi-arid Andes as their formation is favoured by very low humidity, persistently low temperatures and sustained high solar radiation. While the conditions of their formation are relatively well constrained it is not yet clear how their presence influences the rate of mass loss and meltwater production from the mountain cryosphere and there is a need for accurate measurements of ablation within penitente fields through time in order to evaluate how well existing energy balance models perform for surfaces with penitentes. The complex surface morphology poses a challenge to measuring the mass loss at snow or glacier surfaces as (i) the spatial distribution of surface lowering within a penitente field is very heterogeneous, and (ii) the steep walls and sharp edges of the penitentes limit the line of sight view for surveying from fixed positions. In this work we explored whether these problems can be solved by using the Xbox Kinect sensor to generate small scale digital terrain models (DTMs) of sample areas of snow and ice penitentes. The study site was Glaciar Tapado in Chile (30°08'S; 69°55'W) where three sample sites were monitored from November 2013 to January 2014. The range of the Kinect sensor was found to be restricted to about 1 m over snow and ice, and scanning was only possible after dusk. Moving the sensor around the penitente field was challenging and often resulted in fragmented scans. However, despite these challenges, the scans obtained could be successfully combined in MeshLab software to produce good surface representations of the penitentes. GPS locations of target stakes in the sample plots allow the DTMs to be orientated correctly in space so the morphology of the penitente field and the volume loss through time can be fully described. At the study site in snow penitentes the Kinect DTM was compared with the quality

  18. Computational methods for constructing protein structure models from 3D electron microscopy maps.

    PubMed

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2013-10-01

    Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided.

  19. Multi-scale modelling of strongly heterogeneous 3D composite structures using spatial Voronoi tessellation

    NASA Astrophysics Data System (ADS)

    El Said, Bassam; Ivanov, Dmitry; Long, Andrew C.; Hallett, Stephen R.

    2016-03-01

    3D composite materials are characterized by complex internal yarn architectures, leading to complex deformation and failure development mechanisms. Net-shaped preforms, which are originally periodic in nature, lose their periodicity when the fabric is draped, deformed on a tool, and consolidated to create geometrically complex composite components. As a result, the internal yarn architecture, which dominates the mechanical behaviour, becomes dependent on the structural geometry. Hence, predicting the mechanical behaviour of 3D composites requires an accurate representation of the yarn architecture within structural scale models. When applied to 3D composites, conventional finite element modelling techniques are limited to either homogenised properties at the structural scale, or the unit cell scale for a more detailed material property definition. Consequently, these models fail to capture the complex phenomena occurring across multiple length scales and their effects on a 3D composite's mechanical response. Here a multi-scale modelling approach based on a 3D spatial Voronoi tessellation is proposed. The model creates an intermediate length scale suitable for homogenisation to deal with the non-periodic nature of the final material. Information is passed between the different length scales to allow for the effect of the structural geometry to be taken into account on the smaller scales. The stiffness and surface strain predictions from the proposed model have been found to be in good agreement with experimental results. The proposed modelling framework has been used to gain important insight into the behaviour of this category of materials. It has been observed that the strain and stress distributions are strongly dependent on the internal yarn architecture and consequently on the final component geometry. Even for simple coupon tests, the internal architecture and geometric effects dominate the mechanical response. Consequently, the behaviour of 3D woven

  20. SimRNAweb: a web server for RNA 3D structure modeling with optional restraints.

    PubMed

    Magnus, Marcin; Boniecki, Michał J; Dawson, Wayne; Bujnicki, Janusz M

    2016-07-08

    RNA function in many biological processes depends on the formation of three-dimensional (3D) structures. However, RNA structure is difficult to determine experimentally, which has prompted the development of predictive computational methods. Here, we introduce a user-friendly online interface for modeling RNA 3D structures using SimRNA, a method that uses a coarse-grained representation of RNA molecules, utilizes the Monte Carlo method to sample the conformational space, and relies on a statistical potential to describe the interactions in the folding process. SimRNAweb makes SimRNA accessible to users who do not normally use high performance computational facilities or are unfamiliar with using the command line tools. The simplest input consists of an RNA sequence to fold RNA de novo. Alternatively, a user can provide a 3D structure in the PDB format, for instance a preliminary model built with some other technique, to jump-start the modeling close to the expected final outcome. The user can optionally provide secondary structure and distance restraints, and can freeze a part of the starting 3D structure. SimRNAweb can be used to model single RNA sequences and RNA-RNA complexes (up to 52 chains). The webserver is available at http://genesilico.pl/SimRNAweb.

  1. Segmented images and 3D images for studying the anatomical structures in MRIs

    NASA Astrophysics Data System (ADS)

    Lee, Yong Sook; Chung, Min Suk; Cho, Jae Hyun

    2004-05-01

    For identifying the pathological findings in MRIs, the anatomical structures in MRIs should be identified in advance. For studying the anatomical structures in MRIs, an education al tool that includes the horizontal, coronal, sagittal MRIs of entire body, corresponding segmented images, 3D images, and browsing software is necessary. Such an educational tool, however, is hard to obtain. Therefore, in this research, such an educational tool which helps medical students and doctors study the anatomical structures in MRIs was made as follows. A healthy, young Korean male adult with standard body shape was selected. Six hundred thirteen horizontal MRIs of the entire body were scanned and inputted to the personal computer. Sixty anatomical structures in the horizontal MRIs were segmented to make horizontal segmented images. Coronal, sagittal MRIs and coronal, sagittal segmented images were made. 3D images of anatomical structures in the segmented images were reconstructed by surface rendering method. Browsing software of the MRIs, segmented images, and 3D images was composed. This educational tool that includes horizontal, coronal, sagittal MRIs of entire body, corresponding segmented images, 3D images, and browsing software is expected to help medical students and doctors study anatomical structures in MRIs.

  2. Automated Breast Volume Scanning: Identifying 3-D Coronal Plane Imaging Features May Help Categorize Complex Cysts.

    PubMed

    Wang, Hong-Yan; Jiang, Yu-Xin; Zhu, Qing-Li; Zhang, Jing; Xiao, Meng-Su; Liu, He; Dai, Qing; Li, Jian-Chu; Sun, Qiang

    2016-03-01

    The study described here sought to identify specific ultrasound (US) automated breast volume scanning (ABVS) features that distinguish benign from malignant lesions. Medical records of 750 patients with 792 breast lesions were retrospectively reviewed. Of the 750 patients, 101 with 122 cystic lesions were included in this study, and the results ABVS results were compared with biopsy pathology results. These lesions were classified into six categories based on ABVS sonographic features: type I = simple cyst; type II = clustered cyst; type III = cystic masses with thin septa; type IV = complex cyst; type V = predominantly cystic masses; and type VI = predominantly solid masses. Comparisons were conducted between the ABVS coronal plane features of the lesions and histopathology results, and the positive predictive value (PPV) was calculated for each feature. Of the 122 lesions, 90 (73.8%) were classified as benign, and 32 (26.2%) were classified as malignant. The sensitivity, specificity and accuracy associated with ABVS features for cystic lesions were 78.1%, 74.4% and 75.4%, respectively. The 11 cases (8.9%) of type I-IV cysts were all benign. Of the 22 (18.0%) type V cysts, 16 (13.1%) were benign and 6 (4.9%) were malignant. Of the 89 (72.9%) type VI cysts, 63 (51.7%) were benign and 26 (21.3%) were malignant. The typical symptoms of malignancy on ABVS include retraction (PPV = 100%, p < 0.05), hyper-echoic halos (PPV = 85.7%, p < 0.05), microcalcification (PPV = 66.7%, p < 0.05), thick walls or thick septa (PPV = 62.5%, p < 0.05), irregular shape (PPV: 51.2%, p < 0.05), indistinct margin (PPV: 48.6%, p < 0.05) and predominantly solid masses with eccentric cystic foci (PPV = 46.8%, p < 0.05). ABVS can reveal sonographic features of the lesions along the coronal plane, which may be of benefit in the detection of malignant, predominantly cystic masses and provide high clinical values.

  3. Seismic source inversion using Green's reciprocity and a 3-D structural model for the Japanese Islands

    NASA Astrophysics Data System (ADS)

    Simutė, S.; Fichtner, A.

    2015-12-01

    We present a feasibility study for seismic source inversions using a 3-D velocity model for the Japanese Islands. The approach involves numerically calculating 3-D Green's tensors, which is made efficient by exploiting Green's reciprocity. The rationale for 3-D seismic source inversion has several aspects. For structurally complex regions, such as the Japan area, it is necessary to account for 3-D Earth heterogeneities to prevent unknown structure polluting source solutions. In addition, earthquake source characterisation can serve as a means to delineate existing faults. Source parameters obtained for more realistic Earth models can then facilitate improvements in seismic tomography and early warning systems, which are particularly important for seismically active areas, such as Japan. We have created a database of numerically computed 3-D Green's reciprocals for a 40°× 40°× 600 km size area around the Japanese Archipelago for >150 broadband stations. For this we used a regional 3-D velocity model, recently obtained from full waveform inversion. The model includes attenuation and radial anisotropy and explains seismic waveform data for periods between 10 - 80 s generally well. The aim is to perform source inversions using the database of 3-D Green's tensors. As preliminary steps, we present initial concepts to address issues that are at the basis of our approach. We first investigate to which extent Green's reciprocity works in a discrete domain. Considering substantial amounts of computed Green's tensors we address storage requirements and file formatting. We discuss the importance of the initial source model, as an intelligent choice can substantially reduce the search volume. Possibilities to perform a Bayesian inversion and ways to move to finite source inversion are also explored.

  4. Advanced resin systems and 3D textile preforms for low cost composite structures

    NASA Technical Reports Server (NTRS)

    Shukla, J. G.; Bayha, T. D.

    1993-01-01

    Advanced resin systems and 3D textile preforms are being evaluated at Lockheed Aeronautical Systems Company (LASC) under NASA's Advanced Composites Technology (ACT) Program. This work is aimed towards the development of low-cost, damage-tolerant composite fuselage structures. Resin systems for resin transfer molding and powder epoxy towpreg materials are being evaluated for processability, performance and cost. Three developmental epoxy resin systems for resin transfer molding (RTM) and three resin systems for powder towpregging are being investigated. Various 3D textile preform architectures using advanced weaving and braiding processes are also being evaluated. Trials are being conducted with powdered towpreg, in 2D weaving and 3D braiding processes for their textile processability and their potential for fabrication in 'net shape' fuselage structures. The progress in advanced resin screening and textile preform development is reviewed here.

  5. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression

    PubMed Central

    Jacob, J. Augustin; Kumar, N. Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation. PMID:26601120

  6. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression.

    PubMed

    Jacob, J Augustin; Kumar, N Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation.

  7. Protein-protein interaction networks studies and importance of 3D structure knowledge.

    PubMed

    Lu, Hui-Chun; Fornili, Arianna; Fraternali, Franca

    2013-12-01

    Protein-protein interaction networks (PPINs) are a powerful tool to study biological processes in living cells. In this review, we present the progress of PPIN studies from abstract to more detailed representations. We will focus on 3D interactome networks, which offer detailed information at the atomic level. This information can be exploited in understanding not only the underlying cellular mechanisms, but also how human variants and disease-causing mutations affect protein functions and complexes' stability. Recent studies have used structural information on PPINs to also understand the molecular mechanisms of binding partner selection. We will address the challenges in generating 3D PPINs due to the restricted number of solved protein structures. Finally, some of the current use of 3D PPINs will be discussed, highlighting their contribution to the studies in genotype-phenotype relationships and in the optimization of targeted studies to design novel chemical compounds for medical treatments.

  8. Region-Based Feature Interpretation for Recognizing 3D Models in 2D images

    DTIC Science & Technology

    1991-06-01

    Likewise, if two model lines are colinear or are connected at their endpoints, they must do the same in the image (again, within some bounds, to account...not well defined. Is a flowerpot part of the plant object? The answer depends on the vision task, and even then may be ambiguous or allow overlapping...However, not all have been tried, either in psychological tests or in vision systems. Proximity: Features are close to each other. Edge Connectivity

  9. Identifiability of 3D attributed scattering features from sparse nonlinear apertures

    NASA Astrophysics Data System (ADS)

    Jackson, Julie Ann; Moses, Randolph L.

    2007-04-01

    Attributed scattering feature models have shown potential in aiding automatic target recognition and scene visualization from radar scattering measurements. Attributed scattering features capture physical scattering geometry, including the non-isotropic response of target scattering over wide angles, that is not discerned from traditional point scatter models. In this paper, we study the identifiability of canonical scattering primitives from complex phase history data collected over sparse nonlinear apertures that have both azimuth and elevation diversity. We study six canonical shapes: a flat plate, dihedral, trihedral, cylinder, top-hat, and sphere, and three flight path scenarios: a monostatic linear path, a monostatic nonlinear path, and a bistatic case with a fixed transmitter and a nonlinear receiver flight path. We modify existing scattering models to account for nonzero object radius and to scale peak scattering intensities to equate to radar cross section. Similarities in some canonical scattering responses lead to confusion among multiple shapes when considering only model fit errors. We present additional model discriminators including polarization consistency between the model and the observed feature and consistency of estimated object size with radar cross section. We demonstrate that flight path diversity and combinations of model discriminators increases identifiability of canonical shapes.

  10. 3D watershed-based segmentation of internal structures within MR brain images

    NASA Astrophysics Data System (ADS)

    Bueno, Gloria; Musse, Olivier; Heitz, Fabrice; Armspach, Jean-Paul

    2000-06-01

    In this paper an image-based method founded on mathematical morphology is presented in order to facilitate the segmentation of cerebral structures on 3D magnetic resonance images (MRIs). The segmentation is described as an immersion simulation, applied to the modified gradient image, modeled by a generated 3D region adjacency graph (RAG). The segmentation relies on two main processes: homotopy modification and contour decision. The first one is achieved by a marker extraction stage where homogeneous 3D regions are identified in order to attribute an influence zone only to relevant minima of the image. This stage uses contrasted regions from morphological reconstruction and labeled flat regions constrained by the RAG. The goal of the decision stage is to precisely locate the contours of regions detected by the marker extraction. This decision is performed by a 3D extension of the watershed transform. Upon completion of the segmentation, the outcome of the preceding process is presented to the user for manual selection of the structures of interest (SOI). Results of this approach are described and illustrated with examples of segmented 3D MRIs of the human head.

  11. Voxel-coding method for quantification of vascular structure from 3D images

    NASA Astrophysics Data System (ADS)

    Soltanian-Zadeh, Hamid; Shahrokni, Ali; Zoroofi, Reza A.

    2001-05-01

    This paper presents an image processing method for information extraction from 3D images of vasculature. It automates the study of vascular structures by extracting quantitative information such as skeleton, length, diameter, and vessel-to- tissue ratio for different vessels as well as their branches. Furthermore, it generates 3D visualization of vessels based on desired anatomical characteristics such as vessel diameter or 3D connectivity. Steps of the proposed approach are as follows. (1) Preprocessing, in which intensity adjustment, optimal thresholding, and median filtering are done. (2) 3D thinning, in which medial axis and skeleton of the vessels are found. (3) Branch labeling, in which different branches are identified and each voxel is assigned to the corresponding branch. (4) Quantitation, in which length of each branch is estimated, based on the number of voxels assigned to it, and its diameter is calculated using the medial axis direction. (5) Visualization, in which vascular structure is shown in 3D, using color coding and surface rendering methods. We have tested and evaluated the proposed algorithms using simulated images of multi-branch vessels and real confocal microscopic images of the vessels in rat brains. Experimental results illustrate performance of the methods and usefulness of the results for medical image analysis applications.

  12. 3D shape shearography with integrated structured light projection for strain inspection of curved objects

    NASA Astrophysics Data System (ADS)

    Anisimov, Andrei G.; Groves, Roger M.

    2015-05-01

    Shearography (speckle pattern shearing interferometry) is a non-destructive testing technique that provides full-field surface strain characterization. Although real-life objects especially in aerospace, transport or cultural heritage are not flat (e.g. aircraft leading edges or sculptures), their inspection with shearography is of interest for both hidden defect detection and material characterization. Accurate strain measuring of a highly curved or free form surface needs to be performed by combining inline object shape measuring and processing of shearography data in 3D. Previous research has not provided a general solution. This research is devoted to the practical questions of 3D shape shearography system development for surface strain characterization of curved objects. The complete procedure of calibration and data processing of a 3D shape shearography system with integrated structured light projector is presented. This includes an estimation of the actual shear distance and a sensitivity matrix correction within the system field of view. For the experimental part a 3D shape shearography system prototype was developed. It employs three spatially-distributed shearing cameras, with Michelson interferometers acting as the shearing devices, one illumination laser source and a structured light projector. The developed system performance was evaluated with a previously reported cylinder specimen (length 400 mm, external diameter 190 mmm) loaded by internal pressure. Further steps for the 3D shape shearography prototype and the technique development are also proposed.

  13. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGES

    Zhang, Xing; Zhang, Lei; Tong, Huimin; ...

    2015-05-05

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

  14. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    SciTech Connect

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

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

  15. Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions

    PubMed Central

    Shi, Ya-Zhou; Jin, Lei; Wang, Feng-Hua; Zhu, Xiao-Long; Tan, Zhi-Jie

    2015-01-01

    A full understanding of RNA-mediated biology would require the knowledge of three-dimensional (3D) structures, structural flexibility, and stability of RNAs. To predict RNA 3D structures and stability, we have previously proposed a three-bead coarse-grained predictive model with implicit salt/solvent potentials. In this study, we further develop the model by improving the implicit-salt electrostatic potential and including a sequence-dependent coaxial stacking potential to enable the model to simulate RNA 3D structure folding in divalent/monovalent ion solutions. The model presented here can predict 3D structures of RNA hairpins with bulges/internal loops (<77 nucleotides) from their sequences at the corresponding experimental ion conditions with an overall improved accuracy compared to the experimental data; the model also makes reliable predictions for the flexibility of RNA hairpins with bulge loops of different lengths at several divalent/monovalent ion conditions. In addition, the model successfully predicts the stability of RNA hairpins with various loops/stems in divalent/monovalent ion solutions. PMID:26682822

  16. Liquid immersion thermal crosslinking of 3D polymer nanopatterns for direct carbonisation with high structural integrity

    PubMed Central

    Kang, Da-Young; Kim, Cheolho; Park, Gyurim; Moon, Jun Hyuk

    2015-01-01

    The direct pyrolytic carbonisation of polymer patterns has attracted interest for its use in obtaining carbon materials. In the case of carbonisation of nanopatterned polymers, the polymer flow and subsequent pattern change may occur in order to relieve their high surface energies. Here, we demonstrated that liquid immersion thermal crosslinking of polymer nanopatterns effectively enhanced the thermal resistance and maintained the structure integrity during the heat treatment. We employed the liquid immersion thermal crosslinking for 3D porous SU8 photoresist nanopatterns and successfully converted them to carbon nanopatterns while maintaining their porous features. The thermal crosslinking reaction and carbonisation of SU8 nanopatterns were characterised. The micro-crystallinity of the SU8-derived carbon nanopatterns was also characterised. The liquid immersion heat treatment can be extended to the carbonisation of various polymer or photoresist nanopatterns and also provide a facile way to control the surface energy of polymer nanopatterns for various purposes, for example, to block copolymer or surfactant self-assemblies. PMID:26677949

  17. Proteopedia: A Collaborative, Virtual 3D Web-Resource for Protein and Biomolecule Structure and Function

    ERIC Educational Resources Information Center

    Hodis, Eran; Prilusky, Jaime, Sussman, Joel L.

    2010-01-01

    Protein structures are hard to represent on paper. They are large, complex, and three-dimensional (3D)--four-dimensional if conformational changes count! Unlike most of their substrates, which can easily be drawn out in full chemical formula, drawing every atom in a protein would usually be a mess. Simplifications like showing only the surface of…

  18. Graphene originated 3D structures grown on the assembled nickel particles

    NASA Astrophysics Data System (ADS)

    Paronyan, Tereza; Harutyunyan, Avetik; Honda Research Institute USA Inc. Team

    2013-03-01

    Recently, the fabrication of various morphologies of graphene originated structures became very important due to the perspective of wide range of new applications. Particularly, free standing 3D structured graphene foams could be imperative in energy related areas . Here, we present the new approach of the CVD growth of 3D graphene network by using primarily sintered Ni particle's (~40 μm size) assembles as a template-catalyst via decomposition of low rate of CH4 at 1100° C based on synthesis method described earlier. SEM and Raman spectra analysis revealed the formation of graphene structure containing a single up to few layers grown on the sintered metal particles served as a catalyst-template. After etching the metal frame without using any support polymer, 3D free-standing graphene microporous structure was formed demonstrating high BET surface area. Two probe measurements of frame resistance were ~2-8 Ω. Our approach allows controllable tune the pore size and thereby the surface area of 3D graphene network through the variation of the template-catalyst particles size.

  19. Ion Beam Etching: Replication of Micro Nano-structured 3D Stencil Masks

    SciTech Connect

    Weber, Patrick; Guibert, Edouard; Mikhailov, Serguei; Bruegger, Juergen; Villanueva, Guillermo

    2009-03-10

    Ion beam LIGA allows the etching of 3D nano-structures by direct writing with a nano-sized beam. However, this is a relatively time consuming process. We propose here another approach for etching structures on large surfaces and faster, compared to the direct writing process. This approach consists of replicating 3D structured masks, by scanning an unfocused ion beam. A polymer substrate is placed behind the mask, as in UV photolithography. But the main advantage is that the 3D structure of the mask can be replicated into the polymer. For that purpose, the masks (developped at LMIS1, EPFL) are made of a silicon nitride membrane 100 nm thick, on which 3D gold structures up to 200 nm thick, are deposited. The 3D Au structures are made with the nanostencil method, based on successive gold deposition. The IMA institute, from HE-Arc, owns a High Voltage Engineering 1.7 MV Tandetron with both solid and gaseous negative ion sources, able to generate ions from almost every chemical element in a broad range of energies comprised between 400 keV and 6.8 MeV. The beam composition and energy are chosen in such a way, that ions lose a significant fraction of their energy when passing through the thickest regions of the mask. Ions passing through thinner regions of the mask loose a smaller fraction of their energy and etch the polymer with larger thicknesses, allowing a replication of the mask into the polymer. For our trials, we have used a carbon beam with an energy of 500 keV. The beam was focussed to a diameter of 5 mm with solid slits, in order to avoid border effects and thus ensure a homogeneous dose distribution on the beam diameter. The feasibility of this technique has been demonstrated, allowing industrial applications for micro-mould fabrication, micro-fluidics and micro-optics.

  20. Non-contact 3D fingerprint scanner using structured light illumination

    NASA Astrophysics Data System (ADS)

    Troy, Mike; Hassebrook, Laurence; Yalla, Veeraganesh; Daley, Raymond

    2011-03-01

    As crime prevention and national security remain a top priority, requirements for the use of fingerprints for identification continue to grow. While the size of fingerprint databases continues to expand, new technologies that can improve accuracy and ultimately matching performance will become more critical to maintain the effectiveness of the systems. FlashScan3D has developed non-contact, fingerprint scanners based on the principles of Structured Light Illumination (SLI) that capture 3Dimensional data of fingerprints quickly, accurately and independently of an operator. FlashScan3D will present findings from various research projects performed for the US Army and the Department of Homeland Security.

  1. A Patterned 3D Silicon Anode Fabricated by Electrodeposition on a Virus-Structured Current Collector

    SciTech Connect

    Chen, X L; Gerasopoulos, K; Guo, J C; Brown, A; Wang, Chunsheng; Ghodssi, Reza; Culver, J N

    2010-11-09

    Electrochemical methods were developed for the deposition of nanosilicon onto a 3D virus-structured nickel current collector. This nickel current collector is composed of self-assembled nanowire-like rods of genetically modified tobacco mosaic virus (TMV1cys), chemically coated in nickel to create a complex high surface area conductive substrate. The electrochemically depo­sited 3D silicon anodes demonstrate outstanding rate performance, cycling stability, and rate capability. Electrodeposition thus provides a unique means of fabricating silicon anode materials on complex substrates at low cost.

  2. Studies of the 3D Structure of the Nucleon at Jlab

    SciTech Connect

    Avakian, Harut

    2016-07-01

    Studies of the 3D structure of the nucleon encoded in Transverse Momentum Dependent distribution and fragmentation functions of partons and Generalized Parton Distributions are among the key objectives of the JLab 12 GeV upgrade and the Electron Ion Collider. Main challenges in extracting 3D partonic distributions from precision measurements of hard scattering processes include clear understanding of leading twist QCD fundamentals, higher twist effects, and also correlations of hadron production in target and current fragmentation regions. In this contribution we discuss some ongoing studies and future measurements of spin-orbit correlations at Jefferson Lab.

  3. Holographic particle velocimetry - A 3D measurement technique for vortex interactions, coherent structures and turbulence

    NASA Astrophysics Data System (ADS)

    Meng, Hui; Hussain, Fazle

    1991-10-01

    To understand the topology and dynamics of coherent structures (CS), the interactions of CS with fine-scale turbulence, and the effects of CS on entrainment, mixing and combustion, experimental tools are needed that can measure velocity (preferably vorticity) vector fields in both 3D space and time. While traditional measurement techniques are not able to serve this purpose, holographic particle velocimetry (HPV) appears to be promising. In a demonstration experiment, the instantaneous 3D velocity vector fields in some simple vortical flows have been obtained using the HPV technique. In this preliminary report, the principles of the HPV technique are illustrated and the key issues in its implementation are discussed.

  4. Features of the Ti-40Nb alloy prototype formation by 3D additive method

    NASA Astrophysics Data System (ADS)

    Sharkeev, Yu. P.; Kovalevskaya, Zh. G.; Khimich, M. A.; Eroshenko, A. Yu.; Saprykin, A. A.; Ibragimov, E. A.; Glukhov, I. A.

    2016-11-01

    The structure of Ti-40Nb alloy prototype obtained by selective laser melting (SLM) on "VARISKAF 100MV" installation was considered by the methods of optical metallography, scanning and transmission electron microscopy. It was revealed that the most of the specimens' surface is uniform flowed surface with typical banded structure formed by laying-on molten pools. The process of the individual layer formation was followed by drop formation. This leads to the porosity formation on the specimen's surface. The structure of entire specimen is not homogeneous throughout the transverse section. The porosity of three kinds is observed. They are cavities of not full contact and melting of the layers, drawholes, gas pores. The porosity optimization requires more careful SLM modes selection. The alloy has a grain structure with anisotropy from small (2-8 µm) to medium (8-20 µm) grain size. The anisotropy of the specimen is formed in each layer and is retained during building of the specimen. The grains of microstructure are formed by the main β-phase with precipitations of nonequilibrium α″-martensite on the boundaries and within the grains.

  5. Two nanosized 3d-4f clusters featuring four Ln6 octahedra encapsulating a Zn4 tetrahedron.

    PubMed

    Zheng, Xiu-Ying; Wang, Shi-Qiang; Tang, Wen; Zhuang, Gui-Lin; Kong, Xiang-Jian; Ren, Yan-Ping; Long, La-Sheng; Zheng, Lan-Sun

    2015-07-07

    Two high-nuclearity 3d-4f clusters Ln24Zn4 (Ln = Gd and Sm) featuring four Ln6 octahedra encapsulating a Zn4 tetrahedron were obtained through the self-assembly of Zn(OAc)2 and Ln(ClO4)3. Quantum Monte Carlo (QMC) simulations show the antiferromagnetic coupling between Gd(3+) ions. Studies of the magnetocaloric effect (MCE) show that the Gd24Zn4 cluster exhibits the entropy change (-ΔSm) of 31.4 J kg(-1) K(-1).

  6. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells.

    PubMed

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L; Han, Jessica H; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H; Bussey, Kimberly J; Meldrum, Deirdre R

    2016-08-09

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an 'epigenetic' drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat's differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action.

  7. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells

    PubMed Central

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L.; Han, Jessica H.; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H.; Bussey, Kimberly J.; Meldrum, Deirdre R.

    2016-01-01

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an ‘epigenetic’ drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat’s differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action. PMID:27503568

  8. Recursive estimation of 3D motion and surface structure from local affine flow parameters.

    PubMed

    Calway, Andrew

    2005-04-01

    A recursive structure from motion algorithm based on optical flow measurements taken from an image sequence is described. It provides estimates of surface normals in addition to 3D motion and depth. The measurements are affine motion parameters which approximate the local flow fields associated with near-planar surface patches in the scene. These are integrated over time to give estimates of the 3D parameters using an extended Kalman filter. This also estimates the camera focal length and, so, the 3D estimates are metric. The use of parametric measurements means that the algorithm is computationally less demanding than previous optical flow approaches and the recursive filter builds in a degree of noise robustness. Results of experiments on synthetic and real image sequences demonstrate that the algorithm performs well.

  9. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures

    PubMed Central

    Zenou, M.; Sa’ar, A.; Kotler, Z.

    2015-01-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures. PMID:26602432

  10. 3D electrical structure of porphyry copper deposit: A case study of Shaxi copper deposit

    NASA Astrophysics Data System (ADS)

    Chen, Xiang-Bin; Lü, Qing-Tian; Yan, Jia-Yong

    2012-06-01

    Located in Lu-Zong ore concentration area, middle-lower Yangtze metallogenic belt, ShaXi porphyry copper deposit is a typical hydrothermal deposit. To investigate the distribution of deep ore bodies and spatial characteristics of host structures, an AMT survey was conducted in mining area. Eighteen pseudo-2D resistivity sections were constructed through careful processing and inversion. These sections clearly show resistivity difference between the Silurian sandstones formation and quartz diorite porphyry and this porphyry copper formation was controlled by the highly resistive anticlines. Using 3D block Kriging interpolation method and 3D visualization techniques, we constructed a detailed 3D resistivity model of quartz diorite porphyry which shows the shape and spatial distribution of deep ore bodies. This case study can serve as a good example for future ore prospecting in and around this mining area.

  11. 3D shape measurement of shoeprint impression with structured illumination and fringe pattern analysis

    NASA Astrophysics Data System (ADS)

    Su, Xianyu; Cao, Yiping; Xiang, Liqun; Chen, Wenjing

    2002-06-01

    The shoeprint impressions of suspect left at the crime scene can sometimes tell investigators what type of shoes to be looked for. These shoeprint impressions as one of the important evidence are useful in the detection of criminals. In this paper we propose a novel technique for identifying and analyzing the 3D characteristics of shoeprint impressions. We also design 3D shoeprint impression analysis system based on the combination the 3D shape measurement with structured illumination and fringe pattern analysis. We give a detail discussion on the principle and configuration of the system. Laboratory experiments show the technique is efficient in the detection of shoeprint and in the offering the reference for judicial evidence.

  12. A series of novel lanthanide carboxyphosphonates with a 3D framework structure: synthesis, structure, and luminescent and magnetic properties.

    PubMed

    Chen, Kai; Dong, Da-Peng; Sun, Zhen-Gang; Jiao, Cheng-Qi; Li, Chao; Wang, Cheng-Lin; Zhu, Yan-Yu; Zhao, Yan; Zhu, Jiang; Sun, Shou-Hui; Zheng, Ming-Jing; Tian, Hui; Chu, Wei

    2012-08-28

    By introduction of 1,4-benzenedicarboxylic acid as the second organic ligand, a series of novel lanthanide carboxyphosphonates with a 3D framework structure, namely, [Ln(3)(H(2)L)(HL)(2)(bdc)(2)(H(2)O)]·7H(2)O (Ln = La (1), Ce (2), Pr (3), Nd (4), Sm (5), Eu (6), Gd (7), Tb (8); H(3)L = H(2)O(3)PCH(2)NC(5)H(9)COOH; H(2)bdc = HOOCC(6)H(4)COOH) have been synthesized under hydrothermal conditions. Compounds are isostructural and feature a 3D framework in which Ln(III) polyhedra are interconnected by bridging {CPO(3)} tetrahedra into 2D inorganic layers parallel to the ab plane. The organic groups of H(2)L(-) are grafted on the two sides of the layer. These layers are further cross-linked by the bdc(2-) ligands from one layer to the Ln atoms from the other into a pillared-layered architecture with one-dimensional channel system along the a axis. The thermal stability of compounds has been investigated. Luminescent properties of compounds , and the magnetic properties of compound have also been studied.

  13. Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity.

    PubMed

    Lee, Karen J I; Calder, Grant M; Hindle, Christopher R; Newman, Jacob L; Robinson, Simon N; Avondo, Jerome J H Y; Coen, Enrico S

    2016-12-26

    Optical projection tomography (OPT) is a well-established method for visualising gene activity in plants and animals. However, a limitation of conventional OPT is that the specimen upper size limit precludes its application to larger structures. To address this problem we constructed a macro version called Macro OPT (M-OPT). We apply M-OPT to 3D live imaging of gene activity in growing whole plants and to visualise structural morphology in large optically cleared plant and insect specimens up to 60 mm tall and 45 mm deep. We also show how M-OPT can be used to image gene expression domains in 3D within fixed tissue and to visualise gene activity in 3D in clones of growing young whole Arabidopsis plants. A further application of M-OPT is to visualise plant-insect interactions. Thus M-OPT provides an effective 3D imaging platform that allows the study of gene activity, internal plant structures and plant-insect interactions at a macroscopic scale.

  14. 3D P-Wave Velocity Structure of the Deep Galicia Rifted Margin

    NASA Astrophysics Data System (ADS)

    Bayrakci, Gaye; Minshull, Timothy; Davy, Richard; Sawyer, Dale; Klaeschen, Dirk; Papenberg, Cord; Reston, Timothy; Shillington, Donna; Ranero, Cesar

    2015-04-01

    The combined wide-angle reflection-refraction and multi-channel seismic (MCS) experiment, Galicia 3D, was carried out in 2013 at the Galicia rifted margin in the northeast Atlantic Ocean, west of Spain. The main geological features within the 64 by 20 km (1280 km²) 3D box investigated by the survey are the peridotite ridge (PR), the fault bounded, rotated basement blocks and the S reflector, which has been interpreted to be a low angle detachment fault. 44 short period four-component ocean bottom seismometers and 28 ocean bottom hydrophones were deployed in the 3D box. 3D MCS profiles sampling the whole box were acquired with two airgun arrays of 3300 cu.in. fired alternately every 37.5 m. We present the results from 3D first-arrival time tomography that constrains the P-wave velocity in the 3D box, for the entire depth sampled by reflection data. Results are validated by synthetic tests and by the comparison with Galicia 3D MCS lines. The main outcomes are as follows: 1- The 3.5 km/s iso-velocity contour mimics the top of the acoustic basement observed on MCS profiles. Block bounding faults are imaged as velocity contrasts and basement blocks exhibit 3D topographic variations. 2- On the southern profiles, the top of the PR rises up to 5.5 km depth whereas, 20 km northward, its basement expression (at 6.5 km depth) nearly disappears. 3- The 6.5 km/s iso-velocity contour matches the topography of the S reflector where the latter is visible on MCS profiles. Within a depth interval of 0.6 km (in average), velocities beneath the S reflector increase from 6.5 km/s to 7 km/s, which would correspond to a decrease in the degree of serpentinization from ~45 % to ~30 % if these velocity variations are caused solely by variations in hydration. At the intersections between the block bounding normal faults and the S reflector, this decrease happens over a larger depth interval (> 1 km), suggesting that faults act as conduit for the water flow in the upper mantle.

  15. 3D P-Wave Velocity Structure of the Deep Galicia Rifted Margin

    NASA Astrophysics Data System (ADS)

    Bayrakci, G.; Minshull, T. A.; Davy, R. G.; Sawyer, D. S.; Klaeschen, D.; Papenberg, C. A.; Reston, T. J.; Shillington, D. J.; Ranero, C. R.

    2014-12-01

    The combined wide-angle reflection-refraction and multi-channel seismic (MCS) experiment, Galicia 3D, was carried out in 2013 at the Galicia rifted margin in the northeast Atlantic Ocean, west of Spain. The main geological features within the 64 by 20 km (1280 km²) 3D box investigated by the survey are the peridotite ridge (PR), the fault bounded, rotated basement blocks and the S reflector, which has been interpreted to be a low angle detachment fault. 44 short period four-component ocean bottom seismometers and 28 ocean bottom hydrophones were deployed in the 3D box. 3D MCS profiles sampling the whole box were acquired with two airgun arrays of 3300 cu.in. fired alternately every 37.5 m. We present the results from 3D first-arrival time tomography that constrains the P-wave velocity in the 3D box, for the entire depth sampled by reflection data. Results are validated by synthetic tests and by the comparison with Galicia 3D MCS lines. The main outcomes are as follows: 1- The 3.5 km/s iso-velocity contour mimics the top of the acoustic basement observed on MCS profiles. Block bounding faults are imaged as velocity contrasts and basement blocks exhibit 3D topographic variations. 2- On the southern profiles, the top of the PR rises up to 5.5 km depth whereas, 20 km northward, its basement expression (at 6.5 km depth) nearly disappears. 3- The 6.5 km/s iso-velocity contour matches the topography of the S reflector where the latter is visible on MCS profiles. Within a depth interval of 0.6 km (in average), velocities beneath the S reflector increase from 6.5 km/s to 7 km/s, which would correspond to a decrease in the degree of serpentinization from ~45 % to ~30 % if these velocity variations are caused solely by variations in hydration. At the intersections between the block bounding normal faults and the S reflector, this decrease happens over a larger depth interval (> 1 km), suggesting that faults act as conduit for the water flow in the upper mantle.

  16. Modeling and characterization of 2-D and 3-D textile structural composites

    SciTech Connect

    Yang, J.M.

    1986-01-01

    This dissertation studies the analytical modeling and experimental characterization of various two-dimensional and three-dimensional textile structure composites. In the analytical approach, various theoretical models were established to predict the stiffness, strength, nonlinear deformation, and failure behavior of triaxial woven-fabric composites, 3-D braided composites, and multilayer multidirectional warp knit fabric composites in polymer and metal matrices. The structure performance maps of various textile structural composites were also established, based upon these analytical methods. In the experimental approach, extensive mechanical testing and microstructural characterization were performed to investigate the thermomechanical properties and failure behavior of 3-D braided FP/Al composites. Results of this research will serve as the basis for assessing the potential of textile composites for structural applications.

  17. Parametric estimation of 3D tubular structures for diffuse optical tomography

    PubMed Central

    Larusson, Fridrik; Anderson, Pamela G.; Rosenberg, Elizabeth; Kilmer, Misha E.; Sassaroli, Angelo; Fantini, Sergio; Miller, Eric L.

    2013-01-01

    We explore the use of diffuse optical tomography (DOT) for the recovery of 3D tubular shapes representing vascular structures in breast tissue. Using a parametric level set method (PaLS) our method incorporates the connectedness of vascular structures in breast tissue to reconstruct shape and absorption values from severely limited data sets. The approach is based on a decomposition of the unknown structure into a series of two dimensional slices. Using a simplified physical model that ignores 3D effects of the complete structure, we develop a novel inter-slice regularization strategy to obtain global regularity. We report on simulated and experimental reconstructions using realistic optical contrasts where our method provides a more accurate estimate compared to an unregularized approach and a pixel based reconstruction. PMID:23411913

  18. Cryo-EM structure of a 3D DNA-origami object

    PubMed Central

    Bai, Xiao-chen; Martin, Thomas G.; Scheres, Sjors H. W.; Dietz, Hendrik

    2012-01-01

    A key goal for nanotechnology is to design synthetic objects that may ultimately achieve functionalities known today only from natural macromolecular complexes. Molecular self-assembly with DNA has shown potential for creating user-defined 3D scaffolds, but the level of attainable positional accuracy has been unclear. Here we report the cryo-EM structure and a full pseudoatomic model of a discrete DNA object that is almost twice the size of a prokaryotic ribosome. The structure provides a variety of stable, previously undescribed DNA topologies for future use in nanotechnology and experimental evidence that discrete 3D DNA scaffolds allow the positioning of user-defined structural motifs with an accuracy that is similar to that observed in natural macromolecules. Thereby, our results indicate an attractive route to fabricate nanoscale devices that achieve complex functionalities by DNA-templated design steered by structural feedback. PMID:23169645

  19. Parametric estimation of 3D tubular structures for diffuse optical tomography.

    PubMed

    Larusson, Fridrik; Anderson, Pamela G; Rosenberg, Elizabeth; Kilmer, Misha E; Sassaroli, Angelo; Fantini, Sergio; Miller, Eric L

    2013-02-01

    We explore the use of diffuse optical tomography (DOT) for the recovery of 3D tubular shapes representing vascular structures in breast tissue. Using a parametric level set method (PaLS) our method incorporates the connectedness of vascular structures in breast tissue to reconstruct shape and absorption values from severely limited data sets. The approach is based on a decomposition of the unknown structure into a series of two dimensional slices. Using a simplified physical model that ignores 3D effects of the complete structure, we develop a novel inter-slice regularization strategy to obtain global regularity. We report on simulated and experimental reconstructions using realistic optical contrasts where our method provides a more accurate estimate compared to an unregularized approach and a pixel based reconstruction.

  20. 3-D Facial Landmark Localization With Asymmetry Patterns and Shape Regression from Incomplete Local Features.

    PubMed

    Sukno, Federico M; Waddington, John L; Whelan, Paul F

    2015-09-01

    We present a method for the automatic localization of facial landmarks that integrates nonrigid deformation with the ability to handle missing points. The algorithm generates sets of candidate locations from feature detectors and performs combinatorial search constrained by a flexible shape model. A key assumption of our approach is that for some landmarks there might not be an accurate candidate in the input set. This is tackled by detecting partial subsets of landmarks and inferring those that are missing, so that the probability of the flexible model is maximized. The ability of the model to work with incomplete information makes it possible to limit the number of candidates that need to be retained, drastically reducing the number of combinations to be tested with respect to the alternative of trying to always detect the complete set of landmarks. We demonstrate the accuracy of the proposed method in the face recognition grand challenge database, where we obtain average errors of approximately 3.5 mm when targeting 14 prominent facial landmarks. For the majority of these our method produces the most accurate results reported to date in this database. Handling of occlusions and surfaces with missing parts is demonstrated with tests on the Bosphorus database, where we achieve an overall error of 4.81 and 4.25 mm for data with and without occlusions, respectively. To investigate potential limits in the accuracy that could be reached, we also report experiments on a database of 144 facial scans acquired in the context of clinical research, with manual annotations performed by experts, where we obtain an overall error of 2.3 mm, with averages per landmark below 3.4 mm for all 14 targeted points and within 2 mm for half of them. The coordinates of automatically located landmarks are made available on-line.

  1. Solar Prominences Embedded in Flux Ropes: Morphological Features and Dynamics from 3D MHD Simulations

    NASA Astrophysics Data System (ADS)

    Terradas, J.; Soler, R.; Luna, M.; Oliver, R.; Ballester, J. L.; Wright, A. N.

    2016-04-01

    The temporal evolution of a solar prominence inserted in a three-dimensional magnetic flux rope is investigated numerically. Using the model of Titov & Démoulin under the regime of weak twist, the cold and dense prominence counteracts gravity by modifying the initially force-free magnetic configuration. In some cases a quasi-stationary situation is achieved after the relaxation phase, characterized by the excitation of standing vertical oscillations. These oscillations show a strong attenuation with time produced by the mechanism of continuum damping due to the inhomogeneous transition between the prominence and solar corona. The characteristic period of the vertical oscillations does not depend strongly on the twist of the flux rope. Nonlinearity is responsible for triggering the Kelvin-Helmholtz instability associated with the vertical oscillations and that eventually produces horizontal structures. Contrary to other configurations in which the longitudinal axis of the prominence is permeated by a perpendicular magnetic field, like in unsheared arcades, the orientation of the prominence along the flux rope axis prevents the development of Rayleigh-Taylor instabilities and therefore the appearance of vertical structuring along this axis.

  2. SOLAR PROMINENCES EMBEDDED IN FLUX ROPES: MORPHOLOGICAL FEATURES AND DYNAMICS FROM 3D MHD SIMULATIONS

    SciTech Connect

    Terradas, J.; Soler, R.; Oliver, R.; Ballester, J. L.; Luna, M.; Wright, A. N.

    2016-04-01

    The temporal evolution of a solar prominence inserted in a three-dimensional magnetic flux rope is investigated numerically. Using the model of Titov and Démoulin under the regime of weak twist, the cold and dense prominence counteracts gravity by modifying the initially force-free magnetic configuration. In some cases a quasi-stationary situation is achieved after the relaxation phase, characterized by the excitation of standing vertical oscillations. These oscillations show a strong attenuation with time produced by the mechanism of continuum damping due to the inhomogeneous transition between the prominence and solar corona. The characteristic period of the vertical oscillations does not depend strongly on the twist of the flux rope. Nonlinearity is responsible for triggering the Kelvin–Helmholtz instability associated with the vertical oscillations and that eventually produces horizontal structures. Contrary to other configurations in which the longitudinal axis of the prominence is permeated by a perpendicular magnetic field, like in unsheared arcades, the orientation of the prominence along the flux rope axis prevents the development of Rayleigh–Taylor instabilities and therefore the appearance of vertical structuring along this axis.

  3. Determining the 3D Subsurface Density Structure of Taurus Littrow Valley Using Apollo 17 Gravity Data

    NASA Technical Reports Server (NTRS)

    Urbancic, N.; Ghent, R.; Stanley, S,; Johnson, C. L.; Carroll, K. A.; Hatch, D.; Williamson, M. C.; Garry, W. B.; Talwani, M.

    2016-01-01

    Surface gravity surveys can detect subsurface density variations that can reveal subsurface geologic features. In 1972, the Apollo 17 (A17) mission conducted the Traverse Gravimeter Experiment (TGE) using a gravimeter that measured the local gravity field near Taurus Littrow Valley (TLV), located on the south-eastern rim of the Serenitatis basin. TLV is hypothesized to be a basaltfilled radial graben resulting from the impact that formed Mare Serenitatis. It is bounded by both the North and South Massifs (NM and SM) as well as other smaller mountains to the East that are thought to be mainly composed of brecciated highland material. The TGE is the first and only successful gravity survey on the surface of the Moon. Other more recent satellite surveys, such as NASA's Gravity Recovery and Interior Laboratory (GRAIL) mission (2011- 2012), have produced the best global gravity field to date (approx. 13km resolution). However, these satellite surveys are not sensitive enough to detect fine-scale (<1km) lunar subsurface structures. This underscores the value of the data collected at the surface by A17. In the original analysis of the data a 2D forward-modelling approach was used to derive a thickness of the subsurface basalt layer of 1.0 km by assuming a simple flat-faced rectangular geometry and using densities derived from Apollo lunar samples. We are investigating whether modern 3D modelling techniques in combination with high-resolution topographical and image datasets can reveal additional fine-scale subsurface structure in TLV.

  4. Optimization of a 3D Dynamic Culturing System for In Vitro Modeling of Frontotemporal Neurodegeneration-Relevant Pathologic Features

    PubMed Central

    Tunesi, Marta; Fusco, Federica; Fiordaliso, Fabio; Corbelli, Alessandro; Biella, Gloria; Raimondi, Manuela T.

    2016-01-01

    Frontotemporal lobar degeneration (FTLD) is a severe neurodegenerative disorder that is diagnosed with increasing frequency in clinical setting. Currently, no therapy is available and in addition the molecular basis of the disease are far from being elucidated. Consequently, it is of pivotal importance to develop reliable and cost-effective in vitro models for basic research purposes and drug screening. To this respect, recent results in the field of Alzheimer’s disease have suggested that a tridimensional (3D) environment is an added value to better model key pathologic features of the disease. Here, we have tried to add complexity to the 3D cell culturing concept by using a microfluidic bioreactor, where cells are cultured under a continuous flow of medium, thus mimicking the interstitial fluid movement that actually perfuses the body tissues, including the brain. We have implemented this model using a neuronal-like cell line (SH-SY5Y), a widely exploited cell model for neurodegenerative disorders that shows some basic features relevant for FTLD modeling, such as the release of the FTLD-related protein progranulin (PRGN) in specific vesicles (exosomes). We have efficiently seeded the cells on 3D scaffolds, optimized a disease-relevant oxidative stress experiment (by targeting mitochondrial function that is one of the possible FTLD-involved pathological mechanisms) and evaluated cell metabolic activity in dynamic culture in comparison to static conditions, finding that SH-SY5Y cells cultured in 3D scaffold are susceptible to the oxidative damage triggered by a mitochondrial-targeting toxin (6-OHDA) and that the same cells cultured in dynamic conditions kept their basic capacity to secrete PRGN in exosomes once recovered from the bioreactor and plated in standard 2D conditions. We think that a further improvement of our microfluidic system may help in providing a full device where assessing basic FTLD-related features (including PRGN dynamic secretion) that may

  5. 3D scanning of internal structure in gel engineering materials with visual scanning microscopic light scattering

    NASA Astrophysics Data System (ADS)

    Watanabe, Yosuke; Gong, Jing; Masato, Makino; Kabir, M. Hasnat; Furukawa, Hidemitsu

    2014-04-01

    The 3D printing technology, causing much attention from the beginning of 2013, will be possibly an alternative method to fabricate the biological soft tissues. Recently our group of Yamagata University has developed the world-first 3D Gel Printer to fabricate the complicated gel-materials with high-strength and biocompatibility. However, there are no 3D scanners that collect the data from the internal structure of complicated gel objects such as eye lens. It means that a new system for scanning the internal structure is needed now. In this study, firstly, we have tried to investigate the gel network of synthetic and biological gel with scanning microscopic light scattering (SMILS). We calculated the Young's modulus of synthetic gels with the SMILS and with the tensile test, and precisely compared the results between them. The temperature dependences of the inside structure and the transparency are observed in the pig crystalline lens. The quantitative analysis indicates the importance of the internal structure of real object. Secondary, we show the new system named Gel-scanner that can provide the 2-dimentional data of the internal structure. From examining our findings, the scanning of internal structure will enable us to expect physical properties of the real object. We convince that the gelscanner will play major role in the various fields.

  6. ConvNet-Based Localization of Anatomical Structures in 3D Medical Images.

    PubMed

    de Vos, Bob; Wolterink, Jelmer; de Jong, Pim; Leiner, Tim; Viergever, Max; Isgum, Ivana

    2017-02-23

    Localization of anatomical structures is a prerequisite for many tasks in medical image analysis. We propose a method for automatic localization of one or more anatomical structures in 3D medical images through detection of their presence in 2D image slices using a convolutional neural network (ConvNet). A single ConvNet is trained to detect presence of the anatomical structure of interest in axial, coronal, and sagittal slices extracted from a 3D image. To allow the ConvNet to analyze slices of different sizes, spatial pyramid pooling is applied. After detection, 3D bounding boxes are created by combining the output of the ConvNet in all slices. In the experiments 200 chest CT, 100 cardiac CT angiography (CTA), and 100 abdomen CT scans were used. The heart, ascending aorta, aortic arch, and descending aorta were localized in chest CT scans, the left cardiac ventricle in cardiac CTA scans, and the liver in abdomen CT scans. Localization was evaluated using the distances between automatically and manually defined reference bounding box centroids and walls. The best results were achieved in localization of structures with clearly defined boundaries (e.g. aortic arch) and the worst when the structure boundary was not clearly visible (e.g. liver). The method was more robust and accurate in localization multiple structures.

  7. Deformable modeling using a 3D boundary representation with quadratic constraints on the branching structure of the Blum skeleton.

    PubMed

    Yushkevich, Paul A; Zhang, Hui Gary

    2013-01-01

    We propose a new approach for statistical shape analysis of 3D anatomical objects based on features extracted from skeletons. Like prior work on medial representations, the approach involves deforming a template to target shapes in a way that preserves the branching structure of the skeleton and provides intersubject correspondence. However, unlike medial representations, which parameterize the skeleton surfaces explicitly, our representation is boundary-centric, and the skeleton is implicit. Similar to prior constrained modeling methods developed 2D objects or tube-like 3D objects, we impose symmetry constraints on tuples of boundary points in a way that guarantees the preservation of the skeleton's topology under deformation. Once discretized, the problem of deforming a template to a target shape is formulated as a quadratically constrained quadratic programming problem. The new technique is evaluated in terms of its ability to capture the shape of the corpus callosum tract extracted from diffusion-weighted MRI.

  8. Validation of a numerical 3-D fluid-structure interaction model for a prosthetic valve based on experimental PIV measurements.

    PubMed

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

    2009-10-01

    A numerical 3-D fluid-structure interaction (FSI) model of a prosthetic aortic valve was developed, based on a commercial computational fluid dynamics (CFD) software program using an Arbitrary Eulerian Lagrangian (ALE) formulation. To make sure of the validity of this numerical model, an equivalent experimental model accounting for both the geometrical features and the hydrodynamic conditions was also developed. The leaflet and the flow behaviours around the bileaflet valve were investigated numerically and experimentally by performing particle image velocimetry (PIV) measurements. Through quantitative and qualitative comparisons, it was shown that the leaflet behaviour and the velocity fields were similar in both models. The present study allows the validation of a fully coupled 3-D FSI numerical model. The promising numerical tool could be therefore used to investigate clinical issues involving the aortic valve.

  9. Modeling ionospheric disturbance features in quasi-vertically incident ionograms using 3-D magnetoionic ray tracing and atmospheric gravity waves

    NASA Astrophysics Data System (ADS)

    Cervera, M. A.; Harris, T. J.

    2014-01-01

    The Defence Science and Technology Organisation (DSTO) has initiated an experimental program, Spatial Ionospheric Correlation Experiment, utilizing state-of-the-art DSTO-designed high frequency digital receivers. This program seeks to understand ionospheric disturbances at scales < 150 km and temporal resolutions under 1 min through the simultaneous observation and recording of multiple quasi-vertical ionograms (QVI) with closely spaced ionospheric control points. A detailed description of and results from the first campaign conducted in February 2008 were presented by Harris et al. (2012). In this paper we employ a 3-D magnetoionic Hamiltonian ray tracing engine, developed by DSTO, to (1) model the various disturbance features observed on both the O and X polarization modes in our QVI data and (2) understand how they are produced. The ionospheric disturbances which produce the observed features were modeled by perturbing the ionosphere with atmospheric gravity waves.

  10. Novel 3D bismuth-based coordination polymers: Synthesis, structure, and second harmonic generation properties

    NASA Astrophysics Data System (ADS)

    Wibowo, Arief C.; Smith, Mark D.; Yeon, Jeongho; Halasyamani, P. Shiv; zur Loye, Hans-Conrad

    2012-11-01

    Two new 3D bismuth containing coordination polymers are reported along with their single crystal structures and SHG properties. Compound 1: Bi2O2(pydc) (pydc=pyridine-2, 5-dicarboxylate), crystallizes in the monoclinic, polar space group, P21 (a=9.6479(9) Å, b=4.2349(4) Å, c=11.9615(11) Å, β=109.587(1)°), which contains Bi2O2 chains that are connected into a 3D structure via the pydc ligands. Compound 2: Bi4Na4(1R3S-cam)8(EtOH)3.1(H2O)3.4 (1R3S cam=1R3S-camphoric acid) crystallizes in the monoclinic, polar space group, P21 (a=19.0855(7) Å, b=13.7706(5) Å, c=19.2429(7) Å, β=90.701(1)°) and is a true 3D coordination polymer. These are two example of SHG compounds prepared using unsymmetric ligands (compound 1) or chiral ligands (compound 2), together with metals that often exhibit stereochemically-active lone pairs, such as Bi3+, a synthetic approach that resulted in polar, non-centrosymmetric, 3D metal-organic coordination polymer.

  11. Structural and functional imaging of 3D microfluidic mixers using optical coherence tomography.

    PubMed

    Xi, Chuanwu; Marks, Daniel L; Parikh, Devang S; Raskin, Lutgarde; Boppart, Stephen A

    2004-05-18

    To achieve high mixing efficiency in microfluidic devices, complex designs are often required. Microfluidic devices have been evaluated with light and confocal microscopy, but fluid-flow characteristics at different depths are difficult to separate from the en face images produced. By using optical coherence tomography (OCT), an imaging modality capable of imaging 3D microstructures at micrometer-scale resolutions over millimeter-size scales, we obtained 3D dynamic functional and structural data for three representative microfluidic mixers: a Y channel mixer, a 3D serpentine mixer, and a vortex mixer. In the serpentine mixer, OCT image analysis revealed that the mixing efficiency was linearly dependent on the Reynolds number, whereas it appeared to have exponential dependence when imaged with light microscopy. The visual overlap of fluid flows in light-microscopy images leads to an overestimation of the mixing efficiency, an effect that was eliminated with OCT imaging. Doppler OCT measurements determined velocity profiles at various points in the serpentine mixer. Mixing patterns in the vortex mixer were compared with light-microscopy and OCT image analysis. These results demonstrate that OCT can significantly improve the characterization of 3D microfluidic device structure and function.

  12. Factors Affecting Dimensional Accuracy of 3-D Printed Anatomical Structures Derived from CT Data.

    PubMed

    Ogden, Kent M; Aslan, Can; Ordway, Nathaniel; Diallo, Dalanda; Tillapaugh-Fay, Gwen; Soman, Pranav

    2015-12-01

    Additive manufacturing and bio-printing, with the potential for direct fabrication of complex patient-specific anatomies derived from medical scan data, are having an ever-increasing impact on the practice of medicine. Anatomic structures are typically derived from CT or MRI scans, and there are multiple steps in the model derivation process that influence the geometric accuracy of the printed constructs. In this work, we compare the dimensional accuracy of 3-D printed constructs of an L1 vertebra derived from CT data for an ex vivo cadaver T-L spine with the original vertebra. Processing of segmented structures using binary median filters and various surface extraction algorithms is evaluated for the effect on model dimensions. We investigate the effects of changing CT reconstruction kernels by scanning simple geometric objects and measuring the impact on the derived model dimensions. We also investigate if there are significant differences between physical and virtual model measurements. The 3-D models were printed using a commercial 3-D printer, the Replicator 2 (MakerBot, Brooklyn, NY) using polylactic acid (PLA) filament. We found that changing parameters during the scan reconstruction, segmentation, filtering, and surface extraction steps will have an effect on the dimensions of the final model. These effects need to be quantified for specific situations that rely on the accuracy of 3-D printed models used in medicine or tissue engineering applications.

  13. Optimal Image Stitching for Concrete Bridge Bottom Surfaces Aided by 3d Structure Lines

    NASA Astrophysics Data System (ADS)

    Liu, Yahui; Yao, Jian; Liu, Kang; Lu, Xiaohu; Xia, Menghan

    2016-06-01

    Crack detection for bridge bottom surfaces via remote sensing techniques is undergoing a revolution in the last few years. For such applications, a large amount of images, acquired with high-resolution industrial cameras close to the bottom surfaces with some mobile platform, are required to be stitched into a wide-view single composite image. The conventional idea of stitching a panorama with the affine model or the homographic model always suffers a series of serious problems due to poor texture and out-of-focus blurring introduced by depth of field. In this paper, we present a novel method to seamlessly stitch these images aided by 3D structure lines of bridge bottom surfaces, which are extracted from 3D camera data. First, we propose to initially align each image in geometry based on its rough position and orientation acquired with both a laser range finder (LRF) and a high-precision incremental encoder, and these images are divided into several groups with the rough position and orientation data. Secondly, the 3D structure lines of bridge bottom surfaces are extracted from the 3D cloud points acquired with 3D cameras, which impose additional strong constraints on geometrical alignment of structure lines in adjacent images to perform a position and orientation optimization in each group to increase the local consistency. Thirdly, a homographic refinement between groups is applied to increase the global consistency. Finally, we apply a multi-band blending algorithm to generate a large-view single composite image as seamlessly as possible, which greatly eliminates both the luminance differences and the color deviations between images and further conceals image parallax. Experimental results on a set of representative images acquired from real bridge bottom surfaces illustrate the superiority of our proposed approaches.

  14. Pipeline inwall 3D measurement system based on the cross structured light

    NASA Astrophysics Data System (ADS)

    Shen, Da; Lin, Zhipeng; Xue, Lei; Zheng, Qiang; Wang, Zichi

    2014-01-01

    In order to accurately realize the defect detection of pipeline inwall, this paper proposes a measurement system made up of cross structured light, single CCD camera and a smart car, etc. Based on structured light measurement technology, this paper mainly introduces the structured light measurement system, the imaging mathematical model, and the parameters and method of camera calibration. Using these measuring principles and methods, the camera in remote control car platform achieves continuous shooting of objects and real-time rebound processing as well as utilizing established model to extract 3D point cloud coordinate to reconstruct pipeline defects, so it is possible to achieve 3D automatic measuring, and verifies the correctness and feasibility of this system. It has been found that this system has great measurement accuracy in practice.

  15. The crystal structure of Aspergillus fumigatus cyclophilin reveals 3D domain swapping of a central element.

    PubMed

    Limacher, Andreas; Kloer, Daniel P; Flückiger, Sabine; Folkers, Gerd; Crameri, Reto; Scapozza, Leonardo

    2006-02-01

    The crystal structure of Aspergillus fumigatus cyclophilin (Asp f 11) was solved by the multiwavelength anomalous dispersion method and was refined to a resolution of 1.85 A with R and R(free) values of 18.9% and 21.4%, respectively. Many cyclophilin structures have been solved to date, all showing the same monomeric conformation. In contrast, the structure of A. fumigatus cyclophilin reveals dimerization by 3D domain swapping and represents one of the first proteins with a swapped central domain. The domain-swapped element consists of two beta strands and a subsequent loop carrying a conserved tryptophan. The tryptophan binds into the active site, inactivating cis-trans isomerization. This might be a means of biological regulation. The two hinge loops leave the protein prone to misfolding. In this context, alternative forms of 3D domain swapping that can lead to N- or C-terminally swapped dimers, oligomers, and aggregates are discussed.

  16. Band like Electronic Structures in Square Hollow Quantum Dots by 3D-MHFKS Calculation

    NASA Astrophysics Data System (ADS)

    Takizawa, Tokihiro; Okada, Hoshihito; Matsuse, Takehiro

    To find novel aspects of the electronic structures in quantum dots (QD) from a view point of spatial broken symmetry, 3-dimensional-mesh Hartree-Fock-Kohn-Sham (3D-MHFKS) calculations1 are applied to the interacting electron system of electron number N in a symmetry broken hollow QD. For the case of a square hollow quantum dot confined in square hard wall (HW) potential (SSHQD), the magnetic (B) field dependence of the obtained single particle energy levels and chemical potentials in B-N diagram are shown to have a band like electronic structures over the wide B-field range up to 20T. To clarify the origin of the band like electronic structures in SSHQD, 3D-MHFKS calculations are also applied for the mixed symmetry QD's with a circular hollow in square HW potential (SCHQD) and with a square hollow in circular HW potential (CSHQD).

  17. Effective 3D protein structure prediction with local adjustment genetic-annealing algorithm.

    PubMed

    Zhang, Xiao-Long; Lin, Xiao-Li

    2010-09-01

    The protein folding problem consists of predicting protein tertiary structure from a given amino acid sequence by minimizing the energy function. The protein folding structure prediction is computationally challenging and has been shown to be NP-hard problem when the 3D off-lattice AB model is employed. In this paper, the local adjustment genetic-annealing (LAGA) algorithm was used to search the ground state of 3D offlattice AB model for protein folding structure. The algorithm included an improved crossover strategy and an improved mutation strategy, where a local adjustment strategy was also used to enhance the searching ability. The experiments were carried out with the Fibonacci sequences. The experimental results demonstrate that the LAGA algorithm appears to have better performance and accuracy compared to the previous methods.

  18. Fabrication of 3D embedded hollow structures inside polymer dielectric PMMA with femtosecond laser

    NASA Astrophysics Data System (ADS)

    Zheng, Chong; Chen, Tao; Hu, Anming; Liu, Shibing; Li, Junwei

    2016-11-01

    Recent progresses in femtosecond laser (fs) manufacturing have already proved that fs laser is a powerful tool in three dimensional internal structure fabrications. However, most studies are mainly focused on realize such structures in inorganic transparent dielectric, such as photosensitive glass and fused silica, etc. In this study, we present two methods to fabricate embedded internal 3D structures in a polymer dielectric material polymethyl methacrylate (PMMA). Both continuous hollow structure such as microfluidic channels and discrete hollow structures such as single microcavities are successfully fabricated with the help of femtosecond lasers. Among them, complicated 3D microchannel with a total length longer than 10mm and diameters around 80μm to 200μm are fabricated with a low repetition rate Ti: sapphire femtosecond laser by direct laser writing at a speed ranging from 25μm/s to 2000μm/s microcavities which function as concave microball lenses (CMBLs) and can be applied in super-wide-angle imaging are fabricated with a high repetition rate femtosecond fiber laser due to the distinct heat accumulation effect after 5s irradiation with the tightly focused fs laser beam. These new approaches proved that femtosecond laser direct writing technology has great application potential in 3D integrated devices manufacturing in the future.

  19. Techniques for Revealing 3d Hidden Archeological Features: Morphological Residual Models as Virtual-Polynomial Texture Maps

    NASA Astrophysics Data System (ADS)

    Pires, H.; Martínez Rubio, J.; Elorza Arana, A.

    2015-02-01

    The recent developments in 3D scanning technologies are not been accompanied by visualization interfaces. We are still using the same types of visual codes as when maps and drawings were made by hand. The available information in 3D scanning data sets is not being fully exploited by current visualization techniques. In this paper we present recent developments regarding the use of 3D scanning data sets for revealing invisible information from archaeological sites. These sites are affected by a common problem, decay processes, such as erosion, that never ceases its action and endangers the persistence of last vestiges of some peoples and cultures. Rock art engravings, or epigraphical inscriptions, are among the most affected by these processes because they are, due to their one nature, carved at the surface of rocks often exposed to climatic agents. The study and interpretation of these motifs and texts is strongly conditioned by the degree of conservation of the imprints left by our ancestors. Every single detail in the remaining carvings can make a huge difference in the conclusions taken by specialists. We have selected two case-studies severely affected by erosion to present the results of the on-going work dedicated to explore in new ways the information contained in 3D scanning data sets. A new method for depicting subtle morphological features in the surface of objects or sites has been developed. It allows to contrast human patterns still present at the surface but invisible to naked eye or by any other archaeological inspection technique. It was called Morphological Residual Model (MRM) because of its ability to contrast the shallowest morphological details, to which we refer as residuals, contained in the wider forms of the backdrop. Afterwards, we have simulated the process of building Polynomial Texture Maps - a widespread technique that as been contributing to archaeological studies for some years - in a 3D virtual environment using the results of MRM

  20. Optically coupled 3D common memory with GaAs on Si structure

    NASA Astrophysics Data System (ADS)

    Hirose, M.; Takata, H.; Koyanagi, M.

    1991-02-01

    An ultra fast data transfer speed is demonstrated for a novel three-dimensional (3D) Static Random Access Memory (SRAM) consisting of multilayer silicon LSI chips on which GaAs LEDs and photodetectors are monolithically integrated for vertical optical interconnections. A unique feature of this system is the capability of parallel data transfer from one memory layer to the upper and lower memory layers by the optical interconnections. The results of static and dynamic simulations of the optically coupled 3D common memory have indicated that a block of 512 bits data can be transferred through four memory layers within 16 nsec. This is an equivalent data transfer speed of 128 Gbits/sec/layer.

  1. The Deep Structure and 3D Thermo-geodynamics of the Caucasus by Geophysical Data.

    NASA Astrophysics Data System (ADS)

    Chelidze, T.; Gugunava, G.; Gamkrelidze, N.; Mindeli, P.; Kiria, J.; Ghonghadze, S.; Janovskaya, O.

    2012-04-01

    allows the construction of three-dimensional non-stationary geothermal and thermo-elastic models of the Caucasus and the Black and the Caspian seas water areas proposed by the authors of this paper. Paleo-reconstruction schemes of development of sedimentary cover of the Caucasus (Sholpo, 1978) and the Black sea area (Kasmin at al. 2000) and a lot of other data regarding the Caspian sea area have been used for the construction of three-dimensional non-stationary models of investigated region. Numerical modeling of thermal and thermo-elastic processes allows revealing the temporal distribution of a number of thermo-geodynamic events including the formation of some deep faults and active seismic zones. The above preliminary results on 3D structure and temperature fields in Caucasus were compared to recent publication on 3D crust structure and thermal model of Western and Central Europe (Tesauro, Kaban, and Cloetingh, 2010) and quite satisfactory agreement with our results was found for matching areas (North Turley, Black Sea, Crimea) of considered regions.

  2. 3D Printed Modeling of the Mitral Valve for Catheter-Based Structural Interventions.

    PubMed

    Vukicevic, Marija; Puperi, Daniel S; Jane Grande-Allen, K; Little, Stephen H

    2017-02-01

    As catheter-based structural heart interventions become increasingly complex, the ability to effectively model patient-specific valve geometry as well as the potential interaction of an implanted device within that geometry will become increasingly important. Our aim with this investigation was to combine the technologies of high-spatial resolution cardiac imaging, image processing software, and fused multi-material 3D printing, to demonstrate that patient-specific models of the mitral valve apparatus could be created to facilitate functional evaluation of novel trans-catheter mitral valve repair strategies. Clinical 3D transesophageal echocardiography and computed tomography images were acquired for three patients being evaluated for a catheter-based mitral valve repair. Target anatomies were identified, segmented and reconstructed into 3D patient-specific digital models. For each patient, the mitral valve apparatus was digitally reconstructed from a single or fused imaging data set. Using multi-material 3D printing methods, patient-specific anatomic replicas of the mitral valve were created. 3D print materials were selected based on the mechanical testing of elastomeric TangoPlus materials (Stratasys, Eden Prairie, Minnesota, USA) and were compared to freshly harvested porcine leaflet tissue. The effective bending modulus of healthy porcine MV tissue was significantly less than the bending modulus of TangoPlus (p < 0.01). All TangoPlus varieties were less stiff than the maximum tensile elastic modulus of mitral valve tissue (3697.2 ± 385.8 kPa anterior leaflet; 2582.1 ± 374.2 kPa posterior leaflet) (p < 0.01). However, the slopes of the stress-strain toe regions of the mitral valve tissues (532.8 ± 281.9 kPa anterior leaflet; 389.0 ± 156.9 kPa posterior leaflet) were not different than those of the Shore 27, Shore 35, and Shore 27 with Shore 35 blend TangoPlus material (p > 0.95). We have demonstrated that patient-specific mitral valve models can be

  3. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.

    PubMed

    Miao, Zhichao; Adamiak, Ryszard W; Antczak, Maciej; Batey, Robert T; Becka, Alexander J; Biesiada, Marcin; Boniecki, Michał J; Bujnicki, Janusz; Chen, Shi-Jie; Cheng, Clarence Yu; Chou, Fang-Chieh; Ferré-D'Amaré, Adrian R; Das, Rhiju; Dawson, Wayne K; Feng, Ding; Dokholyan, Nikolay V; Dunin-Horkawicz, Stanisław; Geniesse, Caleb; Kappel, Kalli; Kladwang, Wipapat; Krokhotin, Andrey; Łach, Grzegorz E; Major, François; Mann, Thomas H; Magnus, Marcin; Pachulska-Wieczorek, Katarzyna; Patel, Dinshaw J; Piccirilli, Joseph A; Popenda, Mariusz; Purzycka, Katarzyna J; Ren, Aiming; Rice, Greggory M; Santalucia, John; Sarzynska, Joanna; Szachniuk, Marta; Tandon, Arpit; Trausch, Jeremiah J; Tian, Siqi; Wang, Jian; Weeks, Kevin M; Williams, Benfeard; Xiao, Yi; Xu, Xiaojun; Zhang, Dong; Zok, Tomasz; Westhof, Eric

    2017-01-30

    RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF) and one set describes large conformational changes between ligand-free and ligand-bound states; the Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All the puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homology-derived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal notable need for algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.u-strasbg.fr/rnapuzzles/.

  4. 3D structure tensor analysis of light microscopy data for validating diffusion MRI

    PubMed Central

    Khan, Ahmad Raza; Cornea, Anda; Leigland, Lindsey A.; Kohama, Steven G.; Jespersen, Sune Nørhøj; Kroenke, Christopher D.

    2015-01-01

    Diffusion magnetic resonance imaging (d-MRI) is a powerful non-invasive and non-destructive technique for characterizing brain tissue on the microscopic scale. However, the lack of validation of d-MRI by independent experimental means poses an obstacle to accurate interpretation of data acquired using this method. Recently, structure tensor analysis has been applied to light microscopy images, and this technique holds promise to be a powerful validation strategy for d-MRI. Advantages of this approach include its similarity to d-MRI in terms of averaging the effects of a large number of cellular structures, and its simplicity, which enables it to be implemented in a high-throughput manner. However, a drawback of previous implementations of this technique arises from it being restricted to 2D. As a result, structure tensor analyses have been limited to tissue sectioned in a direction orthogonal to the direction of interest. Here we describe the analytical framework for extending structure tensor analysis to 3D, and utilize the results to analyze serial image “stacks” acquired with confocal microscopy of rhesus macaque hippocampal tissue. Implementation of 3D structure tensor procedures requires removal of sources of anisotropy introduced in tissue preparation and confocal imaging. This is accomplished with image processing steps to mitigate the effects of anisotropic tissue shrinkage, and the effects of anisotropy in the point spread function (PSF). In order to address the latter confound, we describe procedures for measuring the dependence of PSF anisotropy on distance from the microscope objective within tissue. Prior to microscopy, ex vivo d-MRI measurements performed on the hippocampal tissue revealed three regions of tissue with mutually orthogonal directions of least restricted diffusion that correspond to CA1, alveus and inferior longitudinal fasciculus. We demonstrate the ability of 3D structure tensor analysis to identify structure tensor orientations

  5. 3D printing of layered brain-like structures using peptide modified gellan gum substrates.

    PubMed

    Lozano, Rodrigo; Stevens, Leo; Thompson, Brianna C; Gilmore, Kerry J; Gorkin, Robert; Stewart, Elise M; in het Panhuis, Marc; Romero-Ortega, Mario; Wallace, Gordon G

    2015-10-01

    The brain is an enormously complex organ structured into various regions of layered tissue. Researchers have attempted to study the brain by modeling the architecture using two dimensional (2D) in vitro cell culturing methods. While those platforms attempt to mimic the in vivo environment, they do not truly resemble the three dimensional (3D) microstructure of neuronal tissues. Development of an accurate in vitro model of the brain remains a significant obstacle to our understanding of the functioning of the brain at the tissue or organ level. To address these obstacles, we demonstrate a new method to bioprint 3D brain-like structures consisting of discrete layers of primary neural cells encapsulated in hydrogels. Brain-like structures were constructed using a bio-ink consisting of a novel peptide-modified biopolymer, gellan gum-RGD (RGD-GG), combined with primary cortical neurons. The ink was optimized for a modified reactive printing process and developed for use in traditional cell culturing facilities without the need for extensive bioprinting equipment. Furthermore the peptide modification of the gellan gum hydrogel was found to have a profound positive effect on primary cell proliferation and network formation. The neural cell viability combined with the support of neural network formation demonstrated the cell supportive nature of the matrix. The facile ability to form discrete cell-containing layers validates the application of this novel printing technique to form complex, layered and viable 3D cell structures. These brain-like structures offer the opportunity to reproduce more accurate 3D in vitro microstructures with applications ranging from cell behavior studies to improving our understanding of brain injuries and neurodegenerative diseases.

  6. Comparison of low cost 3D structured light scanners for face modeling.

    PubMed

    Bakirman, Tolga; Gumusay, Mustafa Umit; Reis, Hatice Catal; Selbesoglu, Mahmut Oguz; Yosmaoglu, Serra; Yaras, Mehmet Cem; Seker, Dursun Zafer; Bayram, Bulent

    2017-02-01

    This study aims to compare three different structured light scanner systems to generate accurate 3D human face models. Among these systems, the most dense and expensive one was denoted as the reference and the other two that were low cost and low resolution were compared according to the reference system. One female face and one male face were scanned with three light scanner systems. Point-cloud filtering, mesh generation, and hole-filling steps were carried out using a trial version of commercial software; moreover, the data evaluation process was realized using CloudCompare open-source software. Various filtering and mesh smoothing levels were applied on reference data to compare with other low-cost systems. Thus, the optimum reduction level of reference data was evaluated to continue further processes. The outcome of the presented study shows that low-cost structured light scanners have a great potential for 3D object modeling, including the human face. A considerable cheap structured light system has been used due to its capacity to obtain spatial and morphological information in the case study of 3D human face modeling. This study also discusses the benefits and accuracy of low-cost structured light systems.

  7. Low-cost impact detection and location for automated inspections of 3D metallic based structures.

    PubMed

    Morón, Carlos; Portilla, Marina P; Somolinos, José A; Morales, Rafael

    2015-05-28

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach.

  8. Rapid Fabrication of Cell-Laden Alginate Hydrogel 3D Structures by Micro Dip-Coating

    PubMed Central

    Ghanizadeh Tabriz, Atabak; Mills, Christopher G.; Mullins, John J.; Davies, Jamie A.; Shu, Wenmiao

    2017-01-01

    Development of a simple, straightforward 3D fabrication method to culture cells in 3D, without relying on any complex fabrication methods, remains a challenge. In this paper, we describe a new technique that allows fabrication of scalable 3D cell-laden hydrogel structures easily, without complex machinery: the technique can be done using only apparatus already available in a typical cell biology laboratory. The fabrication method involves micro dip-coating of cell-laden hydrogels covering the surface of a metal bar, into the cross-linking reagents calcium chloride or barium chloride to form hollow tubular structures. This method can be used to form single layers with thickness ranging from 126 to 220 µm or multilayered tubular structures. This fabrication method uses alginate hydrogel as the primary biomaterial and a secondary biomaterial can be added depending on the desired application. We demonstrate the feasibility of this method, with survival rate over 75% immediately after fabrication and normal responsiveness of cells within these tubular structures using mouse dermal embryonic fibroblast cells and human embryonic kidney 293 cells containing a tetracycline-responsive, red fluorescent protein (tHEK cells). PMID:28286747

  9. Low-Cost Impact Detection and Location for Automated Inspections of 3D Metallic Based Structures

    PubMed Central

    Morón, Carlos; Portilla, Marina P.; Somolinos, José A.; Morales, Rafael

    2015-01-01

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach. PMID:26029951

  10. LigandBox: A database for 3D structures of chemical compounds.

    PubMed

    Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

    2013-01-01

    A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  12. Propagation of Coronal Mass Ejections in 3D and the Structure of the Inner Heliosphere

    NASA Astrophysics Data System (ADS)

    Gallagher, P. T.; Byrne, J. P.; Maloney, S. A.; McAteer, J.

    2011-12-01

    Solar coronal mass ejections (CMEs) are the most significant drivers of adverse space weather on Earth, but the physics governing their propagation through the heliosphere is not well understood. Although stereoscopic imaging of CMEs with NASA's Solar Terrestrial Relations Observatory (STEREO) has provided some insight into their three-dimensional (3D) propagation, the mechanisms governing their evolution remain unclear because of difficulties in reconstructing their true 3D structure. In this talk I will describe the use of an elliptical tie-pointing technique to reconstruct a CME front in 3D, enabling us to quantify its deflected trajectory from high latitudes along the ecliptic, and measure its increasing angular width and propagation. At large distances from the Sun (>7 R_sun), I will describe how its motion is determined by drag effects in the solar wind, using ENLIL simulations of the inner heliosphere. By combining a 3D reconstruction with modelling of the solar wind, we predict an arrival time within 30 mins of the in-situ detection of the CME at ACE

  13. 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.

  14. Multi Length Scale Imaging of Flocculated Estuarine Sediments; Insights into their Complex 3D Structure

    NASA Astrophysics Data System (ADS)

    Wheatland, Jonathan; Bushby, Andy; Droppo, Ian; Carr, Simon; Spencer, Kate

    2015-04-01

    Suspended estuarine sediments form flocs that are compositionally complex, fragile and irregularly shaped. The fate and transport of suspended particulate matter (SPM) is determined by the size, shape, density, porosity and stability of these flocs and prediction of SPM transport requires accurate measurements of these three-dimensional (3D) physical properties. However, the multi-scaled nature of flocs in addition to their fragility makes their characterisation in 3D problematic. Correlative microscopy is a strategy involving the spatial registration of information collected at different scales using several imaging modalities. Previously, conventional optical microscopy (COM) and transmission electron microscopy (TEM) have enabled 2-dimensional (2D) floc characterisation at the gross (> 1 µm) and sub-micron scales respectively. Whilst this has proven insightful there remains a critical spatial and dimensional gap preventing the accurate measurement of geometric properties and an understanding of how structures at different scales are related. Within life sciences volumetric imaging techniques such as 3D micro-computed tomography (3D µCT) and focused ion beam scanning electron microscopy [FIB-SEM (or FIB-tomography)] have been combined to characterise materials at the centimetre to micron scale. Combining these techniques with TEM enables an advanced correlative study, allowing material properties across multiple spatial and dimensional scales to be visualised. The aims of this study are; 1) to formulate an advanced correlative imaging strategy combining 3D µCT, FIB-tomography and TEM; 2) to acquire 3D datasets; 3) to produce a model allowing their co-visualisation; 4) to interpret 3D floc structure. To reduce the chance of structural alterations during analysis samples were first 'fixed' in 2.5% glutaraldehyde/2% formaldehyde before being embedding in Durcupan resin. Intermediate steps were implemented to improve contrast and remove pore water, achieved by the

  15. 2D and 3D GPR imaging of structural ceilings in historic and existing constructions

    NASA Astrophysics Data System (ADS)

    Colla, Camilla

    2014-05-01

    GPR applications in civil engineering are to date quite diversified. With respect to civil constructions and monumental buildings, detection of voids, cavities, layering in structural elements, variation of geometry, of moisture content, of materials, areas of decay, defects, cracks have been reported in timber, concrete and masonry elements. Nonetheless, many more fields of investigation remain unexplored. This contribution gives an account of a variety of examples of structural ceilings investigation by GPR radar in reflection mode, either as 2D or 3D data acquisition and visualisation. Ceilings have a pre-eminent role in buildings as they contribute to a good structural behaviour of the construction. Primarily, the following functions can be listed for ceilings: a) they carry vertical dead and live loads on floors and distribute such loads to the vertical walls; b) they oppose to external horizontal forces such as wind loads and earthquakes helping to transfer such forces from the loaded element to the other walls; c) they contribute to create the box skeleton and behaviour of a building, connecting the different load bearing walls and reducing the slenderness and flexural instability of such walls. Therefore, knowing how ceilings are made in specific buildings is of paramount importance for architects and structural engineers. According to the type of building and age of construction, ceilings may present very different solutions and materials. Moreover, in existing constructions, ceilings may have been substituted, modified or strengthened due to material decay or to change of use of the building. These alterations may often go unrecorded in technical documentation or technical drawings may be unavailable. In many cases, the position, orientation and number of the load carrying elements in ceilings may be hidden or not be in sight, due for example to the presence of false ceilings or to technical plants. GPR radar can constitute a very useful tool for

  16. The 3D crustal structure of Northeastern Tibetan area from seismic tomography

    NASA Astrophysics Data System (ADS)

    Sun, Anhui

    2015-04-01

    The Northeastern Tibetan region is located in the border area of three sub-plates in China, i.e. the Tibetan plateau, North China block and Xinjiang block. Effected simultaneously by the extrusion driven by the India-Eurasia plat collision and the blockage of the Ordos basin, this area has complex geology, strong tectonics activities and suffered from several large historic earthquakes, such as the Haiyuan earthquake (M8.6) in 1920, the Gulang earthquake (M8.0) in 1927. To enhance our understanding of the crustal structure and the interaction between different tectonic blocks of this region, we conduct a three-dimensional (3D) tomographic study by using the arrival time date recorded by regional seismic network. We used 101101 P and 103313 S wave arrival times from 11650 local earthquakes during 1970 to 2013 recorded by 154 permanent seismic stations of the local Seismic Network, installed over five provinces in China, i.e. Gansu, Ningxia, Qinghai, Shanxi, Neimenggu. We first established a 1D primary crustal model from LITHO1.0, an updated crust and lithospheric model of the Earth by weighted averaging. To better performer ray tracing, our inversion involved three discontinuities (including the Moho) with depth variation over the mantle derived from LITHO1.0. Detailed three-dimensional seismic velocity (Vp and Vs) structures of the crust of the Northeastern Tibetan are determined with a horizontal resolution of about 35 km and a depth resolution of 6-20 km. The Poisson's ratio (σ) structure was also estimated after obtained Vp and Vs structures. We detected low-velocity anomalies in the lower crust and relative high-velocity anomalies in the upper crust beneath the Longmenshan faults zone, which are in good agreement with the results of most previous geophysical studies. Our results revealed clear different velocity variation beneath both sides of different tectonic blocks. In addition, we found the correlation between our tomographic result and previous

  17. Determination and validation of mTOR kinase-domain 3D structure by homology modeling.

    PubMed

    Lakhlili, Wiame; Chevé, Gwénaël; Yasri, Abdelaziz; Ibrahimi, Azeddine

    2015-01-01

    The AKT/mammalian target of rapamycin (mTOR) pathway is considered as one of the commonly activated and deregulated signaling pathways in human cancer. mTOR is associated with other proteins in two molecular complexes: mTOR complex 1/Raptor and the mTOR complex 2/Rictor. Using the crystal structure of the related lipid kinase PI3Kγ, we built a model of the catalytic region of mTOR. The modeling of the three-dimensional (3D) structure of the mTOR was performed by homology modeling program SWISS-MODEL. The quality and validation of the obtained model were performed using PROCHECK and PROVE softwares. The overall stereochemical property of the protein was assessed by the Ramachandran plot. The model validation was also done by docking of known inhibitors. In this paper, we describe and validate a 3D model for the mTOR catalytic site.

  18. Utilizing in-situ resources and 3D printing structures for a manned Mars mission

    NASA Astrophysics Data System (ADS)

    Kading, Benjamin; Straub, Jeremy

    2015-02-01

    This paper presents a manned Mars mission, which is based on the use of in-situ resources for the fabrication of structures. First, it provides an overview of the two-phase mission. In phase one, robotic construction units prepare a functional base for phase-two human habitation. Then, it describes a set of prospective structures that can be created utilizing additive manufacturing (commonly known as 3D printing) techniques and in situ materials. Next, the technological advancements required to allow this type of mission are considered and their feasibility is discussed. Specific focus is given to the topics of basalt 3D printing and the maintenance of the pressure environment. The process of the construction of the base is also discussed. Finally the proposed approach is analyzed through comparison to prior missions, before concluding.

  19. Construction of topological structure of 3D coronary vessels for analysis of catheter navigation in interventional cardiology simulation

    NASA Astrophysics Data System (ADS)

    Wang, Yaoping; Chui, Cheekong K.; Cai, Yiyu; Mak, KoonHou

    1998-06-01

    This study presents an approach to build a 3D vascular system of coronary for the development of a virtual cardiology simulator. The 3D model of the coronary arterial tree is reconstructed from the geometric information segmented from the Visible Human data set for physical analysis of catheterization. The process of segmentation is guided by a 3D topologic hierarchy structure of coronary vessels which is obtained from a mechanical model by using Coordinate Measuring Machine (CMM) probing. This mechanical professional model includes all major coronary arterials ranging from right coronary artery to atrioventricular branch and from left main trunk to left anterior descending branch. All those branches are considered as the main operating sites for cardiology catheterization. Along with the primary arterial vasculature and accompanying secondary and tertiary networks obtained from a previous work, a more complete vascular structure can then be built for the simulation of catheterization. A novel method has been developed for real time Finite Element Analysis of catheter navigation based on this featured vasculature of vessels.

  20. 3D reconstruction of internal structure of animal body using near-infrared light

    NASA Astrophysics Data System (ADS)

    Tran, Trung Nghia; Yamamoto, Kohei; Namita, Takeshi; Kato, Yuji; Shimizu, Koichi

    2014-03-01

    To realize three-dimensional (3D) optical imaging of the internal structure of animal body, we have developed a new technique to reconstruct CT images from two-dimensional (2D) transillumination images. In transillumination imaging, the image is blurred due to the strong scattering in the tissue. We had developed a scattering suppression technique using the point spread function (PSF) for a fluorescent light source in the body. In this study, we have newly proposed a technique to apply this PSF for a light source to the image of unknown light-absorbing structure. The effectiveness of the proposed technique was examined in the experiments with a model phantom and a mouse. In the phantom experiment, the absorbers were placed in the tissue-equivalent medium to simulate the light-absorbing organs in mouse body. Near-infrared light was illuminated from one side of the phantom and the image was recorded with CMOS camera from another side. Using the proposed techniques, the scattering effect was efficiently suppressed and the absorbing structure can be visualized in the 2D transillumination image. Using the 2D images obtained in many different orientations, we could reconstruct the 3D image. In the mouse experiment, an anesthetized mouse was held in an acrylic cylindrical holder. We can visualize the internal organs such as kidneys through mouse's abdomen using the proposed technique. The 3D image of the kidneys and a part of the liver were reconstructed. Through these experimental studies, the feasibility of practical 3D imaging of the internal light-absorbing structure of a small animal was verified.

  1. Analysis and 3D visualization of structures of animal brains obtained from histological sections

    NASA Astrophysics Data System (ADS)

    Forero-Vargas, Manuel G.; Fuentes, Veronica; Lopez, D.; Moscoso, A.; Merchan, Miguel A.

    2002-11-01

    This paper presents a new application for the analysis of histological sections and their 3D visualization. The process is performed in few steps. First, a manual process is necessary to determine the regions of interest, including image digitalization, drawing of borders and alignment between all images. Then, a reconstruction process is made. After sampling the contour, the structure of interest is displayed. The application is experimentally validated and some results on histological sections of a rodent's brain (hamster and rat) are shown.

  2. Dynamic Characteristics of a Model and Prototype for 3D-RC Structure

    NASA Astrophysics Data System (ADS)

    Moniuddin, Md. Khaja; Vasanthalakshmi, G.; Chethan, K.; Babu, R. Ramesh

    2016-06-01

    Infill walls provide durable and economical partitions that have relatively excellent thermal and sound insulation with high fire resistance. Monolithic infilled walls are provided within RC structures without being analyzed as a combination of concrete and brick elements, although in reality they act as a single unit during earthquakes. The performance of such structures during earthquakes has proved to be superior in comparison to bare frames in terms of stiffness, strength and energy dissipation. To know the dynamic characteristics of monolithic infill wall panels and masonry infill, modal, response spectrum and time history analyses have been carried out on a model and prototype of a 3D RC structure for a comparative study.

  3. Segmentation of bone structures in 3D CT images based on continuous max-flow optimization

    NASA Astrophysics Data System (ADS)

    Pérez-Carrasco, J. A.; Acha-Piñero, B.; Serrano, C.

    2015-03-01

    In this paper an algorithm to carry out the automatic segmentation of bone structures in 3D CT images has been implemented. Automatic segmentation of bone structures is of special interest for radiologists and surgeons to analyze bone diseases or to plan some surgical interventions. This task is very complicated as bones usually present intensities overlapping with those of surrounding tissues. This overlapping is mainly due to the composition of bones and to the presence of some diseases such as Osteoarthritis, Osteoporosis, etc. Moreover, segmentation of bone structures is a very time-consuming task due to the 3D essence of the bones. Usually, this segmentation is implemented manually or with algorithms using simple techniques such as thresholding and thus providing bad results. In this paper gray information and 3D statistical information have been combined to be used as input to a continuous max-flow algorithm. Twenty CT images have been tested and different coefficients have been computed to assess the performance of our implementation. Dice and Sensitivity values above 0.91 and 0.97 respectively were obtained. A comparison with Level Sets and thresholding techniques has been carried out and our results outperformed them in terms of accuracy.

  4. 3-D Structure of the Slave and Rae Cratons Provides Clues to Their Construction

    NASA Astrophysics Data System (ADS)

    Snyder, D. B.

    2013-12-01

    Deep geologic structures within cratons that make up continental cores were long neglected. Recently acquired geophysical data from large observational arrays and geochemical data resulting from exploration for diamond has now made possible co-registration of large-scale (400-km depth), truly 3-dimensional data sets. P-waves, surface waves and magnetotelluric observations provide 3-D wavespeed and conductivity models. Multi-azimuthal receiver functions map seismic discontinuity surfaces in 3-D. Xenolith suites erupted in kimberlites provide rock samples at key lithospheric depths, albeit at sparsely distributed locations. These multi-disciplinary models are becoming available for several key cratons worldwide; here the deep structure of the Slave and Rae cratons of the Canadian Shield is described. Lithospheric layers with tapered, wedge-shaped margins are common. Slave craton layers are sub-horizontal and indicate construction of the craton core at 2.7 Ga by underthrusting and flat stacking of lithosphere. The central Rae craton has predominantly dipping discontinuities that indicate construction at 1.9 Ga by thrusting similar to that observed in crustal ';thick-skinned' fold-and-thrust belts. 3-D mapping of conductivity and metasomatism, the latter via mineral recrystallization and resetting of isotopic ages, overprints primary structures in both cratons. Distribution of more conductivitve mantle suggests that assumed causative pervasive metasomatism occurs at 100-200 km depths with ';chimneys' reaching to shallower depths, typically in locations where kimberlites or mineralization has occurred.

  5. SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures

    PubMed Central

    Nadzirin, Nurul; Gardiner, Eleanor J.; Willett, Peter; Artymiuk, Peter J.; Firdaus-Raih, Mohd

    2012-01-01

    Similarities in the 3D patterns of amino acid side chains can provide insights into their function despite the absence of any detectable sequence or fold similarities. Search for protein sites (SPRITE) and amino acid pattern search for substructures and motifs (ASSAM) are graph theoretical programs that can search for 3D amino side chain matches in protein structures, by representing the amino acid side chains as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. Both programs require the input file to be in the PDB format. The objective of using SPRITE is to identify matches of side chains in a query structure to patterns with characterized function. In contrast, a 3D pattern of interest can be searched for existing occurrences in available PDB structures using ASSAM. Both programs are freely accessible without any login requirement. SPRITE is available at http://mfrlab.org/grafss/sprite/ while ASSAM can be accessed at http://mfrlab.org/grafss/assam/. PMID:22573174

  6. Enhanced hybrid search algorithm for protein structure prediction using the 3D-HP lattice model.

    PubMed

    Zhou, Changjun; Hou, Caixia; Zhang, Qiang; Wei, Xiaopeng

    2013-09-01

    The problem of protein structure prediction in the hydrophobic-polar (HP) lattice model is the prediction of protein tertiary structure. This problem is usually referred to as the protein folding problem. This paper presents a method for the application of an enhanced hybrid search algorithm to the problem of protein folding prediction, using the three dimensional (3D) HP lattice model. The enhanced hybrid search algorithm is a combination of the particle swarm optimizer (PSO) and tabu search (TS) algorithms. Since the PSO algorithm entraps local minimum in later evolution extremely easily, we combined PSO with the TS algorithm, which has properties of global optimization. Since the technologies of crossover and mutation are applied many times to PSO and TS algorithms, so enhanced hybrid search algorithm is called the MCMPSO-TS (multiple crossover and mutation PSO-TS) algorithm. Experimental results show that the MCMPSO-TS algorithm can find the best solutions so far for the listed benchmarks, which will help comparison with any future paper approach. Moreover, real protein sequences and Fibonacci sequences are verified in the 3D HP lattice model for the first time. Compared with the previous evolutionary algorithms, the new hybrid search algorithm is novel, and can be used effectively to predict 3D protein folding structure. With continuous development and changes in amino acids sequences, the new algorithm will also make a contribution to the study of new protein sequences.

  7. [MOLECULAR EVOLUTION OF ION CHANNELS: AMINO ACID SEQUENCES AND 3D STRUCTURES].

    PubMed

    Korkosh, V S; Zhorov, B S; Tikhonov, D B

    2016-01-01

    An integral part of modern evolutionary biology is comparative analysis of structure and function of macromolecules such as proteins. The first and critical step to understand evolution of homologous proteins is their amino acid sequence alignment. However, standard algorithms fop not provide unambiguous sequence alignments for proteins of poor homology. More reliable results can be obtained by comparing experimental 3D structures obtained at atomic resolution, for instance, with the aid of X-ray structural analysis. If such structures are lacking, homology modeling is used, which may take into account indirect experimental data on functional roles of individual amino-acid residues. An important problem is that the sequence alignment, which reflects genetic modifications, does not necessarily correspond to the functional homology. The latter depends on three-dimensional structures which are critical for natural selection. Since alignment techniques relying only on the analysis of primary structures carry no information on the functional properties of proteins, including 3D structures into consideration is very important. Here we consider several examples involving ion channels and demonstrate that alignment of their three-dimensional structures can significantly improve sequence alignments obtained by traditional methods.

  8. Novel 3D bismuth-based coordination polymers: Synthesis, structure, and second harmonic generation properties

    SciTech Connect

    Wibowo, Arief C.; Smith, Mark D.; Yeon, Jeongho; Halasyamani, P. Shiv; Loye, Hans-Conrad zur

    2012-11-15

    Two new 3D bismuth containing coordination polymers are reported along with their single crystal structures and SHG properties. Compound 1: Bi{sub 2}O{sub 2}(pydc) (pydc=pyridine-2, 5-dicarboxylate), crystallizes in the monoclinic, polar space group, P2{sub 1} (a=9.6479(9) A, b=4.2349(4) A, c=11.9615(11) A, {beta}=109.587(1) Degree-Sign ), which contains Bi{sub 2}O{sub 2} chains that are connected into a 3D structure via the pydc ligands. Compound 2: Bi{sub 4}Na{sub 4}(1R3S-cam){sub 8}(EtOH){sub 3.1}(H{sub 2}O){sub 3.4} (1R3S cam=1R3S-camphoric acid) crystallizes in the monoclinic, polar space group, P2{sub 1} (a=19.0855(7) A, b=13.7706(5) A, c=19.2429(7) A, {beta}=90.701(1) Degree-Sign ) and is a true 3D coordination polymer. These are two example of SHG compounds prepared using unsymmetric ligands (compound 1) or chiral ligands (compound 2), together with metals that often exhibit stereochemically-active lone pairs, such as Bi{sup 3+}, a synthetic approach that resulted in polar, non-centrosymmetric, 3D metal-organic coordination polymer. - Graphical Abstract: Structures of two new, polar, 3D Bismuth(III)-based coordination polymers: Bi{sub 2}O{sub 2}(pydc) (compound 1), and Bi{sub 4}Na{sub 4}(1R3S-cam){sub 8}(EtOH){sub 3.1}(H{sub 2}O){sub 3.4} (compound 2). Highlights: Black-Right-Pointing-Pointer New, polar, 3D Bismuth(III)-based coordination polymers. Black-Right-Pointing-Pointer First polar bismuth-based coordination polymers synthesized via a 'hybrid' strategy. Black-Right-Pointing-Pointer Combination of stereochemically-active lone pairs and unsymmetrical or chiral ligands. Black-Right-Pointing-Pointer Synthesis of class C-SHG materials based on Kurtz-Perry categories.

  9. Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA.

    PubMed

    Mrozek, Dariusz; Brożek, Miłosz; Małysiak-Mrozek, Bożena

    2014-02-01

    Searching for similar 3D protein structures is one of the primary processes employed in the field of structural bioinformatics. However, the computational complexity of this process means that it is constantly necessary to search for new methods that can perform such a process faster and more efficiently. Finding molecular substructures that complex protein structures have in common is still a challenging task, especially when entire databases containing tens or even hundreds of thousands of protein structures must be scanned. Graphics processing units (GPUs) and general purpose graphics processing units (GPGPUs) can perform many time-consuming and computationally demanding processes much more quickly than a classical CPU can. In this paper, we describe the GPU-based implementation of the CASSERT algorithm for 3D protein structure similarity searching. This algorithm is based on the two-phase alignment of protein structures when matching fragments of the compared proteins. The GPU (GeForce GTX 560Ti: 384 cores, 2GB RAM) implementation of CASSERT ("GPU-CASSERT") parallelizes both alignment phases and yields an average 180-fold increase in speed over its CPU-based, single-core implementation on an Intel Xeon E5620 (2.40GHz, 4 cores). In this paper, we show that massive parallelization of the 3D structure similarity search process on many-core GPU devices can reduce the execution time of the process, allowing it to be performed in real time. GPU-CASSERT is available at: http://zti.polsl.pl/dmrozek/science/gpucassert/cassert.htm.

  10. Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities

    PubMed Central

    Dai, Chao; Li, Wenyuan; Tjong, Harianto; Hao, Shengli; Zhou, Yonggang; Li, Qingjiao; Chen, Lin; Zhu, Bing; Alber, Frank; Jasmine Zhou, Xianghong

    2016-01-01

    Three-dimensional (3D) genome structures vary from cell to cell even in an isogenic sample. Unlike protein structures, genome structures are highly plastic, posing a significant challenge for structure-function mapping. Here we report an approach to comprehensively identify 3D chromatin clusters that each occurs frequently across a population of genome structures, either deconvoluted from ensemble-averaged Hi-C data or from a collection of single-cell Hi-C data. Applying our method to a population of genome structures (at the macrodomain resolution) of lymphoblastoid cells, we identify an atlas of stable inter-chromosomal chromatin clusters. A large number of these clusters are enriched in binding of specific regulatory factors and are therefore defined as ‘Regulatory Communities.' We reveal two major factors, centromere clustering and transcription factor binding, which significantly stabilize such communities. Finally, we show that the regulatory communities differ substantially from cell to cell, indicating that expression variability could be impacted by genome structures. PMID:27240697

  11. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers

    PubMed Central

    Mao, Yiqi; Yu, Kai; Isakov, Michael S.; Wu, Jiangtao; Dunn, Martin L.; Jerry Qi, H.

    2015-01-01

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations. PMID:26346202

  12. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers.

    PubMed

    Mao, Yiqi; Yu, Kai; Isakov, Michael S; Wu, Jiangtao; Dunn, Martin L; Jerry Qi, H

    2015-09-08

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations.

  13. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers

    NASA Astrophysics Data System (ADS)

    Mao, Yiqi; Yu, Kai; Isakov, Michael S.; Wu, Jiangtao; Dunn, Martin L.; Jerry Qi, H.

    2015-09-01

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations.

  14. Combination of photogrammetric and geoelectric methods to assess 3d structures associated to natural hazards

    NASA Astrophysics Data System (ADS)

    Fargier, Yannick; Dore, Ludovic; Antoine, Raphael; Palma Lopes, Sérgio; Fauchard, Cyrille

    2016-04-01

    The extraction of subsurface materials is a key element for the economy of a nation. However, natural degradation of underground quarries is a major issue from an economic and public safety point of view. Consequently, the quarries stakeholders require relevant tools to define hazards associated to these structures. Safety assessment methods of underground quarries are recent and mainly based on rock physical properties. This kind of method leads to a certain homogeneity assumption of pillar internal properties that can cause an underestimation of the risk. Electrical Resistivity Imaging (ERI) is a widely used method that possesses two advantages to overcome this limitation. The first is to provide a qualitative understanding for the detection and monitoring of anomalies in the pillar body (e.g. faults). The second is to provide a quantitative description of the electrical resistivity distribution inside the pillar. This quantitative description can be interpreted with constitutive laws to help decision support (water content decreases the mechanical resistance of a chalk). However, conventional 2D and 3D Imaging techniques are usually applied to flat surface surveys or to surfaces with moderate topography. A 3D inversion of more complex media (case of the pillar) requires a full consideration of the geometry that was never taken into account before. The Photogrammetric technique presents a cost effective solution to obtain an accurate description of the external geometry of a complex media. However, this method has never been fully coupled with a geophysical method to enhance/improve the inversion process. Consequently we developed a complete procedure showing that photogrammetric and ERI tools can be efficiently combined to assess a complex 3D structure. This procedure includes in a first part a photogrammetric survey, a processing stage with an open source software and a post-processing stage finalizing a 3D surface model. The second part necessitates the

  15. An intelligent recovery progress evaluation system for ACL reconstructed subjects using integrated 3-D kinematics and EMG features.

    PubMed

    Malik, Owais A; Senanayake, S M N Arosha; Zaheer, Dansih

    2015-03-01

    An intelligent recovery evaluation system is presented for objective assessment and performance monitoring of anterior cruciate ligament reconstructed (ACL-R) subjects. The system acquires 3-D kinematics of tibiofemoral joint and electromyography (EMG) data from surrounding muscles during various ambulatory and balance testing activities through wireless body-mounted inertial and EMG sensors, respectively. An integrated feature set is generated based on different features extracted from data collected for each activity. The fuzzy clustering and adaptive neuro-fuzzy inference techniques are applied to these integrated feature sets in order to provide different recovery progress assessment indicators (e.g., current stage of recovery, percentage of recovery progress as compared to healthy group, etc.) for ACL-R subjects. The system was trained and tested on data collected from a group of healthy and ACL-R subjects. For recovery stage identification, the average testing accuracy of the system was found above 95% (95-99%) for ambulatory activities and above 80% (80-84%) for balance testing activities. The overall recovery evaluation performed by the proposed system was found consistent with the assessment made by the physiotherapists using standard subjective/objective scores. The validated system can potentially be used as a decision supporting tool by physiatrists, physiotherapists, and clinicians for quantitative rehabilitation analysis of ACL-R subjects in conjunction with the existing recovery monitoring systems.

  16. Quantification of telomere features in tumor tissue sections by an automated 3D imaging-based workflow.

    PubMed

    Gunkel, Manuel; Chung, Inn; Wörz, Stefan; Deeg, Katharina I; Simon, Ronald; Sauter, Guido; Jones, David T W; Korshunov, Andrey; Rohr, Karl; Erfle, Holger; Rippe, Karsten

    2017-02-01

    The microscopic analysis of telomere features provides a wealth of information on the mechanism by which tumor cells maintain their unlimited proliferative potential. Accordingly, the analysis of telomeres in tissue sections of patient tumor samples can be exploited to obtain diagnostic information and to define tumor subgroups. In many instances, however, analysis of the image data is conducted by manual inspection of 2D images at relatively low resolution for only a small part of the sample. As the telomere feature signal distribution is frequently heterogeneous, this approach is prone to a biased selection of the information present in the image and lacks subcellular details. Here we address these issues by using an automated high-resolution imaging and analysis workflow that quantifies individual telomere features on tissue sections for a large number of cells. The approach is particularly suited to assess telomere heterogeneity and low abundant cellular subpopulations with distinct telomere characteristics in a reproducible manner. It comprises the integration of multi-color fluorescence in situ hybridization, immunofluorescence and DNA staining with targeted automated 3D fluorescence microscopy and image analysis. We apply our method to telomeres in glioblastoma and prostate cancer samples, and describe how the imaging data can be used to derive statistically reliable information on telomere length distribution or colocalization with PML nuclear bodies. We anticipate that relating this approach to clinical outcome data will prove to be valuable for pretherapeutic patient stratification.

  17. Characterization of ABS specimens produced via the 3D printing technology for drone structural components

    NASA Astrophysics Data System (ADS)

    Ferro, Carlo Giovanni; Brischetto, Salvatore; Torre, Roberto; Maggiore, Paolo

    2016-07-01

    The Fused Deposition Modelling (FDM) technology is widely used in rapid prototyping. 3D printers for home desktop applications are usually employed to make non-structural objects. When the mechanical stresses are not excessive, this technology can also be successfully employed to produce structural objects, not only in prototyping stage but also in the realization of series pieces. The innovative idea of the present work is the application of this technology, implemented in a desktop 3D printer, to the realization of components for aeronautical use, especially for unmanned aerial systems. For this purpose, the paper is devoted to the statistical study of the performance of a desktop 3D printer to understand how the process performs and which are the boundary limits of acceptance. Mechanical and geometrical properties of ABS (Acrylonitrile Butadiene Styrene) specimens, such as tensile strength and stiffness, have been evaluated. ASTM638 type specimens have been used. A capability analysis has been applied for both mechanical and dimensional performances. Statistically stable limits have been determined using experimentally collected data.

  18. Development of biologically active compounds by combining 3D QSAR and structure-based design methods

    NASA Astrophysics Data System (ADS)

    Sippl, Wolfgang

    2002-11-01

    One of the major challenges in computational approaches to drug design is the accurate prediction of the binding affinity of novel biomolecules. In the present study an automated procedure which combines docking and 3D-QSAR methods was applied to several drug targets. The developed receptor-based 3D-QSAR methodology was tested on several sets of ligands for which the three-dimensional structure of the target protein has been solved - namely estrogen receptor, acetylcholine esterase and protein-tyrosine-phosphatase 1B. The molecular alignments of the studied ligands were determined using the docking program AutoDock and were compared with the X-ray structures of the corresponding protein-ligand complexes. The automatically generated protein-based ligand alignment obtained was subsequently taken as basis for a comparative field analysis applying the GRID/GOLPE approach. Using GRID interaction fields and applying variable selection procedures, highly predictive models were obtained. It is expected that concepts from receptor-based 3D QSAR will be valuable tools for the analysis of high-throughput screening as well as virtual screening data

  19. 3D Density Structure and LOS Observations of a Model CME

    NASA Astrophysics Data System (ADS)

    Manchester, W. B.; Lugaz, N.; Gombosi, T.; de Zeeuw, D.; Sokolov, I.; Toth, G.

    2004-12-01

    We present synthetic Thomson-scattered white-light images of a simulated coronal mass ejection (CME). The simulations are based on a 3-D MHD model of a CME propagating through a bimodal solar wind characteristic of solar minimum. The CME is driven by a 3-D Gibson-Low flux rope inserted in the helmet streamer of the steady-state corona. Synthetic coronograph images are produced that follow the evolution of the CME to 1 AU from several points of view. The white light images provide a basis for comparison with wide angle coronographs, like those of SMEI or STEREO. We find that a large amount of plasma is swept up from the solar wind by the CME-driven shock wave, which dominates the density structure far from the Sun. We also find that the shape of this compressed plasma is highly distorted by the variation in speed of the ambient solar wind. Comparisons of 2-D integrated images to the 3-D density structure show that the viewing angle severely effects the line-of-sight appearance of the CME, as well as the estimated mass of the CME from such 2D images.

  20. The lithospheric-scale 3D structural configuration of the North Alpine Foreland Basin constrained by gravity modelling and the calculation of the 3D load distribution

    NASA Astrophysics Data System (ADS)

    Przybycin, Anna M.; Scheck-Wenderoth, Magdalena; Schneider, Michael

    2014-05-01

    The North Alpine Foreland Basin is situated in the northern front of the European Alps and extends over parts of France, Switzerland, Germany and Austria. It formed as a wedge shaped depression since the Tertiary in consequence of the Euro - Adriatic continental collision and the Alpine orogeny. The basin is filled with clastic sediments, the Molasse, originating from erosional processes of the Alps and underlain by Mesozoic sedimentary successions and a Paleozoic crystalline crust. For our study we have focused on the German part of the basin. To investigate the deep structure, the isostatic state and the load distribution of this region we have constructed a 3D structural model of the basin and the Alpine area using available depth and thickness maps, regional scale 3D structural models as well as seismic and well data for the sedimentary part. The crust (from the top Paleozoic down to the Moho (Grad et al. 2008)) has been considered as two-parted with a lighter upper crust and a denser lower crust; the partition has been calculated following the approach of isostatic equilibrium of Pratt (1855). By implementing a seismic Lithosphere-Asthenosphere-Boundary (LAB) (Tesauro 2009) the crustal scale model has been extended to the lithospheric-scale. The layer geometry and the assigned bulk densities of this starting model have been constrained by means of 3D gravity modelling (BGI, 2012). Afterwards the 3D load distribution has been calculated using a 3D finite element method. Our results show that the North Alpine Foreland Basin is not isostatically balanced and that the configuration of the crystalline crust strongly controls the gravity field in this area. Furthermore, our results show that the basin area is influenced by varying lateral load differences down to a depth of more than 150 km what allows a first order statement of the required compensating horizontal stress needed to prevent gravitational collapse of the system. BGI (2012). The International

  1. Shape optimization of 3D continuum structures via force approximation techniques

    NASA Technical Reports Server (NTRS)

    Vanderplaats, Garret N.; Kodiyalam, Srinivas

    1988-01-01

    The existing need to develop methods whereby the shape design efficiency can be improved through the use of high quality approximation methods is addressed. An efficient approximation method for stress constraints in 3D shape design problems is proposed based on expanding the nodal forces in Taylor series with respect to shape variations. The significance of this new method is shown through elementary beam theory calculations and via numerical computations using 3D solid finite elements. Numerical examples including the classical cantilever beam structure and realistic automotive parts like the engine connecting rod are designed for optimum shape using the proposed method. The numerical results obtained from these methods are compared with other published results, to assess the efficiency and the convergence rate of the proposed method.

  2. Structured light 3D tracking system for measuring motions in PET brain imaging

    NASA Astrophysics Data System (ADS)

    Olesen, Oline V.; Jørgensen, Morten R.; Paulsen, Rasmus R.; Højgaard, Liselotte; Roed, Bjarne; Larsen, Rasmus

    2010-02-01

    Patient motion during scanning deteriorates image quality, especially for high resolution PET scanners. A new proposal for a 3D head tracking system for motion correction in high resolution PET brain imaging is set up and demonstrated. A prototype tracking system based on structured light with a DLP projector and a CCD camera is set up on a model of the High Resolution Research Tomograph (HRRT). Methods to reconstruct 3D point clouds of simple surfaces based on phase-shifting interferometry (PSI) are demonstrated. The projector and camera are calibrated using a simple stereo vision procedure where the projector is treated as a camera. Additionally, the surface reconstructions are corrected for the non-linear projector output prior to image capture. The results are convincing and a first step toward a fully automated tracking system for measuring head motions in PET imaging.

  3. Imaging and 3D reconstruction of cerebrovascular structures in embryonic zebrafish.

    PubMed

    Ethell, Douglas W; Cameron, D Joshua

    2014-04-22

    Zebrafish are a powerful tool to study developmental biology and pathology in vivo. The small size and relative transparency of zebrafish embryos make them particularly useful for the visual examination of processes such as heart and vascular development. In several recent studies transgenic zebrafish that express EGFP in vascular endothelial cells were used to image and analyze complex vascular networks in the brain and retina, using confocal microscopy. Descriptions are provided to prepare, treat and image zebrafish embryos that express enhanced green fluorescent protein (EGFP), and then generate comprehensive 3D renderings of the cerebrovascular system. Protocols include the treatment of embryos, confocal imaging, and fixation protocols that preserve EGFP fluorescence. Further, useful tips on obtaining high-quality images of cerebrovascular structures, such as removal the eye without damaging nearby neural tissue are provided. Potential pitfalls with confocal imaging are discussed, along with the steps necessary to generate 3D reconstructions from confocal image stacks using freely available open source software.

  4. Constructing a 3D structural block diagram of the Central Basin in Marmara Sea by means of bathymetric and seismic data

    NASA Astrophysics Data System (ADS)

    Demirbağ, Emin; Kurt, Hülya; Düşünür, Doğa; Sarıkavak, Kerim; Çetin, Suna

    2007-12-01

    In this study we made a comparative interpretation of multibeam bathymetric and seismic reflection data with different resolutions and penetration properties collected in the Central Basin of the Marmara Sea. Our main objectives were (i) to investigate and compare the active tectonic deformation observed on the sea bottom and within the uppermost sedimentary layers to that of the deep-seated deformation within the limits of resolution and penetration of the available geophysical data and (ii) to build a three-dimensional (3D) block diagram of the active tectonic and buried features by means of a sliced mapping technique. In this approach, we produced slice maps of the active and buried structural features at selected depths and then combined them to form a 3D structural block diagram. Motivation for our work was to produce a 3D structural diagram to derive a more detailed image of the structural features in the Central Basin where there is no available 3D seismic data. The observations from the bathymetry and seismic data and developed 3D diagram support the presence of a through-going strike-slip fault that forms a rotational depression zone against a right-stepping strike-slip faulting causing a pull-apart basin in the Central Depression zone.

  5. Loading mode dependent effective properties of octet-truss lattice structures using 3D-printing

    NASA Astrophysics Data System (ADS)

    Challapalli, Adithya

    Cellular materials, often called lattice materials, are increasingly receiving attention for their ultralight structures with high specific strength, excellent impact absorption, acoustic insulation, heat dissipation media and compact heat exchangers. In alignment with emerging additive manufacturing (AM) technology, realization of the structural applications of the lattice materials appears to be becoming faster. Considering the direction dependent material properties of the products with AM, by directionally dependent printing resolution, effective moduli of lattice structures appear to be directionally dependent. In this paper, a constitutive model of a lattice structure, which is an octet-truss with a base material having an orthotropic material property considering AM is developed. In a case study, polyjet based 3D printing material having an orthotropic property with a 9% difference in the principal direction provides difference in the axial and shear moduli in the octet-truss by 2.3 and 4.6%. Experimental validation for the effective properties of a 3D printed octet-truss is done for uniaxial tension and compression test. The theoretical value based on the micro-buckling of truss member are used to estimate the failure strength. Modulus value appears a little overestimate compared with the experiment. Finite element (FE) simulations for uniaxial compression and tension of octettruss lattice materials are conducted. New effective properties for the octet-truss lattice structure are developed considering the observed behavior of the octet-truss structure under macroscopic compression and tension trough simulations.

  6. 3D visualization of deformation structures and potential fluid pathways at the Grimsel Test Site

    NASA Astrophysics Data System (ADS)

    Schneeberger, Raphael; Kober, Florian; Berger, Alfons; Spillmann, Thomas; Herwegh, Marco

    2015-04-01

    Knowledge on the ability of fluids to infiltrate subsurface rocks is of major importance for underground constructions, geothermal or radioactive waste disposal projects. In this study, we focus on the characterization of water infiltration pathways, their 3D geometries and origins. Based on surface and subsurface mapping in combination with drill core data, we developed by the use of MoveTM (Midland Valley Exploration Ltd.) a 3D structural model of the Grimsel Test Site (GTS). GTS is an underground laboratory operated by NAGRA, the Swiss organisation responsible for the management of nuclear waste. It is located within a suite of post-Variscan magmatic bodies comprising former granitic and granodioritic melts, which are dissected by mafic and aplitic dikes. During Alpine orogeny, the suite was tectonically overprinted within two stages of ductile deformation (Wehrens et al., in prep.) followed by brittle overprint of some of the shear zones during the retrograde exhumation history. It is this brittle deformation, which controls today's water infiltration network. However, the associated fractures, cataclasites and fault gouges are controlled themselves by aforementioned pre-existing mechanical discontinuities, whose origin ranges back as far as to the magmatic stage. For example, two sets of vertically oriented mafic dikes (E-W and NW-SE striking) and compositional heterogeneities induced by magmatic segregation processes in the plutonic host rocks served as nucleation sites for Alpine strain localization. Subsequently, NE-SW, E-W and NW-SE striking ductile shear zones were formed, in combination with high temperature fracturing while dissecting the host rocks in a complex 3D pattern (Wehrens et al, in prep.). Whether the ductile shear zones have been subjected to brittle reactivation and can serve as infiltration pathways or not, depends strongly on their orientations with respect to the principal stress field. Especially where deformation structures intersect

  7. 3D crustal and lithospheric structure of the Pyrenean orogenic wedge

    NASA Astrophysics Data System (ADS)

    Theunissen, Thomas; Chevrot, Sébastien; Sylvander, Matthieu; Monteiller, Vadim; Villasenor, Antonio; Benahmed, Sébastien; Calvet, Marie

    2013-04-01

    The Pyrenean orogenic wedge is the consequence of the collision between the Iberian microplate and the southwesternmost part of the Eurasian plate from 55 to 25 Ma (Eocene to Oligocene). The shortening began since Late Cretaceous, about 100 My ago, leading to about 75 km from the west to 125 km to the east of continental crustal shortening. Before this period of time, the region was characterized by a sedimentary basin associated with a very important thinning that later controlled the deformation during the shortening process. Mantle outcrops are therefore present along and north of the North Pyrenean Fault with a scattered localization to the west toward the Mauleon basin. Today, the horizontal deformation rate is very low and the recent seismicity, mainly normal faulting mechanisms, is certainly caused by coupling between erosion and isostatic readjustments. Images from seismic reflection, gravity modeling, local and teleseismic seismic waves inversions and magnetotellurics inversions are in agreement with the subduction of Iberia beneath Aquitania. The 3D crustal structure reveals the presence of an important thickening of the continental crust associated with the subduction of the Iberian lower crust through the north beneath Aquitania at the favor of a detachment. Lateral variations of the geometry (including that of the Moho) and the wave propagation properties are important. In order to better analyze waveforms from local, regional or teleseismic earthquakes and to better constrain the geodynamical evolution of the Pyrenean chain over the time, PYROPE and TOPO-IBERIA projects were born. Two temporary seismic arrays (using broadband seismometers), on the French and Spanish sides, have been deployed between 2010 and 2013. We present here preliminary results on 3D crustal structures (approximately in the window 40° N-45° N and -4° E and 5° E) from arrival-times of about 20000 earthquakes recorded at about 200 seismic stations between 1978 and 2012

  8. The “lnc” between 3D Chromatin Structure and X Chromosome Inactivation

    PubMed Central

    Pandya-Jones, Amy; Plath, Kathrin

    2016-01-01

    The long non-coding RNA Xist directs a remarkable instance of developmentally regulated, epigenetic change known as X Chromosome Inactivation (XCI). By spreading in cis across the X chromosome from which it is expressed, Xist RNA facilities the creation of a heritably silent, heterochromatic nuclear territory that displays a three-dimensional structure distinct from that of the active X chromosome. How Xist RNA attaches to and propagates across a chromosome and its influence over the three-dimensional (3D) structure of the inactive X are aspects of XCI that have remained largely unclear. Here, we discuss studies that have made significant contributions towards answering these open questions. PMID:27062886

  9. Protein contact maps: A binary depiction of protein 3D structures

    NASA Astrophysics Data System (ADS)

    Emerson, Isaac Arnold; Amala, Arumugam

    2017-01-01

    In recent years, there has been a considerable interest in examining the structure and dynamics of complex networks. Proteins in 3D space may also be considered as complex systems emerged through the interactions of their constituent amino acids. This representation provides a powerful framework to uncover the general organized principle of protein contact network. Here we reviewed protein contact map in terms of protein structure prediction and analyses. In addition, we had also discussed the various computational techniques for the prediction of protein contact maps and the tools to visualize contact maps.

  10. 3D structures of the crust and upper mantle in Atlas Mountains of Morocco from magnetotelluric data

    NASA Astrophysics Data System (ADS)

    Kiyan, D.; Jones, A.; Ledo, J.; Fullea, J.; Sinischalchi, A.; Romano, G.; Campanya, J.

    2012-04-01

    As a part of the PICASSO (Program to Investigate Convective Alboran Sea System Overturn) and concomitant TopoMed (Plate re-organization in the western Mediterranean: Lithospheric causes and topographic consequences - an ESF EUROCORES TOPO-EUROPE project) projects, a multi-institutional magnetotelluric (MT) experiment across the Atlas Mountains initiated in September 2009 and ended in February 2010. The overarching objective of the project is to provide new constrains on the lithospheric structure of the Atlas Mountains, and to aid in discriminating between competing models describing the tectonics of the region. The experiment comprised acquisition of broad-band (crustal probing) and long period (mantle probing) MT data along two profiles: a N-S oriented profile crossing the Middle Atlas through the Central High Atlas to the east (profile MEK) and a NE-SW oriented profile crossing the western High Atlas towards the Anti Atlas in the west (profile MAR). Our MT inversion results from the MEK profile (Ledo et al., 2011), assuming that the Earth can be validly represented by two-dimensional (2D) structures, reveal two major mid- to lower crustal scale conductive features. The first anomaly is stretching from the Middle Atlas southward towards the High Moulouya basin and the second one is located beneath the Anti Atlas. There is a gradual increase in mantle resistivity to the south which may indicate a thickening lithosphere beneath the Anti Atlas. To validate the 2D inversion results, the MT data on the same profile were inverted for 3<